Imperial College London

ProfessorCharlesCoombes

Faculty of MedicineDepartment of Surgery & Cancer

Emeritus Professor of Medical Oncology
 
 
 
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Contact

 

+44 (0)20 7594 2135c.coombes

 
 
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Assistant

 

Mrs Suzy Ford +44 (0)20 7594 2135

 
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Location

 

145ICTEM buildingHammersmith Campus

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Summary

 

Publications

Publication Type
Year
to

976 results found

Ali SN, Jayasena CN, Sam AH, 2018, Which patients with gynaecomastia require more detailed investigation?, CLINICAL ENDOCRINOLOGY, Vol: 88, Pages: 360-363, ISSN: 0300-0664

Gynaecomastia may be due to medication, chronic liver or kidney disease, hypogonadism (primary or secondary to pituitary disease) or hyperthyroidism. Having excluded these aetiologies, it is imperative to be vigilant for underlying malignancy causing gynaecomastia. These include human chorionic gonadotrophin‐secreting testicular and extratesticular tumours and oestrogen‐secreting testicular tumours and feminising adrenal tumours.

Journal article

Coombes RC, Tovey H, Kilburn L, Mansi J, Palmieri C, Bartlett J, Hicks J, Makris A, Evans A, Loibl S, Denkert C, Murray E, Grieve R, Coleman R, Schmidt M, Klare P, Rezai M, Rautenberg B, Klutinus N, Rhein U, Mousa K, Ricardo-Vitorino S, von Minckwitz G, Bliss Jet al., 2018, A phase III multicentre double blind randomised trial of celecoxib versus placebo in primary breast cancer patients (REACT - Randomised EuropeAn celecoxib trial), San Antonio Breast Cancer Symposium, Publisher: AMER ASSOC CANCER RESEARCH, ISSN: 0008-5472

Conference paper

Hazel P, Kroll SHB, Bondke A, Barbazanges M, Patel H, Fuchter MJ, Coombes RC, Ali S, Barrett AGM, Freemont PSet al., 2018, Corrigendum: Inhibitor selectivity for cyclin-dependent kinase 7: a structural, thermodynamic, and modelling study, ChemMedChem, Vol: 13, Pages: 207-207, ISSN: 1860-7187

Journal article

Asaduzzaman M, Constantinou S, Min H, Gallon J, Lin M-L, Singh P, Raguz S, Ali S, Shousha S, Charles Coombes R, Lam EW-F, Hu Y, Yagüe Eet al., 2018, Correction to: Tumour suppressor EP300, a modulator of paclitaxel resistance and stemness, is downregulated in metaplastic breast cancer, Breast Cancer Research and Treatment, Vol: 167, Pages: 605-606, ISSN: 0167-6806

In the original publication, Fig. 1 depicting the blot for EP300 in CAL51 cells (Fig. 1c) was unintentionally duplicated with that from MDA-MB-231 cells (Fig. 1d). The new figure given in this erratum depicts the correct EP300 blot in Fig. 1c.

Journal article

Alberro JA, Ballester B, Deulofeu P, Fabregas R, Fraile M, Gubern JM, Janer J, Moral A, de Pablo JL, Penalva G, Puig P, Ramos M, Rojo R, Santesteban P, Serra C, Sola M, Solarnau L, Solsona J, Veloso E, Vidal S, Abe O, Abe R, Enomoto K, Kikuchi K, Koyama H, Masuda H, Nomura Y, Ohashi Y, Sakai K, Sugimachi K, Toi M, Tominaga T, Uchino J, Yoshida M, Coles CE, Haybittle JL, Moebus V, Leonard CF, Calais G, Garaud P, Collett V, Davies C, Delmestri A, Sayer J, Harvey VJ, Holdaway IM, Kay RG, Mason BH, Forbe JF, Franci PA, Wilcken N, Balic M, Bartsch R, Fesl C, Fitzal F, Fohler H, Gnant M, Greil R, Jakesz R, Marth C, Mlineritsch B, Pfeiler G, Singer CF, Steger GG, Stoeger H, Canney P, Yosef HMA, Focan C, Peek U, Oates GD, Powell J, Durand M, Mauriac L, Di Leo A, Dolci S, Larsimont D, Nogaret JM, Philippson C, Piccart MJ, Masood MB, Parker D, Price JJ, Lindsay MA, Mackey J, Martin M, Hupperets PSGJ, Bates T, Blamey RW, Chetty U, Ellis IO, Mallon E, Morgan DAL, Patnick J, Pinder S, Lohrisch C, Nichol A, Bartlett JMS, Bramwell VH, Chen BE, Chia SKL, Gelmon K, Goss PE, Levine MN, Parulekar W, Pater JL, Pritchard KI, Shepherd LE, Tu D, Whelan T, Berry D, Broadwater G, Cirrincione C, Muss H, Norton L, Weiss RB, Abu-Zahara HT, Karpov A, Portnoj SL, Bowden S, Brookes C, Dunn J, Fernando I, Lee M, Poole C, Rea D, Spooner D, Barrett-Lee PJ, Manse RE, Monypenny IJ, Gordon NH, Davis HL, Cuzick J, Sestak I, Lehingue Y, Romestaing P, Dubois JB, Delozier T, Griffon B, Lesec'h JM, Mustacchi G, Petruzelka L, Pribylova O, Owen JR, Meier P, Shan Y, Shao YF, Wang X, Zhao DB, Howell A, Swindell R, Albano J, de Oliveira CF, Gervasio H, Gordilho J, Ejlertsen B, Jensen M-B, Mouridsen H, Gelman RS, Harris JR, Hayes D, Henderson C, Shapiro CL, Christiansen P, Ejlertsen B, Ewertz M, Jensen MB, Mouridsen HT, Fehm T, Trampisch HJ, Dalesio O, de Vries EGE, Rodenhuis S, van Tinteren H, Comis RL, Davidson NE, Gray R, Robert N, Sledge G, Solin LJ, Sparano JA, Tormey DC, Wood W, Cameron D, Chetty U, Dixon Jet al., 2018, Long-term outcomes for neoadjuvant versus adjuvant chemotherapy in early breast cancer: meta-analysis of individual patient data from ten randomised trials, LANCET ONCOLOGY, Vol: 19, Pages: 27-39, ISSN: 1470-2045

BackgroundNeoadjuvant chemotherapy (NACT) for early breast cancer can make breast-conserving surgery more feasible and might be more likely to eradicate micrometastatic disease than might the same chemotherapy given after surgery. We investigated the long-term benefits and risks of NACT and the influence of tumour characteristics on outcome with a collaborative meta-analysis of individual patient data from relevant randomised trials.MethodsWe obtained information about prerandomisation tumour characteristics, clinical tumour response, surgery, recurrence, and mortality for 4756 women in ten randomised trials in early breast cancer that began before 2005 and compared NACT with the same chemotherapy given postoperatively. Primary outcomes were tumour response, extent of local therapy, local and distant recurrence, breast cancer death, and overall mortality. Analyses by intention-to-treat used standard regression (for response and frequency of breast-conserving therapy) and log-rank methods (for recurrence and mortality).FindingsPatients entered the trials from 1983 to 2002 and median follow-up was 9 years (IQR 5–14), with the last follow-up in 2013. Most chemotherapy was anthracycline based (3838 [81%] of 4756 women). More than two thirds (1349 [69%] of 1947) of women allocated NACT had a complete or partial clinical response. Patients allocated NACT had an increased frequency of breast-conserving therapy (1504 [65%] of 2320 treated with NACT vs 1135 [49%] of 2318 treated with adjuvant chemotherapy). NACT was associated with more frequent local recurrence than was adjuvant chemotherapy: the 15 year local recurrence was 21·4% for NACT versus 15·9% for adjuvant chemotherapy (5·5% increase [95% CI 2·4–8·6]; rate ratio 1·37 [95% CI 1·17–1·61]; p=0·0001). No significant difference between NACT and adjuvant chemotherapy was noted for distant recurrence (15 year risk 38·2% for NACT vs 38&

Journal article

Palmieri C, Stein RC, Liu X, Hudson E, Nicholas H, Sasano H, Guestini F, Holcombe C, Barrett S, Kenny L, Reed S, Lim A, Hayward L, Howell S, Coombes RCet al., 2018, Correction to: IRIS study: a phase II study of the steroid sulfatase inhibitor Irosustat when added to an aromatase inhibitor in ER-positive breast cancer patients (vol 165, pg 343, 2017), Breast Cancer Research and Treatment, Vol: 167, Pages: 407-407, ISSN: 0167-6806

Journal article

Martin L-A, Ribas R, Simigdala N, Schuster E, Pancholi S, Tenev T, Gellert P, Buluwela L, Harrod A, Thornhill A, Nikitorowicz-Buniak J, Bhamra A, Turgeon M-O, Poulogiannis G, Gao Q, Martins V, Hills M, Garcia-Murillas I, Fribbens C, Patani N, Li Z, Sikora MJ, Turner N, Zwart W, Oesterreich S, Carroll J, Ali S, Dowsett Met al., 2017, Discovery of naturally occurring ESR1 mutations in breast cancer cell lines modelling endocrine resistance., Nature Communications, Vol: 8, ISSN: 2041-1723

Resistance to endocrine therapy remains a major clinical problem in breast cancer. Genetic studies highlight the potential role of estrogen receptor-α (ESR1) mutations, which show increased prevalence in the metastatic, endocrine-resistant setting. No naturally occurring ESR1 mutations have been reported in in vitro models of BC either before or after the acquisition of endocrine resistance making functional consequences difficult to study. We report the first discovery of naturally occurring ESR1 Y537C and ESR1 Y537S mutations in MCF7 and SUM44 ESR1-positive cell lines after acquisition of resistance to long-term-estrogen-deprivation (LTED) and subsequent resistance to fulvestrant (ICIR). Mutations were enriched with time, impacted on ESR1 binding to the genome and altered the ESR1 interactome. The results highlight the importance and functional consequence of these mutations and provide an important resource for studying endocrine resistance.

Journal article

Cheang MCU, Bliss JM, Viale G, Speirs V, Palmieri C, Shaaban A, Lønning PE, Morden J, Porta N, Jassem J, van De Velde CJ, Rasmussen BB, Verhoeven D, Bartlett JMS, Coombes RC, PathIES Sub-Committeeet al., 2017, Evaluation of applying IHC4 as a prognostic model in the translational study of Intergroup Exemestane Study (IES): PathIES, Breast Cancer Research and Treatment, Vol: 168, Pages: 169-178, ISSN: 0167-6806

BACKGROUND: Intergroup Exemestane Study (IES) was a randomised study that showed a survival benefit of switching adjuvant endocrine therapy after 2-3 years from tamoxifen to exemestane. This PathIES aimed to assess the role of immunohistochemical (IHC)4 score in determining the relative sensitivity to either tamoxifen or sequential treatment with tamoxifen and exemestane. PATIENTS AND METHODS: Primary tumour samples were available for 1274 patients (27% of IES population). Only patients for whom the IHC4 score could be calculated (based on oestrogen receptor, progesterone receptor, HER2 and Ki67) were included in this analysis (N = 430 patients). The clinical score (C) was based on age, grade, tumour size and nodal status. The association of clinicopathological parameters, IHC4(+C) scores and treatment effect with time to distant recurrence-free survival (TTDR) was assessed in univariable and multivariable Cox regression analyses. A modified clinical score (PathIEscore) (N = 350) was also estimated. RESULTS: Our results confirm the prognostic importance of the original IHC4, alone and in conjunction with clinical scores, but no significant difference with treatment effects was observed. The combined IHC4 + Clinical PathIES score was prognostic for TTDR (P < 0.001) with a hazard ratio (HR) of 5.54 (95% CI 1.29-23.70) for a change from 1st quartile (Q1) to Q1-Q3 and HR of 15.54 (95% CI 3.70-65.24) for a change from Q1 to Q4. CONCLUSION: In the PathIES population, the IHC4 score is useful in predicting long-term relapse in patients who remain disease-free after 2-3 years. This is a first trial to suggest the extending use of IHC4+C score for prognostic indication for patients who have switched endocrine therapies at 2-3 years and who remain disease-free after 2-3 years.

Journal article

Smith L, Farzan R, Ali S, Buluwela L, Saurin AT, Meek DWet al., 2017, Author Correction: The responses of cancer cells to PLK1 inhibitors reveal a novel protective role for p53 in maintaining centrosome separation, Scientific Reports, Vol: 8, ISSN: 2045-2322

The original version of this Article contained a typographical error in the spelling of the author Adrian T. Saurin, which was incorrectly given as Adrian Saurin. This has now been corrected in the PDF and HTML versions of the Article, and in the accompanying Supplementary Material.

Journal article

Smith L, Farzan R, Ali S, Buluwela L, Saurin A, Meek DWet al., 2017, The responses of cancer cells to PLK1 inhibitors reveal a novel protective role for p53 in maintaining centrosome separation., Scientific Reports, Vol: 7, ISSN: 2045-2322

Polo-like kinase-1 (PLK1) plays a major role in driving mitotic events, including centrosome disjunction and separation, and is frequently over-expressed in human cancers. PLK1 inhibition is a promising therapeutic strategy and works by arresting cells in mitosis due to monopolar spindles. The p53 tumour suppressor protein is a short-lived transcription factor that can inhibit the growth, or stimulate the death, of developing cancer cells. Curiously, although p53 normally acts in an anti-cancer capacity, it can offer significant protection against inhibitors of PLK1, but the events underpinning this effect are not known. Here, we show that functional p53 reduces the sensitivity to PLK1 inhibitors by permitting centrosome separation to occur, allowing cells to traverse mitosis and re-enter cycle with a normal complement of 2N chromosomes. Protection entails the activation of p53 through the DNA damage-response enzymes, ATM and ATR, and requires the phosphorylation of p53 at the key regulatory site, Ser15. These data highlight a previously unrecognised link between p53, PLK1 and centrosome separation that has therapeutic implications for the use of PLK1 inhibitors in the clinic.

Journal article

Pan H, Gray R, Braybrooke J, Davies C, Taylor C, McGale P, Peto R, Pritchard KI, Bergh J, Dowsett M, Hayes DFet al., 2017, 20-Year Risks of Breast-Cancer Recurrence after Stopping Endocrine Therapy at 5 Years, NEW ENGLAND JOURNAL OF MEDICINE, Vol: 377, Pages: 1836-1846, ISSN: 0028-4793

Journal article

Palmieri C, Szydlo R, Miller M, Barker L, Patel NH, Sasano H, Barwick T, Tam H, Hadjiminas D, Lee J, Shaaban A, Nicholas H, Coombes RC, Kenny LMet al., 2017, IPET study: an FLT-PET window study to assess the activity of the steroid sulfatase inhibitor irosustat in early breast cancer, Breast Cancer Research and Treatment, Vol: 166, Pages: 527-539, ISSN: 0167-6806

BACKGROUND: Steroid sulfatase (STS) is involved in oestrogen biosynthesis and irosustat is a first generation, irreversible steroid sulfatase inhibitor. A pre-surgical window-of-opportunity study with irosustat was undertaken in estrogen receptor-positive (ER+) breast cancer to assess the effect of irosustat on tumour cell proliferation as measured by 3'-deoxy-3'-[18F] fluorothymidine uptake measured by PET scanning (FLT-PET) and Ki67. METHODS: Postmenopausal women with untreated ER+ early breast cancer were recruited, and imaged with FLT-PET at baseline and after at least 2 weeks treatment with irosustat, 40 mg once daily orally. The primary endpoint was changed in FLT uptake; secondary endpoints included safety and tolerability of irosustat, changes in tumoral Ki67 and steroidogenic enzymes expression and circulating steroid hormone levels. RESULTS: Thirteen women were recruited, and ten started irosustat for 2 weeks, followed by repeat FLT-PET scans in eight. Defining response as decreases of ≥20% in standardized uptake value (SUV) or ≥30% in Ki, 1 (12.5% (95% CI 2-47%, p = 0.001)) and 3 (43% (95% CI 16-75%, p = <0.001) patients, respectively, responded. 6 out of 7 patients had a Ki67 reduction (range = -19.3 to 76.4%), and median percentage difference in Ki67 was 52.3% (p = 0.028). In one patient with a low baseline STS expression, a 19.7% increase in Ki67 was recorded. STS decreases were seen in tumours with high basal STS expression, significant decreases were also noted in aromatase, and 17β-hydroxysteroid dehydrogenase type 1 and 2. Irosustat was generally well tolerated with all adverse event CTCAE Grade ≤2. CONCLUSIONS: Irosustat resulted in a significant reduction in FLT uptake and Ki67, and is well tolerated. These data are the first demonstrating clinical activity of irosustat in early breast cancer. Baseline expression of STS may be a biomarker of sensitivity to irosustat.

Journal article

Dubash SR, Merchant S, Mauri F, Kozlowski K, Lim A, Patel N, Steel J, Heinzmann K, Azeem S, Cleator S, Coombes RC, Aboagye EO, Kenny Let al., 2017, Clinical translation of the caspase 3/7 specific PET radiotracer [<SUP>18</SUP>F]ICMT-11 for measuring chemotherapy induced apoptosis in breast and lung cancer, Publisher: SPRINGER, Pages: S378-S379, ISSN: 1619-7070

Conference paper

Saleem A, Searle GE, Kenny LM, Huiban M, Kozlowski K, Waldman AD, Woodley L, Palmieri C, Lowdell C, Kaneko T, Murphy PS, Lau MR, Aboagye EO, Coombes RCet al., 2017, Lapatinib access into normal brain and brain metastases in patients with Her-2 overexpressing breast cancer (vol 5, 30, 2015), EJNMMI RESEARCH, Vol: 7, ISSN: 2191-219X

Journal article

Saleem A, Searle GE, Kenny LM, Huiban M, Kozlowski K, Waldman AD, Woodley L, Palmieri C, Lowdell C, Kaneko T, Murphy PS, Lau MR, Aboagye EO, Coombes RCet al., 2017, Erratum to: Lapatinib access into normal brain and brain metastases in patients with Her-2 overexpressing breast cancer., EJNMMI Research, Vol: 7, Pages: 74-74, ISSN: 2191-219X

Journal article

Periyasamy M, Singh A, Gemma C, Kranjec C, Farzan R, Leach D, Navaratnam N, Palinkas HL, Vertessy BG, Fenton TR, Doorbar J, Fuller-Pace F, Meek DW, Coombes RC, Buluwela L, Ali Set al., 2017, p53 controls expression of the DNA deaminase APOBEC3B to limit its potential mutagenic activity in cancer cells, Nucleic Acids Research, Vol: 45, Pages: 11056-11069, ISSN: 1362-4962

Cancer genome sequencing has implicated the cytosine deaminase activity of apolipoprotein B mRNA editing enzyme catalytic polypeptide-like (APOBEC) genes as an important source of mutations in diverse cancers, with APOBEC3B (A3B) expression especially correlated with such cancer mutations. To better understand the processes directing A3B over-expression in cancer, and possible therapeutic avenues for targeting A3B, we have investigated the regulation of A3B gene expression. Here, we show that A3B expression is inversely related to p53 status in different cancer types and demonstrate that this is due to a direct and pivotal role for p53 in repressing A3B expression. This occurs through the induction of p21 (CDKN1A) and the recruitment of the repressive DREAM complex to the A3B gene promoter, such that loss of p53 through mutation, or human papilloma virus-mediated inhibition, prevents recruitment of the complex, thereby causing elevated A3B expression and cytosine deaminase activity in cancer cells. As p53 is frequently mutated in cancer, our findings provide a mechanism by which p53 loss can promote cancer mutagenesis.

Journal article

Palmieri C, Stein RC, Liu X, Hudson E, Nicholas H, Sasano H, Guestini F, Holcombe C, Barrett S, Kenny L, Reed S, Lim A, Hayward L, Howell S, Coombes RCet al., 2017, IRIS study: a phase II study of the steroid sulfatase inhibitor Irosustat when added to an aromatase inhibitor in ER-positive breast cancer patients, Breast Cancer Research and Treatment, Vol: 165, Pages: 343-353, ISSN: 0167-6806

Purpose Irosustat is a first-generation, orally active, irreversiblesteroid sulfatase inhibitor. We performed a multicentre,open label phase II trial of the addition of Irosustatto a first-line aromatase inhibitor (AI) in patients withadvanced BC to evaluate the safety of the combination andto test the hypothesis that the addition of Irosustat to AImay further suppress estradiol levels and result in clinicalbenefit.Experimental design Postmenopausal women with ERpositivelocally advanced or metastatic breast cancer whohad derived clinical benefit from a first-line AI and whosubsequently progressed were enrolled. The first-line AIwas continued and Irosustat (40 mg orally daily) added.The primary endpoint was clinical benefit rate (CBR).Secondary endpoints included safety, tolerability, andpharmacodynamic end points.Results Twenty-seven women were recruited, four discontinuedtreatment without response assessment. Basedon local reporting, the CBR was 18.5% (95% CI6.3–38.1%) on an intent to treat basis, increasing to 21.7%(95% CI 7.4–43.7%) by per-protocol analysis. In thosepatients that achieved clinical benefit (n = 5), the median(interquartile range) duration was 9.4 months (8.1–11.3)months. The median progression-free survival time was2.7 months (95% CI 2.5–4.6) in both the ITT and perprotocolanalyses. The most frequently reported grade 3/4toxicities were dry skin (28%), nausea (13%), fatigue(13%), diarrhoea (8%), headache (7%), anorexia (7%) andlethargy (7%).Conclusions The addition of Irosustat to aromatase inhibitortherapy resulted in clinical benefit with an acceptablesafety profile. The study met its pre-defined successcriterion by both local and central radiological assessments.

Journal article

Morden JP, Alvarez I, Bertelli G, Coates AS, Coleman R, Fallowfield L, Jassem J, Jones S, Kilburn L, Lonning PE, Ortmann O, Snowdon C, van de Velde C, Andersen J, Del Mastro L, Dodwell D, Holmberg S, Nicholas H, Paridaens R, Bliss JM, Coombes RCet al., 2017, Long-Term Follow-Up of the Intergroup Exemestane Study, JOURNAL OF CLINICAL ONCOLOGY, Vol: 35, Pages: 2507-2514, ISSN: 0732-183X

PurposeThe Intergroup Exemestane Study, an investigator-led study of 4,724 postmenopausal patients with early breast cancer (clinical trial information: ISRCTN11883920), has previously demonstrated that a switch from adjuvant endocrine therapy after 2 to 3 years of tamoxifen to exemestane was associated with clinically relevant improvements in efficacy. Here, we report the final efficacy analyses of this cohort.Patients and MethodsPatients who remained disease free after 2 to 3 years of adjuvant tamoxifen were randomly assigned to continue tamoxifen or switch to exemestane to complete a total of 5 years of adjuvant endocrine therapy. Given the large number of non–breast cancer–related deaths now reported, breast cancer–free survival (BCFS), with censorship of intercurrent deaths, was the primary survival end point of interest. Analyses focus on patients with estrogen receptor-positive or unknown tumors (n = 4,599).ResultsAt the time of the data snapshot, median follow-up was 120 months. In the population that was estrogen receptor positive or had unknown estrogen receptor status, 1,111 BCFS events were observed with 508 (22.1%) of 2,294 patients in the exemestane group and 603 (26.2%) of 2,305 patients in the tamoxifen group. The data corresponded to an absolute difference (between exemestane and tamoxifen) at 10 years of 4.0% (95% CI, 1.2% to 6.7%), and the hazard ratio (HR) of 0.81 (95% CI, 0.72 to 0.92) favored exemestane. This difference remained in multivariable analysis that was adjusted for nodal status, prior use of hormone replacement therapy, and prior chemotherapy (HR, 0.80; 95% CI, 0.71 to 0.90; P < .001). A modest improvement in overall survival was seen with exemestane; the absolute difference (between exemestane and tamoxifen) at 10 years in the population that was estrogen receptor positive or had unknown estrogen receptor status was 2.1% (95% CI, −0.5% to 4.6%), and the HR was 0.89 (95% CI, 0.78 to 1.01; P = .08). For the

Journal article

Martin M, Dragoš A, Hölscher T, Maróti G, Bálint B, Westermann M, Kovács ÁTet al., 2017, De novo evolved interference competition promotes the spread of biofilm defectors., Nat Commun, Vol: 8

Biofilms are social entities where bacteria live in tightly packed agglomerations, surrounded by self-secreted exopolymers. Since production of exopolymers is costly and potentially exploitable by non-producers, mechanisms that prevent invasion of non-producing mutants are hypothesized. Here we study long-term dynamics and evolution in Bacillus subtilis biofilm populations consisting of wild-type (WT) matrix producers and mutant non-producers. We show that non-producers initially fail to incorporate into biofilms formed by the WT cells, resulting in 100-fold lower final frequency compared to the WT. However, this is modulated in a long-term scenario, as non-producers evolve the ability to better incorporate into biofilms, thereby slightly decreasing the productivity of the whole population. Detailed molecular analysis reveals that the unexpected shift in the initially stable biofilm is coupled with newly evolved phage-mediated interference competition. Our work therefore demonstrates how collective behaviour can be disrupted as a result of rapid adaptation through mobile genetic elements.

Journal article

Coombes RC, Caballero OL, Shousha S, Ghaem-Maghami S, Woodley-Barker L, Wilhelm-Benartzi CS, Neville AMet al., 2017, NY-ESO-1 expression in DCIS: A new predictor of good prognosis, Oncoscience, Vol: 4, Pages: 33-40, ISSN: 2331-4737

BACKGROUND: At present, it is difficult to predict which patients with ductal carcinoma-in-situ (DCIS) will subsequently develop frank invasive breast cancer (IDC). A recent survey by our group has shown that NY-ESO-1 and MAGEA are both expressed in DCIS. This study was aimed at determining whether expression of these antigens was related to the later development of IDC. RESULTS: 14 of 42 (33%) of patients developed invasive breast cancer during the follow up period. Only one of those DCIS cases that relapsed was positive for NYESO-1 at diagnosis. In contrast, DCIS samples of 15 of the 28 (54%) of those patients who remained disease-free expressed NY-ESO-1. (Permutation chi square p=0.0033). METHODS: We identified 42 patients with DCIS, and followed them up for more than 10 years. NY-ESO-1 and MAGEA were demonstrated by immunostaining as were CD8+ infiltrates on all sections together with the conventional markers, ER, PR, and HER2. CONCLUSIONS: Expression of NY-ESO-1 may predict those patients who will not subsequently develop invasive breast cancer and could therefore potentially be helpful in defining prognosis in patients with DCIS.

Journal article

Yague E, Asaduzzaman M, Constantinou S, Haoxiang M, Gallon J, Lin ML, Singh P, Raguz S, Ali S, Shousha S, Coombes RC, Lam EWF, Hu Y, Yague Eet al., 2017, Tumour suppressor EP300, a modulator of paclitaxel resistance and stemness, is down-regulated in metaplastic breast cancer, Breast Cancer Research and Treatment, Vol: 163, Pages: 461-474, ISSN: 1573-7217

PurposeWe have previously described a novel pathway controlling drug resistance, epithelial-to-mesenchymal transition (EMT) and stemness in breast cancer cells. Upstream in the pathway, three miRs (miR-106b, miR-93 and miR-25) target EP300, a transcriptional activator of E-cadherin. Upregulation of these miRs leads to the downregulation of EP300 and E-cadherin with initiation of an EMT. However, miRs regulate the expression of many genes, and the contribution to EMT by miR targets other than EP300 cannot be ruled out.MethodsWe used lentiviruses expressing EP300-targeting shRNA to downregulate its expression in MCF-7 cells as well as an EP300-knocked-out colon carcinoma cell line. An EP300-expression plasmid was used to upregulate its expression in basal-like CAL51 and MDA-MB-231 breast cancer cells. Drug resistance was determined by short-term proliferation and long-term colony formation assays. Stemness was determined by tumour sphere formation in both soft agar and liquid cultures as well as by the expression of CD44/CD24/ALDH markers. Gene expression microarray analysis was performed in MCF-7 cells lacking EP300. EP300 expression was analysed by immunohistochemistry in 17 samples of metaplastic breast cancer.ResultsCells lacking EP300 became more resistant to paclitaxel whereas EP300 overexpression increased their sensitivity to the drug. Expression of cancer stem cell markers, as well as tumour sphere formation, was also increased in EP300-depleted cells, and was diminished in EP300-overexpressing cells. The EP300-regulated gene signature highlighted genes associated with adhesion (CEACAM5), cytoskeletal remodelling (CAPN9), stemness (ABCG2), apoptosis (BCL2) and metastasis (TGFB2). Some genes in this signature were also validated in a previously generated EP300-depleted model of breast cancer using minimally transformed mammary epithelial cells. Importantly, two key genes in apoptosis and stemness, BCL2 and ABCG2, were also upregulated in EP300-knockout colon c

Journal article

Fulton J, Mazumder B, Whitchurch JB, Monteiro CJ, Collins HM, Chan CM, Clemente MP, Hernandez-Quiles M, Stewart EA, Amoaku WM, Moran PM, Mongan NP, Persson JL, Ali S, Heery DMet al., 2017, Heterodimers of photoreceptor-specific nuclear receptor (PNR/NR2E3) and peroxisome proliferator-activated receptor-gamma (PPAR gamma) are disrupted by retinal disease-associated mutations, Cell Death and Disease, Vol: 8, ISSN: 2041-4889

Photoreceptor-specific nuclear receptor (PNR/NR2E3) and Tailless homolog (TLX/NR2E1) are human orthologs of the NR2E group,a subgroup of phylogenetically related members of the nuclear receptor (NR) superfamily of transcription factors. We assessed theability of these NRs to form heterodimers with other members of the human NRs representing all major subgroups. The TLXligand-binding domain (LBD) did not appear to form homodimers or interact directly with any other NR tested. The PNR LBD wasable to form homodimers, but also exhibited robust interactions with the LBDs of peroxisome proliferator-activated receptor-γ(PPARγ)/NR1C3 and thyroid hormone receptor b (TRb) TRβ/NR1A2. The binding of PNR to PPARγ was specific for this paralog, asno interaction was observed with the LBDs of PPARα/NR1C1 or PPARδ/NR1C2. In support of these findings, PPARγ and PNR werefound to be co-expressed in human retinal tissue extracts and could be co-immunoprecipitated as a native complex. Selectedsequence variants in the PNR LBD associated with human retinopathies, or a mutation in the dimerization region of PPARγ LBDassociated with familial partial lipodystrophy type 3, were found to disrupt PNR/PPARγ complex formation. Wild-type PNR, but nota PNR309G mutant, was able to repress PPARγ-mediated transcription in reporter assays. In summary, our results reveal novelheterodimer interactions in the NR superfamily, suggesting previously unknown functional interactions of PNR with PPARγ andTRβ that have potential importance in retinal development and disease.

Journal article

Magnani L, Frige G, Gadaleta RM, Corleone G, Fabris S, Kempe MH, Vershure PJ, Barozzi I, Vircillo V, Hong S, Perone Y, Saini M, Trumpp A, Viale G, Neri A, Simak A, Colleoni MA, Pruneri G, Minucci Set al., 2017, Acquired CYP19A1 amplification is an early specific mechanism of aromatase inhibitor resistance in ERα metastatic breast cancer, Nature Genetics, Vol: 49, Pages: 444-450, ISSN: 1546-1718

Tumor evolution is shaped by many variables, potentially involving external selective pressures induced by therapies1. After surgery, patients with estrogen receptor (ERα)-positive breast cancer are treated with adjuvant endocrine therapy2, including selective estrogen receptor modulators (SERMs) and/or aromatase inhibitors (AIs)3. However, more than 20% of patients relapse within 10 years and eventually progress to incurable metastatic disease4. Here we demonstrate that the choice of therapy has a fundamental influence on the genetic landscape of relapsed diseases. We found that 21.5% of AI-treated, relapsed patients had acquired CYP19A1 (encoding aromatase) amplification (CYP19A1amp). Relapsed patients also developed numerous mutations targeting key breast cancer–associated genes, including ESR1 and CYP19A1. Notably, CYP19A1amp cells also emerged in vitro, but only in AI-resistant models. CYP19A1 amplification caused increased aromatase activity and estrogen-independent ERα binding to target genes, resulting in CYP19A1amp cells showing decreased sensitivity to AI treatment. These data suggest that AI treatment itself selects for acquired CYP19A1amp and promotes local autocrine estrogen signaling in AI-resistant metastatic patients.

Journal article

Page K, Guttery DS, Fernandez-Garcia D, Hills A, Hastings RK, Luo J, Goddard K, Shahin V, Woodley-Barker L, Rosales BM, Coombes RC, Stebbing J, Shaw JAet al., 2017, Next Generation Sequencing of Circulating Cell-Free DNA for Evaluating Mutations and Gene Amplification in Metastatic Breast Cancer, CLINICAL CHEMISTRY, Vol: 63, Pages: 532-541, ISSN: 0009-9147

Journal article

Hazel P, Kroll SH, Bondke A, Barbazanges M, Patel H, Fuchter MJ, Coombes RC, Ali S, Barrett AG, Freemont PSet al., 2017, Inhibitor selectivity for cyclin-dependent kinase 7: a structural, thermodynamic, and modelling study, Chemmedchem, Vol: 12, Pages: 372-380, ISSN: 1860-7187

Deregulation of the cell cycle by mechanisms that lead to elevated activities of cyclin-dependent kinases (CDK) is a feature of many human diseases, cancer in particular. We identified small-molecule inhibitors that selectively inhibit CDK7, the kinase that phosphorylates cell-cycle CDKs to promote their activities. To investigate the selectivity of these inhibitors we used a combination of structural, biophysical, and modelling approaches. We determined the crystal structures of the CDK7-selective compounds ICEC0942 and ICEC0943 bound to CDK2, and used these to build models of inhibitor binding to CDK7. Molecular dynamics (MD) simulations of inhibitors bound to CDK2 and CDK7 generated possible models of inhibitor binding. To experimentally validate these models, we gathered isothermal titration calorimetry (ITC) binding data for recombinant wild-type and binding site mutants of CDK7 and CDK2. We identified specific residues of CDK7, notably Asp155, that are involved in determining inhibitor selectivity. Our MD simulations also show that the flexibility of the G-rich and activation loops of CDK7 is likely an important determinant of inhibitor specificity similar to CDK2.

Journal article

Shaw JA, Guttery DS, Hills A, Fernandez-Garcia D, Page K, Rosales BM, Goddard KS, Hastings RK, Luo J, Ogle O, Woodley L, Ali S, Stebbing J, Coombes RCet al., 2017, Mutation analysis of cell-free DNA and single circulating tumor cells in metastatic breast cancer patients with high CTC counts, Clinical Cancer Research, Vol: 22, ISSN: 1557-3265

Purpose: The purpose of this study was to directly compare mutation profiles in multiple single CTCs and cfDNA isolated from the same blood samples taken from patients with metastaic breast cancer (MBC). We aimed to determine whether cell-free DNA would reflect the heterogeneity observed in 40 single CTCs. Experimental design: CTCs were enumerated by Cellsearch. CTC count was compared with the quantity of matched cfDNA and serum CA15-3 and alkaline phosphatase (ALP) in 112 patients with metastatic breast cancer. In 5 patients with {greater than or equal to}100 CTCs, multiple individual EpCAM-positive CTCs were isolated by DEPArray and compared with matched cfDNA and primary tumour tissue by targeted next generation sequencing (NGS) of ~2200 mutations in 50 cancer genes. Results: In the whole cohort, total cfDNA levels and cell counts ({greater than or equal to}5 CTCs) were both significantly associated with overall survival, unlike CA15-3 and ALP. NGS analysis of 40 individual EpCAM-positive CTCs from 5 patients with MBC revealed mutational heterogeneity in PIK3CA, TP53, ESR1 and KRAS genes between individual CTCs. In all 5 patients cfDNA profiles provided an accurate reflection of mutations seen in individual CTCs. ESR1 and KRAS gene mutations were absent from primary tumour tissue and therefore likely reflect either a minor sub-clonal mutation or were acquired with disease progression. Conclusion: Our results demonstrate that cfDNA reflects persisting EpCAM-positive CTCs in patients with high CTC counts and therefore may enable monitoring of the metastatic burden for clinical decision-making.Experimental Design: DNA methylation was investigated in independent tumor cohorts using Illumina HumanMethylation arrays and gene expression by Affymetrix arrays and qRT-PCR. The role of Msh homeobox 1 (MSX1) in drug sensitivity was investigated by gene reintroduction and siRNA knockdown of ovarian cancer cell lines.Results: CpG sites at contiguous genomic locations within th

Journal article

Kotwinski P, Smith G, Cooper J, Sanders J, Ma L, Teis A, Kotwinski D, Mythen M, Pennell DJ, Jones A, Montgomery H, Breast cancer Early disease Toxicity from Therapy with Epirubicin RegimensCardiac Assessment and Risk Evaluation BETTER-CARE Study Investigatorset al., 2016, Body surface area and baseline blood pressure predict subclinical anthracycline cardiotoxicity in women treated for early breast cancer., PLOS One, Vol: 11, Pages: e0165262-e0165262, ISSN: 1932-6203

BACKGROUND AND AIMS: Anthracyclines are highly effective chemotherapeutic agents which may cause long-term cardiac damage (chronic anthracycline cardiotoxicity) and heart failure. The pathogenesis of anthracycline cardiotoxicity remains incompletely understood and individual susceptibility difficult to predict. We sought clinical features which might contribute to improved risk assessment. METHODS: Subjects were women with early breast cancer, free of pre-existing cardiac disease. Left ventricular ejection fraction was measured using cardiovascular magnetic resonance before and >12 months after anthracycline-based chemotherapy (>3 months post-Trastuzumab). Variables associated with subclinical cardiotoxicity (defined as a fall in left ventricular ejection fraction of ≥5%) were identified by logistic regression. RESULTS: One hundred and sixty-five women (mean age 48.3 years at enrollment) completed the study 21.7 months [IQR 18.0-26.8] after starting chemotherapy. All received anthracyclines (98.8% epirubicin, cumulative dose 400 [300-450] mg/m2); 18% Trastuzumab. Baseline blood pressure was elevated (≥140/90mmHg, mean 147.3/86.1mmHg) in 18 subjects. Thirty-four subjects (20.7%) were identified with subclinical cardiotoxicity, independent predictors of which were the number of anthracycline cycles (odds ratio, OR 1.64 [1.17-2.30] per cycle), blood pressure ≥140/90mmHg (OR 5.36 [1.73-17.61]), body surface area (OR 2.08 [1.36-3.20] per standard deviation (0.16m2) increase), and Trastuzumab therapy (OR 3.35 [1.18-9.51]). The resultant predictive-model had an area under the receiver operating characteristics curve of 0.78 [0.70-0.86]. CONCLUSIONS: We found subclinical cardiotoxicity to be common even within this low risk cohort. Risk of cardiotoxicity was associated with modestly elevated baseline blood pressure-indicating that close attention should be paid to blood pressure in patients considered for anthracycline based chemotherapy. The association with

Journal article

Harrod A, Fulton J, Nguyen VTM, Periyasamy M, Ramos Garcia L, Lai C-F, Metodieva G, de Giorgio A, Williams RL, Santos DB, Jimenez Gomez P, Lin M-L, Metodiev MV, Stebbing J, Castellano L, Magnani L, Coombes RC, Buluwela L, Ali Set al., 2016, Genomic modelling of the ESR1 Y537S mutation for evaluating function and new therapeutic approaches for metastatic breast cancer, Oncogene, Vol: 36, Pages: 2286-2296, ISSN: 1476-5594

Drugs that inhibit estrogen receptor-α (ER) activity have been highlysuccessful in treating and reducing breast cancer progression in ER-positivedisease. However, resistance to these therapies presents a major clinicalproblem. Recent genetic studies have shown that mutations in the ER geneare found in >20% of tumours that progress on endocrine therapies.Remarkably, the great majority of these mutations localise to just a few aminoacids within or near the critical helix 12 region of the ER hormone bindingdomain, where they are likely to be single allele mutations. Understandinghow these mutations impact on ER function is a prerequiste for identifyingmethods to treat breast cancer patients featuring such mutations. Towardsthis end, we used CRISPR-Cas9 genome editing to make a single alleleknockin of the most commonly mutated amino acid residue, tyrosine 537, inthe estrogen-responsive MCF7 breast cancer cell line. Genomic analysesusing RNA-seq and ER ChIP-seq demonstrated that the Y537S mutationpromotes constitutive ER activity globally, resulting in estrogen-independentgrowth. MCF7-Y537S cells were resistant to the anti-estrogen tamoxifen andfulvestrant. Further, we show that the basal transcription factor TFIIH isconstitutively recruited by ER-Y537S, resulting in ligand-independentphosphorylation of Serine 118 (Ser118) by the TFIIH kinase, CDK7. TheCDK7 inhibitor, THZ1 prevented Ser118 phosphorylation and inhibited growthof MCF7-Y537S cells. These studies confirm the functional importance of ERmutations in endocrine resistance, demonstrate the utility of knockinmutational models for investigating alternative therapeutic approaches andhighlight CDK7 inhibition as a potential therapy for endocrine resistant breastcancer mediated by ER mutations.

Journal article

Ali S, Patel H, Periyasamy M, Bondke A, Slafer BW, Ottaviani S, Harrod A, Buluwela L, Fuchter MJ, Barrett AGM, Coombes RCet al., 2016, ICEC0942, an orally bioavailable selective inhibitor of CDK7 for breast cancer, UK Breast Cancer Research Symposium, Publisher: Springer Verlag, Pages: 195-195, ISSN: 0167-6806

Conference paper

Aleskandarany MA, Abduljabbar R, Ashankyty I, Elmouna A, Jerjees D, Ali S, Buluwela L, Diez-Rodriguez M, Caldas C, Green AR, Ellis IO, Rakha EAet al., 2016, Prognostic significance of androgen receptor expression in invasive breast cancer: transcriptomic and protein expression analysis, Breast Cancer Research and Treatment, Vol: 159, Pages: 215-227, ISSN: 1573-7217

Differential prognostic roles of Androgen Receptor (AR) have been proposed in breast cancer (BC) depending on tumour oestrogen receptor (ER) status. This study aimed to evaluate the prognostic and/or predictive significance of AR expression in invasive BC. In this study AR expression was studied on a large (n = 1141) consecutive series of early-stage (I-III) BC using tissue microarray and immunohistochemistry (IHC). AR mRNA expression was assessed in a subset of cases. The prognostic impact of AR mRNA expression was externally validated using the online BC gene expression data sets (n = 25 data sets, 4078 patients). Nuclear AR IHC expression was significantly associated with features of good prognosis including older age, smaller tumour size, lower grade and lobular histology particularly in the ER-positive tumours. AR was associated with ER-related markers GATA3, FOXa1, RERG and BEX1. Negative association was observed with HER2, p53, Ki67, TK1, CD71 and AGTR1. AR Overexpression was associated with longer survival (p < 0.001), independent of tumour size, grade, stage [p = 0.033, hazard ratio (HR) = 0.80 95 % CI = 0.64-0.98]. Similar associations were maintained in ER+ tumours in univariate and multivariate analysis (p < 0.01) both in patients with and without adjuvant endocrine or chemotherapy. AR mRNA expression showed significant association with tumour grade, molecular subtypes, and longer 10 and 15 years survival in luminal BC. In the external validation cohorts, AR gene expression data were associated with improved patients' outcome (p < 0.001, HR = 0.84, 95 % CI 0.79-0.90). AR is not only an independent prognostic factor in ER-positive luminal BC but is also expressed in ER-negative tumours. AR could act as a molecular target in patients with ER-positive disease predicting response to adjuvant therapy.

Journal article

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