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Bartlett JM, Xu K, Wong J, Pond G, Zhang Y, Spears M, Salunga R, Mallon E, Taylor KJ, Hasenburg A, Markopoulos C, Dirix L, van de Velde CJ, Rea D, Schnabel CA, Treuner K, Bayani J. Validation of the Prognostic Performance of Breast Cancer Index in Hormone Receptor-Positive Postmenopausal Breast Cancer Patients in the TEAM Trial. Clin Cancer Res 2024; 30:1509-1517. [PMID: 38345755 PMCID: PMC11016895 DOI: 10.1158/1078-0432.ccr-23-2436] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/01/2023] [Accepted: 02/08/2024] [Indexed: 04/16/2024]
Abstract
PURPOSE Patients with early-stage hormone receptor-positive (HR+) breast cancer face a prolonged risk of recurrence even after adjuvant endocrine therapy. The Breast Cancer Index (BCI) is significantly prognostic for overall (0-10 years) and late (5-10 years) distant recurrence (DR) risk in N0 and N1 patients. Here, BCI prognostic performance was evaluated in HR+ postmenopausal women from the Tamoxifen and Exemestane Adjuvant Multinational (TEAM) trial. EXPERIMENTAL DESIGN 3,544 patients were included in the analysis (N = 1,519 N0, N = 2,025 N+). BCI risk groups were calculated using pre-specified cutoff points. Kaplan-Meier analyses and log-rank tests were used to assess the prognostic significance of BCI risk groups based on DR. Hazard ratios (HR) and confidence intervals (CI) were calculated using Cox models with and without clinical covariates. RESULTS For overall 10-year DR, BCI was significantly prognostic in Ni0 (N = 1,196) and N1 (N = 1,234) patients who did not receive prior chemotherapy (P < 0.001). In patients who were DR-free for 5 years, 10-year late DR rates for low- and high-risk groups were 5.4% and 9.3% (N0 cohort, N = 1,285) and 4.8% and 12.2% (N1 cohort, N = 1,625) with multivariate HRs of 2.25 (95% CI, 1.30-3.88; P = 0.004) and 2.67 (95% CI, 1.53-4.63; P < 0.001), respectively. Late DR performance was substantially improved using previously optimized cutoff points, identifying BCI low-risk groups with even lower 10-year late DR rates of 3.8% and 2.7% in N0 and N1 patients, respectively. CONCLUSIONS The TEAM trial represents the largest prognostic validation study for BCI to date and provides a more representative assessment of late DR risk to guide individualized treatment decision-making for HR+ patients with early-stage breast cancer.
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Affiliation(s)
- John M.S. Bartlett
- Cancer Research UK Scotland Centre, University of Edinburgh, Edinburgh, United Kingdom
| | - Keying Xu
- Diagnostic Development, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jenna Wong
- Biotheranostics, A Hologic Company, San Diego, California
| | - Gregory Pond
- Department of Biostatistics, McMaster University, Hamilton, Ontario
| | - Yi Zhang
- Biotheranostics, A Hologic Company, San Diego, California
| | - Melanie Spears
- Diagnostic Development, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario
| | | | | | - Karen J. Taylor
- Cancer Research UK Scotland Centre, University of Edinburgh, Edinburgh, United Kingdom
| | - Annette Hasenburg
- Department of Gynecology and Obstetrics, University Center Mainz, Mainz, Germany
| | | | - Luc Dirix
- St. Augustinus Hospital, Antwerp, Belgium
| | | | - Daniel Rea
- Cancer Research UK Clinical Trials Unit, University of Birmingham, Birmingham, United Kingdom
| | | | - Kai Treuner
- Biotheranostics, A Hologic Company, San Diego, California
| | - Jane Bayani
- Diagnostic Development, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario
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Raman B, McCracken C, Cassar MP, Moss AJ, Finnigan L, Samat AHA, Ogbole G, Tunnicliffe EM, Alfaro-Almagro F, Menke R, Xie C, Gleeson F, Lukaschuk E, Lamlum H, McGlynn K, Popescu IA, Sanders ZB, Saunders LC, Piechnik SK, Ferreira VM, Nikolaidou C, Rahman NM, Ho LP, Harris VC, Shikotra A, Singapuri A, Pfeffer P, Manisty C, Kon OM, Beggs M, O'Regan DP, Fuld J, Weir-McCall JR, Parekh D, Steeds R, Poinasamy K, Cuthbertson DJ, Kemp GJ, Semple MG, Horsley A, Miller CA, O'Brien C, Shah AM, Chiribiri A, Leavy OC, Richardson M, Elneima O, McAuley HJC, Sereno M, Saunders RM, Houchen-Wolloff L, Greening NJ, Bolton CE, Brown JS, Choudhury G, Diar Bakerly N, Easom N, Echevarria C, Marks M, Hurst JR, Jones MG, Wootton DG, Chalder T, Davies MJ, De Soyza A, Geddes JR, Greenhalf W, Howard LS, Jacob J, Man WDC, Openshaw PJM, Porter JC, Rowland MJ, Scott JT, Singh SJ, Thomas DC, Toshner M, Lewis KE, Heaney LG, Harrison EM, Kerr S, Docherty AB, Lone NI, Quint J, Sheikh A, Zheng B, Jenkins RG, Cox E, Francis S, Halling-Brown M, Chalmers JD, Greenwood JP, Plein S, Hughes PJC, Thompson AAR, Rowland-Jones SL, Wild JM, Kelly M, Treibel TA, Bandula S, Aul R, Miller K, Jezzard P, Smith S, Nichols TE, McCann GP, Evans RA, Wain LV, Brightling CE, Neubauer S, Baillie JK, Shaw A, Hairsine B, Kurasz C, Henson H, Armstrong L, Shenton L, Dobson H, Dell A, Lucey A, Price A, Storrie A, Pennington C, Price C, Mallison G, Willis G, Nassa H, Haworth J, Hoare M, Hawkings N, Fairbairn S, Young S, Walker S, Jarrold I, Sanderson A, David C, Chong-James K, Zongo O, James WY, Martineau A, King B, Armour C, McAulay D, Major E, McGinness J, McGarvey L, Magee N, Stone R, Drain S, Craig T, Bolger A, Haggar A, Lloyd A, Subbe C, Menzies D, Southern D, McIvor E, Roberts K, Manley R, Whitehead V, Saxon W, Bularga A, Mills NL, El-Taweel H, Dawson J, Robinson L, Saralaya D, Regan K, Storton K, Brear L, Amoils S, Bermperi A, Elmer A, Ribeiro C, Cruz I, Taylor J, Worsley J, Dempsey K, Watson L, Jose S, Marciniak S, Parkes M, McQueen A, Oliver C, Williams J, Paradowski K, Broad L, Knibbs L, Haynes M, Sabit R, Milligan L, Sampson C, Hancock A, Evenden C, Lynch C, Hancock K, Roche L, Rees M, Stroud N, Thomas-Woods T, Heller S, Robertson E, Young B, Wassall H, Babores M, Holland M, Keenan N, Shashaa S, Price C, Beranova E, Ramos H, Weston H, Deery J, Austin L, Solly R, Turney S, Cosier T, Hazelton T, Ralser M, Wilson A, Pearce L, Pugmire S, Stoker W, McCormick W, Dewar A, Arbane G, Kaltsakas G, Kerslake H, Rossdale J, Bisnauthsing K, Aguilar Jimenez LA, Martinez LM, Ostermann M, Magtoto MM, Hart N, Marino P, Betts S, Solano TS, Arias AM, Prabhu A, Reed A, Wrey Brown C, Griffin D, Bevan E, Martin J, Owen J, Alvarez Corral M, Williams N, Payne S, Storrar W, Layton A, Lawson C, Mills C, Featherstone J, Stephenson L, Burdett T, Ellis Y, Richards A, Wright C, Sykes DL, Brindle K, Drury K, Holdsworth L, Crooks MG, Atkin P, Flockton R, Thackray-Nocera S, Mohamed A, Taylor A, Perkins E, Ross G, McGuinness H, Tench H, Phipps J, Loosley R, Wolf-Roberts R, Coetzee S, Omar Z, Ross A, Card B, Carr C, King C, Wood C, Copeland D, Calvelo E, Chilvers ER, Russell E, Gordon H, Nunag JL, Schronce J, March K, Samuel K, Burden L, Evison L, McLeavey L, Orriss-Dib L, Tarusan L, Mariveles M, Roy M, Mohamed N, Simpson N, Yasmin N, Cullinan P, Daly P, Haq S, Moriera S, Fayzan T, Munawar U, Nwanguma U, Lingford-Hughes A, Altmann D, Johnston D, Mitchell J, Valabhji J, Price L, Molyneaux PL, Thwaites RS, Walsh S, Frankel A, Lightstone L, Wilkins M, Willicombe M, McAdoo S, Touyz R, Guerdette AM, Warwick K, Hewitt M, Reddy R, White S, McMahon A, Hoare A, Knighton A, Ramos A, Te A, Jolley CJ, Speranza F, Assefa-Kebede H, Peralta I, Breeze J, Shevket K, Powell N, Adeyemi O, Dulawan P, Adrego R, Byrne S, Patale S, Hayday A, Malim M, Pariante C, Sharpe C, Whitney J, Bramham K, Ismail K, Wessely S, Nicholson T, Ashworth A, Humphries A, Tan AL, Whittam B, Coupland C, Favager C, Peckham D, Wade E, Saalmink G, Clarke J, Glossop J, Murira J, Rangeley J, Woods J, Hall L, Dalton M, Window N, Beirne P, Hardy T, Coakley G, Turtle L, Berridge A, Cross A, Key AL, Rowe A, Allt AM, Mears C, Malein F, Madzamba G, Hardwick HE, Earley J, Hawkes J, Pratt J, Wyles J, Tripp KA, Hainey K, Allerton L, Lavelle-Langham L, Melling L, Wajero LO, Poll L, Noonan MJ, French N, Lewis-Burke N, Williams-Howard SA, Cooper S, Kaprowska S, Dobson SL, Marsh S, Highett V, Shaw V, Beadsworth M, Defres S, Watson E, Tiongson GF, Papineni P, Gurram S, Diwanji SN, Quaid S, Briggs A, Hastie C, Rogers N, Stensel D, Bishop L, McIvor K, Rivera-Ortega P, Al-Sheklly B, Avram C, Faluyi D, Blaikely J, Piper Hanley K, Radhakrishnan K, Buch M, Hanley NA, Odell N, Osbourne R, Stockdale S, Felton T, Gorsuch T, Hussell T, Kausar Z, Kabir T, McAllister-Williams H, Paddick S, Burn D, Ayoub A, Greenhalgh A, Sayer A, Young A, Price D, Burns G, MacGowan G, Fisher H, Tedd H, Simpson J, Jiwa K, Witham M, Hogarth P, West S, Wright S, McMahon MJ, Neill P, Dougherty A, Morrow A, Anderson D, Grieve D, Bayes H, Fallon K, Mangion K, Gilmour L, Basu N, Sykes R, Berry C, McInnes IB, Donaldson A, Sage EK, Barrett F, Welsh B, Bell M, Quigley J, Leitch K, Macliver L, Patel M, Hamil R, Deans A, Furniss J, Clohisey S, Elliott A, Solstice AR, Deas C, Tee C, Connell D, Sutherland D, George J, Mohammed S, Bunker J, Holmes K, Dipper A, Morley A, Arnold D, Adamali H, Welch H, Morrison L, Stadon L, Maskell N, Barratt S, Dunn S, Waterson S, Jayaraman B, Light T, Selby N, Hosseini A, Shaw K, Almeida P, Needham R, Thomas AK, Matthews L, Gupta A, Nikolaidis A, Dupont C, Bonnington J, Chrystal M, Greenhaff PL, Linford S, Prosper S, Jang W, Alamoudi A, Bloss A, Megson C, Nicoll D, Fraser E, Pacpaco E, Conneh F, Ogg G, McShane H, Koychev I, Chen J, Pimm J, Ainsworth M, Pavlides M, Sharpe M, Havinden-Williams M, Petousi N, Talbot N, Carter P, Kurupati P, Dong T, Peng Y, Burns A, Kanellakis N, Korszun A, Connolly B, Busby J, Peto T, Patel B, Nolan CM, Cristiano D, Walsh JA, Liyanage K, Gummadi M, Dormand N, Polgar O, George P, Barker RE, Patel S, Price L, Gibbons M, Matila D, Jarvis H, Lim L, Olaosebikan O, Ahmad S, Brill S, Mandal S, Laing C, Michael A, Reddy A, Johnson C, Baxendale H, Parfrey H, Mackie J, Newman J, Pack J, Parmar J, Paques K, Garner L, Harvey A, Summersgill C, Holgate D, Hardy E, Oxton J, Pendlebury J, McMorrow L, Mairs N, Majeed N, Dark P, Ugwuoke R, Knight S, Whittaker S, Strong-Sheldrake S, Matimba-Mupaya W, Chowienczyk P, Pattenadk D, Hurditch E, Chan F, Carborn H, Foot H, Bagshaw J, Hockridge J, Sidebottom J, Lee JH, Birchall K, Turner K, Haslam L, Holt L, Milner L, Begum M, Marshall M, Steele N, Tinker N, Ravencroft P, Butcher R, Misra S, Walker S, Coburn Z, Fairman A, Ford A, Holbourn A, Howell A, Lawrie A, Lye A, Mbuyisa A, Zawia A, Holroyd-Hind B, Thamu B, Clark C, Jarman C, Norman C, Roddis C, Foote D, Lee E, Ilyas F, Stephens G, Newell H, Turton H, Macharia I, Wilson I, Cole J, McNeill J, Meiring J, Rodger J, Watson J, Chapman K, Harrington K, Chetham L, Hesselden L, Nwafor L, Dixon M, Plowright M, Wade P, Gregory R, Lenagh R, Stimpson R, Megson S, Newman T, Cheng Y, Goodwin C, Heeley C, Sissons D, Sowter D, Gregory H, Wynter I, Hutchinson J, Kirk J, Bennett K, Slack K, Allsop L, Holloway L, Flynn M, Gill M, Greatorex M, Holmes M, Buckley P, Shelton S, Turner S, Sewell TA, Whitworth V, Lovegrove W, Tomlinson J, Warburton L, Painter S, Vickers C, Redwood D, Tilley J, Palmer S, Wainwright T, Breen G, Hotopf M, Dunleavy A, Teixeira J, Ali M, Mencias M, Msimanga N, Siddique S, Samakomva T, Tavoukjian V, Forton D, Ahmed R, Cook A, Thaivalappil F, Connor L, Rees T, McNarry M, Williams N, McCormick J, McIntosh J, Vere J, Coulding M, Kilroy S, Turner V, Butt AT, Savill H, Fraile E, Ugoji J, Landers G, Lota H, Portukhay S, Nasseri M, Daniels A, Hormis A, Ingham J, Zeidan L, Osborne L, Chablani M, Banerjee A, David A, Pakzad A, Rangelov B, Williams B, Denneny E, Willoughby J, Xu M, Mehta P, Batterham R, Bell R, Aslani S, Lilaonitkul W, Checkley A, Bang D, Basire D, Lomas D, Wall E, Plant H, Roy K, Heightman M, Lipman M, Merida Morillas M, Ahwireng N, Chambers RC, Jastrub R, Logan S, Hillman T, Botkai A, Casey A, Neal A, Newton-Cox A, Cooper B, Atkin C, McGee C, Welch C, Wilson D, Sapey E, Qureshi H, Hazeldine J, Lord JM, Nyaboko J, Short J, Stockley J, Dasgin J, Draxlbauer K, Isaacs K, Mcgee K, Yip KP, Ratcliffe L, Bates M, Ventura M, Ahmad Haider N, Gautam N, Baggott R, Holden S, Madathil S, Walder S, Yasmin S, Hiwot T, Jackson T, Soulsby T, Kamwa V, Peterkin Z, Suleiman Z, Chaudhuri N, Wheeler H, Djukanovic R, Samuel R, Sass T, Wallis T, Marshall B, Childs C, Marouzet E, Harvey M, Fletcher S, Dickens C, Beckett P, Nanda U, Daynes E, Charalambou A, Yousuf AJ, Lea A, Prickett A, Gooptu B, Hargadon B, Bourne C, Christie C, Edwardson C, Lee D, Baldry E, Stringer E, Woodhead F, Mills G, Arnold H, Aung H, Qureshi IN, Finch J, Skeemer J, Hadley K, Khunti K, Carr L, Ingram L, Aljaroof M, Bakali M, Bakau M, Baldwin M, Bourne M, Pareek M, Soares M, Tobin M, Armstrong N, Brunskill N, Goodman N, Cairns P, Haldar P, McCourt P, Dowling R, Russell R, Diver S, Edwards S, Glover S, Parker S, Siddiqui S, Ward TJC, Mcnally T, Thornton T, Yates T, Ibrahim W, Monteiro W, Thickett D, Wilkinson D, Broome M, McArdle P, Upthegrove R, Wraith D, Langenberg C, Summers C, Bullmore E, Heeney JL, Schwaeble W, Sudlow CL, Adeloye D, Newby DE, Rudan I, Shankar-Hari M, Thorpe M, Pius R, Walmsley S, McGovern A, Ballard C, Allan L, Dennis J, Cavanagh J, Petrie J, O'Donnell K, Spears M, Sattar N, MacDonald S, Guthrie E, Henderson M, Guillen Guio B, Zhao B, Lawson C, Overton C, Taylor C, Tong C, Mukaetova-Ladinska E, Turner E, Pearl JE, Sargant J, Wormleighton J, Bingham M, Sharma M, Steiner M, Samani N, Novotny P, Free R, Allen RJ, Finney S, Terry S, Brugha T, Plekhanova T, McArdle A, Vinson B, Spencer LG, Reynolds W, Ashworth M, Deakin B, Chinoy H, Abel K, Harvie M, Stanel S, Rostron A, Coleman C, Baguley D, Hufton E, Khan F, Hall I, Stewart I, Fabbri L, Wright L, Kitterick P, Morriss R, Johnson S, Bates A, Antoniades C, Clark D, Bhui K, Channon KM, Motohashi K, Sigfrid L, Husain M, Webster M, Fu X, Li X, Kingham L, Klenerman P, Miiler K, Carson G, Simons G, Huneke N, Calder PC, Baldwin D, Bain S, Lasserson D, Daines L, Bright E, Stern M, Crisp P, Dharmagunawardena R, Reddington A, Wight A, Bailey L, Ashish A, Robinson E, Cooper J, Broadley A, Turnbull A, Brookes C, Sarginson C, Ionita D, Redfearn H, Elliott K, Barman L, Griffiths L, Guy Z, Gill R, Nathu R, Harris E, Moss P, Finnigan J, Saunders K, Saunders P, Kon S, Kon SS, O'Brien L, Shah K, Shah P, Richardson E, Brown V, Brown M, Brown J, Brown J, Brown A, Brown A, Brown M, Choudhury N, Jones S, Jones H, Jones L, Jones I, Jones G, Jones H, Jones D, Davies F, Davies E, Davies K, Davies G, Davies GA, Howard K, Porter J, Rowland J, Rowland A, Scott K, Singh S, Singh C, Thomas S, Thomas C, Lewis V, Lewis J, Lewis D, Harrison P, Francis C, Francis R, Hughes RA, Hughes J, Hughes AD, Thompson T, Kelly S, Smith D, Smith N, Smith A, Smith J, Smith L, Smith S, Evans T, Evans RI, Evans D, Evans R, Evans H, Evans J. Multiorgan MRI findings after hospitalisation with COVID-19 in the UK (C-MORE): a prospective, multicentre, observational cohort study. Lancet Respir Med 2023; 11:1003-1019. [PMID: 37748493 PMCID: PMC7615263 DOI: 10.1016/s2213-2600(23)00262-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/16/2023] [Accepted: 06/30/2023] [Indexed: 09/27/2023]
Abstract
INTRODUCTION The multiorgan impact of moderate to severe coronavirus infections in the post-acute phase is still poorly understood. We aimed to evaluate the excess burden of multiorgan abnormalities after hospitalisation with COVID-19, evaluate their determinants, and explore associations with patient-related outcome measures. METHODS In a prospective, UK-wide, multicentre MRI follow-up study (C-MORE), adults (aged ≥18 years) discharged from hospital following COVID-19 who were included in Tier 2 of the Post-hospitalisation COVID-19 study (PHOSP-COVID) and contemporary controls with no evidence of previous COVID-19 (SARS-CoV-2 nucleocapsid antibody negative) underwent multiorgan MRI (lungs, heart, brain, liver, and kidneys) with quantitative and qualitative assessment of images and clinical adjudication when relevant. Individuals with end-stage renal failure or contraindications to MRI were excluded. Participants also underwent detailed recording of symptoms, and physiological and biochemical tests. The primary outcome was the excess burden of multiorgan abnormalities (two or more organs) relative to controls, with further adjustments for potential confounders. The C-MORE study is ongoing and is registered with ClinicalTrials.gov, NCT04510025. FINDINGS Of 2710 participants in Tier 2 of PHOSP-COVID, 531 were recruited across 13 UK-wide C-MORE sites. After exclusions, 259 C-MORE patients (mean age 57 years [SD 12]; 158 [61%] male and 101 [39%] female) who were discharged from hospital with PCR-confirmed or clinically diagnosed COVID-19 between March 1, 2020, and Nov 1, 2021, and 52 non-COVID-19 controls from the community (mean age 49 years [SD 14]; 30 [58%] male and 22 [42%] female) were included in the analysis. Patients were assessed at a median of 5·0 months (IQR 4·2-6·3) after hospital discharge. Compared with non-COVID-19 controls, patients were older, living with more obesity, and had more comorbidities. Multiorgan abnormalities on MRI were more frequent in patients than in controls (157 [61%] of 259 vs 14 [27%] of 52; p<0·0001) and independently associated with COVID-19 status (odds ratio [OR] 2·9 [95% CI 1·5-5·8]; padjusted=0·0023) after adjusting for relevant confounders. Compared with controls, patients were more likely to have MRI evidence of lung abnormalities (p=0·0001; parenchymal abnormalities), brain abnormalities (p<0·0001; more white matter hyperintensities and regional brain volume reduction), and kidney abnormalities (p=0·014; lower medullary T1 and loss of corticomedullary differentiation), whereas cardiac and liver MRI abnormalities were similar between patients and controls. Patients with multiorgan abnormalities were older (difference in mean age 7 years [95% CI 4-10]; mean age of 59·8 years [SD 11·7] with multiorgan abnormalities vs mean age of 52·8 years [11·9] without multiorgan abnormalities; p<0·0001), more likely to have three or more comorbidities (OR 2·47 [1·32-4·82]; padjusted=0·0059), and more likely to have a more severe acute infection (acute CRP >5mg/L, OR 3·55 [1·23-11·88]; padjusted=0·025) than those without multiorgan abnormalities. Presence of lung MRI abnormalities was associated with a two-fold higher risk of chest tightness, and multiorgan MRI abnormalities were associated with severe and very severe persistent physical and mental health impairment (PHOSP-COVID symptom clusters) after hospitalisation. INTERPRETATION After hospitalisation for COVID-19, people are at risk of multiorgan abnormalities in the medium term. Our findings emphasise the need for proactive multidisciplinary care pathways, with the potential for imaging to guide surveillance frequency and therapeutic stratification. FUNDING UK Research and Innovation and National Institute for Health Research.
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Arnaout A, Robertson S, Keyhanian K, Hopkins M, Liao L, Talebian V, Awan A, Bartlett JMS, Pond GR, Radvanyi L, Bender LH, Walters IB, Ozuna VL, Spears M. Abstract PD11-02: PD11-02 A Phase II Randomized Window of Opportunity Trial Evaluating Cytotoxic and Immunomodulatory effects of Intratumoral INT230-6 in Early Stage Breast Cancer: the INVINCIBLE Trial. Cancer Res 2023. [DOI: 10.1158/1538-7445.sabcs22-pd11-02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Abstract
Background: The majority of breast cancers outside of the triple negative subtype are considered immunological quiescent and are therefore minimally responsive to immunotherapies. One potential method to combat this is through local therapies that induce cell death, thereby exposing tumor antigens, providing adjuvants for anti-tumor immune priming, and potentially increasing responsiveness to immunotherapies. We have conducted a randomized, Phase 2 presurgical Window-Of-Opportunity trial for intratumoral (IT) INT230-6 (comprising VINblastine (VIN) Cisplatin (VIN)) evaluating clinical and BioLogical Effects in patients with early-stage operable Breast Cancer (the INVINCIBLE trial- https://clinicaltrials.gov/ct2/show/NCT04781725). INT230-6 contains a dispersion enhancer molecule (SHAO) with the cytotoxic agents and is designed to cause tumor necrosis by dispersion throughout the tumor and diffusion into cancer cells. Previous in vitro studies have demonstrated that INT230-6 halts cancer cell replication and induces cell death recruiting dendritic cells and T-cells to the tumor microenvironment. In this trial, IT injections of INT230-6 are conducted to 1) exploit the potential of regional cytotoxic chemotherapy on breast cancer in vivo and 2) assess the immune response within the tumor, microenvironment and systemically in the host blood prior to surgical resection. Methods: Women with newly diagnosed and awaiting surgery for early-stage intermediate or high-grade T1-T2 invasive breast cancers were recruited to the trial. The study has two parts. Part I was a randomized (2:1) open label trial comparing 1-3 doses of INT230-6 injected weekly versus no treatment prior to surgery to evaluate safety, feasibility, and optimal drug dosing. Part II was a double-blinded randomized (2:1) trial where patients received one IT dose of INT230-6 vs saline injection. The primary objective was to estimate the proportion of patients with tumor necrosis and complete cell cycle arrest (CCCA) at the time of surgery compared to control. In addition, we performed targeted sequencing and proteomic profiling in tumour samples from the INT230-6 clinical trial. Results: The study recruited 90 patients with age ranges of 40-77 yrs (mean = 60 yrs) with tumors ranging from 1.5-4.3 cm (mean = 2.4cm). No surgeries were delayed or altered as a result of trial participation and the most common (>10%) AEs were injection site pain, injection site reaction and nausea/vomiting. Compared to the control group, up to 95% tumor necrosis was present in varying biologic subtypes and histologies, including invasive lobular carcinoma. Preliminary gene expression analysis showed significant differential gene expression between the baseline biopsy and surgical specimens. Pathway analysis identified genes associated with TCR signaling, B cells, T cells, chemokine signaling and NF-κB signaling were significantly changed in the post treatment samples. There was a relative increase in CD4 and CD8 T cells and B and NK cells within the tumor and in the tumour microenvironment. Conclusion: Preliminary evidence shows that a single dose of INT230-6 can cause substantial tumor necrosis and stimulate an immune response in breast cancers prior to surgery with minimal adverse effects and good tolerability. This window of opportunity clinical trial demonstrates that INT230-6 injection is a novel and simple method to convert traditionally immune quiescent breast cancers into immunogenic tumors. This can open the door to future potential immunotherapeutic options in early stage breast cancer.
Citation Format: Angel Arnaout, Susan Robertson, Kianoosh Keyhanian, Megan Hopkins, Linda Liao, Vida Talebian, Arif Awan, John MS Bartlett, Gregory R. Pond, Lazlo Radvanyi, Lewis H. Bender, Ian B. Walters, Vanessa Lopez Ozuna, Melanie Spears. PD11-02 A Phase II Randomized Window of Opportunity Trial Evaluating Cytotoxic and Immunomodulatory effects of Intratumoral INT230-6 in Early Stage Breast Cancer: the INVINCIBLE Trial [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD11-02.
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Affiliation(s)
- Angel Arnaout
- 1Ottawa Hospital/Ottawa Hospital Research Institute/Ontario Institute of Cancer Research, Ottawa, Ontario, Canada
| | | | | | | | - Linda Liao
- 5Ontario Institute for Cancer Research, Canada
| | | | - Arif Awan
- 7The Ottawa Hospital Cancer Centre, Canada
| | - John MS Bartlett
- 8University of Edinburgh, Scotland, United Kingdom, United Kingdom
| | | | | | | | | | | | - Melanie Spears
- 14Diagnostic Development, Ontario Institute for Cancer Research, Toronto. Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario
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Bartlett JMS, Xu K, Wong J, Pond GR, Zhang Y, Spears M, Salunga R, Mallon E, Taylor KJ, Hasenburg A, Markopoulos C, Dirix L, Seynaeve C, van de Velde CJ, Rea D, Schnabel CA, Treuner K, Bayani J. Abstract P2-11-10: Validation of the Breast Cancer Index (BCI) prognostic models optimized for late distant recurrence in postmenopausal women with early-stage HR+ breast cancer in the TEAM trial. Cancer Res 2023. [DOI: 10.1158/1538-7445.sabcs22-p2-11-10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Abstract
Background: Women with HR+ breast cancer experience a persistent risk of distant recurrence (DR) even after completion of 5 years of adjuvant endocrine therapy, with more than 50% of DR occurring after 5 years (late DR). The prognostic genomic signatures currently being used in the clinic were not developed or optimized specifically for late DR. We have previously shown that the Breast Cancer Index (BCI) and BCIN+ prognostic models were significantly prognostic for risk of overall (0-10y) and late (5-10y) distant recurrence (DR) in N0 and N1 HR+ patients in the Tamoxifen and Exemestane Adjuvant Multinational (TEAM) trial. Here, the prognostic performance of the BCI and BCIN+ models with alternative cut-points optimized for late DR were evaluated in patients from the TEAM trial, who were free from DR for at least 5 years.
Methods: BCI testing was performed blinded to clinical outcome. The pre-specified alternative cut-points 4.4 and 1.8 for BCI and BCIN+ models were determined previously from Trans-aTTom and IDEAL studies, respectively (ESMO 2021). Kaplan-Meier analysis and log-rank test were used to evaluate the prognostic significance of BCI/BCIN+ risk groups based on DR. Univariate and multivariate Cox models were used to estimate hazard ratios (HRs) and the associated 95% confidence intervals (CIs).
Results: 1285 HR+ N0 (median age 69.2, 54.2% T1, 92.5% G2-3, 21.3% chemotherapy) and 1762 N1 (median age 68.5, 49.7% T1, 80.8% G2-3, 42.6% chemotherapy) patients who remained free from DR at 5 years post randomization were included in the current analysis. For N0 patients, BCI identified 439 (34%) and 846 (66%) patients as low and high-risk with late 10-year DR rates of 3.8% (95% CI: 1.5-6.0%) and 9.1% (95% CI: 6.8-11.4%), respectively (HR: 2.6, 95% CI: 1.4-5.0; p=0.0025). For N1 patients, BCIN+ identified 287 (16%) and 1475 (84%) patients as low and high-risk with late 10-year DR rates of 3.4% (95% CI: 1.2-5.5%) and 12.3% (95% CI: 10.4-14.2%), respectively (HR: 3.5, 95% CI: 1.8-6.9; p< 0.0001). Similar results were observed in the HER2- patients. Notably, BCI/BCIN+ remained a statistically significant prognostic factor in the multivariate analysis after controlling for age, tumor size, grade, treatment. (Table).
Conclusions: Compared to the original BCI/BCIN+ models, the optimized BCI and BCIN+ models showed improved prognostic performance for identifying low-risk patients with a very low risk of late DR (< 4%), for both N0 and N1 patients. These results provide further validation of BCI clinical utility as an aid in the decision-making for extended endocrine therapies for HR+ breast cancer, particularly in patients with N1 disease that may be spared extended endocrine treatment.
Table
Citation Format: John MS Bartlett, Keying Xu, Jenna Wong, Gregory R. Pond, Yi Zhang, Melanie Spears, Ranelle Salunga, Elizabeth Mallon, Karen J. Taylor, Annette Hasenburg, Christos Markopoulos, Luc Dirix, Caroline Seynaeve, Cornelis J.H. van de Velde, Daniel Rea, Catherine A. Schnabel, Kai Treuner, Jane Bayani. Validation of the Breast Cancer Index (BCI) prognostic models optimized for late distant recurrence in postmenopausal women with early-stage HR+ breast cancer in the TEAM trial [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-11-10.
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Affiliation(s)
| | - Keying Xu
- 2Diagnostic Development, Ontario Institute for Cancer Research, Toronto. Ontario, Canada
| | - Jenna Wong
- 3Biotheranostics, A Hologic Company, San Diego
| | | | - Yi Zhang
- 5Biotheranostics, A Hologic Company
| | - Melanie Spears
- 6Diagnostic Development, Ontario Institute for Cancer Research, Toronto. Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario
| | - Ranelle Salunga
- 7Biotheranostics, A Hologic Company; Diagnostics Oncology Research & Development
| | - Elizabeth Mallon
- 8Department of Pathology, University of Glasgow, Glasgow, United Kingdom
| | - Karen J. Taylor
- 9University of Edinburgh Cancer Research Centre, Institute of Genetics and Cancer
| | - Annette Hasenburg
- 10University Medical Center Mainz, Johannes Gutenberg University, Mainz, Germany
| | - Christos Markopoulos
- 11National and Kapodistrian University of Athens, Medical School, Athens, Greece
| | - Luc Dirix
- 12Translational Cancer Research Unit, GZA Hospitals & CORE, MIPRO, University of Antwerp, Antwerp, Belgium
| | | | | | - Daniel Rea
- 15Cancer Research UK Clinical Trials Unit (CRCTU), Institute of Cancer and Genomic Sciences. College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | | | | | - Jane Bayani
- 18Diagnostic Development, Ontario Institute for Cancer Research Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto. Toronto, Ontario, Canada
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Ozuna VL, Pond GR, Bartlett JMS, Radvanyi L, Spears M, Petrocelli T, Gordon C, Rose RJ, Arnaout A. Abstract P6-05-12: Understanding Patient Perspectives on Window of Opportunity Clinical Trial Participation in Breast Cancer. Cancer Res 2023. [DOI: 10.1158/1538-7445.sabcs22-p6-05-12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Abstract
Background: Window of opportunity (WOO) clinical trials take advantage of the waiting period between a patient’s cancer diagnosis and standard treatment (usually surgery) to evaluate novel cancer therapies and their biologic effects in vivo. These types of trials are being increasingly harnessed in the clinical setting for the safe and rapid evaluation of novel therapeutic strategies in treatment naive patients, thereby expediting drug development. Distinct from neoadjuvant trials, no therapeutic benefit is envisaged and the patient’s standard treatments are not intentionally delayed. The purpose of this study was to understand the patient motivations and perspectives for participating in WOO trials. Methods: This study was conducted at an academic cancer center where two breast cancer WOO trials were ongoing (NCT04781725 and NCT04676516). Eligible patients with newly diagnosed operable invasive breast cancers participating in either of these WOO trials were recruited to this separate study. Patients were provided with a questionnaire that surveyed their motivation and perspectives for participation or lack of participation in the WOO trial Results: From April 2021- May 2022, the study recruited 89 patients with age ranging from of 40-78 yrs with tumors ranging from 1.5-4.3 cm. Surgical wait times ranged from 2-8 weeks. Of the 83 patients that participated in a WOO trial, the most common reasons for participation included (a) the potential to benefit other patients in the future (90%) (b) trust in their treating doctor (88%), (c) desire to contribute to scientific research (62%) and (d) a belief that they may benefit from the therapy (39%). For these patients, 49% reported that the possibility of a repeat biopsy would not deter them from trial participation; whereas 11% said that it definitely would. Of the 6 patients that chose not to participate in a WOO trial the most common reasons included (a) travel or transportation issues (50%) and (b) lack of belief of potential benefit to them (33%). For these patients, when asked whether the participation of a cancer patient in the design of the WOO trial would change their mind, all reported that it would not make a difference. Conclusion: WOO trials are becoming increasingly common in oncology research. Understanding patient perspectives for WOO trial participation is useful to inform trial design and communication approaches in future WOO trial efforts.
Citation Format: Vanessa Lopez Ozuna, Gregory R. Pond, John MS Bartlett, Lazlo Radvanyi, Melanie Spears, Teresa Petrocelli, Carol Gordon, Rebecca J. Rose, Angel Arnaout. Understanding Patient Perspectives on Window of Opportunity Clinical Trial Participation in Breast Cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P6-05-12.
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Affiliation(s)
| | | | - John MS Bartlett
- 3University of Edinburgh, Scotland, United Kingdom, United Kingdom
| | | | - Melanie Spears
- 5Diagnostic Development, Ontario Institute for Cancer Research, Toronto. Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario
| | | | | | | | - Angel Arnaout
- 9Ottawa Hospital/Ottawa Hospital Research Institute/Ontario Institute of Cancer Research, Ottawa, Ontario, Canada
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Bartlett J, Xu K, Wong J, Pond G, Zhang Y, Spears M, Salunga R, Mallon E, Taylor K, Hasenburg A, Markopoulos C, Dirix L, Seynaeve C, van de Velde C, Rea D, Schnabel C, Treuner K, Bayani J. 138MO Prognostic performance of Breast Cancer Index (BCI) in postmenopausal women with early-stage HR+ breast cancer in the TEAM trial. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.173] [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: 11/26/2022] Open
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Evans RA, Leavy OC, Richardson M, Elneima O, McAuley HJC, Shikotra A, Singapuri A, Sereno M, Saunders RM, Harris VC, Houchen-Wolloff L, Aul R, Beirne P, Bolton CE, Brown JS, Choudhury G, Diar-Bakerly N, Easom N, Echevarria C, Fuld J, Hart N, Hurst J, Jones MG, Parekh D, Pfeffer P, Rahman NM, Rowland-Jones SL, Shah AM, Wootton DG, Chalder T, Davies MJ, De Soyza A, Geddes JR, Greenhalf W, Greening NJ, Heaney LG, Heller S, Howard LS, Jacob J, Jenkins RG, Lord JM, Man WDC, McCann GP, Neubauer S, Openshaw PJM, Porter JC, Rowland MJ, Scott JT, Semple MG, Singh SJ, Thomas DC, Toshner M, Lewis KE, Thwaites RS, Briggs A, Docherty AB, Kerr S, Lone NI, Quint J, Sheikh A, Thorpe M, Zheng B, Chalmers JD, Ho LP, Horsley A, Marks M, Poinasamy K, Raman B, Harrison EM, Wain LV, Brightling CE, Abel K, Adamali H, Adeloye D, Adeyemi O, Adrego R, Aguilar Jimenez LA, Ahmad S, Ahmad Haider N, Ahmed R, Ahwireng N, Ainsworth M, Al-Sheklly B, Alamoudi A, Ali M, Aljaroof M, All AM, Allan L, Allen RJ, Allerton L, Allsop L, Almeida P, Altmann D, Alvarez Corral M, Amoils S, Anderson D, Antoniades C, Arbane G, Arias A, Armour C, Armstrong L, Armstrong N, Arnold D, Arnold H, Ashish A, Ashworth A, Ashworth M, Aslani S, Assefa-Kebede H, Atkin C, Atkin P, Aung H, Austin L, Avram C, Ayoub A, Babores M, Baggott R, Bagshaw J, Baguley D, Bailey L, Baillie JK, Bain S, Bakali M, Bakau M, Baldry E, Baldwin D, Ballard C, Banerjee A, Bang B, Barker RE, Barman L, Barratt S, Barrett F, Basire D, Basu N, Bates M, Bates A, Batterham R, Baxendale H, Bayes H, Beadsworth M, Beckett P, Beggs M, Begum M, Bell D, Bell R, Bennett K, Beranova E, Bermperi A, Berridge A, Berry C, Betts S, Bevan E, Bhui K, Bingham M, Birchall K, Bishop L, Bisnauthsing K, Blaikely J, Bloss A, Bolger A, Bonnington J, Botkai A, Bourne C, Bourne M, Bramham K, Brear L, Breen G, Breeze J, Bright E, Brill S, Brindle K, Broad L, Broadley A, Brookes C, Broome M, Brown A, Brown A, Brown J, Brown J, Brown M, Brown M, Brown V, Brugha T, Brunskill N, Buch M, Buckley P, Bularga A, Bullmore E, Burden L, Burdett T, Burn D, Burns G, Burns A, Busby J, Butcher R, Butt A, Byrne S, Cairns P, Calder PC, Calvelo E, Carborn H, Card B, Carr C, Carr L, Carson G, Carter P, Casey A, Cassar M, Cavanagh J, Chablani M, Chambers RC, Chan F, Channon KM, Chapman K, Charalambou A, Chaudhuri N, Checkley A, Chen J, Cheng Y, Chetham L, Childs C, Chilvers ER, Chinoy H, Chiribiri A, Chong-James K, Choudhury N, Chowienczyk P, Christie C, Chrystal M, Clark D, Clark C, Clarke J, Clohisey S, Coakley G, Coburn Z, Coetzee S, Cole J, Coleman C, Conneh F, Connell D, Connolly B, Connor L, Cook A, Cooper B, Cooper J, Cooper S, Copeland D, Cosier T, Coulding M, Coupland C, Cox E, Craig T, Crisp P, Cristiano D, Crooks MG, Cross A, Cruz I, Cullinan P, Cuthbertson D, Daines L, Dalton M, Daly P, Daniels A, Dark P, Dasgin J, David A, David C, Davies E, Davies F, Davies G, Davies GA, Davies K, Dawson J, Daynes E, Deakin B, Deans A, Deas C, Deery J, Defres S, Dell A, Dempsey K, Denneny E, Dennis J, Dewar A, Dharmagunawardena R, Dickens C, Dipper A, Diver S, Diwanji SN, Dixon M, Djukanovic R, Dobson H, Dobson SL, Donaldson A, Dong T, Dormand N, Dougherty A, Dowling R, Drain S, Draxlbauer K, Drury K, Dulawan P, Dunleavy A, Dunn S, Earley J, Edwards S, Edwardson C, El-Taweel H, Elliott A, Elliott K, Ellis Y, Elmer A, Evans D, Evans H, Evans J, Evans R, Evans RI, Evans T, Evenden C, Evison L, Fabbri L, Fairbairn S, Fairman A, Fallon K, Faluyi D, Favager C, Fayzan T, Featherstone J, Felton T, Finch J, Finney S, Finnigan J, Finnigan L, Fisher H, Fletcher S, Flockton R, Flynn M, Foot H, Foote D, Ford A, Forton D, Fraile E, Francis C, Francis R, Francis S, Frankel A, Fraser E, Free R, French N, Fu X, Furniss J, Garner L, Gautam N, George J, George P, Gibbons M, Gill M, Gilmour L, Gleeson F, Glossop J, Glover S, Goodman N, Goodwin C, Gooptu B, Gordon H, Gorsuch T, Greatorex M, Greenhaff PL, Greenhalgh A, Greenwood J, Gregory H, Gregory R, Grieve D, Griffin D, Griffiths L, Guerdette AM, Guillen Guio B, Gummadi M, Gupta A, Gurram S, Guthrie E, Guy Z, H Henson H, Hadley K, Haggar A, Hainey K, Hairsine B, Haldar P, Hall I, Hall L, Halling-Brown M, Hamil R, Hancock A, Hancock K, Hanley NA, Haq S, Hardwick HE, Hardy E, Hardy T, Hargadon B, Harrington K, Harris E, Harrison P, Harvey A, Harvey M, Harvie M, Haslam L, Havinden-Williams M, Hawkes J, Hawkings N, Haworth J, Hayday A, Haynes M, Hazeldine J, Hazelton T, Heeley C, Heeney JL, Heightman M, Henderson M, Hesselden L, Hewitt M, Highett V, Hillman T, Hiwot T, Hoare A, Hoare M, Hockridge J, Hogarth P, Holbourn A, Holden S, Holdsworth L, Holgate D, Holland M, Holloway L, Holmes K, Holmes M, Holroyd-Hind B, Holt L, Hormis A, Hosseini A, Hotopf M, Howard K, Howell A, Hufton E, Hughes AD, Hughes J, Hughes R, Humphries A, Huneke N, Hurditch E, Husain M, Hussell T, Hutchinson J, Ibrahim W, Ilyas F, Ingham J, Ingram L, Ionita D, Isaacs K, Ismail K, Jackson T, James WY, Jarman C, Jarrold I, Jarvis H, Jastrub R, Jayaraman B, Jezzard P, Jiwa K, Johnson C, Johnson S, Johnston D, Jolley CJ, Jones D, Jones G, Jones H, Jones H, Jones I, Jones L, Jones S, Jose S, Kabir T, Kaltsakas G, Kamwa V, Kanellakis N, Kaprowska S, Kausar Z, Keenan N, Kelly S, Kemp G, Kerslake H, Key AL, Khan F, Khunti K, Kilroy S, King B, King C, Kingham L, Kirk J, Kitterick P, Klenerman P, Knibbs L, Knight S, Knighton A, Kon O, Kon S, Kon SS, Koprowska S, Korszun A, Koychev I, Kurasz C, Kurupati P, Laing C, Lamlum H, Landers G, Langenberg C, Lasserson D, Lavelle-Langham L, Lawrie A, Lawson C, Lawson C, Layton A, Lea A, Lee D, Lee JH, Lee E, Leitch K, Lenagh R, Lewis D, Lewis J, Lewis V, Lewis-Burke N, Li X, Light T, Lightstone L, Lilaonitkul W, Lim L, Linford S, Lingford-Hughes A, Lipman M, Liyanage K, Lloyd A, Logan S, Lomas D, Loosley R, Lota H, Lovegrove W, Lucey A, Lukaschuk E, Lye A, Lynch C, MacDonald S, MacGowan G, Macharia I, Mackie J, Macliver L, Madathil S, Madzamba G, Magee N, Magtoto MM, Mairs N, Majeed N, Major E, Malein F, Malim M, Mallison G, Mandal S, Mangion K, Manisty C, Manley R, March K, Marciniak S, Marino P, Mariveles M, Marouzet E, Marsh S, Marshall B, Marshall M, Martin J, Martineau A, Martinez LM, Maskell N, Matila D, Matimba-Mupaya W, Matthews L, Mbuyisa A, McAdoo S, Weir McCall J, McAllister-Williams H, McArdle A, McArdle P, McAulay D, McCormick J, McCormick W, McCourt P, McGarvey L, McGee C, Mcgee K, McGinness J, McGlynn K, McGovern A, McGuinness H, McInnes IB, McIntosh J, McIvor E, McIvor K, McLeavey L, McMahon A, McMahon MJ, McMorrow L, Mcnally T, McNarry M, McNeill J, McQueen A, McShane H, Mears C, Megson C, Megson S, Mehta P, Meiring J, Melling L, Mencias M, Menzies D, Merida Morillas M, Michael A, Milligan L, Miller C, Mills C, Mills NL, Milner L, Misra S, Mitchell J, Mohamed A, Mohamed N, Mohammed S, Molyneaux PL, Monteiro W, Moriera S, Morley A, Morrison L, Morriss R, Morrow A, Moss AJ, Moss P, Motohashi K, Msimanga N, Mukaetova-Ladinska E, Munawar U, Murira J, Nanda U, Nassa H, Nasseri M, Neal A, Needham R, Neill P, Newell H, Newman T, Newton-Cox A, Nicholson T, Nicoll D, Nolan CM, Noonan MJ, Norman C, Novotny P, Nunag J, Nwafor L, Nwanguma U, Nyaboko J, O'Donnell K, O'Brien C, O'Brien L, O'Regan D, Odell N, Ogg G, Olaosebikan O, Oliver C, Omar Z, Orriss-Dib L, Osborne L, Osbourne R, Ostermann M, Overton C, Owen J, Oxton J, Pack J, Pacpaco E, Paddick S, Painter S, Pakzad A, Palmer S, Papineni P, Paques K, Paradowski K, Pareek M, Parfrey H, Pariante C, Parker S, Parkes M, Parmar J, Patale S, Patel B, Patel M, Patel S, Pattenadk D, Pavlides M, Payne S, Pearce L, Pearl JE, Peckham D, Pendlebury J, Peng Y, Pennington C, Peralta I, Perkins E, Peterkin Z, Peto T, Petousi N, Petrie J, Phipps J, Pimm J, Piper Hanley K, Pius R, Plant H, Plein S, Plekhanova T, Plowright M, Polgar O, Poll L, Porter J, Portukhay S, Powell N, Prabhu A, Pratt J, Price A, Price C, Price C, Price D, Price L, Price L, Prickett A, Propescu J, Pugmire S, Quaid S, Quigley J, Qureshi H, Qureshi IN, Radhakrishnan K, Ralser M, Ramos A, Ramos H, Rangeley J, Rangelov B, Ratcliffe L, Ravencroft P, Reddington A, Reddy R, Redfearn H, Redwood D, Reed A, Rees M, Rees T, Regan K, Reynolds W, Ribeiro C, Richards A, Richardson E, Rivera-Ortega P, Roberts K, Robertson E, Robinson E, Robinson L, Roche L, Roddis C, Rodger J, Ross A, Ross G, Rossdale J, Rostron A, Rowe A, Rowland A, Rowland J, Roy K, Roy M, Rudan I, Russell R, Russell E, Saalmink G, Sabit R, Sage EK, Samakomva T, Samani N, Sampson C, Samuel K, Samuel R, Sanderson A, Sapey E, Saralaya D, Sargant J, Sarginson C, Sass T, Sattar N, Saunders K, Saunders P, Saunders LC, Savill H, Saxon W, Sayer A, Schronce J, Schwaeble W, Scott K, Selby N, Sewell TA, Shah K, Shah P, Shankar-Hari M, Sharma M, Sharpe C, Sharpe M, Shashaa S, Shaw A, Shaw K, Shaw V, Shelton S, Shenton L, Shevket K, Short J, Siddique S, Siddiqui S, Sidebottom J, Sigfrid L, Simons G, Simpson J, Simpson N, Singh C, Singh S, Sissons D, Skeemer J, Slack K, Smith A, Smith D, Smith S, Smith J, Smith L, Soares M, Solano TS, Solly R, Solstice AR, Soulsby T, Southern D, Sowter D, Spears M, Spencer LG, Speranza F, Stadon L, Stanel S, Steele N, Steiner M, Stensel D, Stephens G, Stephenson L, Stern M, Stewart I, Stimpson R, Stockdale S, Stockley J, Stoker W, Stone R, Storrar W, Storrie A, Storton K, Stringer E, Strong-Sheldrake S, Stroud N, Subbe C, Sudlow CL, Suleiman Z, Summers C, Summersgill C, Sutherland D, Sykes DL, Sykes R, Talbot N, Tan AL, Tarusan L, Tavoukjian V, Taylor A, Taylor C, Taylor J, Te A, Tedd H, Tee CJ, Teixeira J, Tench H, Terry S, Thackray-Nocera S, Thaivalappil F, Thamu B, Thickett D, Thomas C, Thomas S, Thomas AK, Thomas-Woods T, Thompson T, Thompson AAR, Thornton T, Tilley J, Tinker N, Tiongson GF, Tobin M, Tomlinson J, Tong C, Touyz R, Tripp KA, Tunnicliffe E, Turnbull A, Turner E, Turner S, Turner V, Turner K, Turney S, Turtle L, Turton H, Ugoji J, Ugwuoke R, Upthegrove R, Valabhji J, Ventura M, Vere J, Vickers C, Vinson B, Wade E, Wade P, Wainwright T, Wajero LO, Walder S, Walker S, Walker S, Wall E, Wallis T, Walmsley S, Walsh JA, Walsh S, Warburton L, Ward TJC, Warwick K, Wassall H, Waterson S, Watson E, Watson L, Watson J, Welch C, Welch H, Welsh B, Wessely S, West S, Weston H, Wheeler H, White S, Whitehead V, Whitney J, Whittaker S, Whittam B, Whitworth V, Wight A, Wild J, Wilkins M, Wilkinson D, Williams N, Williams N, Williams J, Williams-Howard SA, Willicombe M, Willis G, Willoughby J, Wilson A, Wilson D, Wilson I, Window N, Witham M, Wolf-Roberts R, Wood C, Woodhead F, Woods J, Wormleighton J, Worsley J, Wraith D, Wrey Brown C, Wright C, Wright L, Wright S, Wyles J, Wynter I, Xu M, Yasmin N, Yasmin S, Yates T, Yip KP, Young B, Young S, Young A, Yousuf AJ, Zawia A, Zeidan L, Zhao B, Zongo O. Clinical characteristics with inflammation profiling of long COVID and association with 1-year recovery following hospitalisation in the UK: a prospective observational study. Lancet Respir Med 2022; 10:761-775. [PMID: 35472304 PMCID: PMC9034855 DOI: 10.1016/s2213-2600(22)00127-8] [Citation(s) in RCA: 144] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/23/2022] [Accepted: 03/31/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND No effective pharmacological or non-pharmacological interventions exist for patients with long COVID. We aimed to describe recovery 1 year after hospital discharge for COVID-19, identify factors associated with patient-perceived recovery, and identify potential therapeutic targets by describing the underlying inflammatory profiles of the previously described recovery clusters at 5 months after hospital discharge. METHODS The Post-hospitalisation COVID-19 study (PHOSP-COVID) is a prospective, longitudinal cohort study recruiting adults (aged ≥18 years) discharged from hospital with COVID-19 across the UK. Recovery was assessed using patient-reported outcome measures, physical performance, and organ function at 5 months and 1 year after hospital discharge, and stratified by both patient-perceived recovery and recovery cluster. Hierarchical logistic regression modelling was performed for patient-perceived recovery at 1 year. Cluster analysis was done using the clustering large applications k-medoids approach using clinical outcomes at 5 months. Inflammatory protein profiling was analysed from plasma at the 5-month visit. This study is registered on the ISRCTN Registry, ISRCTN10980107, and recruitment is ongoing. FINDINGS 2320 participants discharged from hospital between March 7, 2020, and April 18, 2021, were assessed at 5 months after discharge and 807 (32·7%) participants completed both the 5-month and 1-year visits. 279 (35·6%) of these 807 patients were women and 505 (64·4%) were men, with a mean age of 58·7 (SD 12·5) years, and 224 (27·8%) had received invasive mechanical ventilation (WHO class 7-9). The proportion of patients reporting full recovery was unchanged between 5 months (501 [25·5%] of 1965) and 1 year (232 [28·9%] of 804). Factors associated with being less likely to report full recovery at 1 year were female sex (odds ratio 0·68 [95% CI 0·46-0·99]), obesity (0·50 [0·34-0·74]) and invasive mechanical ventilation (0·42 [0·23-0·76]). Cluster analysis (n=1636) corroborated the previously reported four clusters: very severe, severe, moderate with cognitive impairment, and mild, relating to the severity of physical health, mental health, and cognitive impairment at 5 months. We found increased inflammatory mediators of tissue damage and repair in both the very severe and the moderate with cognitive impairment clusters compared with the mild cluster, including IL-6 concentration, which was increased in both comparisons (n=626 participants). We found a substantial deficit in median EQ-5D-5L utility index from before COVID-19 (retrospective assessment; 0·88 [IQR 0·74-1·00]), at 5 months (0·74 [0·64-0·88]) to 1 year (0·75 [0·62-0·88]), with minimal improvements across all outcome measures at 1 year after discharge in the whole cohort and within each of the four clusters. INTERPRETATION The sequelae of a hospital admission with COVID-19 were substantial 1 year after discharge across a range of health domains, with the minority in our cohort feeling fully recovered. Patient-perceived health-related quality of life was reduced at 1 year compared with before hospital admission. Systematic inflammation and obesity are potential treatable traits that warrant further investigation in clinical trials. FUNDING UK Research and Innovation and National Institute for Health Research.
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Arnaout A, Spears M, Awan AA, Robertson S, Keyhanian K, Pond GR, Bartlett J, Lopez-Ozuna V, Mahmood S, Bender LH, Walters IB. Intratumoral (IT) INT230-6 can cause tumor necrosis in vivo: Preliminary results of a phase II randomized presurgical window-of-opportunity study in early breast cancers (the INVINCIBLE study). J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
605 Background: The INVINCIBLE study is a randomized, Phase 2 presurgical Window-Of-Opportunity trial for IT INT230-6 (comprising VINblastine (VIN) Cisplatin (VIN)) evaluating clinical and BioLogical Effects in patients with early-stage operable Breast Cancer. INT230-6 also contains a dispersion enhancer molecule designed to facilitate diffusion of the cytotoxic agents into cancer cells and cause tumor necrosis. We have previously demonstrated that INT230-6 halts cancer cell replication and induces apoptosis while maturing dendritic cells and recruiting T-cells to the tumor microenvironment. In this trial, IT injections of INT230-6 are conducted to 1) exploit the potential of regional cytotoxic chemotherapy on breast cancer in vivo and 2) assess the potential for an immune response in the tumor microenvironment and host prior to surgical resection. Methods: Up to 90 women with newly diagnosed operable early-stage intermediate or high-grade T1-T2 invasive breast cancers are randomly allocated (2:1) prior to resection to IT injections of INT230-6, no treatment or saline sham. This study has two parts. Part I (N=29) was a randomized trial comparing 1-3 doses of INT230-6 injected weekly vs no treatment prior to surgery to evaluate safety, feasibility, and optimal drug dosing. Part II is a double-blinded randomized trial of up to 60 patients where patients will receive one IT dose of INT230-6 vs saline injection (2:1). The primary endpoint is to estimate the proportion of patients who achieve a complete cell cycle arrest post-surgery compared to the diagnosis biopsy. Secondary endpoints include an evaluation of the rate of pathological complete response, the percent of residual cancer, and safety. The study will also profile changes in CD4/CD8 and the T-cell repertoire. Results: Part I demonstrated feasibility, safety and tolerability of presurgical IT injections in breast cancer patients. Twenty patients with tumors ranging from 1-4.4cm were injected with at least one dose up to 48 hours prior to surgery. No surgeries were delayed or altered and the most common (>10%) AEs were injection site pain (100%), infusion site extravasation, injection site reaction and vomiting (10% each). Preliminary data show histologic evidence of up to 95% tumor necrosis in varying biologic subtypes and an increase in intratumoral TILs in injected tumors compared to controls. Part II is ongoing. Conclusions: Preliminary evidence shows that a single dose of INT230-6 can cause intratumoral necrosis and stimulate an immune response in breast cancers prior to surgery with minimal adverse effects and good tolerability. The results of Part II of the study will further evaluate the potential cytotoxic, immunomodulatory and other biologic effects of INT230-6 and its role as a potential cancer therapy in breast cancer patients awaiting surgery. Clinical trial information: NCT04781725.
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Affiliation(s)
- Angel Arnaout
- Department of Surgery, The Ottawa Hospital, University of Ottawa & The Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Melanie Spears
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Arif Ali Awan
- Division of Medical Oncology, The Ottawa Hospital Cancer Centre, Department of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Susan Robertson
- Eastern Ontario Regional Laboratory Association, Department of Pathology and Laboratory Medicine, University of Ottawa, Ottawa, ON, Canada
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Spears M, Talebian V, Liao L, Hopkins M, Jain D, Quintayo MA, Bayani J, Cheung A, Yaffe M, Bartlett JM. Abstract 2698: Spatial gene expression profiling in breast cancer. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Over the last decade breast cancer survival has improved, largely due to the therapies offered to patients with the disease. However, despite the advances in diagnosis and treatment of breast cancer, it is still remains the second leading cause of death from cancer in women. Breast cancer is a heterogeneous disease, this in part, explains why the majority of current therapeutic approaches for cancer work best when multiple agents are combined. The interaction between immune and tumor cells is critical in the development and progression of breast cancer. Here we present in situ transcriptomic profiling, using the NanoString Digital Spatial Profiler (DSP) cancer transcriptomic atlas (CTA) assay, of a cohort of breast cancer lumpectomies to reveal the extent of heterogeneity in pathologically defined unifocal and multifocal cancers. In this study, lumpectomies were processed as whole mounts with serial blocks reviewed. Tissue cores were taken from at least three different regions through the lumpectomy for tissue microarray (TMA) construction, focusing on morphologic/histological differences in addition to the spatial orientation of the sampled region within the lumpectomy. In situ quantification of 1800 tumor and immune genes across 60 patients revealed heterogeneity of tumor and immune genes in most patients. Expression of genes such as HER2, ER and AKT were enriched in the tumor compartment. Whereas, genes such as COLA1, CD68 and CD3 were enriched in the immune compartment. Using a SpatialDecon algorithm for mixed cell deconvolution on the immune areas heterogeneity of the tumor infiltrate at a cell type levels was observed. Fibroblasts and macrophages were prevalent in all samples while immune dense areas also contained B-cells and T-cells. While there are a number of clinically validated transcriptional assays available for breast cancer, we have demonstrated that the immune microenvironment needs to be considered to develop rational stratification of patients to currently available targeted therapies.
Citation Format: Melanie Spears, Vida Talebian, Linda Liao, Megan Hopkins, Drashti Jain, Mary Anne Quintayo, Jane Bayani, Alison Cheung, Martin Yaffe, John M. Bartlett. Spatial gene expression profiling in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2698.
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Affiliation(s)
- Melanie Spears
- 1Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Vida Talebian
- 1Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Linda Liao
- 1Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Megan Hopkins
- 1Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Drashti Jain
- 1Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Jane Bayani
- 1Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Alison Cheung
- 2Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Martin Yaffe
- 1Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - John M. Bartlett
- 1Ontario Institute for Cancer Research, Toronto, Ontario, Canada
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Spears M, Talebian V, Liao L, Hopkins M, Lynn K, Lock M, Kornecki A, Bartlett JM, Brackstone M. Abstract 2701: Molecular profiling to assess the immune response to neoadjuvant SABR in early breast cancer. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Radiation therapy is used successfully in the treatment of breast cancer. Stereotactic radiation therapy (SBRT) is well established in the treatment of lung cancer, brain metastases and various other metastatic sites. Localized radiotherapy can promote dendritic cells maturations and activation and enhances phagocytosis of cells by antigen-presenting cells (APCs) increased presentation of tumor-associated antigenic peptides, and T cells being primed from naïve towards memory phenotypes In this study we evaluated the ability to implement a three fraction SBRT regimen for low-risk primary carcinoma of the breast prior to lumpectomy and profiled the immune microenvironment using NanoString's GeoMx Digital Spatial Profiling (DSP) platform and we performed NanoString gene expression profiling using the Human v.1.1 PanCancer immune profiling panel.
NanoString's DSP platform was used to analyze 25 patient samples from the SIGNAL 2.0 clinical trial. For analysis, region of interest were selected comparing the tumor microenvironment (TME, CD45+ve) and tumor (pan cytokeratin) in pre and post treated FFPE slides. A panel of 60-antibodies were analyzed in each region. For gene expression profiling total RNA was extracted from the frozen tissue and the human V.1.1 PanCancer Immune Profiling Panel was used. We observed notable differences in the immune microenvironment gene expression patterns in samples pre- and post-treatment. We identified a total of 175 differentially expressed genes (DEGs) using a 5% adjusted p-value across the entire patient population regardless of which radiation arm. Pathway analysis identified genes associated with activation of immune response, signaling by interleukins and adaptive immune response were significantly changed in the post treatment samples. Deconvolution of the immune cell mRNA gene expression data demonstrated that there were significant changes in the cellular composition after radiotherapy. There were significant increase in expression levels of macrophages, dendritic cells, neutrophils and CD8 T cells post radiation treatment. In conclusion we have demonstrated through proteomic and transcriptomic profiling, SBRT elicits an immune response with increases in the innate response.
Citation Format: Melanie Spears, Vida Talebian, Linda Liao, Megan Hopkins, Kalan Lynn, Michael Lock, Anat Kornecki, John M. Bartlett, Muriel Brackstone. Molecular profiling to assess the immune response to neoadjuvant SABR in early breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2701.
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Affiliation(s)
- Melanie Spears
- 1Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Vida Talebian
- 1Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Linda Liao
- 1Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Megan Hopkins
- 1Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Kalan Lynn
- 2Lawson Health Research Institute, London, Ontario, Canada
| | - Michael Lock
- 3London Health Sciences Centre, London, Ontario, Canada
| | | | - John M. Bartlett
- 1Ontario Institute for Cancer Research, Toronto, Ontario, Canada
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Bayani J, Trinh QM, Quintayo MA, Crozier C, Hopkins M, Qiao J, Cheung A, Mainprize J, Morris Q, Spears M, Yaffe M, Stein L, Bartlett JM. Abstract 3131: Tumour spatial heterogeneity in breast cancer and the impact on clinical management. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-3131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
We recognize that many cancers are highly complex mixtures of sub-populations of cells, which are also influenced by their microenvironment. This heterogeneity explains in part, why the majority of current therapeutic approaches for cancer work best when multiple agents are combined. Therefore, in an era of targeted therapeutics it becomes critical to understand the complexity of tumors both at diagnosis and over the course of therapy, including measures of heterogeneity. Here we present genomic, transcriptomic and in situ proteomic profiling of a cohort of breast cancer (BCa) lumpectomies to reveal the extent of heterogeneity in pathologically defined unifocal and multifocal cancers. Integration of molecular profiling, phylogenetic analyses and radiomics has the potential to significantly improve BCa clinical management and stratification to targeted therapies that are already available in the clinic. In this study, lumpectomies with imaging data were processed as whole mounts with serial blocks reviewed. Tissue cores were taken from at least three different regions through the lumpectomy for nucleic acid extraction and tissue microarray (TMA) construction, focusing on morphologic/histological differences in addition to the spatial orientation of the sampled region within the lumpectomy. Targeted sequencing using the Oncomine Comprehensive Assay v3 (OCAv3); transcriptional profiling using the NanoString Breast Cancer 360 Panel; in situ profiling by multiplex fluorescence immunohistochemistry (MxIF) and Digital Spatial Profiling (see abstract Spears et al) were performed. From this cohort of 60 patients, we present a subset of patients demonstrating integration of the molecular profiling to reveal the phylogenetic relationship between the multiple samplings and the impact on clinical decision making in BCa. Briefly, we identified differences in the molecular subtypes between the different sample regions from the same unifocal cancer as well as differences in the predicted responses to anti-PDL1 therapy by transcriptional profiling; while targeted sequencing of driver mutations suggested the likelihood of an ancestral tumor cell giving rise to the lesions in pathologically defined multifocal cancers. However it was evident that genes and pathways found to be aberrant in these different lesions from the same cancer could impact the response to standard BCa treatment, or the selection of targeted therapies. In situ proteomics demonstrated differences in the expression of standard BCa markers ER, PgR, HER2 and Ki67 in addition to immune markers in the tumor and tumor microenvironment. While there are clinically validated transcriptional risk test available for BCa, we have demonstrated that transcriptomics or genomics alone is insufficient for a rational stratification of patients to currently available targeted therapies; therefore supporting the need for an integrative approach.
Citation Format: Jane Bayani, Quang M. Trinh, Mary Anne Quintayo, Cheryl Crozier, Megan Hopkins, Jingping Qiao, Alison Cheung, James Mainprize, Quaid Morris, Melanie Spears, Martin Yaffe, Lincoln Stein, John M. Bartlett. Tumour spatial heterogeneity in breast cancer and the impact on clinical management [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 3131.
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Affiliation(s)
- Jane Bayani
- 1Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Quang M. Trinh
- 1Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Cheryl Crozier
- 1Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Megan Hopkins
- 1Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jingping Qiao
- 1Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Alison Cheung
- 2Sunnybrook Research Institute, Toronto, Ontario, Canada
| | | | | | - Melanie Spears
- 1Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Martin Yaffe
- 2Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Lincoln Stein
- 1Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - John M. Bartlett
- 1Ontario Institute for Cancer Research, Toronto, Ontario, Canada
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Bayani J, Trinh QM, Quintayo MA, Crozier C, Hopkins M, Qiao J, Cheung A, Mainprize JG, Morris Q, Spears M, Yaffe MJ, Stein LD, Bartlett JM. Abstract PO-002: Revealing tumour spatial heterogeneity in breast cancer and the impact on clinical management. Cancer Res 2020. [DOI: 10.1158/1538-7445.tumhet2020-po-002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Many cancers are highly complex mixtures of many sub-populations of cells, also influenced by their microenvironment. This heterogeneity explains, in part, why the majority of current therapeutic approaches for cancer work best when multiple agents are combined. Therefore, in an era of targeted therapeutics it becomes critical to understand the complexity of tumours both at diagnosis and over the course of therapy, including measures of heterogeneity. Here we present genomic, transcriptomic and in situ proteomic profiling of a cohort of breast cancer (BCa) lumpectomies with associated imaging data to reveal the extent of heterogeneity in pathologically defined unifocal and multifocal cancers. Integration of molecular profiling, phylogenetic analyses and radiomics has the potential to significantly improve BCa clinical management and stratification to targeted therapies that are already available in the clinic. In this study, lumpectomies were processed as whole mounts with serial blocks reviewed. Tissue cores were taken from at least three different regions throughout the lumpectomy for nucleic acid extraction and tissue microarray (TMA) construction, focusing on morphologic/histological differences in addition to the spatial orientation of the sampled region within the lumpectomy. Targeted sequencing using the Oncomine Comprehensive Assay v3 (OCAv3); transcriptional profiling using the NanoString Breast Cancer 360 Panel; and in situ profiling by multiplex fluorescence immunohistochemistry (MxIF) performed (see abstract Cheung et al). From this cohort of 60 patients, we present a subset of patients demonstrating integration of the molecular profiling to reveal the phylogenetic relationship between the multiple samplings and the potential impact on clinical decision making in BCa. We identified differences in the molecular subtypes between the different sample regions from the same unifocal cancer as well as differences in the predicted responses to anti-PDL1 therapy by transcriptional profiling. Targeted sequencing of driver mutations suggested the likelihood of an ancestral tumour cell giving rise to the lesions in pathologically defined multifocal cancers; however it was evident that genes and pathways found to be aberrant in these different lesions from the same cancer could impact the response to standard BCa treatment, or the selection of targeted therapies. In situ proteomics demonstrated differences in the expression of standard BCa markers ER, PgR, HER2 and Ki67, in addition to immune markers in the tumour and its microenvironment. While there are clinically validated transcriptional risk tests available for BCa, we have demonstrated that transcriptomics or genomics alone is insufficient for a rational stratification of patients to currently available targeted therapies, therefore, supporting the need for an integrative approach.
Citation Format: Jane Bayani, Quang M. Trinh, Mary Anne Quintayo, Cheryl Crozier, Megan Hopkins, Jingping Qiao, Alison Cheung, James G Mainprize, Quaid Morris, Melanie Spears, Martin J. Yaffe, Lincoln D. Stein, John M.S. Bartlett. Revealing tumour spatial heterogeneity in breast cancer and the impact on clinical management [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr PO-002.
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Affiliation(s)
- Jane Bayani
- 1Ontario Institute for Cancer Research, Toronto, ON, Canada,
| | - Quang M. Trinh
- 1Ontario Institute for Cancer Research, Toronto, ON, Canada,
| | | | - Cheryl Crozier
- 1Ontario Institute for Cancer Research, Toronto, ON, Canada,
| | - Megan Hopkins
- 1Ontario Institute for Cancer Research, Toronto, ON, Canada,
| | - Jingping Qiao
- 1Ontario Institute for Cancer Research, Toronto, ON, Canada,
| | - Alison Cheung
- 2Sunnybrook Research Institute, Toronto, ON, Canada,
| | | | - Quaid Morris
- 3Memorial Sloan Kettering Cancer Center, New York, NY
| | - Melanie Spears
- 1Ontario Institute for Cancer Research, Toronto, ON, Canada,
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Lungu IM, De Luca A, Li J, Bayani J, Spears M, Pugh TJ, Bartlett JM. Abstract PO-075: Performance comparison of five extraction kits for SARS-CoV-2 RNA extraction. Clin Cancer Res 2020. [DOI: 10.1158/1557-3265.covid-19-po-075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
A new type of coronavirus, SARS-CoV-2, was identified in January 2020. Its associated disease, COVID-19, was announced as a pandemic by the World Health Organization in March 2020. The Ontario Institute for Cancer Research quickly engaged to support viral sequencing, not only in frontline health care workers but in cancer patients. A key deliverable was the selection of an extraction methodology that would not impact the supply of approved diagnostic testing reagents. This consideration was in response to reports of possible shortages predicted early in the pandemic and as indicated by the Public Health Agency of Canada (PHAC), through their call for reagents in April 2020. Five commercially available kits for automated nucleic acid extraction were compared. The KingFisher Flex Purification System (ThermoFisher, 5400610) was used for nucleic acid extraction. Four kits were selected based on availability, system compatibility, and exclusion from PHAC’s call for COVID-19 testing reagents. The MagMAX CORE Nucleic Acid Purification Kit (CORE; ThermoFisher, A32702), MagMAX Total Nucleic Acid Isolation Kit (Total NA; ThermoFisher, AM1840), MagMAX Total RNA Isolation Kit (Total RNA; ThermoFisher, AM1830), and Mag-Bind Viral DNA/RNA 96 Kit (Omega; Omega BioTek, M6246-03) were evaluated. The MagMAX Viral/Pathogen Kit (MVP; ThermoFisher, A42352), approved by the Food and Drug Administration of Canada for diagnostic testing, was used as a benchmark. Test samples were prepared using Universal Human RNA (Agilent, 740000), lambda DNA solution (Sigma Aldrich, ERMAD442K), SARS-CoV-2 RNA (ATCC, VR1986D) and heat-inactivated virus (ATCC, VR-1986HK). Extractions were performed by two operators on replicate samples. Protocols were assessed on reproducibility, yield, reagent availability, run time, and ease of use. The top two kits were validated with nasopharyngeal swab samples from SARS-CoV-2-positive patients. Four of five kits demonstrated reproducible yields, while yields from the Total RNA kit were inconsistent. The CORE and Omega kits possessed the best overall extraction efficiencies (both 70%). The MVP kit and Total NA kit were 59% and 44% efficient in recovery, respectively. The CORE and Omega kits ranked best after overall assessment. Patient samples were subsequently extracted using both kits and successfully sequenced. Extraction kits do not all perform to the same specification. In our hands, we found the MVP kit did not perform as well as others, despite being approved for diagnostic use, and the Total RNA kit showed inconsistent results. Many reagents are commercially available and should be explored as alternatives to the approved SARS-CoV-2 diagnostic reagents, particularly during a global crisis. Interestingly, following our validation testing, supply of the CORE kit became limited with unknown future availability. This illustrated the need to validate multiple methods during uncertain times in order to maintain critical testing.
Citation Format: Ilinca M. Lungu, Angela De Luca, Jason Li, Jane Bayani, Melanie Spears, Trevor J. Pugh, John M.S. Bartlett. Performance comparison of five extraction kits for SARS-CoV-2 RNA extraction [abstract]. In: Proceedings of the AACR Virtual Meeting: COVID-19 and Cancer; 2020 Jul 20-22. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(18_Suppl):Abstract nr PO-075.
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Affiliation(s)
| | - Angela De Luca
- Ontario Institute of Cancer Research, Toronto, ON, Canada
| | - Jason Li
- Ontario Institute of Cancer Research, Toronto, ON, Canada
| | - Jane Bayani
- Ontario Institute of Cancer Research, Toronto, ON, Canada
| | - Melanie Spears
- Ontario Institute of Cancer Research, Toronto, ON, Canada
| | - Trevor J. Pugh
- Ontario Institute of Cancer Research, Toronto, ON, Canada
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Bayani J, Hopkins M, Spears M, Bartlett JMS. Abstract A03: Evaluation of the Oncomine Pan-Cancer Cell-Free Assay for liquid biopsy profiling. Clin Cancer Res 2020. [DOI: 10.1158/1557-3265.liqbiop20-a03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Genomic profiling of liquid biopsies is no longer an emerging area of clinical research, but quickly becoming translated as part of contemporary clinical trials for use in the diagnostic setting. Comparatively less invasive than traditional solid tissue biopsy approaches, liquid biopsy specimens such as blood or urine can be used not only for early detection, but also for the monitoring of therapeutic response and progression. While custom circulating tumor DNA (ctDNA) assays are being academically developed for the profiling of specific biomarkers in a specific disease or therapeutic context, there are commercially available pan-cancer circulating nucleic acid (cNA) panels available. These commercially available panels can be used to reveal the spectrum of genomic changes within liquid biopsies and determine the level of sensitivity that can be obtained. In this study, we profiled 39 patients (n= 78 samples) with matched plasma and solid tumor to evaluate the Oncomine Pan-Cancer Cell-Free Assay, a 52-gene total nucleic acid panel for the detection of hotspot mutation and copy-number changes in key cancer driving genes. The evaluation cohort comprises 30 invasive breast cancers, 5 lung cancers, and 4 cancers of indeterminate origin, ranging from early and localized cancers to those that were characterized as late or metastatic. The Oncomine Pan-Cancer Cell-Free Assay utilizes molecular tagging technology to enable variant detection as low as 0.1%, given an optimal input of 20 ng of ctDNA. To determine whether variants detected using the Oncomine Pan-Cancer Cell-Free Assay were represented in the solid tumor, the solid tumor tissues were assayed using the Oncomine Pan-Cancer Cell-Free Assay in addition to the Oncomine Comprehensive Assay v3 (OCAv3). The OCAv3 profiles 161 pan-cancer genes for both full exon coverage as well as hotspot mutation and copy-number detection. Using these commercially available panels, for which OCAv3 is currently being utilized in the NCI-MATCH Trial (NCT02465060), we were able to validate the detection of genomic changes in the ctDNAs to the matching solid tissues; among them, MET mutations detected in the plasma of invasive breast cancers were identified in the matching solid tumor, as were PIK3CA and TP53 mutations, in addition to amplification of ERBB2. Similarly, KRAS mutations detected in the plasma of lung cancer patients were identified in the matched solid tumor. This presentation will summarize those findings with respect to the limit of detection obtained and the implications of monitoring progression and therapeutic response. These data suggest that existing commercial panels such as the Oncomine Pan-Cancer Cell-Free Assay, the Ion Torrent Platform, and Ion Reporter have the potential to be used in a routine clinical setting.
Citation Format: Jane Bayani, Megan Hopkins, Melanie Spears, John M. S. Bartlett. Evaluation of the Oncomine Pan-Cancer Cell-Free Assay for liquid biopsy profiling [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr A03.
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Affiliation(s)
- Jane Bayani
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Megan Hopkins
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Melanie Spears
- Ontario Institute for Cancer Research, Toronto, ON, Canada
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Taylor KJ, Lyttle N, Lao L, Gourley C, Cameron DA, Bartlett JMS, Spears M. Abstract P6-03-21: Identification of mechanisms driving acquired chemoresistance in preclinical breast cancer models of taxane resistance. Cancer Res 2020. [DOI: 10.1158/1538-7445.sabcs19-p6-03-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Taxanes are an established part of the treatment regime for early and metastatic breast cancer. However acquired chemoresistance remains a major factor in therapeutic failure in these patients. Treatment options thereafter are limited. It is key that the underlying molecular mechanisms of the taxane resistance are elucidated to drive the development of novel targeted therapies to treat chemorefractory disease.
Methods: In vitro models of taxane resistance in breast cancer were developed through continuous exposure of MDA-MB-231 and MCF7 cell lines to either paclitaxel or docetaxel. Differential gene expression analysis was performed comparing the resistant cells to chemosensitive parent lines using the Nanostring PanCancer Pathway panel. Further, RPPA analysis was utilised to investigate the proteomic signature of the chemoresistant lines and Western blotting performed to confirm key changes. A small molecule kinase screen was performed to identify candidate inhibitors with activity in the taxane resistant models.
Results: Nanostring gene expression analysis resulted in the identification of 204 significantly altered mRNA in MDA-MB-231 PACR, 231 mRNA altered in MDA-MB-231 DOCR and 88 mRNA significantly altered in MCF7 PACR (1.5 fold, p-value<0.05). Of these genes, 93 were altered in both the paclitaxel and docetaxel MDA-MB-231 models. Pathway analysis of the differentially expressed genes highlighted involvement of the MAPK and PI3K/Akt pathways in the evolution of chemoresistance. RPPA analysis predicted alterations in the protein expression of a number of select members of these pathways and Western blotting confirmed expression changes in phosphorylation of FAK, Akt and MAPK1. PI3K inhibitors BKM-120 and PIK-75 were identified as part of a small molecule kinase screen and found to inhibit cell growth in both taxane sensitive and resistant cell lines.
Table 1: Sensitivity of taxane resistant cell lines models to BKM-120 and PIK-75Cell line modelBKM-120 IC50 (µM)PIK-75 IC50 (µM)MDA-MB-231 Parent3.284 ± 0.5820.033 ± 0.008MDA-MB-231 PACR1.512 ± 0.5240.076 ± 0.018MDA-MB-231 DOCR2.267 ± 0.8160.064 ± 0.01MCF7 Parent0.421 ± 0.0440.022 ± 0.015MCF7 PACR0.289 ± 0.0410.01 ± 0.003
Conclusion: Candidate resistance-associated pathways were identified by differential gene expression analysis and proteomic analysis by RPPA. Western blotting confirmed alterations in the PI3K/Akt and MAPK pathways. PI3K inhibitors were found to have potent activity against the taxane resistant cell line models. Further investigations to confirm their potential as a therapeutic in the treatment of chemoresistant breast cancer is required.
Citation Format: Karen J Taylor, Nicola Lyttle, Linda Lao, Charlie Gourley, David A Cameron, John MS Bartlett, Melanie Spears. Identification of mechanisms driving acquired chemoresistance in preclinical breast cancer models of taxane resistance [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-03-21.
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Affiliation(s)
| | - Nicola Lyttle
- 2Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Linda Lao
- 2Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | | | | | - Melanie Spears
- 2Ontario Institute for Cancer Research, Toronto, ON, Canada
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Acs B, Leung SC, Kidwell KM, Arun I, Augulis R, Badve SS, Bai Y, Bane AL, Bartlett JM, Bayani J, Bigras G, Blank A, Borgquist S, Buikema H, Chang MC, Dietz RL, Dodson A, Ehinger A, Fineberg S, Focke CM, Gao D, Gown AM, Gutierrez C, Hartman J, Hugh JC, Kos Z, Lænkholm AV, Laurinavicius A, Levenson RM, Mahboubi-Ardakani R, Mastropasqua MG, Moriya T, Nofech-Mozes S, Osborne CK, Pantanowitz L, Penault-Llorca FM, Piper T, Quintayo MA, Rau TT, Reinhard S, Robertson S, Sakatani T, Salgado R, Spears M, Starczynski J, Sugie T, van der Vegt B, Viale G, Virk S, Zabaglo LA, Hayes DF, Dowsett M, Nielsen TO, Rimm DL. Abstract P5-02-01: Analytical validation and prognostic potential of an automated digital scoring protocol for Ki67: An International Ki67 Working Group study. Cancer Res 2020. [DOI: 10.1158/1538-7445.sabcs19-p5-02-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: The nuclear proliferation biomarker Ki67 has multiple potential roles in breast cancer, including aiding decisions based on prognosis, but has unacceptable between-laboratory variability. Here we tested an open source and calibrated automated digital image analysis (DIA) platform to: (i) Assess inter-laboratory reproducibility of automated Ki67 measurement among 17 participating labs and compare those with standardized pathologist-based visual scoring. (ii) Investigate the comparability of Ki67 measurement across corresponding core biopsy and whole section cases. (iii) Test prognostic potential of the built Ki67 scoring algorithms on an independent cohort.
Methods: Two sets of 60 previously stained slides containing 30 core-cut biopsy and 30 corresponding whole tumor sections from 30 ER+ breast cancer cases were sent to 17 participating labs for automated assessment of average Ki67 expression. The blocks were centrally cut and stained for Ki67 using the Mib-1 antibody. The QuPath (open-source software) DIA platform was used to evaluate tumoral Ki67 expression. Calibration of the DIA method was performed in our previous study (Acs et al, Lab Invest 2019). A detailed guideline for building an automated Ki67 scoring algorithm was sent to the participating labs. Visual scoring of average Ki67 expression was performed by pathologists according to published standardized methods (Leung et al, NPJ Br Cancer 2016; Leung et al, Histopath 2019). Locked down DIA Ki67 scoring algorithms were applied to a validation cohort: 222 breast cancer cases from the Karolinska University Hospital in whole section format. Sufficient reproducibility to declare analytical validity was defined as an Intra Class Correlation (ICC) with lower limit of 95% credible interval (CI) >0.80. Markov Chain Monte Carlo routines for generalized linear mixed models were used to estimate ICCs and calculate corresponding CIs.
Results: The same-section ICC was 0.902 (CI: 0.852-0.949) across 17 labs using calibrated DIA platform on core biopsy slides and 0.845 (CI: 0.778-0.912) on whole sections. The different-section ICC across the 17 labs was 0.873 (CI: 0.806-0.932) scoring on core biopsy slides and 0.777 (CI: 0.670-0.874) on whole sections. The pathologist-based visual Ki67 scoring showed ICC of 0.860 for all comparisons, respectively (CI: 0.795-0.927). Similar to what was observed for visual Ki67 scoring, the DIA scores are higher for core biopsy slides compared to paired whole sections (p≤0.001; median difference: 5.31%; IQR: 11.50%). Ki67 scores of all locked down DIA algorithms correlates significantly (p≤0.023) with outcome on the validation cohort (observed hazard ratios range: 2.518-2.922).
Conclusions: Automated Ki67 evaluation using a calibrated, open-source DIA platform (QuPath) met the pre-specified criterion of success on core biopsies but not on whole sections in the multi-institutional setting. The systematic discrepancy between core biopsy and corresponding whole sections was likely due to pre-analytical factors (tissue handling, fixation) and intratumor heterogeneity. We found that different algorithms built according to calibrated DIA methods had similar prognostic potential. Assessment of clinical utility is planned.
Citation Format: Balazs Acs, Samuel C.Y. Leung, Kelley M. Kidwell, Indu Arun, Renaldas Augulis, Sunil S. Badve, Yalai Bai, Anita L. Bane, John M.S. Bartlett, Jane Bayani, Gilbert Bigras, Annika Blank, Signe Borgquist, Henk Buikema, Martin C. Chang, Robin L. Dietz, Andrew Dodson, Anna Ehinger, Susan Fineberg, Cornelia M. Focke, Dongxia Gao, Allen M. Gown, Carolina Gutierrez, Johan Hartman, Judith C. Hugh, Zuzana Kos, Anne-Vibeke Lænkholm, Arvydas Laurinavicius, Richard M. Levenson, Rustin Mahboubi-Ardakani, Mauro G. Mastropasqua, Takuya Moriya, Sharon Nofech-Mozes, C. Kent Osborne, Liron Pantanowitz, Frédérique M. Penault-Llorca, Tammy Piper, Mary Anne Quintayo, Tilman T. Rau, Stefan Reinhard, Stephanie Robertson, Takashi Sakatani, Roberto Salgado, Melanie Spears, Jane Starczynski, Tomoharu Sugie, Bert van der Vegt, Giuseppe Viale, Shakeel Virk, Lila A. Zabaglo, Daniel F. Hayes, Mitch Dowsett, Torsten O. Nielsen, David L. Rimm, International Ki67 in Breast Cancer Working Group, BIG-NABCG. Analytical validation and prognostic potential of an automated digital scoring protocol for Ki67: An International Ki67 Working Group study [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P5-02-01.
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Affiliation(s)
- Balazs Acs
- 1Department of Pathology, Yale University School of Medicine, New Haven, CT
| | | | - Kelley M. Kidwell
- 3Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI
| | - Indu Arun
- 4Tata Medical Center, Kolkata, India
| | - Renaldas Augulis
- 5Vilnius University Faculty of Medicine and National Center of Pathology, Vilnius University Hospital Santaros Clinics, Vilnius, Lithuania
| | - Sunil S. Badve
- 6Indiana University Simon Cancer Center, Indianapolis, IN
| | - Yalai Bai
- 1Department of Pathology, Yale University School of Medicine, New Haven, CT
| | - Anita L. Bane
- 7Juravinski Hospital and Cancer Centre, McMaster University, Hamilton, ON, Canada
| | | | - Jane Bayani
- 8Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Gilbert Bigras
- 9Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada
| | - Annika Blank
- 10Universität Bern Institut für Pathologie, Murtenstrasse, Switzerland
| | | | - Henk Buikema
- 12University Medical Center Groningen, Groningen, Netherlands
| | - Martin C. Chang
- 13Department of Pathology & Laboratory Medicine, University of Vermont Medical Center, Burlington, VT
| | - Robin L. Dietz
- 14Department of Pathology, University of Pittsburgh, Pittsburgh, PA
| | - Andrew Dodson
- 15UK NEQAS for Immunocytochemistry and In-Situ Hybridisation, London, United Kingdom
| | | | - Susan Fineberg
- 16Montefiore Medical Center and the Albert Einstein College of Medicine, Bronx, NY
| | | | - Dongxia Gao
- 2University of British Columbia, Vancouver, BC, Canada
| | | | - Carolina Gutierrez
- 19Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX
| | | | | | - Zuzana Kos
- 22University of Ottawa and The Ottawa Hospital, Ottawa, ON, Canada
| | - Anne-Vibeke Lænkholm
- 23Department of Surgical Pathology, Zealand University Hospital, Slagelse, Denmark
| | - Arvydas Laurinavicius
- 5Vilnius University Faculty of Medicine and National Center of Pathology, Vilnius University Hospital Santaros Clinics, Vilnius, Lithuania
| | - Richard M. Levenson
- 24Department of Medical Pathology and Laboratory Medicine, University of California Davis Medical Center, Sacramento, CA
| | - Rustin Mahboubi-Ardakani
- 24Department of Medical Pathology and Laboratory Medicine, University of California Davis Medical Center, Sacramento, CA
| | | | | | - Sharon Nofech-Mozes
- 27University of Toronto Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - C. Kent Osborne
- 19Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX
| | | | | | - Tammy Piper
- 29Edinburgh Cancer Research Centre, Western General Hospital, Edinburgh, United Kingdom
| | | | - Tilman T. Rau
- 10Universität Bern Institut für Pathologie, Murtenstrasse, Switzerland
| | - Stefan Reinhard
- 10Universität Bern Institut für Pathologie, Murtenstrasse, Switzerland
| | | | | | | | - Melanie Spears
- 8Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Jane Starczynski
- 32Birmingham Heart of England, National Health Service, Birmingham, United Kingdom
| | | | | | | | - Shakeel Virk
- 35Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | | | | | - Mitch Dowsett
- 36The Institute of Cancer Research, London, United Kingdom
| | | | - David L. Rimm
- 1Department of Pathology, Yale University School of Medicine, New Haven, CT
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Spears M, Denkert C, Villagas SL, Lyttle N, Liao L, Quintayo MA, Twelves CJ. Abstract P1-10-08: Assessing immune biomarkers of response to anthracyclines in breast cancer. Cancer Res 2020. [DOI: 10.1158/1538-7445.sabcs19-p1-10-08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Pathologists have long recognized that the interaction between immune and tumour cells is critical in the development and progression of breast cancer. Studies have demonstrated the presence of tumour-infiltrating lymphocytes (TILs) correlates with improved clinical outcome in breast cancer especially in the triple negative and HER-2 positive subtypes. TILs predict for improved response to certain therapies including chemotherapy and trastuzumab. The predictive value of TILs in ER positive tumours is less clear. It has been demonstrated the higher presence of the immune microenvironment is associated with a better prognosis and as a result a higher likelihood of benefit from chemotherapy and possibly from immunotherapy, whereas cold immune microenvironment carries greater risk of relapse and lower benefit from chemotherapy and possibly immuno-therapies. In this study, we evaluated whether TILs could be used to predict chemotherapy response and characterize the pre-existing tumour microenvironment (TME) using NanoString’s GeoMx Digital Spatial Profiling (DSP) platform.
Methods: We assessed haematoxylin and eosin stained slides from the phase III BR9601 adjuvant breast cancer trial using software used in the international ring study 2 for standardized evaluation of TILs integrated in VMscope slide explorer. Evaluation of stromal TILs was based on international guidelines. NanoString’s DSP platform was used to analysis 256 patient samples from the BR9601 clinical trial. For analysis, region of interest were selected and compared for the TME (CD45+ve) and tumour rich (pan cytokeratin) in tissue microarrays. A panel of 56-antibodies were analysed in each ROI.
Results: The mean TIL score in this cohort of patients was 15.58% (ranging from 0 to 66.67%). The presence of higher levels of TILs was significantly associated with ER negativity (p<0.001), high grade (p=0.01) and increased lymph nodal involvement (p=0.002). In multivariate analysis, patients whose tumours had medium/high levels of TILS expression had better DRFS (HR: 0.49, 95%CI 0.24-1.02, p=0.057) when treated with E-CMF than those treated with CMF alone. Highest levels of TILs were found in Basal and HER2-like tumours. A T-cell score was generated using the average expression of CD3, CD4 and CD8. The T-cell score was examined in both the tumour and TME. Using the T cell score it was apparent that the cohort had a range of immune “hot” and immune “cold” tumours. It was demonstrated that immune “hot” TME doesn’t not always correlate with immune “hot” tumour expression. Proteins that were most associated with T-cell exclusion (p<0.01) in the TME were Fibronectin, B7-H3, PTEN, ER-α, TGFB1, FAPα and CD34. This would indicate that these proteins are causal inhibitors of T-cell invasion.
Conclusion: In conclusion, this study highlights the significance of assessing the entire tumour since TILs, tumour and stromal cells collectively engage in a complex interplay that contributes to disease development and progression. NanoString’s GeoMx DSP is a promising technology for multiplexed analysis. TILs, whether measured using automated software, or estimation by protein profiling, are predictive of chemotherapy benefit.
Citation Format: Melanie Spears, Carsten Denkert, Sonia L Villagas, Nicola Lyttle, Linda Liao, Mary Anne Quintayo, Christopher J Twelves. Assessing immune biomarkers of response to anthracyclines in breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P1-10-08.
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Affiliation(s)
- Melanie Spears
- 1Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | | | - Nicola Lyttle
- 1Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Linda Liao
- 1Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Christopher J Twelves
- 3Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom
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Bayani J, Kornaga EN, Crozier C, Jang GH, Bathurst L, Kalatskaya I, Trinh QM, Yao CQ, Livingstone J, Boutros PC, Spears M, McPherson JD, Stein LD, Rea D, Bartlett JM. Identification of Distinct Prognostic Groups: Implications for Patient Selection to Targeted Therapies Among Anti-Endocrine Therapy–Resistant Early Breast Cancers. JCO Precis Oncol 2019; 3:1-13. [DOI: 10.1200/po.18.00373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Hormone receptor–positive breast cancer remains an ongoing therapeutic challenge, despite optimal anti-endocrine therapies. In this study, we assessed the prognostic ability of genomic signatures to identify patients at risk for recurrence after endocrine therapy. Analysis was performed on the basis of an a priori hypothesis related to molecular pathways, which might predict response to existing targeted therapies. PATIENTS AND METHODS A subset of patients from the Tamoxifen Versus Exemestane Adjuvant Multinational trial ( ClinicalTrials.gov identifiers: NCT00279448 and NCT00032136, and NCT00036270) pathology cohort were analyzed to determine the prognostic ability of mutational and copy number aberration biomarkers that represent the cyclin D/cyclin-dependent kinase (CCND/CDK), fibroblast growth factor receptor/fibroblast growth factor (FGFR/FGF), and phosphatidylinositol 3-kinase/protein kinase B (PI3K/ATK) pathways to inform the potential choice of additional therapies to standard endocrine treatment. Copy number analysis and targeted sequencing was performed. Pathways were identified as aberrant if there were copy number aberrations and/or mutations in any of the predetermined pathway genes: CCND1/CCND2/CCND3/CDK4/CDK6, FGFR1/FGFR2/FGFR2/FGFR4, and AKT1/AKT2/PIK3CA/PTEN. RESULTS The 390 of 420 samples that passed quality control were analyzed for distant metastasis–free survival between groups. Patients with no changes in the CCND/CDK pathway experienced a better distant metastasis–free survival (hazard ratio, 1.94; 95% CI, 1.45 to 2.61; P < .001) than those who possessed aberrations. In the FGFR/FGF and PI3K/AKT pathways, a similar outcome was observed (hazard ratio, 1.43 [95% CI, 1.07 to 1.92; P = .017] and 1.34 [95% CI, 1.00 to 1.81; P = .053], respectively). CONCLUSION We show that aberrations of genes in these pathways are independently linked to a higher risk of relapse after endocrine treatment. Improvement of the clinical management of early breast cancers could be made by identifying those for whom current endocrine therapies are sufficient, thus reducing unnecessary treatment, and secondly, by identifying those who are at high risk for recurrence and linking molecular features that drive these cancers to treatment with targeted therapies.
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Affiliation(s)
- Jane Bayani
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Elizabeth N. Kornaga
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Tom Baker Cancer Centre, Calgary, Alberta, Canada
| | - Cheryl Crozier
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Gun Ho Jang
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Lauren Bathurst
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- University of Toronto, Toronto, Ontario, Canada
| | - Irina Kalatskaya
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- EMD Serono Research and Development Institute, Billerica, MA
| | - Quang M. Trinh
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Cindy Q. Yao
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Paul C. Boutros
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- University of Toronto, Toronto, Ontario, Canada
| | - Melanie Spears
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- University of Toronto, Toronto, Ontario, Canada
| | | | - Lincoln D. Stein
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- University of Toronto, Toronto, Ontario, Canada
| | - Daniel Rea
- University of Birmingham, Birmingham, United Kingdom
| | - John M.S. Bartlett
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- University of Toronto, Toronto, Ontario, Canada
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Beckett DJ, Spears M, Thomson E. Reliable consultant level data from an Acute Medical Unit: a powerful tool for improvement. J R Coll Physicians Edinb 2019; 48:108-113. [PMID: 29992198 DOI: 10.4997/jrcpe.2018.202] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The development of a novel database interrogating the patient management system in the Acute Medical Unit at Forth Valley Royal Hospital, Scotland, has allowed, for the first time, acquisition of reliable individual consultant-level process and outcome data over a 2-year period. These data have a number of uses, including understanding the level of variation between consultant physicians in AMU across key indicators, such as direct discharge percentage (67.5-44.3%), and readmission percentage (4.0-6.8%). Looking at overnight admissions only effectively excluded case mix as a confounder to identify variation in 30-day mortality (0-2.8%). This has allowed benchmarking, and exploring of relationships between volume of work, physician experience, and patient outcomes. For example, no significant relationship was seen between direct discharge percentage and readmission percentage. Furthermore it is extremely useful for individual clinician appraisal and governance. Finally it has practical uses when designing consultant rotas in order to minimise system variation. A key consideration throughout this work has been clear provenance and local clinical ownership of these data, unlike centrally generated data that may not accurately reflect Acute Medical Unit activity.
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Affiliation(s)
- D J Beckett
- Department of Acute Medicine, Forth Valley Royal Hospital, Larbert FK5 4WR, UK,
| | - M Spears
- Consultant Respiratory Physician, Forth Valley Royal Hospital, Larbert, UK
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Baker AEG, Bahlmann LC, Tam RY, Liu JC, Ganesh AN, Mitrousis N, Marcellus R, Spears M, Bartlett JMS, Cescon DW, Bader GD, Shoichet MS. Benchmarking to the Gold Standard: Hyaluronan-Oxime Hydrogels Recapitulate Xenograft Models with In Vitro Breast Cancer Spheroid Culture. Adv Mater 2019; 31:e1901166. [PMID: 31322299 DOI: 10.1002/adma.201901166] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/28/2019] [Indexed: 06/10/2023]
Abstract
Many 3D in vitro models induce breast cancer spheroid formation; however, this alone does not recapitulate the complex in vivo phenotype. To effectively screen therapeutics, it is urgently needed to validate in vitro cancer spheroid models against the gold standard of xenografts. A new oxime-crosslinked hyaluronan (HA) hydrogel is designed, manipulating gelation rate and mechanical properties to grow breast cancer spheroids in 3D. This HA-oxime breast cancer model maintains the gene expression profile most similar to that of tumor xenografts based on a pan-cancer gene expression profile (comprising 730 genes) of three different human breast cancer subtypes compared to Matrigel or conventional 2D culture. Differences in gene expression between breast cancer cultures in HA-oxime versus Matrigel or 2D are confirmed for 12 canonical pathways by gene set variation analysis. Importantly, drug response is dependent on the culture method. Breast cancer cells respond better to the Rac inhibitor (EHT-1864) and the PI3K inhibitor (AZD6482) when cultured in HA-oxime versus Matrigel. This study demonstrates the superiority of an HA-based hydrogel as a platform for in vitro breast cancer culture of both primary, patient-derived cells and cell lines, and provides a hydrogel culture model that closely matches that in vivo.
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Affiliation(s)
- Alexander E G Baker
- The Donnelly Centre, University of Toronto, Toronto, 160 College St, Ontario, M5S 3E1, Canada
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
- Institute of Biomaterials and Biomedical Engineering, 164 College Street, Toronto, Ontario, M5S 3G9, Canada
| | - Laura C Bahlmann
- The Donnelly Centre, University of Toronto, Toronto, 160 College St, Ontario, M5S 3E1, Canada
- Institute of Biomaterials and Biomedical Engineering, 164 College Street, Toronto, Ontario, M5S 3G9, Canada
| | - Roger Y Tam
- The Donnelly Centre, University of Toronto, Toronto, 160 College St, Ontario, M5S 3E1, Canada
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
- Institute of Biomaterials and Biomedical Engineering, 164 College Street, Toronto, Ontario, M5S 3G9, Canada
| | - Jeffrey C Liu
- The Donnelly Centre, University of Toronto, Toronto, 160 College St, Ontario, M5S 3E1, Canada
- Institute of Biomaterials and Biomedical Engineering, 164 College Street, Toronto, Ontario, M5S 3G9, Canada
| | - Ahil N Ganesh
- The Donnelly Centre, University of Toronto, Toronto, 160 College St, Ontario, M5S 3E1, Canada
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
- Institute of Biomaterials and Biomedical Engineering, 164 College Street, Toronto, Ontario, M5S 3G9, Canada
| | - Nikolaos Mitrousis
- The Donnelly Centre, University of Toronto, Toronto, 160 College St, Ontario, M5S 3E1, Canada
- Institute of Biomaterials and Biomedical Engineering, 164 College Street, Toronto, Ontario, M5S 3G9, Canada
| | - Richard Marcellus
- Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Toronto, Ontario, M5G 0A3, Canada
| | - Melanie Spears
- Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Toronto, Ontario, M5G 0A3, Canada
- Department of Laboratory Medicine and Pathology, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - John M S Bartlett
- Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Toronto, Ontario, M5G 0A3, Canada
| | - David W Cescon
- Princess Margaret Cancer Centre, University Health Network, 610 University Ave., Toronto, Ontario, M5G 2C1, Canada
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, Toronto, 160 College St, Ontario, M5S 3E1, Canada
| | - Molly S Shoichet
- The Donnelly Centre, University of Toronto, Toronto, 160 College St, Ontario, M5S 3E1, Canada
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
- Institute of Biomaterials and Biomedical Engineering, 164 College Street, Toronto, Ontario, M5S 3G9, Canada
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada
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Taylor KJ, Lyttle N, Liao L, Gourley C, Cameron DA, Bartlett JM, Spears M. Abstract P5-03-11: Sensitivity to cell cycle inhibitors in taxane resistant breast cancer models. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p5-03-11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: The use of anthracycline and taxane chemotherapy has improved overall and disease-free survival in breast cancer. However these agents have significant toxicity. In addition, breast cancers can acquire or possess intrinsic chemoresistance. It is imperative to identify patients who will benefit most from adjuvant taxane treatment and those with resistant tumours who could be spared unnecessary toxicity.
Methods: A panel of in vitro derived cell lines models of taxane resistance were generated by serial culture in escalating doses of either paclitaxel or docetaxel until resistance was achieved. Taxane resistant cells were characterised by 2D growth, cell cycle and apoptosis analyses. Genomic profiling using the NanoString® platform was performed to identify differentially expressed genes. The identification of kinases which target the chemoresistant models was achieved through a small molecule kinase inhibitor screen. Effects of selected target kinases on cell proliferation, cell cycle, apoptosis and protein expression were assessed.
Results:
Resistant cell lines exhibited an IC50 at least 40-fold higher than that of the parental cells and displayed cross-resistance to the non-establishing taxane. Cell cycle analysis revealed taxane treatment failed to induce G2/M arrest in the resistant models. A reduced apoptotic response was demonstrated. Genomic profiling identified pathways associated with the cell cycle as being significantly altered. Dinaciclib, a CDK inhibitor of CDK1, CDK2, CDK5 and CDK9, inhibited taxane resistant cell growth with IC50s comparable to the parental lines. Upon exposure to dinaciclib, cell cycle arrest at G2/M was induced and marked apoptosis demonstrated. A reduction in cyclin B1, PLK1 and pRB was observed by western blotting.
Table 1:Sensitivity of taxane resistant cell lines models to paclitaxel and docetaxelCell line modelPaclitaxel (μM)Docetaxel (μM)MDA-MB-231 Parent0.004 ± 0.0030.002 ± 0.003MDA-MB-231 PACR0.184 ± 0.030.017 ± 0.02MDA-MB-231 DOCR0.414 ± 0.0470.262 ± 0.058MCF7 Parent0.004 ± 0.00050.005 ± 0.001MCF PACR0.769 ± 0.1050.07 ± 0.02
Table 2:Gene ontology enrichment analysis of biological process terms significantly over-represented in MDA-MB-231 PACR cell line modelGO TermP-valueFDRpositive regulation of transcription from RNA polymerase II promoter1.11E-162.44E-13positive regulation of cell proliferation9.99E-161.10E-12activation of cysteine-type endopeptidase activity involved in apoptotic process1.43E-106.27E-08negative regulation of apoptotic process2.13E-095.83E-07extrinsic apoptotic signaling pathway8.33E-091.62E-06cell cycle arrest8.89E-091.62E-06positive regulation of cell migration2.83E-084.42E-06
Conclusion: In this study we identified candidate resistance-associated pathways which were differentially expressed between in vitro derived taxane resistant cell line models and the sensitive parental line. The CDK inhibitor, dinaciclib, demonstrated potent activity against the taxane resistant cell line models. Clinical validation to ascertain the role of dinaciclib as a novel therapeutic in the treatment of chemorefractory breast cancer is required.
Citation Format: Taylor KJ, Lyttle N, Liao L, Gourley C, Cameron DA, Bartlett JM, Spears M. Sensitivity to cell cycle inhibitors in taxane resistant breast cancer models [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-03-11.
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Affiliation(s)
- KJ Taylor
- University of Edinburgh, Cancer Research UK Edinburgh Centre, Western General Hospital, Edinburgh, United Kingdom; Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada
| | - N Lyttle
- University of Edinburgh, Cancer Research UK Edinburgh Centre, Western General Hospital, Edinburgh, United Kingdom; Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada
| | - L Liao
- University of Edinburgh, Cancer Research UK Edinburgh Centre, Western General Hospital, Edinburgh, United Kingdom; Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada
| | - C Gourley
- University of Edinburgh, Cancer Research UK Edinburgh Centre, Western General Hospital, Edinburgh, United Kingdom; Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada
| | - DA Cameron
- University of Edinburgh, Cancer Research UK Edinburgh Centre, Western General Hospital, Edinburgh, United Kingdom; Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada
| | - JM Bartlett
- University of Edinburgh, Cancer Research UK Edinburgh Centre, Western General Hospital, Edinburgh, United Kingdom; Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada
| | - M Spears
- University of Edinburgh, Cancer Research UK Edinburgh Centre, Western General Hospital, Edinburgh, United Kingdom; Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada
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Bathurst L, Liao L, Crozier C, Lyttle N, Marcellus R, Bayani J, Al-awar R, Bartlett J, Spears M. Abstract P5-04-24: Molecular stratification of ER+/HER2- breast cancer cell lines to predict sensitivity to targeted agents. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p5-04-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Approximately 70% of all breast cancers are estrogen receptor positive (ER+) at diagnosis and are dependent on estrogen signaling for tumour growth and proliferation. Some ER+ breast cancers can be effectively treated with adjuvant endocrine therapies including tamoxifen, but despite favorable improvements in overall survival, resistance to endocrine therapy is common and has been associated with dysregulation of several signaling pathways. These pathways can be targeted with specific inhibitors, many of which are currently under clinical investigation. However currently there is a lack of predictive biomarkers to identify which patients should receive treatment with targeted therapy. The goal of this study was to determine whether alterations in specific signaling pathways can be identified and used to stratify breast cancer cell lines to the most effective experimental treatments.
Methods/Results: Fifteen ER+/HER2- cell lines were characterized using a NanoString PAM50-like assay as well as next generation sequencing and were then stratified according to alterations in three key signaling pathways: CCND/CDK, PI3K/AKT/mTOR and FGFR. High-throughput small-molecule screenings were performed to identify the IC50 values of 24 inhibitors across the strata. Variation in inhibitor sensitivity was observed between cell lines based on molecular alterations. Cell lines with a PIK3CA mutation in combination with a CDK-pathway alteration were more sensitive to CDK inhibitors (50 to 120nM) than cell lines with alterations in the CDK-pathway alone or PIK3CA mutations alone (170nM to >5000nM). In addition, cell lines with the dual alterations demonstrated stronger synergy between CDK and PI3K-pathway inhibitors compared to either alteration alone.
Conclusions: The results suggest that stratification according to molecular alterations in specific signaling pathways may predict sensitivity to targeted inhibitors in a panel of ER+/HER2- luminal breast cancer cell lines. Work is ongoing to identify the optimal synergistic inhibitor combinations for each strata. The ultimate goal is to translate this work into a novel personalized medicine approach, using molecular stratification based on a combination of molecular events in a functional pathway as opposed to single genes.
Citation Format: Bathurst L, Liao L, Crozier C, Lyttle N, Marcellus R, Bayani J, Al-awar R, Bartlett J, Spears M. Molecular stratification of ER+/HER2- breast cancer cell lines to predict sensitivity to targeted agents [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-04-24.
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Affiliation(s)
- L Bathurst
- University of Toronto, Toronto, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - L Liao
- University of Toronto, Toronto, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - C Crozier
- University of Toronto, Toronto, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - N Lyttle
- University of Toronto, Toronto, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - R Marcellus
- University of Toronto, Toronto, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - J Bayani
- University of Toronto, Toronto, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - R Al-awar
- University of Toronto, Toronto, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - J Bartlett
- University of Toronto, Toronto, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - M Spears
- University of Toronto, Toronto, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada
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Spears M, Jensen MB, Lyttle N, Liao L, Laenkholm AV, Ejitlertsen B, Bartlett JM. Abstract P3-11-03: Validation of CIN4 in the DBCG 89D clinical cohort. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p3-11-03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Chromosome instability (CIN) in solid tumours is associated with poor prognosis and results in numerical and structural chromosomal aberrations. Our group previously have developed the CIN signatures and have demonstrated the CIN signatures as prognostic biomarkers in breast cancer cohorts. Furthermore, our work in the BR9601 and MA.5 clinical cohorts CIN4 provided level IIB evidence that CIN4 was predictive of anthracycline sensitivity. An analysis of the DBCG 89D clinical trial was now performed to validate the role of CIN gene expression signatures as a marker of anthracycline sensitivity.
Methods: RNA was extracted from patients in DBCG 89D clinical trial analysed through NanoString technology. The prognostic and predictive values of the signatures on distant relapse-free survival (DRFS) were explored using Cox proportional hazard models. Multivariate models included menopausal status, tumour size, nodal status, ER and Her2 status, histological type and grade, and treatment regimen.
Results: All of the 594 samples available from the DBCG 89D we successfully analysed. CIN25 and CIN70 gene expression signatures did not associate with any of the clinicopathological characteristics tested. In addition, CIN25 and CIN70 were not prognostic or predictive of distant relapse free or breast cancer specific survival in this clinical cohort. Low CIN4 score was associated with ER negativity (p=0.02), HER2 normal expression (p<0.05).
Conclusion: In this study we demonstrated that CIN4 was associated with aggressive disease. We were however in DBCG 89D unable to validate the predictive value of CIN4 concerning anthracycline sensitivity.
Citation Format: Spears M, Jensen M-B, Lyttle N, Liao L, Laenkholm A-V, Ejitlertsen B, Bartlett JM. Validation of CIN4 in the DBCG 89D clinical cohort [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-11-03.
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Affiliation(s)
- M Spears
- Ontario Institute for Cancer Research, Toronto, Canada; University of Toronto, Toronto, Canada; Danish Breast Cancer Cooperative Group, Copenhagen, Denmark; Slagelse Hospital, Slagelse, Denmark
| | - M-B Jensen
- Ontario Institute for Cancer Research, Toronto, Canada; University of Toronto, Toronto, Canada; Danish Breast Cancer Cooperative Group, Copenhagen, Denmark; Slagelse Hospital, Slagelse, Denmark
| | - N Lyttle
- Ontario Institute for Cancer Research, Toronto, Canada; University of Toronto, Toronto, Canada; Danish Breast Cancer Cooperative Group, Copenhagen, Denmark; Slagelse Hospital, Slagelse, Denmark
| | - L Liao
- Ontario Institute for Cancer Research, Toronto, Canada; University of Toronto, Toronto, Canada; Danish Breast Cancer Cooperative Group, Copenhagen, Denmark; Slagelse Hospital, Slagelse, Denmark
| | - A-V Laenkholm
- Ontario Institute for Cancer Research, Toronto, Canada; University of Toronto, Toronto, Canada; Danish Breast Cancer Cooperative Group, Copenhagen, Denmark; Slagelse Hospital, Slagelse, Denmark
| | - B Ejitlertsen
- Ontario Institute for Cancer Research, Toronto, Canada; University of Toronto, Toronto, Canada; Danish Breast Cancer Cooperative Group, Copenhagen, Denmark; Slagelse Hospital, Slagelse, Denmark
| | - JM Bartlett
- Ontario Institute for Cancer Research, Toronto, Canada; University of Toronto, Toronto, Canada; Danish Breast Cancer Cooperative Group, Copenhagen, Denmark; Slagelse Hospital, Slagelse, Denmark
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Spears M, Kornaga E, Lyttle N, Liao L, Bayani J, Quintayo MA, Yao CQ, D'Costa A, Boutros PC, Twelves CJ, Pritchard KI, Levine MN, Nielsen TO, Shepherd L, Bartlett JMS. Abstract P2-10-01: Validation that a histone gene signature predicts anthracycline response in early breast cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p2-10-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: The use of anthracycline-based chemotherapies has improved overall and disease free survival in breast cancer. However, anthracyclines can have significant toxicities including cardiotoxicity and leukemia. It is, therefore, imperative to identify those patients who will benefit from adjuvant anthracycline treatment and patients who could be spared unnecessary toxicities and be considered for alternative adjuvant therapy. Previous work performed by our laboratory identified a histone gene expression signature as a predictive marker of anthracycline benefit in the BR9601 clinical trial. In this study we validate the 18 histone gene signature in the MA.5 clinical trial and examine the role of the signature in individual intrinsic subtypes of breast cancer.
Methods We analysed the CCTG MA.5 clinical trial in a prospectively planned retrospective biomarker approach to validate this signature and tested the role of intrinsic subtyping as predictive markers of anthracycline benefit. RNA was extracted from patients in the MA.5 adjuvant trial evaluating the addition of epirubicin (E) to CMF and analysed using NanoString technology. Log-rank analyses validated the predictive values of the signature on distant relapse-free survival (DRFS). Cox-regression models tested independent predictive value on DRFS in the presence of treatment, age, tumour size, nodal status, HER2, ER status and grade, and treatment by marker interactions.
Results Analysis of the MA.5 clinical cohort revealed that patients whose tumour had low histone gene signature expression experienced increased DRFS (HR: 0.54, 95% CI 0.38-0.76, p=0.001) when treated with CEF compared with patients treated with CMF alone. Conversely, there was no apparent benefit of CEF vs CMF in patients with high histone gene expression signature (HR: 1.01, 95%CI 0.66-1.55, p=0.963). After multivariate analysis and adjustment for HER2, nodal status, age, grade and ER, the treatment by marker interaction for the gene signature was 0.54 (95%CI 0.31-0.94, p=0.030) for DRFS.
The predictive impact of the histone signature was independent of intrinsic subtype.
Conclusion The histone gene expression signature is an independent predictor of anthracycline benefit and could be a potential candidate diagnostic assay for patients with early breast cancer.
Citation Format: Spears M, Kornaga E, Lyttle N, Liao L, Bayani J, Quintayo M-A, Yao CQ, D'Costa A, Boutros PC, Twelves CJ, Pritchard KI, Levine MN, Nielsen TO, Shepherd L, Bartlett JMS. Validation that a histone gene signature predicts anthracycline response in early breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-10-01.
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Affiliation(s)
- M Spears
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Tom Baker Cancer Centre, Calgary, AB, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Suunybrook Odette Cancer Centre, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; University of British Columbia, Vancouver, BC, Canada; Canadian Clinical Trials Group, Kingston, ON, Canada; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - E Kornaga
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Tom Baker Cancer Centre, Calgary, AB, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Suunybrook Odette Cancer Centre, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; University of British Columbia, Vancouver, BC, Canada; Canadian Clinical Trials Group, Kingston, ON, Canada; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - N Lyttle
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Tom Baker Cancer Centre, Calgary, AB, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Suunybrook Odette Cancer Centre, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; University of British Columbia, Vancouver, BC, Canada; Canadian Clinical Trials Group, Kingston, ON, Canada; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - L Liao
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Tom Baker Cancer Centre, Calgary, AB, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Suunybrook Odette Cancer Centre, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; University of British Columbia, Vancouver, BC, Canada; Canadian Clinical Trials Group, Kingston, ON, Canada; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - J Bayani
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Tom Baker Cancer Centre, Calgary, AB, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Suunybrook Odette Cancer Centre, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; University of British Columbia, Vancouver, BC, Canada; Canadian Clinical Trials Group, Kingston, ON, Canada; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - M-A Quintayo
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Tom Baker Cancer Centre, Calgary, AB, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Suunybrook Odette Cancer Centre, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; University of British Columbia, Vancouver, BC, Canada; Canadian Clinical Trials Group, Kingston, ON, Canada; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - CQ Yao
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Tom Baker Cancer Centre, Calgary, AB, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Suunybrook Odette Cancer Centre, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; University of British Columbia, Vancouver, BC, Canada; Canadian Clinical Trials Group, Kingston, ON, Canada; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - A D'Costa
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Tom Baker Cancer Centre, Calgary, AB, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Suunybrook Odette Cancer Centre, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; University of British Columbia, Vancouver, BC, Canada; Canadian Clinical Trials Group, Kingston, ON, Canada; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - PC Boutros
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Tom Baker Cancer Centre, Calgary, AB, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Suunybrook Odette Cancer Centre, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; University of British Columbia, Vancouver, BC, Canada; Canadian Clinical Trials Group, Kingston, ON, Canada; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - CJ Twelves
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Tom Baker Cancer Centre, Calgary, AB, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Suunybrook Odette Cancer Centre, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; University of British Columbia, Vancouver, BC, Canada; Canadian Clinical Trials Group, Kingston, ON, Canada; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - KI Pritchard
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Tom Baker Cancer Centre, Calgary, AB, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Suunybrook Odette Cancer Centre, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; University of British Columbia, Vancouver, BC, Canada; Canadian Clinical Trials Group, Kingston, ON, Canada; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - MN Levine
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Tom Baker Cancer Centre, Calgary, AB, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Suunybrook Odette Cancer Centre, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; University of British Columbia, Vancouver, BC, Canada; Canadian Clinical Trials Group, Kingston, ON, Canada; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - TO Nielsen
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Tom Baker Cancer Centre, Calgary, AB, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Suunybrook Odette Cancer Centre, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; University of British Columbia, Vancouver, BC, Canada; Canadian Clinical Trials Group, Kingston, ON, Canada; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - L Shepherd
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Tom Baker Cancer Centre, Calgary, AB, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Suunybrook Odette Cancer Centre, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; University of British Columbia, Vancouver, BC, Canada; Canadian Clinical Trials Group, Kingston, ON, Canada; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - JMS Bartlett
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Tom Baker Cancer Centre, Calgary, AB, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Suunybrook Odette Cancer Centre, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; University of British Columbia, Vancouver, BC, Canada; Canadian Clinical Trials Group, Kingston, ON, Canada; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
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Spears M, Kalatskaya I, Trinh QM, Liao L, Chong TM, Crozier C, Dion D, Heisler L, Timms L, Stein LD, Pritchard KI, Levine MN, Shepherd L, Twelves CJ, Bartlett JMS. Abstract P2-10-04: Targeted sequencing in early breast cancer: Identification of novel candidate mutations predictive of anthracycline benefit. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p2-10-04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background The use of chemotherapies such as anthracyclines and taxanes have improved overall and disease free survival in breast cancer. For all patients, anthracyclines can have significant toxicities including cardiotoxicity and leukemia. It is therefore essential to select the subset of patients who will receive the optimal overall benefit from anthracycline therapy and to identify molecular pathways driving resistance. To fully understand the impact of mutations in the context of current breast cancer therapy, requires a comprehensive mapping of key molecular events in the context of treatment. We sequenced 101 genes, that were prioritized based on not only gene frequency, but also taking into account the importance of amino acid substitution, type of mutation and network connectivity, in 692 primary tumours to both identify driver genes and pathway cassettes and to understand their clinical significance in response to anthracycline treatment.
Methods We performed targeted sequencing in patients from the BR9601 (n=374) and CCTG MA.5 (n=703) clinical trials. The BR9601 and MA.5 clinical trials examined the effectiveness of combination chemotherapy consisting of CMF (cyclophosphamide, methotrexate and 5-fluorouracil) with or without epirubicin. DNA was extracted, samples were sequenced using AmpliSeq Technology adapted to Illumina and somatic mutations were called using a novel mutation calling pipeline (ISOWN). A priori analyses were performed using distant recurrence free survival (DRFS) as the primary endpoint.
Results: In 692 successfully analysed samples 509 (73.6%) samples exhibited at least one single nucleotide mutation (range 0-54). 94/101 genes were mutated in at least one patient. Only variants in PIK3CA, TP53, CDH1, TLE6, MLL3 and USH2A were detected in 5% or more of samples. TSC22D1, RB1 and ZNF565 were associated with increased risk of distant relapse in multivariate analyses corrected for clinic-pathological variables. No single genes were predictive of anthracycline treatment compared to CMF in multivariate analyses corrected for clinic-pathological variables. Signaling cassettes/modules were designed based on the pathway database, Reactome. Within the signaling cassettes one module was predictive of anthracycline failure. Patients with one or more mutations in this module had an increased risk of distant relapse (HR 0.52, 95% CI 0.29-0.95, p=0.034) when treated with an anthracycline containing chemotherapy regimen compared to CMF (HR 1.34 95% CI 1.05-1.72, p=0.019).
Conclusions: We successfully performed a signaling pathway-based targeted sequencing analysis within predefined signaling modules. We identified a single signaling cassette linked to anthracycline resistance in early breast cancer. However, further work to validate this study in a separate clinical trial is warranted.
Citation Format: Spears M, Kalatskaya I, Trinh QM, Liao L, Chong TM, Crozier C, Dion D, Heisler L, Timms L, Stein LD, Pritchard KI, Levine MN, Shepherd L, Twelves CJ, Bartlett JMS. Targeted sequencing in early breast cancer: Identification of novel candidate mutations predictive of anthracycline benefit [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-10-04.
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Affiliation(s)
- M Spears
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - I Kalatskaya
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - QM Trinh
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - L Liao
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - TM Chong
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - C Crozier
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - D Dion
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - L Heisler
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - L Timms
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - LD Stein
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - KI Pritchard
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - MN Levine
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - L Shepherd
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - CJ Twelves
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - JMS Bartlett
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
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Kalatskaya I, Trinh Q, Spears M, Bartlett J, Stein L. Abstract 3571: Precise somatic mutation prediction in the absence of matching normal DNA. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-3571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Accurate identification of somatic mutations is an essential first step for many cancer studies. It is usually done by comparing the genome of the tumour to the reference genome sequence derived from a normal tissue taken from the same donor. However, there are a number of possible scenarios in which matched normal tissues might be not available for comparisons. It is most commonly encountered when performing analysis on retrospective studies with human tissues from clinical trials or pathology archives when normal samples were not collected in the first place or patient consent precludes examination of normal tissue or germline variants. Another common scenario is the use of a cancer cell line as an experimental model, many of which have no information on the donor’s normal genome. In this work, we describe an algorithm to identify somatic single nucleotide variants (SNVs) in Next Generation Sequencing (NGS) data in the absence of normal samples using a machine learning approach. Our algorithm was evaluated using a family of supervised learning classifications across six different cancer types and ~1,600 samples, including cell lines, fresh frozen tissues, and formalin-fixed paraffin-embedded (FFPE) tissues. In addition, our algorithm was tested with both deep targeted sequencing and whole exome sequencing strategies. The algorithm correctly classified between 95% and 98% of somatic mutations with F1-measure ranges from 75.9% to 98.6% depending on the tumour type. We have released the algorithm as a software package called ISOWN (Identification of SOmatic mutations Without matching Normal tissues), which is available as Open Source under Apache License 2.0 from https://github.com/ikalatskaya/ISOWN.
Citation Format: Irina Kalatskaya, Quang Trinh, Melanie Spears, John Bartlett, Lincoln Stein. Precise somatic mutation prediction in the absence of matching normal DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3571. doi:10.1158/1538-7445.AM2017-3571
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Affiliation(s)
- Irina Kalatskaya
- Ontario Instittute for Cancer Research, Toronto, Ontario, Canada
| | - Quang Trinh
- Ontario Instittute for Cancer Research, Toronto, Ontario, Canada
| | - Melanie Spears
- Ontario Instittute for Cancer Research, Toronto, Ontario, Canada
| | - John Bartlett
- Ontario Instittute for Cancer Research, Toronto, Ontario, Canada
| | - Lincoln Stein
- Ontario Instittute for Cancer Research, Toronto, Ontario, Canada
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Kalatskaya I, Trinh QM, Spears M, McPherson JD, Bartlett JMS, Stein L. ISOWN: accurate somatic mutation identification in the absence of normal tissue controls. Genome Med 2017; 9:59. [PMID: 28659176 PMCID: PMC5490163 DOI: 10.1186/s13073-017-0446-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 06/06/2017] [Indexed: 12/31/2022] Open
Abstract
Background A key step in cancer genome analysis is the identification of somatic mutations in the tumor. This is typically done by comparing the genome of the tumor to the reference genome sequence derived from a normal tissue taken from the same donor. However, there are a variety of common scenarios in which matched normal tissue is not available for comparison. Results In this work, we describe an algorithm to distinguish somatic single nucleotide variants (SNVs) in next-generation sequencing data from germline polymorphisms in the absence of normal samples using a machine learning approach. Our algorithm was evaluated using a family of supervised learning classifications across six different cancer types and ~1600 samples, including cell lines, fresh frozen tissues, and formalin-fixed paraffin-embedded tissues; we tested our algorithm with both deep targeted and whole-exome sequencing data. Our algorithm correctly classified between 95 and 98% of somatic mutations with F1-measure ranges from 75.9 to 98.6% depending on the tumor type. We have released the algorithm as a software package called ISOWN (Identification of SOmatic mutations Without matching Normal tissues). Conclusions In this work, we describe the development, implementation, and validation of ISOWN, an accurate algorithm for predicting somatic mutations in cancer tissues in the absence of matching normal tissues. ISOWN is available as Open Source under Apache License 2.0 from https://github.com/ikalatskaya/ISOWN. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0446-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Irina Kalatskaya
- Informatics and Bio-computing, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
| | - Quang M Trinh
- Informatics and Bio-computing, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Melanie Spears
- Transformative Pathology, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - John D McPherson
- Department of Biochemistry and Molecular Medicine, University of California Davis, Sacramento, California, USA
| | - John M S Bartlett
- Transformative Pathology, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Edinburgh Cancer Research UK Centre, MRC IGMM, University of Edinburgh, Edinburgh, UK
| | - Lincoln Stein
- Informatics and Bio-computing, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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Bayani J, Kornaga E, Crozier C, Jang GH, Kalatskaya I, Trinh QM, Yao CQ, Livingstone J, Hasenburg A, Kieback DG, Markopoulos C, Dirix L, Boutros PC, Spears M, Stein LD, Rea D, Bartlett J. Copy-number and targeted sequencing analyses to identify distinct prognostic groups: Implications for patient selection to targeted therapies amongst anti-endocrine therapy resistant early breast cancers. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
524 Background: Hormone receptor positive breast cancer is a therapeutic challenge. Despite optimal anti-endocrine therapies, most breast cancer deaths follow a diagnosis of early luminal cancer. To understand the impact of multiple aberrations in the context of current therapy, we assessed the prognostic ability of genomic signatures as a putative stratification tool to targeted therapies. Methods: This a priori study is based on molecular pathways which might predict response to targeted therapies. DNA from 420 patients from the phase III TEAM pathology cohort were used. Patients with a distant recurrence within 5 years were matched by clinical variables to those disease-free at follow up. Copy number analysis was performed using the Affymetrix Oncoscan Assay. Targeted sequencing was performed in a subset of samples for genes based on signaling cassettes mined from the ICGC. Pathways were identified as aberrant if there were copy number variations (CNVs) and/or mutations in any of the pre-determined pathway genes: 1) CCND1/CCND2/CCND3/CDK4/CDK6; 2) FGFR1/FGFR2/FGFR2/FGFR4; and 3) AKT1/AKT2/PIK3CA/PTEN. Kaplan-Meier and log-rank analyses were used for DFS between groups. Hazard ratios were calculated using the Cox proportional hazard models adjusted for age, tumour size, grade, lymph node and HER2 status. Results: 390/420 samples passed informatics QC filters. For the CCND/CDK pathway, patients with no CNV changes experienced a better DFS (HR = 1.7, 95% CI 1.3-2.3, p < 0.001). For the FGFR/FGF pathway, a similar outcome is seen among patients without CNVs (HR = 1.5, 95% CI 1.1-2.0; p = 0.005). For AKT/PIK3CA, a decrease in DFS was seen in those with aberrations (HR = 1.4, 95% CI 1.0-1.8, p = 0.03). Conclusions: We demonstrated that CNVs of genes within CDK4/CCND, PIK3CA/AKT and FGFR pathways are independently linked to high risk of relapse following endocrine treatment, with implications for identifying those patients who are at high-risk for recurrence despite optimal anti-endocrine therapy and linking molecular features driving these cancers to targeted therapies.
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Affiliation(s)
- Jane Bayani
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Cheryl Crozier
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Gun Ho Jang
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Quang M Trinh
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Cindy Q Yao
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | | | | | | | - Luc Dirix
- Sint-Augustinus Hospital Oncology Center, Medical Oncology, Antwerpen, Belgium
| | | | | | | | - Daniel Rea
- Cancer Research UK Institute for Cancer Studies, Birmingham, United Kingdom
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Taylor KJ, Chong T, D'Costa A, Yao C, Gourley C, Cameron DA, Bartlett JMS, Spears M. Abstract P4-07-06: MicroRNAs associated with acquired taxane resistance in a breast cancer cell line model. Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-p4-07-06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Acquired chemoresistance remains the major cause of therapeutic failure in the treatment of breast cancer. Improved knowledge of the transition from drug sensitive to resistant breast cancer will pave the way for novel preventative and therapeutic strategies. MicroRNAs (miRNA) are endogenous, small non-coding RNAs that regulate gene expression by targeting the 3'UTR region of messenger RNAs. There is a growing body of evidence to suggest miRNAs may be involved in the development of chemoresistance and may play a role in the regulation of drug resistance pathways.
Methods: An in vitro model of paclitaxel resistance was developed through the generation of resistant MDA-MB-231 cell lines by serial culture in escalating doses of taxane until resistance was achieved. The chemoresistant model was used to compare differential miRNA expression with the sensitive, parental line using the Nanostring® platform, analysing 800 human miRNAs. Confirmation of differential expression was performed by QRT-PCR.
Results: This analysis resulted in 30 significantly altered miRNA (1.5 fold, p value < 0.05) at 25nM paclitaxel and 48 significantly altered miRNA at 50nM paclitaxel. The top up-regulated miRNA cluster in MDA-MB-231 25PACR is hsa-miR-548l (fold change: 2.89, p value: 0.016) and top down-regulated was hsa-miR-449a (fold change: -4.1. p value: 0.001). In MDA-MB-231 50PACR the top up-regulated miRNA cluster is hsa-miR-193a-5p (fold change: 3.746, p value: 0.008) and the top down-regulated miRNA cluster is hsa-miR-135a (fold change: -4.085, p value: 0.001). To explore the molecular mechanisms of the differentially expressed miRNAs in paclitaxel resistance, targets were predicted by in silico analysis. Pathways and networks designated by miRNA targets included the cell cycle, PI3K/Akt pathways and focal adhesion.
Conclusion: In this study we identified candidate resistance-associated miRNAs which were differentially expressed between in vitro derived paclitaxel resistant MDA-MB-231 and the sensitive parental line. Further validation to ascertain their role in the transition to a chemoresistant phenotype is currently ongoing.
Citation Format: Taylor KJ, Chong T, D'Costa A, Yao C, Gourley C, Cameron DA, Bartlett JMS, Spears M. MicroRNAs associated with acquired taxane resistance in a breast cancer cell line model [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P4-07-06.
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Affiliation(s)
- KJ Taylor
- Edinburgh Cancer Research Centre, University of Edinburgh, Edinburgh, United Kingdom; Ontario Institute of Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada
| | - T Chong
- Edinburgh Cancer Research Centre, University of Edinburgh, Edinburgh, United Kingdom; Ontario Institute of Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada
| | - A D'Costa
- Edinburgh Cancer Research Centre, University of Edinburgh, Edinburgh, United Kingdom; Ontario Institute of Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada
| | - C Yao
- Edinburgh Cancer Research Centre, University of Edinburgh, Edinburgh, United Kingdom; Ontario Institute of Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada
| | - C Gourley
- Edinburgh Cancer Research Centre, University of Edinburgh, Edinburgh, United Kingdom; Ontario Institute of Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada
| | - DA Cameron
- Edinburgh Cancer Research Centre, University of Edinburgh, Edinburgh, United Kingdom; Ontario Institute of Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada
| | - JMS Bartlett
- Edinburgh Cancer Research Centre, University of Edinburgh, Edinburgh, United Kingdom; Ontario Institute of Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada
| | - M Spears
- Edinburgh Cancer Research Centre, University of Edinburgh, Edinburgh, United Kingdom; Ontario Institute of Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada
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Crawley D, van Hemelrijck M, Chowdhury S, James N, Gilson C, Spears M, Sydes M, Rudman S. Effect of baseline metabolic aberrations in men with locally advanced/metastatic prostate cancer treated with ADT on time to disease progression, prostate cancer specific and all cause death. Ann Oncol 2016. [DOI: 10.1093/annonc/mdw372.46] [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: 11/13/2022] Open
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31
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Spears M, Yousif F, Lyttle N, Boutros PC, Munro AF, Twelves C, Pritchard KI, Levine MN, Shepherd L, Bartlett JMS. A four gene signature predicts benefit from anthracyclines: evidence from the BR9601 and MA.5 clinical trials. Oncotarget 2016; 6:31693-701. [PMID: 26372731 PMCID: PMC4741633 DOI: 10.18632/oncotarget.5562] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 08/10/2015] [Indexed: 12/21/2022] Open
Abstract
Chromosome instability (CIN) in solid tumours results in multiple numerical and structural chromosomal aberrations and is associated with poor prognosis in multiple tumour types. Recent evidence demonstrated CEP17 duplication, a CIN marker, is a predictive marker of anthracycline benefit. An analysis of the BR9601 and MA.5 clinical trials was performed to test the role of existing CIN gene expression signatures as predictive markers of anthracycline sensitivity in breast cancer. Univariate analysis demonstrated, high CIN25 expression score was associated with improved distant relapse free survival (DRFS) (HR: 0.74, 95% CI 0.54-0.99, p = 0.046). High tumour CIN70 and CIN25 scores were associated with aggressive clinicopathological phenotype and increased sensitivity to anthracycline therapy compared to low CIN scores. However, in a prospectively planned multivariate analysis only pathological grade, nodal status and tumour size were significant predictors of outcome for CIN25/CIN70. A limited gene signature was generated, patients with low tumour CIN4 scores benefited from anthracycline treatment significantly more than those with high CIN4 scores (HR 0.37, 95% CI 0.20-0.56, p = 0.001). In multivariate analyses the treatment by marker interaction for CIN4/anthracyclines demonstrated hazard ratio of 0.35 (95% CI 0.15-0.80, p = 0.012) for DRFS. This data shows CIN4 is independent predictor of anthracycline benefit for DRFS in breast cancer.
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Affiliation(s)
- Melanie Spears
- Transformative Pathology, Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada
| | - Fouad Yousif
- Informatics and Bio-Computing, Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada
| | - Nicola Lyttle
- Transformative Pathology, Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada
| | - Paul C Boutros
- Informatics and Bio-Computing, Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Alison F Munro
- Edinburgh Cancer Research UK Centre, MRC IGMM, University of Edinburgh, Crewe Road South, Edinburgh, UK
| | - Chris Twelves
- Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, St James' University Hospital, Leeds, UK
| | - Kathleen I Pritchard
- Sunnybrook Odette Cancer Centre, Toronto, ON, Canada.,University of Toronto, Toronto, ON, Canada
| | - Mark N Levine
- McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada
| | - Lois Shepherd
- NCIC Clinical Trials Group (NCIC CTG] and Queen's University, Kingston, ON, Canada
| | - John M S Bartlett
- Transformative Pathology, Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada.,Edinburgh Cancer Research UK Centre, MRC IGMM, University of Edinburgh, Crewe Road South, Edinburgh, UK
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32
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Spears M, Lyttle N, D'Costa A, Chen BE, Yao CQ, Boutros PC, Burnell M, Levine MN, O'Brien P, Shepherd L, Bartlett JMS. A four gene signature of chromosome instability (CIN4) predicts for benefit from taxanes in the NCIC-CTG MA21 clinical trial. Oncotarget 2016; 7:49099-49106. [PMID: 27056899 PMCID: PMC5226493 DOI: 10.18632/oncotarget.8542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 03/17/2016] [Indexed: 01/26/2023] Open
Abstract
Recent evidence demonstrated CIN4 as a predictive marker of anthracycline benefit in early breast cancer. An analysis of the NCIC CTG MA.21 clinical trial was performed to test the role of existing CIN gene expression signatures as prognostic and predictive markers in the context of taxane based chemotherapy. RNA was extracted from patients in cyclophosphamide, epirubicin and fluorouracil (CEF) and epirubicin, cyclophosphamide and paclitaxel (EC/T) arms of the NCIC CTG MA.21 trial and analysed using NanoString technology. After multivariate analysis both high CIN25 and CIN70 score was significantly associated with an increased in RFS (HR 1.76, 95%CI 1.07-2.86, p=0.0018 and HR 1.59, 95%CI 1.12-2.25, p=0.0096 respectively). Patients whose tumours had low CIN4 gene expression scores were associated with an increase in RFS (HR: 0.64, 95% CI 0.39-1.03, p=0.06) when treated with EC/T compared to patients treated with CEF. In conclusion we have demonstrated CIN25 and CIN70 as prognostic markers in breast cancer and that CIN4 is a potential predictive maker of benefit from taxane treatment.
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Affiliation(s)
- Melanie Spears
- Transformative Pathology, Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Nicola Lyttle
- Transformative Pathology, Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada
| | - Alister D'Costa
- Transformative Pathology, Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada.,Informatics and Bio-Computing, Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada
| | - Bingshu E Chen
- NCIC Clinical Trials Group (NCIC CTG) and Queen's University, Kingston, ON, Canada
| | - Cindy Q Yao
- Transformative Pathology, Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada.,Informatics and Bio-Computing, Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada
| | - Paul C Boutros
- Informatics and Bio-Computing, Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON Canada.,Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON Canada
| | | | - Mark N Levine
- Ontario Clinical Oncology Group, McMaster University, Hamilton, ON, Canada
| | - Patti O'Brien
- NCIC Clinical Trials Group (NCIC CTG) and Queen's University, Kingston, ON, Canada
| | - Lois Shepherd
- NCIC Clinical Trials Group (NCIC CTG) and Queen's University, Kingston, ON, Canada
| | - John M S Bartlett
- Transformative Pathology, Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Edinburgh Cancer Research UK Centre, MRC IGMM, University of Edinburgh, Edinburgh, UK
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Mullen NA, Li J, Russell ML, Spears M, Less BD, Singer BC. Results of the California Healthy Homes Indoor Air Quality Study of 2011-2013: impact of natural gas appliances on air pollutant concentrations. Indoor Air 2016; 26:231-245. [PMID: 25647016 DOI: 10.1111/ina.12190] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 01/27/2015] [Indexed: 06/04/2023]
Abstract
This study was conducted to assess the current impact of natural gas appliances on air quality in California homes. Data were collected via telephone interviews and measurements inside and outside of 352 homes. Passive samplers measured time-resolved CO and time-integrated NOX , NO2 , formaldehyde, and acetaldehyde over ~6-day periods in November 2011 - April 2012 and October 2012 - March 2013. The fraction of indoor NOX and NO2 attributable to indoor sources was estimated. NOX , NO2 , and highest 1-h CO were higher in homes that cooked with gas and increased with amount of gas cooking. NOX and NO2 were higher in homes with cooktop pilot burners, relative to gas cooking without pilots. Homes with a pilot burner on a floor or wall furnace had higher kitchen and bedroom NOX and NO2 compared to homes without a furnace pilot. When scaled to account for varying home size and mixing volume, indoor-attributed bedroom and kitchen NOX and kitchen NO2 were not higher in homes with wall or floor furnace pilot burners, although bedroom NO2 was higher. In homes that cooked 4 h or more with gas, self-reported use of kitchen exhaust was associated with lower NOX , NO2 , and highest 1-h CO. Gas appliances were not associated with higher concentrations of formaldehyde or acetaldehyde.
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Affiliation(s)
- N A Mullen
- Product Regulations, Global Supply Chain, Gap Inc., San Francisco, CA, USA
- Indoor Environment Group, Environmental Technologies Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - J Li
- Indoor Environment Group, Environmental Technologies Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - M L Russell
- Indoor Environment Group, Environmental Technologies Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - M Spears
- Indoor Environment Group, Environmental Technologies Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - B D Less
- Residential Building Systems Group, Environmental Technologies Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - B C Singer
- Indoor Environment Group, Environmental Technologies Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Residential Building Systems Group, Environmental Technologies Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Braunstein M, Yao C, Lyttle N, Liao L, Boutros PC, Twelves CJ, Bartlett JMS, Spears M. Abstract P3-07-32: Tumour infiltrating lymphocyte (TIL) and chemokine gene signature predicts for benefit of anthracycline-containing chemotherapy in breast cancer patients. Cancer Res 2016. [DOI: 10.1158/1538-7445.sabcs15-p3-07-32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: The contribution of immune cells has long been appreciated in tumour development and disease progression; however, their translational potential as cancer-associated prognostic and predictive markers was only recently recognized. High densities of tumour-infiltrating lymphocytes (TILs) correlate with improved clinical outcome in breast cancer; whether TILs also predict anthracycline benefit in all, or only a particular subgroup, of breast cancer patients remains largely unknown. Furthermore, since identification of TILs is generally based on H&E staining, it has not previously been possible to evaluate relative contribution of distinct T-cell types, and B cells, to patient outcome.
Methods: We assessed 290 patient samples from the BR9601 adjuvant breast cancer trial for the capacity of TIL contexture to predict for anthracycline (E-CMF) benefit over CMF. We immunoprofiled patient samples on the Nanostring platform to gain insight into the impact of lymphocyte populations predicting for anthracycline benefit. Our immunoprofiling panel included 38 genes representing TIL-gene signatures and chemokines that may be responsible for recruiting TILs to the tumour site.
Results: The analyses revealed two important findings. First, refinement of the 38-gene panel resulted in the generation of a novel 9-gene signature that includes cytotoxic T lymphocytes (CTL) and chemokine genes. Low CTL gene expression correlated with ER+ expression while high expression correlated with ER- expression (p<0.0001), consistent with the notion that high TIL densities are predominantly observed in non-luminal breast cancers. Second, in an univariate Cox regression analysis, this 9-gene signature was a predictive biomarker of anthracycline benefit with respect to breast-cancer specific OS (HR: 0.371, 95%CI 0.158-0.868, p=0.022) and DRFS (HR: 0.395, 95%CI 0.172-0.907, p=0.028); this effect was no longer significant after adjustment for other prognostic factors (OS HR: 0.437, 95%CI 0.166-1.150, p=0.094; DRFS HR: 0.488, 95%CI 0.185-1.287, p=0.147).
Conclusion: This study highlights the significance of assessing the entire tumour since TILs, tumour and stromal cells collectively engage in a complex interplay that contributes to disease development and progression. Importantly, it reveals that not only CTLs but also chemokines may be clinically relevant and should be validated as potential biomarkers of anthracycline benefit and as therapeutic targets.
Citation Format: Braunstein M, Yao C, Lyttle N, Liao L, Boutros PC, Twelves CJ, Bartlett JMS, Spears M. Tumour infiltrating lymphocyte (TIL) and chemokine gene signature predicts for benefit of anthracycline-containing chemotherapy in breast cancer patients. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P3-07-32.
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Affiliation(s)
- M Braunstein
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, St James' University Hospital, Leeds, United Kingdom; Edinburgh Cancer Research Centre, Western General Hospital, Edinburgh, United Kingdom
| | - C Yao
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, St James' University Hospital, Leeds, United Kingdom; Edinburgh Cancer Research Centre, Western General Hospital, Edinburgh, United Kingdom
| | - N Lyttle
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, St James' University Hospital, Leeds, United Kingdom; Edinburgh Cancer Research Centre, Western General Hospital, Edinburgh, United Kingdom
| | - L Liao
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, St James' University Hospital, Leeds, United Kingdom; Edinburgh Cancer Research Centre, Western General Hospital, Edinburgh, United Kingdom
| | - PC Boutros
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, St James' University Hospital, Leeds, United Kingdom; Edinburgh Cancer Research Centre, Western General Hospital, Edinburgh, United Kingdom
| | - CJ Twelves
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, St James' University Hospital, Leeds, United Kingdom; Edinburgh Cancer Research Centre, Western General Hospital, Edinburgh, United Kingdom
| | - JMS Bartlett
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, St James' University Hospital, Leeds, United Kingdom; Edinburgh Cancer Research Centre, Western General Hospital, Edinburgh, United Kingdom
| | - M Spears
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, St James' University Hospital, Leeds, United Kingdom; Edinburgh Cancer Research Centre, Western General Hospital, Edinburgh, United Kingdom
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Spears M, Braunstein M, Liao L, Yao C, Lyttle N, Lobo N, Taylor KJ, Krzyzanowski PM, Kalatskaya I, Marcellus R, Stein L, Boutros P, Twelves CJ, Bartlett JMS. Abstract P3-06-03: Downregulation of histone H2A and H2B pathways is associated with anthracycline sensitivity in breast cancer. Cancer Res 2016. [DOI: 10.1158/1538-7445.sabcs15-p3-06-03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Meta-analyses performed by the Early Breast Cancer Trialists Collaborative Group demonstrated a significant increase in disease free and overall survival through the addition of anthracyclines to polychemotherapy. Anthracyclines have, however, significant toxicities including cardiotoxicity and leukaemia. It is, therefore, imperative to identify those patients who will benefit from adjuvant anthracycline treatment; other patients could then be spared unnecessary toxicities and be considered for alternative adjuvant therapy. Several markers that may predict anthracycline benefit have been explored in patient cohorts (HER2, TOP2A, Ch17CEP and TIMP1) with limited success.
Methods: To identify markers that are clinically-relevant, we generated MDA-MB-231, MCF7, SKBR3 and ZR-75-1 breast cancer cell lines sensitive and resistant to epirubicin to identify pathways contributing to anthracycline resistance. A complementary approach including gene expression analyses to identify molecular pathways involved in resistance, and small-molecule inhibitors to reverse resistance were performed. RNA was extracted from patients in the BR9601 adjuvant trial evaluating the addition of epirubicin (E) to CMF and analysed through Nanostring technology. Log-rank analyses explored the predictive values of the signatures on distant relapse-free survival (DRFS). Cox-regression models tested independent predictive value on DRFS in the presence of treatment, age, tumour size, nodal status, ER status and grade, and treatment by marker interactions.
Results: Gene expression analysis identified upregulaton of a histone gene module in all four cell lines which was validated by qRT-PCR. Histone deacetylase small-molecule inhibitors reversed resistance and were cytotoxic for epirubicin-resistant cell lines, with IC50's ranging from 0.1-3.69µM, confirming that histone pathways are associated with epirubicin resistance. Gene expression analysis of the 18-gene histone module in the BR9601 clinical cohort revealed that patients whose tumour had low expression had an increased DRFS (HR: 0.35, 95%CI 0.17-0.73, p=0.005) when treated with E-CMF compared with patients treated with CMF alone. Conversely, there was no apparent benefit of E-CMF vs CMF in patients with high histone module expression (HR: 0.96, 95%CI 0.58-1.59, p=0.87). After multivariate analysis and adjustment for HER2 status, nodal status, age, grade and ER status, the treatment by marker interaction was 0.35 (95%CI 0.13-0.96, p=0.042) for DRFS.
Conclusion: Histone gene expression was an independent predictor of anthracycline benefit in terms of DRFS. In vitro data demonstrated that resistance could be reversed with histone deacetylase small-molecule inhibitors. The histone signature identified could be a potential theranostic candidate for patients with early breast cancer.
Citation Format: Spears M, Braunstein M, Liao L, Yao C, Lyttle N, Lobo N, Taylor KJ, Krzyzanowski PM, Kalatskaya I, Marcellus R, Stein L, Boutros P, Twelves CJ, Bartlett JMS. Downregulation of histone H2A and H2B pathways is associated with anthracycline sensitivity in breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P3-06-03.
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Affiliation(s)
- M Spears
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Edinburgh, Edinburgh, United Kingdom; Leeds Institute of Cancer and Pathology and Cancer Research Centre, Leeds, United Kingdom
| | - M Braunstein
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Edinburgh, Edinburgh, United Kingdom; Leeds Institute of Cancer and Pathology and Cancer Research Centre, Leeds, United Kingdom
| | - L Liao
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Edinburgh, Edinburgh, United Kingdom; Leeds Institute of Cancer and Pathology and Cancer Research Centre, Leeds, United Kingdom
| | - C Yao
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Edinburgh, Edinburgh, United Kingdom; Leeds Institute of Cancer and Pathology and Cancer Research Centre, Leeds, United Kingdom
| | - N Lyttle
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Edinburgh, Edinburgh, United Kingdom; Leeds Institute of Cancer and Pathology and Cancer Research Centre, Leeds, United Kingdom
| | - N Lobo
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Edinburgh, Edinburgh, United Kingdom; Leeds Institute of Cancer and Pathology and Cancer Research Centre, Leeds, United Kingdom
| | - KJ Taylor
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Edinburgh, Edinburgh, United Kingdom; Leeds Institute of Cancer and Pathology and Cancer Research Centre, Leeds, United Kingdom
| | - PM Krzyzanowski
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Edinburgh, Edinburgh, United Kingdom; Leeds Institute of Cancer and Pathology and Cancer Research Centre, Leeds, United Kingdom
| | - I Kalatskaya
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Edinburgh, Edinburgh, United Kingdom; Leeds Institute of Cancer and Pathology and Cancer Research Centre, Leeds, United Kingdom
| | - R Marcellus
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Edinburgh, Edinburgh, United Kingdom; Leeds Institute of Cancer and Pathology and Cancer Research Centre, Leeds, United Kingdom
| | - L Stein
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Edinburgh, Edinburgh, United Kingdom; Leeds Institute of Cancer and Pathology and Cancer Research Centre, Leeds, United Kingdom
| | - P Boutros
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Edinburgh, Edinburgh, United Kingdom; Leeds Institute of Cancer and Pathology and Cancer Research Centre, Leeds, United Kingdom
| | - CJ Twelves
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Edinburgh, Edinburgh, United Kingdom; Leeds Institute of Cancer and Pathology and Cancer Research Centre, Leeds, United Kingdom
| | - JMS Bartlett
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Edinburgh, Edinburgh, United Kingdom; Leeds Institute of Cancer and Pathology and Cancer Research Centre, Leeds, United Kingdom
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Braunstein M, Liao L, Lyttle N, Lobo N, Taylor KJ, Krzyzanowski PM, Kalatskaya I, Yao CQ, Stein LD, Boutros PC, Twelves CJ, Marcellus R, Bartlett JMS, Spears M. Downregulation of histone H2A and H2B pathways is associated with anthracycline sensitivity in breast cancer. Breast Cancer Res 2016; 18:16. [PMID: 26852132 PMCID: PMC4744406 DOI: 10.1186/s13058-016-0676-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 01/13/2016] [Indexed: 12/31/2022] Open
Abstract
Background Drug resistance in breast cancer is the major obstacle to effective treatment with chemotherapy. While upregulation of multidrug resistance genes is an important component of drug resistance mechanisms in vitro, their clinical relevance remains to be determined. Therefore, identifying pathways that could be targeted in the clinic to eliminate anthracycline-resistant breast cancer remains a major challenge. Methods We generated paired native and epirubicin-resistant MDA-MB-231, MCF7, SKBR3 and ZR-75-1 epirubicin-resistant breast cancer cell lines to identify pathways contributing to anthracycline resistance. Native cell lines were exposed to increasing concentrations of epirubicin until resistant cells were generated. To identify mechanisms driving epirubicin resistance, we used a complementary approach including gene expression analyses to identify molecular pathways involved in resistance, and small-molecule inhibitors to reverse resistance. In addition, we tested its clinical relevance in a BR9601 adjuvant clinical trial. Results Characterisation of epirubicin-resistant cells revealed that they were cross-resistant to doxorubicin and SN-38 and had alterations in apoptosis and cell-cycle profiles. Gene expression analysis identified deregulation of histone H2A and H2B genes in all four cell lines. Histone deacetylase small-molecule inhibitors reversed resistance and were cytotoxic for epirubicin-resistant cell lines, confirming that histone pathways are associated with epirubicin resistance. Gene expression of a novel 18-gene histone pathway module analysis of the BR9601 adjuvant clinical trial revealed that patients with low expression of the 18-gene histone module benefited from anthracycline treatment more than those with high expression (hazard ratio 0.35, 95 % confidence interval 0.13–0.96, p = 0.042). Conclusions This study revealed a key pathway that contributes to anthracycline resistance and established model systems for investigating drug resistance in all four major breast cancer subtypes. As the histone modification can be targeted with small-molecule inhibitors, it represents a possible means of reversing clinical anthracycline resistance. Trial registration ClinicalTrials.gov identifier NCT00003012. Registered on 1 November 1999. Electronic supplementary material The online version of this article (doi:10.1186/s13058-016-0676-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marsela Braunstein
- Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Toronto, ON, M5G 0A3, Canada. .,Department of Immunology, University of Toronto, Toronto, ON, Canada.
| | - Linda Liao
- Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Toronto, ON, M5G 0A3, Canada.
| | - Nicola Lyttle
- Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Toronto, ON, M5G 0A3, Canada.
| | - Nazleen Lobo
- Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Toronto, ON, M5G 0A3, Canada.
| | - Karen J Taylor
- Edinburgh Cancer Research Centre, Western General Hospital, Edinburgh, UK
| | - Paul M Krzyzanowski
- Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Toronto, ON, M5G 0A3, Canada.
| | - Irina Kalatskaya
- Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Toronto, ON, M5G 0A3, Canada.
| | - Cindy Q Yao
- Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Toronto, ON, M5G 0A3, Canada.
| | - Lincoln D Stein
- Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Toronto, ON, M5G 0A3, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
| | - Paul C Boutros
- Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Toronto, ON, M5G 0A3, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada. .,Department of Pharmacology & Toxicology, University of Toronto, Toronto, Canada.
| | - Christopher J Twelves
- Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, St James's University Hospital, Leeds, UK.
| | - Richard Marcellus
- Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Toronto, ON, M5G 0A3, Canada.
| | - John M S Bartlett
- Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Toronto, ON, M5G 0A3, Canada. .,Edinburgh Cancer Research Centre, Western General Hospital, Edinburgh, UK. .,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
| | - Melanie Spears
- Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Toronto, ON, M5G 0A3, Canada.
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Spears M, Lyttle NS, Yousif F, Munro AF, Twelves C, Pritchard KI, Levine MN, Shepherd L, Bartlett JMS. Abstract P2-05-05: A four gene signature predicts anthracycline benefit: Evidence from the BR9601 and MA5 breast cancer trials. Cancer Res 2015. [DOI: 10.1158/1538-7445.sabcs14-p2-05-05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Chromosome instability (CIN) in solid tumours is associated with poor prognosis and results in numerical and structural chromosomal aberrations. Recent evidence from both the BR9601 and MA.5 trials has demonstrated CEP17 duplication as a predictive marker of anthracycline benefit. CIN25 and CIN70 gene expression profiles have previously been published and predict survival response. An analysis of the BR9601 and MA5 clinical trials was performed to test the role of CIN gene expression signatures as a marker of anthracycline sensitivity.
Methods: RNA was extracted from patients in both the BR9601 and MA5 studies and analysed through Nanostring technology. Log-rank analyses explored the prognostic values of the signatures on distant relapse-free survival (DRFS). Cox-regression models tested independent prognostic value on DRFS in the presence of treatment, age, tumour size, nodal status, ER status and grade, and treatment by marker interactions.
Results: Of the 761 samples available from the BR9601 and MA5 cohorts we successfully analysed 703 (92.4%). High CIN25 and CIN70 scores were associated with age (p<0.0001), grade (p0.0001), PgR negativity (p<0.0001) and ER negativity (p<0.0001). In univariate analysis, high CIN25 score was associated with decreased DRFS (HR: 0.74, 95% CI 0.54-0.99, p=0.046). In a multivariate analysis with adjustment for size, nodal status, ER, pathological grade, HER2, CIN25, treatment and treatment by marker only pathological grade, nodal status and tumour size were significant predictors of outcome.
A more limited set of genes that reflected CIN was established by examining the expression profile of the genes and clustering them. The combined cohort was split into a 60% training and 40% validation set. The area under the curve (AUC) was calculated and the gene signature with the greatest AUC was selected and termed CIN4. Patients with low CIN4 score benefited from anthracycline treatment compared to those that had high CIN4 score (HR 2.72, 95% CI 1.48-5.02, p=0.001). No significant benefit with CMF treatment was observed in (HR: 1.02, 95% CI 0.58-1.82, p=0.92). After multivariate analysis the treatment by marker interaction for CIN4 had a hazard ratio of 2.10 (95% CI 2.18-30.38, p= 0.001).
Conclusion: High CIN70 and CIN25 scores were associated with an aggressive phenotype and showed a potential increased sensitivity to anthracycline therapy compared to those with low CIN scores. CIN4 was an independent predictor of anthracycline benefit for DRFS. However, further work in larger patient cohorts such as NEAT is warranted.
Citation Format: Melanie Spears, Nicola S Lyttle, Fouad Yousif, Alison F Munro, Christopher Twelves, Kathleen I Pritchard, Mark N Levine, Lois Shepherd, John MS Bartlett. A four gene signature predicts anthracycline benefit: Evidence from the BR9601 and MA5 breast cancer trials [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P2-05-05.
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Affiliation(s)
| | | | | | | | | | | | | | | | - John MS Bartlett
- 1Ontario Institute for Cancer Research
- 2Edinburgh Cancer Research Centre
- 5University of Toronto
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Yao CQ, Crozier C, Quintayo MA, Bayani J, Spears M, Livingstone J, Jung E, Fung C, Sabine V, Boutros PC, Bartlett JMS. Abstract P2-03-17: Assessing reproducibility of copy number arrays to assist breast cancer biomarker discovery. Cancer Res 2015. [DOI: 10.1158/1538-7445.sabcs14-p2-03-17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction:
Large-scale interrogation of the genome has emerged as an attractive method for identifying useful characteristics of cancer biology; in particular, the study of copy number aberrations (CNA) has recently received tremendous attention. A number of different technologies have been developed to assess the copy-number landscape, allowing us to better understand the role of CNA in cancer cells. The OncoScan CNA platform (Affymetrix Inc.) has been particularly appealing for oncology due of its ability to work well with formalin-fixed, paraffin-embedded (FFPE) materials, which is the primary form for storage of clinical samples. In addition, its high resolution, rapid analysis time and ability to interrogate different genomic characteristics (CNA, loss of heterozygosity or mutation) make the OncoScan platform highly popular: it has been widely cited in the literature for use in biomarker discovery, clonal evolution and sub-clonal detection, as well as population-based analyses. While CNAs identified by the OncoScan platform have shown good concordance with fluorescence in-situ hybridization (FISH) results, to date, no studies have been conducted to thoroughly assess the reproducibility of the assay. In this study, we have assessed the reproducibility of the OncoScan platform using identical samples performed in replicates across multiple chip batches. Moreover, we have assessed the effect on reproducibility of DNA treatment, including elution in water or TE buffer, as well as in the use of varying amounts of DNA.
Methods:
Affymetrix OncoScan FFPE Express 3.0 SNP Arrays were performed using the optimal input DNA as recommended by the manufacturer as well as fewer input amounts for comparison. CNAs were called using BioDiscovery Nexus Copy Number™ software (http://www.biodiscovery.com/software/nexus-copy-number/) using the SNP-FASST2 algorithm with modified parameters (significance threshold of 1 x 10-9 and minimum number of probes per segment of 10).
Results:
Initial reproducibility analysis involving 12 samples repeated either 2, 4 or 6 times both within a single batch and across different batches has revealed that CNA calls were concordant between replicates for the majority of the genome (ranges between 81% to 100%), suggesting high precision of the assay. In addition, we are in the process of assessing and comparing mutation calls across replicates to gain a more in-depth understanding of the platform.
Conclusion:
This is the first study examining the reproducibility of OncoScan FFPE assays; initial results have suggested that the assay is precise and has the potential for robust biomarker discovery. Additional characterizations would be interesting for evaluating its use as a clinical tool in the long term.
Citation Format: Cindy Q Yao, Cheryl Crozier, Mary Anne Quintayo, Jane Bayani, Melanie Spears, Julie Livingstone, Esther Jung, Clement Fung, Victoria Sabine, Paul C Boutros, John MS Bartlett. Assessing reproducibility of copy number arrays to assist breast cancer biomarker discovery [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P2-03-17.
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Affiliation(s)
- Cindy Q Yao
- 1Ontario Institute for Cancer Research (OICR)
| | | | | | - Jane Bayani
- 1Ontario Institute for Cancer Research (OICR)
| | | | | | - Esther Jung
- 1Ontario Institute for Cancer Research (OICR)
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Kenicer J, Spears M, Lyttle N, Taylor KJ, Liao L, Cunningham CA, Lambros M, MacKay A, Yao C, Reis-Filho J, Bartlett JMS. Molecular characterisation of isogenic taxane resistant cell lines identify novel drivers of drug resistance. BMC Cancer 2014; 14:762. [PMID: 25312014 PMCID: PMC4203938 DOI: 10.1186/1471-2407-14-762] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 10/02/2014] [Indexed: 01/29/2023] Open
Abstract
Background Taxanes such as paclitaxel and docetaxel are used successfully to treat breast cancer, usually in combination with other agents. They interfere with microtubules causing cell cycle arrest; however, the mechanisms underlying the clinical effects of taxanes are yet to be fully elucidated. Methods Isogenic paclitaxel resistant (PACR) MDA‒MB‒231, paclitaxel resistant ZR75‒1 and docetaxel resistant (DOCR) ZR75‒1 cell lines were generated by incrementally increasing taxane dose in native cell lines in vitro. We used aCGH analysis to identify mechanisms driving taxane resistance. Results Taxane resistant cell lines exhibited an 18-170 fold increased resistance to taxanes, with the ZR75-1 resistant cell lines also demonstrating cross resistance to anthracyclines. Paclitaxel treatment of native cells resulted in a G2/M block and a decrease in the G1 phase of the cell cycle. However, in the resistant cell lines, minimal changes were present. Functional network analysis revealed that the mitotic prometaphase was lost in the resistant cell lines. Conclusion This study established a model system for examining taxane resistance and demonstrated that both MDR and mitosis represent common mechanism of taxane resistance. Electronic supplementary material The online version of this article (doi:10.1186/1471-2407-14-762) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - John M S Bartlett
- Biomarkers and Companion Diagnostics, Edinburgh Cancer Research Centre, Crewe Road South, Edinburgh EH4 2XR, UK.
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James N, Spears M, Clarke N, Sydes M, Parker C, Dearnaley D, Russell J, Ritchie A, Thalmann G, de Bono J, Attard G, Amos C, Parmar M, Mason M. Impact of Node Status and Radiotherapy on Failure-Free Survival in Patients with Newly Diagnosed Non-Metastatic Prostate Cancer: Data from >690 Patients in the Control Arm of the Stampede Trial. Ann Oncol 2014. [DOI: 10.1093/annonc/mdu336.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Stallard P, Phillips R, Montgomery AA, Spears M, Anderson R, Taylor J, Araya R, Lewis G, Ukoumunne OC, Millings A, Georgiou L, Cook E, Sayal K. A cluster randomised controlled trial to determine the clinical effectiveness and cost-effectiveness of classroom-based cognitive-behavioural therapy (CBT) in reducing symptoms of depression in high-risk adolescents. Health Technol Assess 2014; 17:vii-xvii, 1-109. [PMID: 24172024 DOI: 10.3310/hta17470] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Depression in adolescents is a significant problem that impairs everyday functioning and increases the risk of severe mental health disorders in adulthood. Although this is a major problem, relatively few adolescents with, or at risk of developing, depression are identified and referred for treatment. This suggests the need to investigate alternative approaches whereby preventative interventions are made widely available in schools. OBJECTIVE To investigate the clinical effectiveness and cost-effectiveness of classroom-based cognitive-behavioural therapy (CBT) in reducing symptoms of depression in high-risk adolescents. DESIGN Cluster randomised controlled trial. Year groups ( n = 28) randomly allocated on a 1 : 1 : 1 basis to one of three trial arms once all schools were recruited and balanced for number of classes, number of students, Personal, Social and Health Education (PSHE) lesson frequency, and scheduling of PSHE. SETTING Year groups 8 to 11 (ages 12-16 years) in mixed-sex secondary schools in the UK. Data were collected between 2009 and 2011. PARTICIPANTS Young people who attended PSHE at participating schools were eligible ( n = 5503). Of the 5030 who agreed to participate, 1064 (21.2%) were classified as 'high risk': 392 in the classroom-based CBT arm, 374 in the attention control PSHE arm and 298 in the usual PSHE arm. Primary outcome data on the high-risk group at 12 months were available for classroom-based CBT ( n = 296), attention control PSHE ( n = 308) and usual PSHE ( n = 242). INTERVENTIONS The Resourceful Adolescent Programme (RAP) is a focused CBT-based intervention adapted for the UK (RAP-UK) and delivered by two facilitators external to the school. Control groups were usual PSHE (usual school curriculum delivered by teachers) and attention control (usual school PSHE with additional support from two facilitators). Interventions were delivered universally to whole classes. PRIMARY OUTCOMES Clinical effectiveness: symptoms of depression [Short Mood and Feelings Questionnaire (SMFQ)] in adolescents at high risk of depression 12 months from baseline. Cost-effectiveness: incremental cost-effectiveness ratios (ICERs) based on SMFQ score and quality-adjusted life-years (from European Quality of Life-5 Dimensions scores) between baseline and 12 months. Process evaluation: reach, attrition and qualitative feedback from service recipients and providers. RESULTS SMFQ scores had decreased for high-risk adolescents in all trial arms at 12 months, but there was no difference between arms [classroom-based CBT vs. usual PSHE adjusted difference in means 0.97, 95% confidence interval (CI) -0.34 to 2.28; classroom-based CBT vs. attention control PSHE -0.63, 95% CI -1.99 to 0.73]. Costs of interventions per child were estimated at £41.96 for classroom-based CBT and £34.45 for attention control PSHE. Fieller's method was used to obtain a parametric estimate of the 95% CI for the ICERs and construct the cost-effectiveness acceptability curve, confirming that classroom-based CBT was not cost-effective relative to the controls. Reach of classroom-based CBT was good and attrition was low (median 80% attending ≥ 60% of sessions), but feedback indicated some difficulties with acceptability and sustainability. CONCLUSIONS Classroom-based CBT, attention control PSHE and usual PSHE produced similar outcomes. Classroom-based CBT may result in increased self-awareness and reporting of depressive symptoms. Classroom-based CBT was not shown to be cost-effective. While schools are a convenient way of reaching a wide range of young people, implementing classroom-based CBT within schools is challenging, particularly with regard to fitting programmes into a busy timetable, the lack of value placed on PSHE, and difficulties engaging with teachers and young people. Wider use of classroom-based depression prevention programmes should not be undertaken without further research. If universal preventative approaches are to be pursued, their clinical effectiveness and cost-effectiveness with younger children (aged 10-11 years), before the incidence of depression increases, should be investigated. Alternatively, the clinical effectiveness of indicated school-based programmes targeting those already displaying symptoms of depression should be investigated. TRIAL REGISTRATION Current Controlled Trials ISRCTN19083628. FUNDING This project was funded by the NIHR Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 17, No. 47. See the HTA programme website for further project information.
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Affiliation(s)
- P Stallard
- Department for Health, University of Bath, Bath, UK
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Thomson NC, Chaudhuri R, Spears M, Messow CM, Jelinsky S, Miele G, Nocka K, Takahashi E, Hilmi OJ, Shepherd MC, Miller DK, McSharry C. Arachidonic acid metabolites and enzyme transcripts in asthma are altered by cigarette smoking. Allergy 2014; 69:527-36. [PMID: 24571371 DOI: 10.1111/all.12376] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2014] [Indexed: 01/18/2023]
Abstract
BACKGROUND Arachidonic acid metabolites are implicated in the pathogenesis of asthma although only limited information is available on the impact of current smoking history on these metabolites. The aim of the study was to examine the effect of smoking status on urinary, sputum, and plasma eicosanoid concentrations and relevant enzyme transcripts in asthma. METHODS In 108 smokers and never smokers with asthma and 45 healthy controls [smokers and never smokers], we measured urinary tetranor prostaglandin (PG)D2 (PGDM) and leukotriene (LT)E4 , induced sputum fluid LTB4 , LTE4 , PGD2 , and PGE2 , plasma secretory phospholipase A2 (sPLA2 ), and 11β prostaglandin F2α (11βPGF2α ), and, in a subgroup with severe asthma, airway leukocyte and epithelial cell mRNA expression levels of arachidonic acid metabolic enzymes. RESULTS Smokers with asthma had higher urinary LTE4 ; 83 (59, 130) vs 59 (40, 90) pg/mg creatinine, P = 0.008, and PGDM; 60 (35, 100) vs 41 (28, 59) ng/mg creatinine, P = 0.012 concentrations, respectively, and lower sputum PGE2 concentrations 80 (46, 157) vs 192 (91, 301) pg/ml, P = 0.001 than never smokers with asthma. Sputum LTB4 (P = 0.013), and plasma 11βPGF2α (P = 0.032), concentrations, respectively, were increased in smokers with asthma compared with healthy smokers. Asthma-specific and smoking-related increases (>1.5-fold expression) in arachidonate 15-lipoxygenase and gamma-glutamyltransferase transcripts were demonstrated. CONCLUSIONS Several arachidonic acid metabolites and enzyme transcripts involving both lipoxygenase and cyclooxygenase pathways are increased in smokers with asthma and differ from never smokers with asthma. Possibly targeting specific lipoxygenase and cyclooxygenase pathways that are activated by asthma and cigarette smoking may optimize therapeutic responses.
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Affiliation(s)
- N. C. Thomson
- Institute of Infection, Immunity & Inflammation; University of Glasgow; Glasgow UK
| | - R. Chaudhuri
- Institute of Infection, Immunity & Inflammation; University of Glasgow; Glasgow UK
| | - M. Spears
- Institute of Infection, Immunity & Inflammation; University of Glasgow; Glasgow UK
| | - C. M. Messow
- Robertson Centre for Biostatistics; University of Glasgow; Glasgow UK
| | - S. Jelinsky
- Pfizer Research/Translational Medicine Research Collaboration; Dundee and Sandwich UK
- Pfizer Research/Translational Medicine Research Collaboration; Cambridge MA USA
- Pfizer Research/Translational Medicine Research Collaboration; Collegeville PA USA
| | - G. Miele
- Pfizer Research/Translational Medicine Research Collaboration; Dundee and Sandwich UK
- Pfizer Research/Translational Medicine Research Collaboration; Cambridge MA USA
- Pfizer Research/Translational Medicine Research Collaboration; Collegeville PA USA
| | - K. Nocka
- Pfizer Research/Translational Medicine Research Collaboration; Dundee and Sandwich UK
- Pfizer Research/Translational Medicine Research Collaboration; Cambridge MA USA
- Pfizer Research/Translational Medicine Research Collaboration; Collegeville PA USA
| | | | - O. J. Hilmi
- Ear, Nose & Throat Department; NHS Greater Glasgow and Clyde; Glasgow UK
| | - M. C. Shepherd
- Institute of Infection, Immunity & Inflammation; University of Glasgow; Glasgow UK
| | - D. K. Miller
- Pfizer Research/Translational Medicine Research Collaboration; Dundee and Sandwich UK
- Pfizer Research/Translational Medicine Research Collaboration; Cambridge MA USA
- Pfizer Research/Translational Medicine Research Collaboration; Collegeville PA USA
| | - C. McSharry
- Institute of Infection, Immunity & Inflammation; University of Glasgow; Glasgow UK
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Bartlett JMS, Pritchard KI, Spears M. Validated or not validated? That is the question. J Natl Cancer Inst 2014; 106:djt360. [PMID: 24402423 DOI: 10.1093/jnci/djt360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- John M S Bartlett
- Affiliations of authors: Transformative Pathology, Ontario Institute for Cancer Research, Toronto, ON, Canada (JMSB, MS); Edinburgh Cancer Research UK Centre, University of Edinburgh, Edinburgh, UK (JMSB); Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada (JMSB); Institute of Health Policy Management and Evaluation, University of Edinburgh, Toronto, ON, Canada (KIP); Sunnybrook Odette Cancer Centre, Toronto, ON, Canada (KIP)
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Braunstein M, Liao L, Lyttle N, Taylor KJ, Krzyzanowski P, Kalatskaya I, Stein L, Marcellus R, Al-Awar R, Bartlett JMS, Spears M. Abstract P5-08-14: Deregulated histone and cell cycle pathways are associated with anthracycline resistance in breast cancer. Cancer Res 2013. [DOI: 10.1158/0008-5472.sabcs13-p5-08-14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Drug resistance in breast cancer is the major obstacle to a successful outcome following chemotherapy treatment. While a well-recognized mechanism of resistance involves upregulation of multidrug resistance (MDR) genes, the complexity and hierarchy of other non-MDR driven pathways are still largely unknown. The aim of this study was to identify pathways contributing to anthracycline resistance using isogenic drug resistant breast cancer cell lines. We generated MDA-MB-231, MCF7, SKBR3 and ZR-75-1 epirubicin-resistant breast cancer cell lines, all of which were cross-resistant to doxorubicin and SN-38; only SKBR3 cell line was also resistant to taxanes. Epirubicin-resistant cells were morphologically different from native cells, and had alterations in apoptosis and cell cycle profile. Using gene expression and small inhibitor analyses we identified deregulation of histone H2A and H2B genes in all four cell lines. These genes contribute to several biological pathways, which include cell cycle, chromosomal maintenance, epigenetics, RNA polymerase and mitochondrial transcription, as well as post-translational protein modifications. Importantly, histone deacetylase and cell cycle/DNA damage small molecule inhibitors reversed resistance and were cytotoxic for all four epirubicin-resistant cell lines confirming that histone and cell cycle pathways are associated with epirubicin resistance. Our study has established a model system for investigating drug resistance in all four breast cancer subtypes and revealed key pathways that contribute to the molecular mechanisms of anthracycline resistance.
Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P5-08-14.
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Affiliation(s)
- M Braunstein
- Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada; Ontario Cancer Institute, Toronto Medical Discovery Tower, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Edinburgh Cancer Research Centre, Western General Hospital, Toronto, ON, Canada
| | - L Liao
- Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada; Ontario Cancer Institute, Toronto Medical Discovery Tower, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Edinburgh Cancer Research Centre, Western General Hospital, Toronto, ON, Canada
| | - N Lyttle
- Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada; Ontario Cancer Institute, Toronto Medical Discovery Tower, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Edinburgh Cancer Research Centre, Western General Hospital, Toronto, ON, Canada
| | - KJ Taylor
- Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada; Ontario Cancer Institute, Toronto Medical Discovery Tower, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Edinburgh Cancer Research Centre, Western General Hospital, Toronto, ON, Canada
| | - P Krzyzanowski
- Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada; Ontario Cancer Institute, Toronto Medical Discovery Tower, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Edinburgh Cancer Research Centre, Western General Hospital, Toronto, ON, Canada
| | - I Kalatskaya
- Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada; Ontario Cancer Institute, Toronto Medical Discovery Tower, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Edinburgh Cancer Research Centre, Western General Hospital, Toronto, ON, Canada
| | - L Stein
- Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada; Ontario Cancer Institute, Toronto Medical Discovery Tower, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Edinburgh Cancer Research Centre, Western General Hospital, Toronto, ON, Canada
| | - R Marcellus
- Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada; Ontario Cancer Institute, Toronto Medical Discovery Tower, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Edinburgh Cancer Research Centre, Western General Hospital, Toronto, ON, Canada
| | - R Al-Awar
- Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada; Ontario Cancer Institute, Toronto Medical Discovery Tower, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Edinburgh Cancer Research Centre, Western General Hospital, Toronto, ON, Canada
| | - JMS Bartlett
- Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada; Ontario Cancer Institute, Toronto Medical Discovery Tower, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Edinburgh Cancer Research Centre, Western General Hospital, Toronto, ON, Canada
| | - M Spears
- Ontario Institute for Cancer Research, MaRS Centre, Toronto, ON, Canada; Ontario Cancer Institute, Toronto Medical Discovery Tower, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Edinburgh Cancer Research Centre, Western General Hospital, Toronto, ON, Canada
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Mendell MJ, Eliseeva EA, Davies MM, Spears M, Lobscheid A, Fisk WJ, Apte MG. Association of classroom ventilation with reduced illness absence: a prospective study in California elementary schools. Indoor Air 2013; 23:515-28. [PMID: 23506393 PMCID: PMC7165692 DOI: 10.1111/ina.12042] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 03/12/2013] [Indexed: 05/20/2023]
Abstract
Limited evidence associates inadequate classroom ventilation rates (VRs) with increased illness absence (IA). We investigated relationships between VRs and IA in California elementary schools over two school years in 162 3rd-5th-grade classrooms in 28 schools in three school districts: South Coast (SC), Bay Area (BA), and Central Valley (CV). We estimated relationships between daily IA and VR (estimated from two year daily real-time carbon dioxide in each classroom) in zero-inflated negative binomial models. We also compared IA benefits and energy costs of increased VRs. All school districts had median VRs below the 7.1 l/s-person California standard. For each additional 1 l/s-person of VR, IA was reduced significantly (p<0.05) in models for combined districts (-1.6%) and for SC (-1.2%), and nonsignificantly for districts providing less data: BA (-1.5%) and CV (-1.0%). Assuming associations were causal and generalizable, increasing classroom VRs from the California average (4 l/s-person) to the State standard would decrease IA by 3.4%, increase attendance-linked funding to schools by $33 million annually, and increase costs by only $4 million. Further increasing VRs would provide additional benefits. These findings, while requiring confirmation, suggest that increasing classroom VRs above the State standard would substantially decrease illness absence and produce economic benefits.
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Affiliation(s)
- M. J. Mendell
- Indoor Environment GroupEnvironmental Energy Technologies DivisionLawrence Berkeley National LaboratoryBerkeleyCAUSA
| | - E. A. Eliseeva
- Indoor Environment GroupEnvironmental Energy Technologies DivisionLawrence Berkeley National LaboratoryBerkeleyCAUSA
| | - M. M. Davies
- Indoor Environment GroupEnvironmental Energy Technologies DivisionLawrence Berkeley National LaboratoryBerkeleyCAUSA
| | - M. Spears
- Indoor Environment GroupEnvironmental Energy Technologies DivisionLawrence Berkeley National LaboratoryBerkeleyCAUSA
| | - A. Lobscheid
- Indoor Environment GroupEnvironmental Energy Technologies DivisionLawrence Berkeley National LaboratoryBerkeleyCAUSA
| | - W. J. Fisk
- Indoor Environment GroupEnvironmental Energy Technologies DivisionLawrence Berkeley National LaboratoryBerkeleyCAUSA
| | - M. G. Apte
- Indoor Environment GroupEnvironmental Energy Technologies DivisionLawrence Berkeley National LaboratoryBerkeleyCAUSA
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Spears M, Cunningham CA, Taylor KJ, Mallon EA, Thomas JSJ, Kerr GR, Jack WJL, Kunkler IH, Cameron DA, Chetty U, Bartlett JMS. Authors' Reply. J Pathol 2013; 229:e2-3. [DOI: 10.1002/path.4144] [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] [Received: 09/24/2012] [Revised: 09/24/2012] [Accepted: 10/17/2012] [Indexed: 11/09/2022]
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Bicknell S, Chaudhuri R, Shepherd M, Lee N, Pitman N, Spears M, Cameron E, Cowan D, Nixon J, Thompson J, Thomson NC. P5 Introducing Bronchial Thermoplasty Treatment into a Severe Asthma Clinical Service: Abstract P5 Table 1. Thorax 2012. [DOI: 10.1136/thoraxjnl-2012-202678.146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Spears M, Pederson HC, Lyttle N, Gray C, Quintayo MA, Brogan L, J Thomas JS, Kerr GR, Jack WJL, Kunkler IH, Cameron DA, Chetty U, Bartlett JMS. Expression of activated type I receptor tyrosine kinases in early breast cancer. Breast Cancer Res Treat 2012; 134:701-8. [PMID: 22562124 DOI: 10.1007/s10549-012-2076-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 04/17/2012] [Indexed: 11/30/2022]
Abstract
Overexpression of EGFR, HER2 and HER3 are known to be associated with poor outcome in breast cancer. Few studies have examined the clinical impact of activation of these proteins. In the present study, we evaluated EGFR, HER2 and HER3 and the activated (phosphorylated) forms of these proteins in patients with early breast cancer. EGFR, HER2, HER3, pEGFR, pHER2 and pHER3 expression was determined by immunohistochemical analysis of tissue microarrays constructed from tumours within the Edinburgh Breast Conservation Series (BCS). The BCS represents a fully-documented consecutive cohort of 1,812 patients treated by breast conservation surgery in a single institution. Our results demonstrate overexpression of HER2 and pHER2 to be associated with a significant reduction in overall survival (OS) (HR: 1.66, 95 % CI 1.22-2.26, p = 0.001 and HR: 1.57, 95 % CI 1.22-2.03, p = 0.001, respectively) and distant relapse-free survival (DRFS) (HR: 1.63, 95 % CI 1.23-2.18, p = 0.001 and HR: 1.55, 95 % CI 1.23-1.97, p = 0.0002, respectively). Paradoxically, expression of pEGFR was associated with a significantly improved OS (HR: 0.67 95 % CI 0.50-0.91, p = 0.01) and DRFS (HR: 0.73, 95 % CI 0.56-0.96, p = 0.025). Expression of activated EGFR/HER2 provides additional information on ER positive breast cancer patients and suggests alternative treatment for those in this subgroup.
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Affiliation(s)
- Melanie Spears
- Transformative Pathology, Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College St, Suite 800, Toronto, ON, M5G 043, Canada
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Spears M, Cunningham CA, Taylor KJ, Mallon EA, Thomas JSJ, Kerr GR, Jack WJL, Kunkler IH, Cameron DA, Chetty U, Bartlett JMS. Proximity ligation assays for isoform-specific Akt activation in breast cancer identify activated Akt1 as a driver of progression. J Pathol 2012; 227:481-9. [PMID: 22430898 DOI: 10.1002/path.4022] [Citation(s) in RCA: 26] [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] [Received: 11/02/2011] [Revised: 03/07/2012] [Accepted: 03/09/2012] [Indexed: 11/08/2022]
Abstract
The PI3K/Akt signal transduction pathway plays an important role in cancer progression and cell survival. Akt activation is associated with poor outcome in endocrine-treated breast cancer, whereas high levels of cytoplasmic Akt2 are associated with an improved overall survival. Proximity ligation assays (PLAs) were used to determine quantitative expression levels of isoform-specific activation (phosphorylation) of Akt1 and Akt2 in formalin-fixed, paraffin-embedded cell lines and breast cancer tumour tissues in situ. PLAs demonstrated a range of expression in breast cancer samples for total pAkt1 and pAkt2. High levels of pAkt1 were associated with reduced DRFS (HR: 1.45, 95% CI 1.14-1.83, p = 0.002) and OS (HR: 1.42, 95% CI 1.10-1.83, p = 0.007). When PLA results were combined, patients that had high levels of pAkt1 only had a significantly decreased DRFS (HR: 1.92, 95% CI 1.34-2.76, p = 0.005) and OS (HR: 1.94, 95% CI 1.32-2.86, p = 0.008) compared to other patients. Using PLAs to discriminate activation of Akt1 versus Akt2 suggests that Akt1 drives progression in early breast cancers. In cases where both Akt1/Akt2 are activated, Akt2 may act to reverse this effect. Using PLAs, we have measured activation of Akt1 and Akt2 proteins separately in situ in FFPE breast cancer samples.
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Affiliation(s)
- Melanie Spears
- Transformative Pathology, Ontario Institute for Cancer Research, MaRS Centre, South Tower, 101 College St, Suite 800, Toronto, Ontario, Canada M5G 043
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Spears M, Dewet C, McSharry C, Chaudhuri R, Donnelly I, Jolly L, Cameron E, Thomson NC. S122 Sputum cytokine profiles in asthma and the impact of smoking-a factor analysis. Thorax 2011. [DOI: 10.1136/thoraxjnl-2011-201054b.122] [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: 11/03/2022]
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