Development and independent validation of a prognostic assay for stage ii colon cancer using formalin-fixed paraffin-embedded tissue

Purpose: Current prognostic factors are poor at identifying patients at risk of disease recurrence after surgery for stage II colon cancer. Here we describe a DNA microarray-based prognostic assay using clinically relevant formalin-fixed paraffin-embedded (FFPE) samples. Patients and Methods: A gene signature was developed from a balanced set of 73 patients with recurrent disease (high risk) and 142 patients with no recurrence (low risk) within 5 years of surgery. Results: The 634-probe set signature identified high-risk patients with a hazard ratio (HR) of 2.62 (P <.001) during cross validation of the training set. In an independent validation set of 144 samples, the signature identified high-risk patients with an HR of 2.53 (P <.001) for recurrence and an HR of 2.21 (P = .0084) for cancer-related death. Additionally, the signature was shown to perform independently from known prognostic factors (P <.001). Conclusion: This gene signature represents a novel prognostic biomarker for patients with stage II colon cancer that can be applied to FFPE tumor samples. © 2011 by American Society of Clinical Oncology.

Fluoroscopic and electrical assessment of a series of defibrillation leads:prevalence of externalized conductors

Introduction : Insulation defects with externalized conductors have been reported in the St. Jude Riata(®) family of defibrillation leads (St. Jude Medical, Sylmar, CA, USA). The objective of the Northern Ireland Riata(®) lead screening program was to identify insulation defects and externalized conductors by systematic fluoroscopic and electrical assessment in a prospectively defined cohort of patients. We sought to estimate the prevalence, identify risk factors, and determine the natural history of this abnormality. Methods : All patients with a Riata(®) lead under follow-up at the Royal Victoria Hospital were invited for fluoroscopic imaging and implantable cardioverter-defibrillator lead parameter checks. Fluoroscopic images were read independently by two cardiologists and the presence of externalized conductors was classified as positive, negative, or borderline. Results: One hundred and sixty-five of 212 patients with a Riata lead were evaluated by fluoroscopy and lead parameter measurements. The mean duration after implantation was 3.98+/-1.43 years. After screening 25 (15%) patients were classified as positive, 137 (83%) negative, and three (1.8%) borderline. Time since implantation (P = 0.001), presence of a single coil lead (P = 0.042), and patient age (P = 0.034) were significantly associated with externalized conductors. The observed rate of externalized conductors was 26.9% for 8-French and 4.7% for 7-French leads. No leads that were identified prospectively with externalized conductors had electrical abnormalities. Seven of 25 (28%) patients had a defective lead extracted by the end of this screening period. Conclusion: A significant proportion (15%) of patients with a Riata lead had an insulation breach 4 years after implantation. High-resolution fluoroscopic imaging in at least two orthogonal views is required to identify this abnormality. (PACE 2012;35:1498-1504).

Identification and Validation of an Anthracycline/Cyclophosphamide–Based Chemotherapy Response Assay in Breast Cancer

Background: There is no method routinely used to predict response to anthracycline and cyclophosphamide–based chemotherapy in the clinic; therefore patients often receive treatment for breast cancer with no benefit. Loss of the Fanconi anemia/BRCA (FA/BRCA) DNA damage response (DDR) pathway occurs in approximately 25% of breast cancer patients through several mechanisms and results in sensitization to DNA-damaging agents. The aim of this study was to develop an assay to detect DDR-deficient tumors associated with loss of the FA/BRCA pathway, for the purpose of treatment selection.

Methods: DNA microarray data from 21 FA patients and 11 control subjects were analyzed to identify genetic processes associated with a deficiency in DDR. Unsupervised hierarchical clustering was then performed using 60 BRCA1/2 mutant and 47 sporadic tumor samples, and a molecular subgroup was identified that was defined by the molecular processes represented within FA patients. A 44-gene microarray-based assay (the DDR deficiency assay) was developed to prospectively identify this subgroup from formalin-fixed, paraffin-embedded samples. All statistical tests were two-sided.

Results: In a publicly available independent cohort of 203 patients, the assay predicted complete pathologic response vs residual disease after neoadjuvant DNA-damaging chemotherapy (5-fluorouracil, anthracycline, and cyclophosphamide) with an odds ratio of 3.96 (95% confidence interval [Cl] =1.67 to 9.41; P = .002). In a new independent cohort of 191 breast cancer patients treated with adjuvant 5-fluorouracil, epirubicin, and cyclophosphamide, a positive assay result predicted 5-year relapse-free survival with a hazard ratio of 0.37 (95% Cl = 0.15 to 0.88; P = .03) compared with the assay negative population.

Conclusions: A formalin-fixed, paraffin-embedded tissue-based assay has been developed and independently validated as a predictor of response and prognosis after anthracycline/cyclophosphamide–based chemotherapy in the neoadjuvant and adjuvant settings. These findings warrant further validation in a prospective clinical study.

Factors influencing success of clinical genome sequencing across a broad spectrum of disorders

To assess factors influencing the success of whole-genome sequencing for mainstream clinical diagnosis, we sequenced 217 individuals from 156 independent cases or families across a broad spectrum of disorders in whom previous screening had identified no pathogenic variants. We quantified the number of candidate variants identified using different strategies for variant calling, filtering, annotation and prioritization. We found that jointly calling variants across samples, filtering against both local and external databases, deploying multiple annotation tools and using familial transmission above biological plausibility contributed to accuracy. Overall, we identified disease-causing variants in 21% of cases, with the proportion increasing to 34% (23/68) for mendelian disorders and 57% (8/14) in family trios. We also discovered 32 potentially clinically actionable variants in 18 genes unrelated to the referral disorder, although only 4 were ultimately considered reportable. Our results demonstrate the value of genome sequencing for routine clinical diagnosis but also highlight many outstanding challenges.

Identification of tubulin as the molecular target of proapoptotic pyrrolo-1,5-benzoxazepines

We have demonstrated previously that certain members of a series of novel pyrrolo-1,5-benzoxazepine (PBOX) compounds potently induce apoptosis in a variety of human chemotherapy-resistant cancer cell lines and in primary ex vivo material derived from cancer patients. A better understanding of the molecular mechanisms underlying the apoptotic effects of these PBOX compounds is essential to their development as antineoplastic therapeutic agents. This study sought to test the hypothesis that proapoptotic PBOX compounds target the microtubules. We show that a representative proapoptotic PBOX compound, PBOX-6, induces apoptosis in both the MCF-7 and K562 cell lines. An accumulation of cells in G2/M precedes apoptosis in response to PBOX-6. PBOX-6 induces prometaphase arrest and causes an accumulation of cyclin B1 levels and activation of cyclin B1/CDK1 kinase in a manner similar to that of two representative antimicrotubule agents, nocodazole and paclitaxel. Indirect immunofluorescence demonstrates that both PBOX-6 and another pro-apoptotic PBOX compound, PBOX-15, cause microtubule depolymerization in MCF-7 cells. They also inhibit the assembly of purified tubulin in vitro, whereas a nonapoptotic PBOX compound (PBOX-21) has no effect on either the cellular microtubule network or on the assembly of purified tubulin. This suggests that the molecular target of the pro-apoptotic PBOX compounds is tubulin. PBOX-6 does not bind to either the vinblastine or the colchicine binding site on tubulin, suggesting that it binds to an as-yet-uncharacterised novel site on tubulin. The ability of PBOX-6 to bind tubulin and cause microtubule depolymerization confirms it as a novel candidate for antineoplastic therapy.

The pyrrolo-1,5-benzoxazepine, PBOX-6, inhibits the growth of breast cancer cells in vitro independent of estrogen receptor status and inhibits breast tumour growth in vivo

Members of a novel series of pyrrolo-1,5-benzoxazepine (PBOX) compounds have been shown to induce apoptosis in a number of human leukemia cell lines of different haematological lineage, suggesting their potential as anti-cancer agents. In this study, we sought to determine if PBOX-6, a well characterised member of the PBOX series of compounds, is also an effective inhibitor of breast cancer growth. Two estrogen receptor (ER)-positive (MCF-7 and T-47-D) and two ER-negative (MDA-MB-231 and SK-BR-3) cell lines were examined. The 3,4,5-dimethylthiazol-2-yl-2,5-diphenyl-tetrazolium bromide (MTT) assay was used to determine reduction in cell viability. PBOX-6 reduced the cell viability of all four cell lines tested, regardless of ER status, with IC(50) values ranging from 1.0 to 2.3 microM. PBOX-6 was most effective in the SK-BR-3 cells, which express high endogenous levels of the HER-2 oncogene. Overexpression of the HER-2 oncogene has been associated with aggressive disease and resistance to chemotherapy. The mechanism of PBOX-6-induced cell death was due to apoptosis, as indicated by the increased proportion of cells in the pre-G1 peak and poly(ADP-ribose) polymerase (PARP) cleavage. Moreover, intratumoural administration of PBOX-6 (7.5 mg/kg) significantly inhibited tumour growth in vivo in a mouse mammary carcinoma model (p=0.04, n=5, Student's t-test). Thus, PBOX-6 could be a promising anti-cancer agent for both hormone-dependent and -independent breast cancers.

Christianity as a Vocation: The Rostrevor Benedictines and the Renewal of Faith in Ireland

This chapter explores how the Benedictine monks at Holy Cross Monastery in Rostrevor, Northern Ireland, have re-introduced the idea of vocation into the minds of a range of Christians on the island of Ireland. A picture of this new vision of the church in Ireland is painted through sections devoted to 'living ecumenism' and 'creating safe spaces'. The work of the Rostrevor Benedictines may seem limited because of the small scale of the changes among individuals. But Holy Cross is just one of multiple 'extra-institutional' spaces in Ireland's changing religious landscape. From their strategic positions on the margins, extra-institutional expressions of religion may prompt more significant changes in religious practice than initially seem possible.

Legendarius per circulum anni, pars.

Légendier disposé dans l'ordre du calendrier liturgique du 20 juillet au 25 novembre et contenant les saints suivants: ss. Margarita, Maria Magdelene, Jacobus major ap., Stephanus, Laurentius, Hippolytus, assumptio b. Mariae, Bartholomaeus, Augustinus, Johannes Baptista, Aegidius, nativitas b. Mariae, Gorgonius, Protus et Hyacinthus, exaltatio s. Crucis, Euphemia, Matthaeus, Mauritius, Cosmas et Damianus, Michael archangelus, Hieronymus, Leodegarius, Dionysius, Lucas, Simon et Judas, Martinus, Caecilia, Clemens, Catharina. F. 1-130. Legendarius. F. 1-3v. "... passio sancte Margarete virginis"; cf. B.H.L. n° 5306. F. 3v-6v. "... vita sancte Marie Magdalene" [ODO Cluniacensis abbas, sermo 2, excerptum] (P.L. 133, 714B-719C); cf. B.H.L. n° 5440. F. 6v-8v. "... passio sancti Jacobi [majoris] apostoli" incomplet des lignes finales par lacune matérielle, à partir de "decollandi erant dixit [Jacobus...]" [Virtutes apostolorum, de s. Jacobo majore] (Mombritius, 2a ed., II, 37-40 lig. 15); cf. B.H.L. n° 4057; C.A.N.T. n° 272. F. 9-12. "Inventio sancti Stephani prothomartyris" [LUCIANUS presbyter, interprete AVITO presbytero Bracarensi ]. "Domino venerabili Nimpsio [sic] episcopo... [Julianus exponctué et corrigé en] Lucianus... Revelationem que mihi ostensa est...-... aperire dignatus est..." recensio mixta suivie d'un court épilogue: "Bovem appellatum... declarata sunt"; cf. C.P.L. n° 575; B.H.L. Suppl. n° 7851n (E. Vanderlinden, Rev. des études byzantines, IV, 1946, 190-216, version A'; ne fait pas partie des mss. recensés pour l'édition). F. 12-16. "... passio sancti [Sixti et sancti] Laurentii". "In illo tempore Decius Caesar et Valerianus prefectus jusserunt...-... participati sunt omnes"; cf. B.H.L. Suppl. n° 7801 avec var. incipit et n° 4754. F. 16-18. "... passio sancti Ypoliti et sociorum ejus". "Egressus itaque Ypolitus post tercium diem...-... vivere male et regnare cum Christo "; cf. B.H.L. n° 3961 avec var. incipit et explicit. F. 18-31. "... [sermo] beati Ieronimi in assumptione sancte Virginis" [PASCHASIUS RADBERTUS, De Adsumptione b. Mariae] (C.C.C.M., LVI C 109-162; édité aussi parmi les apocryphes de saint Jérôme, P.L., XXX, 126-147); cf. C.P.L. n° 633, ep. 9 (18-29). F. 29-31. Addition contemporaine : "In vigilia assumptionis beate Marie legatur: Secundum Lucam (Lc 11, 27). [M]agne devocionis et fidei...-... ubera que suxisti" [BEDA, In Lc, l. IV, excerptum] divisé en trois paragraphes, correspondant sans doute à trois leçons (P.L., XCII, 479 C-480 B; C.C.S.L., CXX, 236-237 lig. 213-244) (29). — "Sermo iste legatur in nativitate beate Marie virginis"; cf. infra f. 56v. "[A]pprobate consuetudinis est apud christianos...-... pacta cessare" [FULBERTUS CARNOTENSIS, sermo 4] incomplet de la fin qui a été laissée en blanc (P.L. CXLI, 320-324 A; J.M. Canal, dans Rech. théol. anc. méd., XXX (1963), 56-61 lig. 168); ne fait pas partie des mss. répertoriés par J.M. Canal, ibid., XXIX (1962), 36-37; division marginale en neuf, puis en trois fois trois leçons; en marge du titre, une note difficilement lisible identifie l'auteur: "sermo Fulberti ep. Carnotensis" (29v-31). F. 32-35. "... vita [sic pro passio] sancti Bartholomei apostoli" [Virtutes apostolorum, de s. Bartholomaeo]; cf. B.H.L. Suppl. n° 1002a; C.A.N.T. n° 259. F. 35-49v. "[Vita s.] Augustini episcopi", sans prologue [POSSIDIUS]. "Ex provincia affricana civitate...-... perfruar"; cf. B.H.L. n° 785; C.P.L. n° 358 (35-49a lig. 7); suivi de la liste des livres de s. Augustin dans l'ordre des Retractations : "Libros vero quod edidit hic breviter enumerare vel annotare non omissi. Et hoc indicium librorum omnium sancti Augustini. Contra paganos achademicos [sic] libri III. De beata vita liber I. De ordine sacro libri II. De soliloquiis...-... et gratia liber. Requievit autem... V. kal. septembris..." (C.C.S.L., LVII (1984), 1-4, var.); texte proche du ms. lat. 5276, ff. 136v-137, répertorié par A. Wilmart, Miscellanea Agostiniana, Roma, 1931, 157 (Testi e studi, 2) (49a lig. 7-49v). F. 49v-52v. "Inventio capitis sancti Johannis Baptiste"; cf. B.H.L. n° 4296 (49v-51). — "De translatione ejusdem [Angeriacum]"; cf. B.H.L. n° 4297 (51-52v). F. 52v-56v. "... vita sancti Egidii"; cf. B.H.L. n° 93. F. 56v-59v. "De nativitate sancte Marie". "Petis a me petitiunculam opere...-... prefationem habuisse"; cf. B.H.L. Suppl. n° 5345 (56v a-b lig. 27) ; suivi de: "Petitis a me...-... scribi potuerunt. Igitur beata et gloriosissima semper virgo Maria..-... docuerunt Dominum..." (éd. parmi les apocryphes de s. Jérôme, P.L., XXX, 2a ed., 307-317); cf. B.H.L. n° 5344-5343; C.P.L., n° 633, ep. 50 (56v b lig. 27-59v). L'attribution à Paschase Radbert des deux lettres regroupées en une seule faite par C. Lambot, dans Rev. bénéd., XLVI (1934), 271-282, est réfutée par R. Beyers, dans Rev. Théol. et Philos., CXXII (1990), 171-188. Voir sa nouv. éd. dans CC Apocrypha, 10. F. 59v-61v. "Passio sancti Gorgonii [et Dorothei]; cf. B.H.L. n° 3617. F. 61v-62. "[Passio ss.] Prothi et Jacincti"; cf. B.H.L. n° 6977. F. 62-63v. "De exaltatione sancte Crucis". "Tempore illo postquam Constantino Augusto contra Maxentium..."; cf. B.H.L. n° 4178, avec var. incipit. F. 64-68v. "[Passio s.] Eufemie virginis". "Quinto persecutionis anno Diocletiani...-... Completum est autem martyrium... Prisco proconsule Europe..."; cf. B.H.L. n° 2709, avec var. explicit. F. 68v-72v. "[Passio] sancti Mathei apostoli" [Virtutes apostolorum, de s. Jacobo majore]; cf. C.A.N.T. n° 270; B.H.L. n° 5690, avec var. explicit de l'épilogue: "Zaroes autem...-... passio eorum ostendit". F. 72v-76. "[Passio s.] [Marcii corrigé en] Mauricii con [sic] sociis suis" [s. EUCHERIUS LUGDUNENSIS] sans le prologue; cf. B.H.L. n° 5738; C.P.L. n° 490. F. 76-79v. "[Passio ss.] Cosme et Damiani"; cf. B.H.L. Suppl. n° 1975. F. 79v-80. "[In festivitate s.] Michaelis archangeli". "Angelorum quippe et hominum naturam...-... medicina Dei." [GREGORIUS MAGNUS, Hom. in Ev., 34, excerptum]; C.P.L. n° 1711 (P.L., LXXVI, 1249 C-1251 A, §§ 6, fin-9 début) divisé en 8 paragraphes; une interpolation a été ajoutée dans la marge inférieure du f. 79v par une main contemporaine qui a également numéroté les paragraphes en IX leçons, le texte ajouté formant la lectio IIa : "[N]ovem esse angelorum ordines ad Dei judicia...-... principantur."; il s'agit d'un court extrait du sermon Legimus in ecclesiasticis historiis édité par J. E. Cross, dans Traditio, 33 (1977), 108-109 lig. 41-47 (Beda, Homilia subditia 71, P.L., XCIV, 453 C); cf. C.P.P.M., I, 4046. F. 80-82v. "[Vita s.] Jeronimi presbiteri". "Hieronimus noster [corrigé en: presbiter] in oppido Stridonis...-... etatis sue anno in Domino requievit cui..." extraits de la Vie apocryphe de Gennadius (P.L., XXII, 175-184, passim, avec var.); cf. C.P.L. n° 623; B.H.L. n° 3869; Lambert, B.H.M., IIIA, 630 (80-81b lig. 26); suivi du miracle du lion extrait de la Vie du Ps. Sebastianus Casinensis: "Contigit autem hujusmodi miraculum in monasterio... Quadam namque die ingens leo... - asserendo narrantur" (P.L., XXII, 210 lig. 11-213 lig. 11); cf. C.P.L. n° 622; B.H.L. n° 3872 avec var. incipit; Lambert, B.H.M., IIIA, 630 (81b lig. 26-82v). F. 82v-88v. "[Vita s.] Leodegarii". "Igitur sanctus Leodegarius ex progenie...-... postmodum cecum. ... adnecteret opera ibidem" [URSINUS LOGOGIACENSIS] sans le prologue et incomplet de la fin (C.C.S.L., CXVII, 589-632 lig. 14, avec var.); cf. C.P.L. n° 1079a; B.H.L. n° 4851; suivi d'un court extrait omis à sa place plus haut dans le texte: "Deinde vero ire ceperunt... Dei opera ibidem" (ed. cit., 631 § 31 lig. 3-7). F. 88v-98. "[Passio] sancti Dyonisii martyris", texte incomplet par suite de la perte de 2 ff. entre les ff. 96 et 97, le texte s'arrête à "...fideliter adhe[-rebat]" et reprend à "[Domitia-]no per tres Cesares..." (P.L., CVI, 23-40 C et 48 A-50); cf. B.H.L. n° 2175. F. 98-100v. "[Laudatio s.] Luce evvangeliste". "Gloriosus igitur evvangelista Jhesu Christi Lucas natione Syrus...-... ubique confluunt qui ..." [PAULUS DIACONUS, hom. 59] incomplet du prologue (P.L., XCV, 1530-1535, avec var.); cf. B.H.L. n° 4974, d'après ce ms. F. 100v-106. "[Passio ss.] Symonis et Jude apostolorum" avec l'épilogue [ABDIAS, Virtutes Simonis et Judae Thaddaei]; cf. B.H.L. n° 7750-7751; C.A.N.T. n° 284. F. 106-107v. "[Laudatio] sancti Martini archiepiscopi" [ALCUINUS, De vita s. Martini, pars I]; cf. B.H.L. n° 5625. — GREGORIUS TURONENSIS, De virtutibus s. Martini; cf. B.H.L. n° 5618; seule l'adresse du prologue, introduite par une initiale filigranée, a été copiée au bas du f. 107v, col. b: "Domnis sanctis et in Christi amore dulcissimis fratribus... Gregorius peccator", le texte lui-même manque, soit en raison de la perte du cahier suivant, soit qu'il n'ait pas été copié. F. 108-115v. "[Passio s.] Cecilie virginis et martyris"; cf. B.H.L. Suppl. n° 1495a. F. 115v-118v. "[Passio s.] Clementis pape". [Prologus] "Postquam igitur beatus Petrus apostolus in Antiochia cathedram... -... passio secuta est"; cf. B.H.L. Suppl. n° 1849, d'après ce ms. (115v-116a, lig. 11); — "Tunc sanctus Clemens romane ecclesie episcopus disciplinam...-... Cersone Licie provincie"; C.P.L. n° 2177; B.H.L. n° 1848 (Mombritius, 2a ed., I, 341-344, var. à l'incipit et à l'explicit); suivi de: "Oremus fratres ut Dominus... participes. Per..." (116a, lig. 11-118v). F.118v-130. "[Passio] sancte Katerine virginis et martyris"; cf. B.H.L. n° 1663, sans le prologue. F. 130-130v. Additions. Table des saints contenus dans le volume, XIVe s. (130). — Prière latine en 10 strophes de deux vers, XVe s.: "Jhesu tue matris prece ab Orci me serva nece...-... ab inferi atris" (130v).