Analytical validation of HER2DX genomic test for early-stage HER2-positive breast cancer

BACKGROUND

HER2DX, a multianalyte genomic test, has been clinically validated to predict breast cancer recurrence risk (relapse risk score), the probability of achieving pathological complete response post-neoadjuvant therapy (pCR likelihood score), and individual ERBB2 messenger RNA (mRNA) expression levels in patients with early-stage human epidermal growth factor receptor 2 (HER2)-positive breast cancer. This study delves into the comprehensive analysis of HER2DX's analytical performance.

MATERIALS AND METHODS

Precision and reproducibility of HER2DX risk, pCR, and ERBB2 mRNA scores were assessed within and between laboratories using formalin-fixed paraffin-embedded (FFPE) tumor tissues and purified RNA. Robustness was appraised by analyzing the impact of tumor cell content and protocol variations including different instruments, reagent lots, and different RNA extraction kits. Variability was evaluated across intratumor biopsies and genomic platforms [RNA sequencing (RNAseq) versus nCounter], and according to protocol variations.

RESULTS

Precision analysis of 10 FFPE tumor samples yielded a maximal standard error of 0.94 across HER2DX scores (1-99 scale). High reproducibility of HER2DX scores across 29 FFPE tumors and 20 RNAs between laboratories was evident (correlation coefficients >0.98). The probability of identifying score differences >5 units was ≤5.2%. No significant variability emerged based on platform instruments, reagent lots, RNA extraction kits, or TagSet thaw/freeze cycles. Moreover, HER2DX displayed robustness at low tumor cell content (10%). Intratumor variability across 212 biopsies (106 tumors) was <4.0%. Concordance between HER2DX scores from 30 RNAs on RNAseq and nCounter platforms exceeded 90.0% (Cohen's κ coefficients >0.80).

CONCLUSIONS

The HER2DX assay is highly reproducible and robust for the quantification of recurrence risk, pCR likelihood, and ERBB2 mRNA expression in early-stage HER2-positive breast cancer.

Prognostic value of HER2DX in early-stage HER2-positive breast cancer: a comprehensive analysis of 757 patients in the Sweden Cancerome Analysis Network-Breast dataset (SCAN-B)

BACKGROUND

The HER2DX risk-score has undergone rigorous validation in prior investigations involving patients with early-stage human epidermal growth factor receptor 2 (HER2)-positive (HER2+) breast cancer. In this study, we present the outcomes of the HER2DX risk-score within the most recent release of the Sweden Cancerome Analysis Network-Breast (SCAN-B) HER2+ cohort. This updated examination benefits from a larger patient sample, an extended follow-up duration, and detailed treatment information.

MATERIALS AND METHODS

Clinical and RNAseq data from the SCAN-B dataset were retrieved from Gene Expression Omnibus (GSE81538). Among the 6600 patients, 819 had HER2+ breast cancer, with 757 individuals with research-based HER2DX risk-scores and corresponding survival outcomes. The HER2DX risk-score was evaluated (i) as a continuous variable and (ii) using predefined cut-offs. The primary endpoint for this study was overall survival (OS). The Kaplan-Meier method and Cox models were used to estimate OS and a multistate model with four states was fitted to better characterize patients' follow-up.

RESULTS

The median follow-up time was 7.5 years (n = 757). The most common systemic therapy was chemotherapy with trastuzumab (82.0%) and most tumors were classified as T1-T2 (97.1%). The HER2DX risk-score as a continuous variable was significantly associated with OS after adjustment for clinical variables and treatment regimen [hazard ratios (HR) per 10-unit increment = 1.31, 95% confidence interval (CI) 1.13-1.51, P < 0.001] as well as within predefined risk groups (high versus low; HR = 2.57, 95% CI 1.36-4.85, P < 0.001). Patients classified as HER2DX high-risk also had higher risk of (i) breast cancer recurrence and (ii) death without previous recurrence. Within the subgroup of HER2+ T1N0 tumors (n = 297), those classified as high-risk demonstrated inferior OS compared to low-risk tumors (7-year OS 77.8% versus 96.8%, P < 0.001). The HER2DX mRNA ERBB2 score was associated with clinical HER2 status (area under the receiver operating characteristic curve = 0.91).

CONCLUSIONS

In patients with early-stage HER2+ breast cancer, HER2DX risk-score provides prognostic information beyond clinicopathological variables, including treatment regimen with or without trastuzumab.

How Would Nature See Our Corneal Triumphs? The LXXIX Edward Jackson Lecture

PURPOSE

To describe discrepancies between clinical observation and current teachings in corneal endothelial disease, particularly in Fuchs endothelial dystrophy and its potential association with primary open angle glaucoma.

DESIGN

Perspective.

METHODS

A perspective is presented on Fuchs dystrophy, a disorder that commonly presents with a compromised endothelium but minimal stromal edema, indicating that the corneal imbibition pressure is relatively "too high."

RESULTS

The discrepancy between the relative lack of stromal edema in the absence of an endothelial cell layer cannot be explained by the current theories involving a circulatory pumping mechanism over the endothelial cell layer, but may point to the following: (1) secondary involvement of the corneal endothelium in Fuchs dystrophy; (2) separate hydration systems for maintaining the imbibition pressure (vertical static hydration) and corneal nutrition (horizontal dynamic hydration); (3) the cornea as net contributor of aqueous humor; (4) a close relationship between the corneal imbibition and intraocular pressure, with potentially a shared regulatory system; and (5) a potential steroid-type hormone dependency of this regulatory system.

CONCLUSIONS

Clinical observation shows that the stromal imbibition pressure is "too high" in Fuchs endothelial dystrophy, indicating that it may not primarily be an endothelial disease, but a type of "corneal glaucoma."

Association of HER2DX with pathological complete response and survival outcomes in HER2-positive breast cancer

BACKGROUND

The HER2DX genomic test predicts pathological complete response (pCR) and survival outcome in early-stage HER2-positive (HER2+) breast cancer. Here, we evaluated the association of HER2DX scores with (i) pCR according to hormone receptor status and various treatment regimens, and (ii) survival outcome according to pCR status.

MATERIALS AND METHODS

Seven neoadjuvant cohorts with HER2DX and clinical individual patient data were evaluated (DAPHNe, GOM-HGUGM-2018-05, CALGB-40601, ISPY-2, BiOnHER, NEOHER and PAMELA). All patients were treated with neoadjuvant trastuzumab (n = 765) in combination with pertuzumab (n = 328), lapatinib (n = 187) or without a second anti-HER2 drug (n = 250). Event-free survival (EFS) and overall survival (OS) outcomes were available in a combined series of 268 patients (i.e. NEOHER and PAMELA) with a pCR (n = 118) and without a pCR (n = 150). Cox models were adjusted to evaluate whether HER2DX can identify patients with low or high risk beyond pCR status.

RESULTS

HER2DX pCR score was significantly associated with pCR in all patients [odds ratio (OR) per 10-unit increase = 1.59, 95% confidence interval 1.43-1.77; area under the ROC curve = 0.75], with or without dual HER2 blockade. A statistically significant increase in pCR rate due to dual HER2 blockade over trastuzumab-only was observed in HER2DX pCR-high tumors treated with chemotherapy (OR = 2.36 (1.09-5.42). A statistically significant increase in pCR rate due to multi-agent chemotherapy over a single taxane was observed in HER2DX pCR-medium tumors treated with dual HER2 blockade (OR = 3.11, 1.54-6.49). The pCR rates in HER2DX pCR-low tumors were ≤30.0% regardless of treatment administered. After adjusting by pCR status, patients identified as HER2DX low-risk had better EFS (P < 0.001) and OS (P = 0.006) compared with patients with HER2DX high-risk.

CONCLUSIONS

HER2DX pCR score and risk score might help identify ideal candidates to receive neoadjuvant dual HER2 blockade in combination with a single taxane in early-stage HER2+ breast cancer.

Intracorneal ring segment implantation in advanced Keratoconus

PURPOSE

To compare the clinical outcomes of intracorneal ring segment (ICRS) implantation in eyes with advanced vs. mild/moderate keratoconus (KCN).

METHODS

A retrospective analysis of 141 eyes of 111 patients with KCN who underwent ICRS implantation. Preoperative maximum keratometry (Kmax) was <57 diopters (D) in 70 eyes and >57 D in 71 eyes. Postoperatively, corrected distance visual acuity (CDVA), Kmax, and intraoperative and postoperative complications were assessed at 1 day, 1 month, and 1 year.

RESULTS

Corneas with a preoperative Kmax >57 D experienced greater reduction in axial curvature after ICRS implantation than corneas with a preoperative Kmax <57 D (7.0 D vs. 5.5 D, p=0.005) and gained more Snellen lines of CDVA (3 vs. 1, p<0.001) by 1 year postoperatively. The incidences of the most prevalent complications (explantation, extrusion, and infectious keratitis) did not differ significantly between the two groups (p=0.29, p=0.99, p=0.98).

CONCLUSIONS

The visual and topographic effects of ICRS implantation are greater in eyes with more advanced KCN, with no increase in the incidence of the most common complications.

Clinical outcomes of Descemet membrane endothelial keratoplasty performed in eyes with keratoconus and corneal endothelial dysfunction

PURPOSE

To evaluate the clinical outcome of Descemet membrane endothelial keratoplasty (DMEK) performed in eyes with comorbid keratoconus (KCN) and corneal endothelial dysfunction.

METHODS

Twenty-five consecutive eyes of 14 patients with comorbid stable KCN underwent DMEK for corneal endothelial dysfunction; best spectacle corrected visual acuity (BSCVA), maximum corneal curvature (Kmax), maximum corneal power (Pmax), central corneal thickness (CCT), and intra- and postoperative complications were assessed.

RESULTS

Excluding eyes requiring re-transplantation for primary graft failure (n = 3), all eyes showed improvement in BSCVA, reaching ≥ 20/40 (0.5) in 86%, ≥ 20/25 (0.8) in 55%, and ≥ 20/20 (1.0) in 27% by one month postoperatively; 90%, 76%, and 48% by 6 months postoperatively; and 88%, 76%, and 47% by 12 months postoperatively. CCT decreased from 571μm preoperatively to 485μm at 1 month (p < 0.001) and 481μm at 12 months (p < 0.001). Kmax decreased by a median of 1.4 diopters (D) at 1 month (p = 0.003) and 3.1 D at 12 months (p = 0.021), and every eye with a preoperative Kmax ≥ 46 D demonstrated flattening. Pmax decreased by 2.1 D at 1 month (p = 0.001) and 4.0 D at 12 months (p = 0.016).

CONCLUSION

DMEK is technically feasible in eyes with comorbid KCN and may give excellent outcomes visual and refractive outcomes, including significant corneal flattening, which may potentially create a visually significant hyperopic shift in patients with severely ectatic corneas.

DMEK Without Postoperative Supine Posturing

PURPOSE

The purpose of this study was to describe the incidence of graft detachment after Descemet membrane endothelial keratoplasty (DMEK) without postoperative supine posturing.

METHODS

A total of 106 eyes of 84 patients with Fuchs endothelial corneal dystrophy or bullous keratopathy (BK) were operated by a single experienced surgeon with DMEK with a 99% anterior chamber air bubble fill, recovered in an upright (seated) position, and then discharged without instructions to remain supine. Postoperatively, all eyes were evaluated for graft detachment through anterior segment optical coherence tomography at predetermined intervals (1 d, 1 wk, and 1 mo). Detachments were regarded as clinically significant if they subtended 30% of the total graft surface area or involved the visual axis.

RESULTS

Clinically significant graft detachments were observed in 23 of 106 eyes (22%) in the no-supine posturing cohort, including 22 of 85 eyes (26%) operated for Fuchs endothelial corneal dystrophy and 1 of 21 eyes (5%) operated for BK. Compared with a historical comparison group of eyes undergoing DMEK with 48 hours of postoperative supine posturing, the risk of graft detachment was not increased. In both cohorts, 6% of operated eyes required regrafting for either persistent detachment or primary graft failure. No additional intraoperative or postoperative complications were experienced.

CONCLUSIONS

Particularly in eyes operated for BK, the supine posturing requirement after DMEK may be eliminated without increasing the absolute risk for clinically significant graft detachment.

DMEK with endophotocoagulation and cyst wall removal for corneal endothelial decompensation due to iris cyst

Purpose

Iris cysts may arise secondary to surgical or nonsurgical trauma, potentially leading to corneal decompensation via mechanical injury to the adjacent endothelium. However, no well-established protocol exists for the treatment for corneal edema arising therefrom.

Observations

A 58-year-old white male presented with an iris mass of his left eye; it occupied 1/3rd the anterior chamber volume and directly contacted the corneal endothelium. The cornea was diffusely edematous, and best corrected visual acuity (BCVA) measured 20/70 (0.3). Corneal endothelial decompensation secondary to iris cyst was diagnosed. Treatment consisted of endophotocoagulation and vitrectomy probe removal of the cyst wall, with Descemet membrane endothelial keratoplasty (DMEK) also performed as a single, combined procedure. The patient subsequently experienced a resolution of his corneal edema and disappearance of his iris cyst, without recurrence of either condition. BCVA improved to 20/25 (0.8).

Conclusions and importance

Iris cyst may be a rare cause of corneal decompensation. Viable treatment may entail a single-stage procedure involving endophotocoagulation and vitrectomy probe application to the cyst wall combined with DMEK.

Bowman Layer Onlay Grafting: Proof-of-Concept of a New Technique to Flatten Corneal Curvature and Reduce Progression in Keratoconus

PURPOSE

The aim of this study was to describe a new surgical technique for flattening the corneal curvature and to reduce progression in eyes with advanced progressive keratoconus (KC) by using Bowman layer (BL) onlay grafting and to report on the preliminary outcomes of this procedure.

METHODS

In this prospective interventional case series, 5 patients with advanced progressive KC underwent BL onlay grafting. After removal of the epithelium, a BL graft was placed and "stretched" onto the stroma, and a bandage lens was placed to cover the BL graft. In 1 case, BL onlay grafting could be performed immediately after ultraviolet corneal crosslinking; all other eyes were ineligible for ultraviolet corneal crosslinking. Best spectacle- and/or best contact lens-corrected visual acuity, refraction, biomicroscopy, corneal tomography, anterior segment optical coherence tomography, and complications were recorded at 1 week and at 1, 3, 6, 9, and 12 to 15 months postoperatively.

RESULTS

All 5 surgeries could be performed successfully. Average maximum keratometry went from 75 diopters (D) preoperatively to 70 D at 1 year postoperatively. All eyes showed a completely reepithelialized and a well-integrated graft. Best spectacle-corrected visual acuity improved at least 2 Snellen lines (or more) in 3 of 5 cases and best contact lens-corrected visual acuity remained stable, improving by 3 Snellen lines in case 1 at 15 months postoperatively. Satisfaction was high, and all eyes again had full contact lens tolerance.

CONCLUSIONS

BL onlay grafting may be a feasible surgical technique, providing up to -5 D of corneal flattening in eyes with advanced KC.

Bowman Layer Transplantation-A Review

Bowman layer (BL) transplantation has been described for various indications, including the treatment of postrefractive corneal haze, postherpetic scarring, and keratoconus. The unique properties of the BL explain its versatility. Robust, thin, and acellular, transplanted BL inhibits stromal scarring, flattens ectatic corneas, and poses minimal risk of immune reaction. This article reviews the history of BL transplantation and recent developments, and anticipated next steps for the procedure.

DMEK in Super-Seniors: Clinical Outcomes of Descemet Membrane Endothelial Keratoplasty Performed in Patients ≥ 90 Years Old

PURPOSE/AIMS OF THE STUDY

To evaluate the clinical outcomes of Descemet membrane endothelial keratoplasty (DMEK) performed in the "oldest old" patients, i.e. ≥ 90 years.

MATERIALS AND METHODS

Between the years of 2009 and 2019, 20 consecutive eyes of 17 patients aged ≥ 90 underwent DMEK for endothelial dysfunction. Best corrected visual acuity (BCVA), central corneal thickness (CCT), endothelial cell density (ECD), graft survival, and intra- and postoperative complications were assessed.

RESULTS

Except in one case in which the DMEK surgery could not be completed, all operated eyes experienced an improvement in BCVA, although only 50% achieved ≥ 20/40 (0.5) by 1 year postoperatively. One year after surgery, median CCT had declined from 641(±161) μm to 480 (±34) μm, and median endothelial cell density was reduced by 53%, from 2574 (±286) to 1226 (±404) cells/mm². Six of 19 eyes receiving DMEK grafts (32%) developed partial graft detachments requiring re-bubbling. One eye experienced a secondary graft failure at 6 months and underwent repeat endothelial keratoplasty.

CONCLUSION

DMEK is technically feasible in the oldest old patients and may yield significant visual improvements, although an elevated risk of some postoperative complications including graft detachment with corresponding need for re-bubbling may be anticipated.

Are Descemet Membrane Ruptures the Root Cause of Corneal Hydrops in Keratoconic Eyes?

PURPOSE

To challenge the current consensus on the mechanism causing corneal hydrops in eyes with keratoconus (KC).

DESIGN

Retrospective, interventional case series.

METHODS

Sixteen eyes of 10 patients with comorbid KC and Fuchs endothelial corneal dystrophy (FECD) underwent uncomplicated Descemet membrane endothelial keratoplasty (DMEK), and 5 eyes of 5 patients with KC alone underwent Bowman layer (BL) transplantation complicated by inadvertent perforation of the posterior corneal stroma and Descemet membrane (DM). The presence or absence of hydrops was assessed by intra- and postoperative optical coherence tomography and by slit-lamp biomicroscopy.

RESULTS

None of the 16 DMEK eyes manifested a hydrops at any time during or after surgery. By contrast, all 5 eyes undergoing BL transplantation complicated by posterior corneal perforation demonstrated a corneal hydrops, evident both intra- and postoperatively.

CONCLUSIONS

In eyes with KC, even the complete removal of DM did not produce a hydrops, whereas a combined defect in DM and the posterior corneal stroma seemed to consistently elicit a typical corneal hydrops.

Perceived difficulties and barriers to uptake of Descemet's membrane endothelial keratoplasty among surgeons

Purpose: To determine barriers related to implementation of Descemet's membrane endothelial keratoplasty (DMEK) among corneal surgeons.

Methods: This was a multicenter survey study of all corneal surgeons who participated in a DMEK wet lab organized by the Netherlands Institute for Innovative Ocular Surgery. Data related to barriers limiting uptake of DMEK surgery, self-perceived levels of competence, and difficulty with different steps of DMEK surgery were analyzed.

Results: The survey response rate was 31% (22 of 72). The most common barrier to uptake of DMEK surgery identified was anxiety related to incorrect insertion of the tissue and the need to regraft (64%, 14 of 22), followed by anxiety related to tissue preparation (50%, eleven of 22). Surgeons also felt anxious regarding the possibility of rebubbling with initial DMEK (41%, nine of 22). Steps related to DMEK graft (76%) preparation, tissue insertion (41%), and graft unfolding (72%) were identified as the most difficult steps to learn by the respondents.

Conclusion: The DMEK learning curve, especially for the novice surgeon, may be shortened by seeking educational resources, including wet labs and surgical videos. Eye banks may facilitate adoption of DMEK by making validated DMEK tissue more accessible to surgeons globally.

Breast cancer PAM50 signature: correlation and concordance between RNA-Seq and digital multiplexed gene expression technologies in a triple negative breast cancer series

Background

Full RNA-Seq is a fundamental research tool for whole transcriptome analysis. However, it is too costly and time consuming to be used in routine clinical practice. We evaluated the transcript quantification agreement between RNA-Seq and a digital multiplexed gene expression platform, and the subtype call after running the PAM50 assay in a series of breast cancer patients classified as triple negative by IHC/FISH. The goal of this study is to analyze the concordance between both expression platforms overall, and for calling PAM50 triple negative breast cancer intrinsic subtypes in particular.

Results

The analyses were performed in paraffin-embedded tissues from 96 patients recruited in a multicenter, prospective, non-randomized neoadjuvant triple negative breast cancer trial (NCT01560663). Pre-treatment core biopsies were obtained following clinical practice guidelines and conserved as FFPE for further RNA extraction. PAM50 was performed on both digital multiplexed gene expression and RNA-Seq platforms. Subtype assignment was based on the nearest centroid classification following this procedure for both platforms and it was concordant on 96% of the cases (N = 96). In four cases, digital multiplexed gene expression analysis and RNA-Seq were discordant. The Spearman correlation to each of the centroids and the risk of recurrence were above 0.89 in both platforms while the agreement on Proliferation Score reached up to 0.97. In addition, 82% of the individual PAM50 genes showed a correlation coefficient > 0.80.

Conclusions

In our analysis, the subtype calling in most of the samples was concordant in both platforms and the potential discordances had reduced clinical implications in terms of prognosis. If speed and cost are the main driving forces then the preferred technique is the digital multiplexed platform, while if whole genome patterns and subtype are the driving forces, then RNA-Seq is the preferred method.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5849-0) contains supplementary material, which is available to authorized users.

Clinical Outcomes of Descemet Membrane Endothelial Keratoplasty in Eyes With a Glaucoma Drainage Device

PURPOSE

To evaluate the feasibility and clinical outcomes of Descemet membrane endothelial keratoplasty (DMEK) in eyes with a glaucoma drainage device (GDD).

DESIGN

Retrospective, interventional case series.

METHODS

Clinical outcomes of 23 DMEK procedures for bullous keratopathy (52%), failed previous transplant (39%), or Fuchs endothelial corneal dystrophy (9%) in 20 eyes (19 patients) with a GDD were retrospectively analyzed at 2 tertiary referral centers. Main outcome measures were best-corrected visual acuity (BCVA), endothelial cell density (ECD), postoperative complications, and graft survival.

RESULTS

Mean length of postoperative follow-up after DMEK was 19 (±17) months. Kaplan-Meier survival analysis showed an 89% cumulative graft success rate at 1 year postoperatively. At 1 year postoperatively (n = 15 eyes), BCVA improved by ≥2 Snellen lines in 11 eyes (73%) and remained stable in 4 eyes (27%). Donor ECD decreased by 37% (n = 14), 60% (n = 11), and 71% (n = 11) at 1, 6, and 12 months postoperatively, respectively. Postoperative complications up to 2 years postoperatively comprised pupillary block in 1 eye (successfully reversed by partial air removal), visually significant graft detachment requiring rebubbling in 5 eyes (22%), allograft rejection successfully reversed with topical steroids in 2 eyes (9%), secondary graft failure in 2 eyes (9%), and cataract in 1 of 3 phakic eyes (33%). Re-keratoplasty was required in 2 eyes (9%).

CONCLUSIONS

With specific surgical modifications, DMEK provided acceptable clinical outcomes when taking the complexity of these eyes into account. However, presence of a GDD may reduce graft survival times and may pose a risk for more frequent regrafting.

Abstract GS1-05: Apobec3 induced mutagenesis sensitizes murine models of triple negative breast cancer to immunotherapy by activating B-cells and CD4+ T-cells

Immune checkpoint inhibitor (ICI) therapies have led to remarkable clinical responses in cancers such as melanoma and non-small cell lung cancer. In breast cancer, current immunotherapy trials have placed an emphasis on triple negative breast cancers (TNBC), where early results suggest response rates of 10-20%. Thus, it is critical to identify predictive biomarkers to enhance patient selection for immunotherapy. With this goal in mind, we simulated a clinical trial employing anti-PD1 and anti-CTLA therapies in immune-intact genetically engineered mouse models (GEMMs) of TNBC. Testing of ICI therapies on 8 different GEMMs demonstrated that each model was resistant. Whole exome sequencing showed that each model also harbored a low mutation burden. Given that mutation load is predictive of immunotherapy response in other cancer types, and that Apobec3B activity is associated with higher tumor mutation burden (TMB) in breast cancer, we created two different tumor lines with overexpression of murine Apobec3.

In contrast to the parental lines, the Apobec3 overexpressing lines showed an elevated tumor mutation burden and new mutations were consistent with the Apobec mutation signature. These TNBC lines with new mutations resulting from Apobec3 activity were exquisitely sensitive to anti-PD1/anti-CTLA4 combination therapy; as assessed by reduction in tumor volume and extended overall survival. To identify features that predict response, we examined resistant and sensitive tumors at pretreatment, at 1 week of treatment, and at end stage by flow cytometry and mRNA-seq. Gene expression profiling identified multiple immune signatures as predictive of response to ICI therapy; specifically CD8+ T-effector memory cells, CD4+ T-cells, and activated B-Cells. Similarly, gene expression analysis showed that these cell types increased at 1 week of therapy in sensitive models but not in resistant models. Flow cytometry confirmed these predictions.

Next, we used an antibody based approach to separately deplete CD4+ T-Cells, CD8+ T-cells, or B-cells in Apobec3 mutagenized murine tumors receiving aPD1/aCTLA4 combination therapy. In each case, depletion of these populations significantly reduced the therapeutic response. However, mice receiving combination immunotherapy and depleted for CD8+ T-cells still exhibited a significant extension in overall survival compared to non-treated controls. In contrast, the CD4+ T-cell depleted mice and B-cell depleted mice exhibited no ICI therapeutic benefit.

Together, these data point to key immune biomarkers of response to anti-PD1/anti-CTLA4 therapy; we have further developed a genomic predictor of ICI response using our murine models and will test this on a human TNBC data set. Lastly, this GEMM system provides a rich RNA-seq resource, and new immune-activated models for TNBC, which uncovered a key role for B-cells and CD4+ T-cells in response to ICI therapies.

Citation Format: Hollern DP, Xu N, Mott KR, He X, Carey-Ewend K, Marron DS, Ford J, Parker JS, Vincent BG, Serody JS, Perou CM. Apobec3 induced mutagenesis sensitizes murine models of triple negative breast cancer to immunotherapy by activating B-cells and CD4+ T-cells [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 GS1-05.

Abstract PD9-04: FGFR4 as a key regulator of HER2E subtype in the primary and metastatic setting

Background: Therapeutic targets in TNBC remain a challenge. We have observed that some Luminal A primary breast tumors give rise to HER2-enriched (HER2E) subtype metastases but remain clinically HER2 negative (HER2E/cHER2-). Molecular features that drive these HER2E/cHER2- tumors may represent key targets of metastatic progression.

Methods: A comparative genetic and transcriptomic analysis in TCGA (1100 patients) related to the FGFR family was performed. We focused on FGFR4, in part, due to its unique association with the HER2E expression subtype and we developed a robust FGFR4-signature based upon a supervised analysis of a HER2E/cHER2- PDX (WHIM11) treated with a FGFR4 inhibitor (BLU9931). We also constructed a new Luminal Tumor Score (LTS) to identify the optimal axis of separation between Luminal A versus HER2E tumors (higher scores represent greater Luminal A phenotype). Univariate and multivariate analyses were performed using TCGA and METABRIC (1971 samples). Finally, we performed RNA-seq on a cohort of 77 matched primary breast cancer and metastatic tissues pairs from the GEICAM/2009-03 and Hospital Clinic of Barcelona study, and did multiple analyses on these cohorts using our FGFR4-signatures.

Results: FGFR4 was significantly higher in HER2E subtype (P&lt;0.0001), independent of HER2 clinical status. FGFR4 amplification/deletions and mutations were rare and did not correlate with FGFR4 high expression. In vivo, BLU9931 treatment of WHIM11 showed a significant tumor growth inhibition (P=0.01), prolonged survival, and a significant higher LTS (P=0.016). We also identified 745 up-regulated genes called FGFR4-repressed (FGFR4-rep) and 427 down regulated genes called FGFR4-induced (FGFR4-ind), after BLU9931 treatment. Gene set enrichment analysis revealed that FGFR4-ind genes were enriched for STAT3, PI3K/AKT/mTOR pathway and KRAS activation, proliferation, hypoxia, glycolysis and metastasis. FGFR4-rep genes were involved with KRAS inhibition, cell polarity, p53 pathway and upregulation of IFNγ response. In the METABRIC cohort, FGFR4-ind and FGFR4-rep each predicted OS (HR=6.30, P&lt;0.0001; HR=0.33; P&lt;0.0001, respectively). Multivariate analysis showed FGFR4-ind (HR=2.34, P=0.014) as a significant independent prognostic factor beyond subtype for OS. Supervised analysis of the 77 primary-met cohort revealed that the FGFR4-ind was significantly higher in luminal metastases compared with their primaries counterparts (P&lt;0.001), along with proliferation, angiogenesis, and a M2 macrophage signature (with most other immune features being unchanged). Finally, univariate and multivariate analysis demonstrated that the FGFR4-related signatures predicted site-specific metastasis for lung, liver and brain, but not for bone and lymph nodes.

Conclusion: FGFR4 is one of the drivers of HER2-enriched subtype tumors, including those that are clinically HER2-. The FGFR4-ind signature was predictive of worse survival, progression in the metastatic setting, and site-specific metastasis. Treatment options in HER2-enriched TNBC, and for HER2E/cHER2+ patients, may benefit from targeting FGFR4, whose high expression is not based upon genomic or genetic features.

Citation Format: Garcia Recio S, Parker JS, Fan C, Mott K, He X, Cejalvo JM, Brasó Maristany F, Galván P, Lluch A, Albanell J, Rojo F, Martinez de Dueñas E, Prat A, Perou CM. FGFR4 as a key regulator of HER2E subtype in the primary and metastatic setting [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 PD9-04.

Abstract P3-08-04: Transient state change, but not permanent subtype change, after HER2-targeted therapy for HER2-positive breast cancer

Background: In CALGB 40601 (Alliance, NCT00770809), a neoadjuvant phase III trial of paclitaxel and trastuzumab with or without lapatinib for 12 weeks for patients with HER2-positive breast cancer, 33% of pretreatment tumors were Luminal A subtype, however, 69% of post-treatment samples with residual disease were Luminal A subtype. In addition, 71% of Luminal B (12/17) and 67% of HER2-Enriched (6/9) tumors changed into Luminal A, while 80% of Luminal A (20/24) remained Luminal A (Carey et al. J Clin Oncol. 2016). It is not known whether this shift to Luminal A was transient or permanent.

Methods: We selected matched pairs of pre- and post-treatment 40601 samples with tumor purity &gt;10% based upon DNA analyses to ensure all samples contained tumor. PAM50 intrinsic subtyping was applied to the 40601 samples gene expression data using a two-step normalization process based on The Genome Cancer Atlas, and PAM50 training set. In addition, a HER2-enriched expression subtype patient-derived xenograft (PDX) tumor called WHIM35, was studied and was either untreated (n=10), or treated with lapatinib at 220 mg/kg for 1 week (wk) (n=5), for 2 wks (n=8), or for 3 wks (n=4). We also treated WHIM35 tumors with lapatinib for 2 wks (on) and then removed laptinib for 1 wk (off) (n=6), or for 2 wks on and 2-4 wk off (n=6), and finally for 3 wks on, and 1 wk off (n=3). PAM50 intrinsic subtyping was applied to the PDX gene expression data and subtype assessed as well as a genomic-based proliferation score. ANOVA p-values were calculated by comparing median values across all gene signature or correlation scores.

Results: We found 10 pairs of 40601 samples that kept their tumor purity values, however, their subtype changed to Luminal A after treatment (i.e., in the residual disease), and in these cases no minor tumor subclone became a dominant clone in the post treatment sample. Pretreatment subtypes were 6 Luminal B, 3 Luminal A, and 1 HER2-enriched. The tumor purity values did not change after the treatments, but correlation to Luminal A was significantly higher (p=0.01), while correlation to HER2-enriched (p=0.004) and proliferation signature scores (p=0.003) were significantly lower in the post-treatment samples. Among the WHIM35 PDX tumors, one sample changed its subtype from HER2-enriched to Luminal A after the lapatinib treatment and the rest remained HER2-enriched, suggesting environmental differences between patient samples and the PDX model. However, correlation to Luminal A was significantly higher in all lapatinib treated WHIM35 samples (p=8.3e-12), and notably went back to the initial low levels just one week after removing lapatinib. Likewise, correlation to HER2-enriched (p=1.2e-10) and proliferation signature scores (p=6.2e-12) also got lower while treated with lapatinib, but went back to the initial levels after cessation of treatment.

Conclusions: Our findings suggest that the apparent subtype change during HER2-targeting therapy is not permanent, but is more likely a transient state change from a HER2-enriched subtype into a more Luminal A-like state. When we plan additional treatment strategies using residual disease phenotypes, it may not be clear what is the true subtype of the sample due to this inherent plasticity.

Citation Format: Tanioka M, Parker JS, Henry LN, Tolaney S, Dang C, Krop IE, Harris L, Polley M, Berry DA, Winer EP, Carey LA, Perou CM. Transient state change, but not permanent subtype change, after HER2-targeted therapy for HER2-positive breast cancer [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 P3-08-04.

Manual mid-stromal dissection as a low risk procedure to stabilize mild to moderate progressive keratoconus

Background

To evaluate the efficacy of manual mid-stromal dissection in stabilizing progressive keratoconus.

Methods

Surgeries were performed in 16 eyes of 14 patients with progressive keratoconus. All eyes were examined before and at 1 day, 1 week, 1, 3, 6 and 12 months after surgery, and every 6 months thereafter. Pentacam (simK, Kmax and pachymetry), best corrected visual acuity (BCVA) and subjective refraction were recorded up to the latest follow-up visit (mean follow-up time 6.6 ± 2.4 years).

Results

All surgeries were uneventful, and no postoperative complications occurred. Keratometry values (n = 15) stabilized in 6/11 eyes (55%) with a preoperative Kmax < 60.0 diopter (D), while all eyes > 60 D showed continued progression. In 11/15 eyes (73%) pachymetry was unchanged. BCVA with spectacles remained stable in 7/12 eyes (58%) and improved ≥2 Snellen lines in 5/12 eyes (42%). BCVA with a contact lens remained stable in 4/9 eyes (44%), improved ≥2 Snellen lines in 3/9 eyes (33%) and deteriorated in 2/9 eyes (22%).

Conclusions

Manual mid-stromal dissection was effective in 50% of keratoconic corneas with Kmax values < 60 D and may be considered in cases ineligible for other interventions such as UV-crosslinking, stromal ring implantation or Bowman layer transplantation. An advantage of the procedure may be that the tissue is unaltered and that no synthetic or biological implant is required.

Bowman layer transplantation: 5-year results

PURPOSE

The purpose of this study was to evaluate the 5-year clinical results of isolated Bowman layer (BL) transplantation in the treatment of advanced keratoconus.

METHODS

In this prospective, single-center, interventional case series at a tertiary referral center, 20 eyes of 17 patients with advanced keratoconus underwent BL transplantation, i.e. an isolated Bowman layer graft was positioned into a manually dissected mid-stromal pocket. Scheimpflug-based corneal tomography measurements, best corrected spectacle and contact lens visual acuities (BSCVA and BCLVA), endothelial cell density, and complications were evaluated up to 5 years after surgery.

RESULTS

Measured simulated and maximum keratometry (Kmean and Kmax) values were stable up to 5 years after surgery (P = .310 and P = .195 for 5 years compared to 1 month follow-up, respectively), following an initial decrease from pre- to 1 month postoperatively (P < .001 each). Mean LogMAR BSCVA remained stable (P > .99), after an initial improvement from pre- to 12 months postoperatively (P = .007). Mean BCLVA did not change from preoperative to 5 years postoperatively (P = .219). During all postoperative follow-ups, mean densitometry values were higher than preoperatively (P < .001). A corneal hydrops occurred in one eye at 4.5 years postoperatively; no other postoperative complications were observed. Kaplan-Meier analysis showed an estimated success rate of 84% at 5 years postoperatively. Endothelial cell density remained stable from before to 5 years after surgery (P = .319).

CONCLUSIONS

After early postoperative corneal flattening, topographies were stable up to 5 years after BL transplantation, preserving BCLVA and contact lens tolerance, potentially allowing long term postponement of penetrating or deep anterior lamellar keratoplasty.

Abstract P1-05-20: Comparing the frequency and types of genetic aberrations between older and younger women with metastatic breast cancer at the University of North Carolina at Chapel Hill

Background: Targeted therapies have the potential to revolutionize cancer treatment in older adults as they are often oral, convenient, may be better tolerated than cytotoxic chemotherapy, and can be tailored to an individual's biomarker profile. We explore the frequency and distribution of potentially actionable genomic alterations among older (≥65) and younger (&lt;65) patients (pts) with metastatic breast cancer (MBC).

Method: Next generation genetic sequencing (UNCseq™) of a dynamic panel of target genes was prospectively offered to pts with MBC treated at the University of North Carolina at Chapel Hill (UNC). DNA libraries were prepared separately from a retrieved archival FFPE tumor sample and a matched normal sample from each pt. Relevant targets were enriched by custom Agilent SureSelect hybrid capture baits using standard protocols. Samples were sequenced on Illumina HiSeq 2000/2500 platforms. Mutational findings were reviewed by a molecular tumor board; variants identified to be potentially actionable underwent confirmatory testing in a CLIA approved laboratory. Confirmed findings were inserted into the pt's EMR accessible by both the pt and the treating oncologist. Two-sided Fisher's exact test was used to compare percentages between age-specific groups.

Results: As of 3/31/16, results were available for 140 pts. 19% were 65 years or older. Breast cancer clinical subtypes were: HR+/HER2- 49%, HER2+ (HR any) 17%, TN 34% and metastatic location was: bone only 5%, visceral only 44%, bone & visceral 51%; no significant differences were observed between older and younger age groups. Older pts were more likely to be Caucasian compared to younger patients (92% v 75%, p=0.06). Overall, older patients had a higher total number of mutations compared to younger patients (see Table) (p=0.04). Mutation types were similar between age groups, although a trend for more PIK3CA mutations among older patients was seen (37% v 20%, p=0.07).

Observed Mutations by Age. ≥ 65 years (%) N=27&lt; 65 years (%) N=113pNumber of Mutations   01127.0414849.0423320.04374.04Type of mutation   PIK3CA3720.07CCND179.99NF-1115.37FGFR144.99PTEN49.69EGFR04.99

Conclusion: Genomic alterations may allow therapeutic tailoring in both older and younger patients with breast cancer. In this cohort with metastatic disease, older patients had significantly more mutations, but no clear difference in mutational types was seen by age. The relative small number of older pts in this cohort limits generalization, but supports the need for more extensive characterization of molecular aberrations among older pts with metastatic breast cancer in the new era of targeted therapy.

Research support by the University Cancer Research Fund, NCI Breast Cancer SPORE grant (CA58223), John A. Hartford Foundation and Susan G. Komen Foundation.

Citation Format: Jolly TA, Grilley-Olson JE, Deal AM, Ivanova A, Hayward MC, Benbow JM, Parker JS, Patel NM, Eberhard DA, Weck KE, Mieczkowski P, Dees EC, Muss HD, Reeder-Hayes KE, Earp HS, Sharpless NE, Carey LA, Hayes DN, Anders CK. Comparing the frequency and types of genetic aberrations between older and younger women with metastatic breast cancer at the University of North Carolina at Chapel Hill [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 P1-05-20.

Gene expression profile of pulpitis

The cost, prevalence and pain associated with endodontic disease necessitate an understanding of the fundamental molecular aspects of its pathogenesis. This study was aimed to identify the genetic contributors to pulpal pain and inflammation. Inflamed pulps were collected from patients diagnosed with irreversible pulpitis (n=20). Normal pulps from teeth extracted for various reasons served as controls (n=20). Pain level was assessed using a visual analog scale (VAS). Genome-wide microarray analysis was performed using Affymetrix GeneTitan Multichannel Instrument. The difference in gene expression levels were determined by the Significance Analysis of Microarray program using a false discovery rate (q-value) of 5%. Genes involved in immune response, cytokine-cytokine receptor interaction and signaling, integrin cell surface interactions, and others were expressed at relatively higher levels in the in the pulpitis group. Moreover, several genes known to modulate pain and inflammation showed differential expression in asymptomatic and mild pain patients (≥30mm on VAS) compared to those with moderate to severe pain. This exploratory study provides a molecular basis for the clinical diagnosis of pulpitis. With an enhanced understanding of pulpal inflammation, future studies on treatment and management of pulpitis and on pain associated with it can have a biological reference to bridge treatment strategies with pulpal biology.

Abstract S4-01: Identification of early versus late drivers of breast tumors and metastasis

Background: The molecular characterization of primary breast cancers has led to signatures identifying risk of future metastasis and survival; however the underlying biology driving metastasis development is largely unknown.

Methods: Utilizing a Rapid Autopsy Program, we have collected 61 metastatic breast cancer tumors from 7 individuals (4 triple negative, 2 HER2+, 1 ER+/HER2-) including primary tumors and 3-6 metastases/patient. We performed mRNA and DNA exome sequencing. We next used DawnRank, a novel network-based method that integrates DNA and RNA data to identify computationally determined "driver" genes (i.e. a DNA variant that significantly alters its gene expression-network) in each individual sample. Phylogenetic tree and clonal analysis were also performed, with the computationally determined drivers mapped onto these trees.

Results: The breast cancer primaries were molecularly subtyped as 5 Basal-like, 1 HER2-Enriched, and 1 Luminal A; in all cases, the metastases clustered immediately adjacent to their primary tumor by hierarchical clustering analysis. Widespread DNA copy number alterations identified in the primary tumors were typically maintained throughout metastasis. On average, 1.9 ± 1.3% of DNA copy number altered genes, and 2.4 ± 0.95% of the somatic mutations per tumor were identified as "drivers" by DawnRank. There were an average of 199 ± 72 total drivers per tumor due to copy number alterations (amplifications or deletions) and 12 ± 23 drivers per tumor from somatic mutations.

Phylogenetic tree analysis demonstrated that the majority of DNA copy number events occurred early in tumor development. Founding clones were defined as genetic events present in the primary and all matched metastases. Chr5q13 loss and TP53 mutation were the only consistent alterations in the founding clones of all 7 patients. Drivers on chr5q13 identified in this cohort include CCNB1, CDK7, and TAF9. Among the basal-like patients, all 5 patients' TP53 mutations were identified as a driver by DawnRank.

39% and 20% of drivers from copy number gains and losses, respectively, were identified in the primary tumor, while another 34% and 30% were not seen in the primary but were present in more than 1 metastasis within each patient. Metastasis-enriched copy number drivers not seen in any primary included FLT1, MAP2KR, and ARNT.

38% of the drivers resulting from somatic mutations were established in the primary and maintained in metastases. Of the remaining drivers from somatic mutation, only 18% were shared among metastases but not seen in the primary while 47% were not seen in any other tumor within a given patient (i.e. private to a single sample). TP53, PSEN1, CDC27, HDAC1, and BRCA1 were somatic mutation drivers established early in metastatic development, while CCNH was a consistent late driver.

Conclusions: We present a novel computationally determined genetic "driver" analysis of matched breast cancer primaries and multi-organ metastases. In this cohort, our results suggest that most genetic drivers in a single tumor are based on copy number aberrations, are established early, and are maintained in metastases. In contrast to copy number, drivers from somatic mutations are acquired later, and most of the metastases continued to acquire new genetic driving features.

Citation Format: Siegel MB, He X, Chen M, Hou JP, Garrett AL, Dye JB, Silva GO, Usary JE, Moylan VJ, Brady CM, Ma J, Thorne LB, Hoadley KA, Parker JS, Anders CK, Carey LA, Perou CM. Identification of early versus late drivers of breast tumors and metastasis. [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 S4-01.

Abstract P2-07-04: A novel diagnostic androgen receptor gene signature links clinical outcomes and preclinical response to enzalutamide, paclitaxel or the combination in triple-negative breast cancer

Background: The androgen receptor (AR) is expressed in ≈70% of all breast cancers (BCs) and may be necessary for proliferation and survival advantage in AR+ tumors. A novel gene signature associated with AR-signaling biology (PREDICT AR) was developed by sequencing triple-negative BC (TNBC) tumors collected in a phase 2 study evaluating enzalutamide (ENZA) monotherapy1; clinical outcomes were superior in patients (pts) with PREDICT AR+ vs PREDICT AR- tumors.1,2 ENZA blocks nuclear localization and suppresses its activity.3 Paclitaxel (PTX) stabilizes microtubules and may also block AR nuclear localization. Thus we hypothesize that response to PTX-based therapy may be additive in PREDICT AR+ vs PREDICT AR- disease. This study sought to identify independent clinical datasets with PREDICT AR+ gene signature to assess outcomes following PTX-based therapy. Preclinically, we investigated the antitumor activity of ENZA, PTX, or ENZA+PTX in AR-driven TNBC models.

Methods: We probed publicly available TNBC clinical databases from Gene Expression Omnibus datasets to assess PREDICT AR status and clinical outcomes. Similarly, we assessed 21 TNBC lines for PREDICT AR status. BT549, MDA-MB-436, and MDA-MB-453 were treated with ENZA, PTX, or ENZA+PTX to determine activity. Cell signaling and pathway activation were assessed by western blot. ENZA and PTX activity was assessed in PREDICT AR+ xenograft models. Tumor RNA sequencing and immunohistochemistry were used to identify gene signatures, potentially predictive biomarkers, and potential synergistic effects of ENZA+PTX.

Results: The prevalence of PREDICT AR+ tumors in one cohort of 182 pts with primary TNBC4 was 51%. Distant relapse-free survival following PTX-based adjuvant/neoadjuvant therapy was not statistically different between pts with PREDICT AR+ vs PREDICT AR- TNBC (p=0.605). Pathologic complete response rates were 12.5% for PREDICT AR+ vs 21.0% for PREDICT AR- TNBC. Additional sets of pts with primary TNBC are being evaluated. Preclinically, we observed a dose-dependent inhibition of cell viability with either ENZA or PTX in AR+ TNBC cell lines and additive effects from ENZA+PTX. In PREDICT AR+ xenograft models, ENZA or PTX treatment resulted in a dose-dependent antitumor response. Combination studies are underway. Tumor RNA sequencing are being evaluated for gene signature of synergistic antitumor response to ENZA+PTX.

Conclusion: Analyzing publicly available clinical datasets, we found that PREDICT AR+ status was not associated with differential outcomes following PTX-based therapy in primary TNBC, suggesting there is potential to provide additive benefits in PTX-based therapy with ENZA. In preclinical studies, we observed additive effects when combining ENZA+PTX in PREDICT AR+ TNBC lines compared with single agent treatments. Taken together, these data suggest ENZA combined with PTX might provide additive benefits in a clinical setting for pts with PREDICT AR+ TNBC.

References

1. Traina TA et al. J Clin Oncol 2015:33(suppl):abstr 1003.

2. Parker J et al. J Clin Oncol 2015;33(suppl):abstr 1083.

3. Tran C et al. Science 2009;324:787-90.

4. Hatzis C et al. JAMA 2011;305:1873-81.

Citation Format: Phan VT, Protter AA, Peterson AC, Parker JS, Yoon K, Tudor IC, Paton V, Noonberg S, Uppal H. A novel diagnostic androgen receptor gene signature links clinical outcomes and preclinical response to enzalutamide, paclitaxel or the combination in triple-negative 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 P2-07-04.

Treatment options for advanced keratoconus: A review

Traditionally, the mainstay of treatment for advanced keratoconus (KC) has been either penetrating or deep anterior lamellar keratoplasty (PK or DALK, respectively). The success of both operations, however, has been somewhat tempered by potential difficulties and complications, both intraoperatively and postoperatively. These include suture and wound-healing problems, progression of disease in the recipient rim, allograft reaction, and persistent irregular astigmatism. Taken together, these have been the inspiration for an ongoing search for less troublesome therapeutic alternatives. These include ultraviolet crosslinking and intracorneal ring segments, both of which were originally constrained in their indication exclusively to eyes with mild to moderate disease. More recently, Bowman layer transplantation has been introduced for reversing corneal ectasia in eyes with advanced KC, re-enabling comfortable contact lens wear and permitting PK and DALK to be postponed or avoided entirely. We offer a summary of the current and emerging treatment options for advanced KC, aiming to provide the corneal specialist useful information in selecting the optimal therapy for individual patients.

Predicting response and survival in chemotherapy-treated triple-negative breast cancer

BACKGROUND

In this study, we evaluated the ability of gene expression profiles to predict chemotherapy response and survival in triple-negative breast cancer (TNBC).

METHODS

Gene expression and clinical-pathological data were evaluated in five independent cohorts, including three randomised clinical trials for a total of 1055 patients with TNBC, basal-like disease (BLBC) or both. Previously defined intrinsic molecular subtype and a proliferation signature were determined and tested. Each signature was tested using multivariable logistic regression models (for pCR (pathological complete response)) and Cox models (for survival). Within TNBC, interactions between each signature and the basal-like subtype (vs other subtypes) for predicting either pCR or survival were investigated.

RESULTS

Within TNBC, all intrinsic subtypes were identified but BLBC predominated (55-81%). Significant associations between genomic signatures and response and survival after chemotherapy were only identified within BLBC and not within TNBC as a whole. In particular, high expression of a previously identified proliferation signature, or low expression of the luminal A signature, was found independently associated with pCR and improved survival following chemotherapy across different cohorts. Significant interaction tests were only obtained between each signature and the BLBC subtype for prediction of chemotherapy response or survival.

CONCLUSIONS

The proliferation signature predicts response and improved survival after chemotherapy, but only within BLBC. This highlights the clinical implications of TNBC heterogeneity, and suggests that future clinical trials focused on this phenotypic subtype should consider stratifying patients as having BLBC or not.

Concordance among gene expression-based predictors for ER-positive breast cancer treated with adjuvant tamoxifen

BACKGROUND

ER-positive (ER+) breast cancer includes all of the intrinsic molecular subtypes, although the luminal A and B subtypes predominate. In this study, we evaluated the ability of six clinically relevant genomic signatures to predict relapse in patients with ER+ tumors treated with adjuvant tamoxifen only.

METHODS

Four microarray datasets were combined and research-based versions of PAM50 intrinsic subtyping and risk of relapse (PAM50-ROR) score, 21-gene recurrence score (OncotypeDX), Mammaprint, Rotterdam 76 gene, index of sensitivity to endocrine therapy (SET) and an estrogen-induced gene set were evaluated. Distant relapse-free survival (DRFS) was estimated by Kaplan-Meier and log-rank tests, and multivariable analyses were done using Cox regression analysis. Harrell's C-index was also used to estimate performance.

RESULTS

All signatures were prognostic in patients with ER+ node-negative tumors, whereas most were prognostic in ER+ node-positive disease. Among the signatures evaluated, PAM50-ROR, OncotypeDX, Mammaprint and SET were consistently found to be independent predictors of relapse. A combination of all signatures significantly increased the performance prediction. Importantly, low-risk tumors (>90% DRFS at 8.5 years) were identified by the majority of signatures only within node-negative disease, and these tumors were mostly luminal A (78%-100%).

CONCLUSIONS

Most established genomic signatures were successful in outcome predictions in ER+ breast cancer and provided statistically independent information. From a clinical perspective, multiple signatures combined together most accurately predicted outcome, but a common finding was that each signature identified a subset of luminal A patients with node-negative disease who might be considered suitable candidates for adjuvant endocrine therapy alone.

Developing the philosophy of recovery in South African mental health services

The recovery movement has emerged as an important and powerful force in the design and implementation of mental health care in many countries around the world. This involves new and more positive understandings of the concept of recovery, both as an individual outcome and as a goal of services. The basis for these understandings is examined, with particular emphasis on long-term outcomes in schizophrenia, and a brief history of the origins of the recovery movement is given. An argument is made for the implementation of a recovery framework within South African mental health services.

The relationship between genetic and cytogenetic maps of pea. I. Standard and translocation karyotypes

A detailed cytogenetical study of inbred lines of pea and their F1 hybrids has been undertaken to study the relationship between the cytogenetic map and the molecular linkage map. The mitotic karyotypes of a standard pea line, JI15, a translocation line, JI61, and line JI281, a line used in the production of a mapping population, are given. A chromosome rearrangement detected by cytogenetic analysis of mitotic chromosomes has been further defined by synaptonemal complex (SC) analysis and the study of metaphase I chromosome behaviour. This meiotic analysis has allowed a comparison of SC physical lengths, observed chiasma frequencies, and recombination frequencies, as estimated from the genetic map, as a means of comparing physical and genetic distances.

The relationship between genetic and cytogenetic maps of pea. II. Physical maps of linkage mapping populations

A cytogenetic analysis of inbred lines that have been used to generate genetic maps of pea is presented. Mitotic karyotyping of the inbred lines and meiotic studies of their F1 hybrids have been used to test the prediction that structural differences exist between the parental lines. The results are not compatible with the previously published molecular data. A reordered and updated linkage map of pea is presented that is consistent with the cytogenetic data.

PAM50 assay and the three-gene model for identifying the major and clinically relevant molecular subtypes of breast cancer

It has recently been proposed that a three-gene model (SCMGENE) that measures ESR1, ERBB2, and AURKA identifies the major breast cancer intrinsic subtypes and provides robust discrimination for clinical use in a manner very similar to a 50-gene subtype predictor (PAM50). However, the clinical relevance of both predictors was not fully explored, which is needed given that a ~30 % discordance rate between these two predictors was observed. Using the same datasets and subtype calls provided by Haibe-Kains and colleagues, we compared the SCMGENE assignments and the research-based PAM50 assignments in terms of their ability to (1) predict patient outcome, (2) predict pathological complete response (pCR) after anthracycline/taxane-based chemotherapy, and (3) capture the main biological diversity displayed by all genes from a microarray. In terms of survival predictions, both assays provided independent prognostic information from each other and beyond the data provided by standard clinical–pathological variables; however, the amount of prognostic information was found to be significantly greater with the PAM50 assay than the SCMGENE assay. In terms of chemotherapy response, the PAM50 assay was the only assay to provide independent predictive information of pCR in multivariate models. Finally, compared to the SCMGENE predictor, the PAM50 assay explained a significantly greater amount of gene expression diversity as captured by the two main principal components of the breast cancer microarray data. Our results show that classification of the major and clinically relevant molecular subtypes of breast cancer are best captured using larger gene panels.

Masked trial of topical anesthesia for retinopathy of prematurity eye examinations

PURPOSE

To observe the effect of a topical anesthetic on pain and corneal clarity in premature infants undergoing eye examinations for retinopathy of prematurity (ROP).

METHODS

ROP examinations were performed on premature infants who were randomized to receive either proparacaine 0.5% or an artificial tear solution in the right eye. All infants received an artificial tear solution in the left eye. Assessment of discomfort was performed by use of the Premature Infant Pain Profile (PIPP) during examination of the right eye, with a painful event defined as a PIPP score≥11. The left eye was then examined and a comparison of corneal clarity was made between the 2 eyes.

RESULTS

A total of 39 examinations were performed on 34 infants: artificial tear solution was administered 17 times and topical proparacaine anesthetic 22 times. The mean PIPP score for those receiving artificial tears was 10.4 compared with 8.8 for the anesthetic group (p=0.17). Of the examinations without anesthetic, 65% were painful, compared with 27% with anesthetic (p=0.04). No effect on corneal clarity was observed in any examination.

CONCLUSIONS

The use of a topical anesthetic appears to marginally decrease pain and has no adverse effect on subjectively assessed corneal clarity during examination of premature infants for ROP.

Abstract PD07-09: Hypoxia (VEGF-S) Signature and CRYAB Predict Response to Neoadjuvant Anthracycline/Taxane Containing Chemotherapy within Triple Negative and Unselected Breast Tumors

Background: Aggressive breast tumors are a clinically challenge to manage. A VEGF-signature (VEGF-s) developed in vivo (Hu et al. BMC Med. 09) and the profile of the anti-apoptotic gene and regulator of tumor angiogenesis, CRYAB (Moyano et al. J Clin Invest 06; Dimberg et al. Blood 08), are both associated with distant metastasis. In this study, we sought to test if these two mechanistically related biomarkers predict pathological complete response(pCR) to anthracyline/taxane-based neoadjuvant chemotherapy.

Methods: Gene expression data of pre-treatment fresh frozen tumors were combined, 149 from the ISPY trial (Agilent 44K) and 225 from MD Anderson Cancer Center(MDACC) (Affymetrix HG U133A). Patients from I-SPY were treated with doxorubicin/cyclophosphamide followed by a taxane. Patients from MDACC were treated with paclitaxel followed by sequential fluorouracil-AC. Tumors were classified into intrinsic subtypes using PAM50(Parker et al. J Clin Oncol 09) and Claudin-low(CL) predictor(Prat et al., Submitted). Odds ratios of biomarkers to pCR were determined using logistic regression. Predictive values of multivariable models were estimated using receiver operating characteristic curve. Results: 319 patients had complete data; the pCR rate was similar between the datasets (ISPY 22%, MDACC 20%). Both the VEGF-s and CRYAB were highly expressed within Basal-like(BL) and CL (P&lt;0.0001); these two biomarkers were positively correlated with each other (r: 0.4, P&lt;0.001). In univariate analysis, both VEGF-s (P&lt;0.001) and CRYAB (P&lt;0.001) were significantly associated with pCR. A multivariable test including tumor size, grade, ER, Her2, intrinsic subtypes, VEGF-s and CRYAB, had an AUC value of 0.86 to predict pCR(Table 1). T stage, Her2, intrinsic subtypes and CRYABwere significant.

82 patients with triple-negative tumors within this combined cohort. In univariate analysis, T stage, grade or classifying tumors into BL vs not did not predict pCR; but VEGF-s (p= 0.04) and CRYAB (p = 0.02) were associated with pCR. Multivariable model, including VEGF-s, CRYAB and the clinical variables, had a predictive value of 0.71 to pCR(Table 1), which identified CRYAB as the most significant factor by likelihood ratio test.

Table 1: Multivariable logistic regression models to predict pCR.

Conclusion: VEGF-s and CRYAB expression are associated with aggressive subtypes and may possibly help to predict response of anthracycline/taxane-based neoadjuvant chemotherapy beyond ER, Her2, and intrinsic subtypes.

A genomic analysis of subclinical hypothyroidism in hippocampus and neocortex of the developing rat brain

Hypothyroidism during pregnancy and the early postnatal period has severe neurological consequences for the developing offspring. The impact of milder degrees of perturbation of the thyroid axis as encompassed in conditions of subclinical hypothyroidism and hypothyroxinemia, however, has not been established. The present investigation examined the effects of graded levels of hypothyroidism, from subclinical to severe, on global gene expression in the developing rodent brain. Thyroid hormone insufficiency was induced by administration of propylthiouracil (PTU) to pregnant rats via drinking water from gestational day 6 until sacrifice of pups prior to weaning. In the first study a specialised microarray, the Affymetrix Rat Neurobiology array RN_U34, was used to contrast gene expression in the hippocampus of animals exposed to 0 or 10 ppm (10 mg/l) PTU, a treatment producing severe hypothyroidism. In the second study, a more complete genome array (Affymetrix Rat 230A) was used to compare gene expression in the neocortex and hippocampus of postnatal day (PN) 14 animals experiencing graded degrees of thyroid hormone insufficiency induced by delivery of 0, 1, 2 or 3 ppm PTU to the dam. Dose-dependent up- and down-regulation were observed for gene transcripts known to play critical roles in brain development and brain function. Expression levels of a subset of approximately 25 genes in each brain region were altered at a dose of PTU (1 ppm) that induced mild hypothyroxinemia in dams and pups. These data indicate that genes driving important developmental processes are sensitive to relatively modest perturbations of the thyroid axis, and that the level of gene expression is related to the degree of hormone reduction. Altered patterns of gene expression during critical windows of brain development indicate that thyroid disease must be viewed as a continuum and that conditions typically considered 'subclinical' may induce structural and functional abnormalities in the developing central nervous system.

The 15th Biannual National Congress of the South African Society of Psychiatrists, 10-14 August 2008, Fancourt, George, W Cape

<p><strong>1. How can we maintain a sustainable private practice in the current political and economic climate?</strong></p><p>Eugene Allers</p><p><strong>2. SASOP Clinical guidelines, protocols and algorithms: Development of treatment guidelines for bipolar mood disorder and major depression</strong></p><p> Eugene Allers, Margaret Nair, Gerhard Grobler</p><p><strong>3. The revolving door phenomenon in psychiatry: Comparing low-frequency and high-frequency users of psychiatric inpatient services in a developing country</strong></p><p>U A Botha, P Oosthuien, L Koen, J A Joska, J Parker, N Horn</p><p><strong>4. Neurophysiology of emotion and senses - The interface between psyche and soma</strong></p><p>Eugene Allers</p><p><strong>5. Suicide prevention: From and beyond the psychiatrist's hands</strong></p><p>O Alonso Betanourt, M Morales Herrera</p><p><strong>6. Treatment of first-episod psychosis: Efficacy and toleabilty of a long-acting typical antipsychotic </strong></p><p>B Chiliza, R Schoeman, R Emsey, P Oosthuizen, L KOen, D Niehaus, S Hawkridge</p><p><strong>7. Treatment of attention deficit hyperactivity disorder in the young child</strong></p><p>Helen Clark</p><p><strong>8. Holistic/ Alternative treatment in psychiatry: The value of indigenous knowledge systems in cllaboration with moral, ethical and religious approaches in the military services</strong></p><p>J Dill</p><p><strong>9. Treating Schizophrenia: Have we got it wrong?</strong></p><p>Robin Emsley</p><p><strong>10.Terminal questions in the elderly</strong></p><p>Mike Ewart Smith</p><p><strong>11. Mental Health Policy development and implementation in Ghana, South Africa, Uganda and Zambia</strong></p><p>Alan J Flisher, Crick Lund, Michelle Frank, Arvin Bhana, Victor Doku, Natalie Drew, Fred N Kigozi, Martin Knapp, Mayeh Omar, Inge Petersen, Andrew Green andthe MHaPP Research Programme Consortium</p><p><strong>12. What indicators should be used to monitor progress in scaling uo services for people with mental disorders?</strong></p><p>Lancet Global Mental Health Group (Alan J Flisher, Dan Chisholm, Crick Lund, Vikram Patel, Shokhar Saxena, Graham Thornicroft, Mark Tomlinson)</p><p><strong>13. Does unipolar mania merit research in South Africa? A look at the literature</strong></p><p>Christoffel Grobler</p><p><strong>14. Revisiting the Cartesian duality of mind and body</strong></p><p>Oye Gureje</p><p><strong>15. Child and adolescent psychopharmacology: Current trends and complexities</strong></p><p>S M Hawkridge</p><p><strong>16. Integrating mental illness, suicide and religion</strong></p><p>Volker Hitzeroth</p><p><strong>17. Cost of acute inpatient mental health care in a 72-hour assessment uniy</strong></p><p>A B R Janse van Rensburg, W Jassat</p><p><strong>18. Management of Schizophrenia according to South African standard treatment guidelines</strong></p><p>A B R Janse van Rensburg</p><p><strong>19. Structural brain imaging in the clinical management of psychiatric illness</strong></p><p>F Y Jeenah</p><p><strong>20. ADHD: Change in symptoms from child to adulthood</strong></p><p>S A Jeeva, A Turgay</p><p><strong>21. HIV-Positive psychiatric patients in antiretrovirals</strong></p><p>G Jonsson, F Y Jeenah, M Y H Moosa</p><p><strong>22. A one year review of patients admitted to tertiary HIV/Neuropsychiatry beds in the Western Cape</strong></p><p>John Joska, Paul Carey, Ian Lewis, Paul Magni, Don Wilson, Dan J Stein</p><p><strong>23. Star'd - Critical review and treatment implications</strong></p><p>Andre Joubert</p><p><strong>24. Options for treatment-resistent depression: Lessons from Star'd; an interactive session</strong></p><p>Andre Joubert</p><p><strong>25. My brain made me do it: How Neuroscience may change the insanity defence</strong></p><p>Sean Kaliski</p><p><strong>26. Child andadolescent mental health services in four African countries</strong></p><p>Sharon Kleintjies, Alan Flisher, Victoruia Campbell-Hall, Arvin Bhana, Phillippa Bird, Victor Doku, Natalie, Drew, Michelle Funk, Andrew Green, Fred Kigozi, Crick Lund, Angela Ofori-Atta, Mayeh Omar, Inge Petersen, Mental Health and Poverty Research Programme Consortium</p><p><strong>27. Individualistic theories of risk behaviour</strong></p><p>Liezl Kramer, Volker Hitzeroth</p><p><strong>28. Development and implementation of mental health poliy and law in South Africa: What is the impact of stigma?</strong></p><p>Ritsuko Kakuma, Sharon Kleintjes, Crick Lund, Alan J Flisher, Paula Goering, MHaPP Research Programme Consortium</p><p><strong>29. Factors contributing to community reintegration of long-term mental health crae users of Weskoppies Hospital</strong></p><p>Carri Lewis, Christa Kruger</p><p><strong>30. Mental health and poverty: A systematic review of the research in low- and middle-income countries</strong></p><p>Crick Lund, Allison Breen, Allan J Flisher, Ritsuko Kakuma, Leslie Swartz, John Joska, Joanne Corrigall, Vikram Patel, MHaPP Research Programe Consortium</p><p><strong>31. The cost of scaling up mental health care in low- and middle-income countries</strong></p><p>Crick Lund, Dan Chishlom, Shekhar Saxena</p><p><strong>32. 'Tikking'Clock: The impact of a methamphetamine epidemic at a psychiatric hospital in the Western Cape</strong></p><p>P Milligan, J S Parker</p><p><strong>33. Durban youth healh-sk behaviour: Prevalence f Violence-related behaviour</strong></p><p>D L Mkize</p><p><strong>34. Profile of morality of patients amitted Weskoppies Psychiatric Hospital in Sout frican over a 5-Year period (2001-2005)</strong></p><p>N M Moola, N Khamker, J L Roos, P Rheeder</p><p><strong>35. One flew over Psychiatry nest</strong></p><p>Leverne Mountany</p><p><strong>36. The ethical relationship betwe psychiatrists and the pharmaceutical indutry</strong></p><p>Margaret  G Nair</p><p><strong>37. Developing the frameor of a postgraduate da programme in mental health</strong></p><p>R J Nichol, B de Klerk, M M Nel, G van Zyl, J Hay</p><p><strong>38. An unfolding story: The experience with HIV-ve patients at a Psychiatric Hospital</strong></p><p>J S Parker, P Milligan</p><p><strong>39. Task shifting: A practical strategy for scalingup mental health care in developing countries</strong></p><p>Vikram Patel</p><p><strong>40. Ethics: Informed consent and competency in the elderly</strong></p><p>Willie Pienaar</p><p><strong>41. Confronting ommonmoral dilemmas. Celebrating uncertainty, while in search  patient good</strong></p><p>Willie Pienaar</p><p><strong>42. Moral dilemmas in the treatment and repatriation of patients with psychtorders while visiting our country</strong></p><p>Duncan Ian Rodseth</p><p><strong>43. Geriatrics workshop (Psegal symposium): Medico-legal issuess in geriatric psyhiatry</strong></p><p>Felix Potocnik</p><p><strong>44. Brain stimulation techniques - update on recent research</strong></p><p>P J Pretorius</p><p><strong>45. Holistic/Alternative treatments in psychiatry</strong></p><p>T Rangaka, J Dill</p><p><strong>46. Cognitive behaviour therapy and other brief interventions for management of substances</strong></p><p>Solomon Rataemane</p><p><strong>47. A Transtheoretical view of change</strong></p><p>Nathan P Rogerson</p><p><strong>48. Profile of security breaches in longerm mental health care users at Weskoppies Hospital over a 6-month period</strong></p><p>Deleyn Rema, Lindiwe Mthethwa, Christa Kruger</p><p><strong>49. Management of psychogenic and chronic pain - A novel approach</strong></p><p>M S Salduker</p><p><strong>50. Childhood ADHD and bipolar mood disorders: Differences and similarities</strong></p><p>L Scribante</p><p><strong>51. The choice of antipsychotic in HIV-infected patients and psychopharmacocal responses to antipsychotic medication</strong></p><p>Dinesh Singh, Karl Goodkin</p><p><strong>52. Pearls in clinical neuroscience: A teaching column in CNS Spectrums</strong></p><p><strong></strong>Dan J Stein</p><p><strong>53. Urinary Cortisol secretion and traumatics in a cohort of SA Metro policemen A longitudinal study</strong></p><p>Ugash Subramaney</p><p><strong>54. Canabis use in Psychiatric inpatients</strong></p><p><strong></strong>M Talatala, G M Nair, D L Mkize</p><p><strong>55. Pathways to care and treatmt in first and multi-episodepsychosis: Findings fm a developing country</strong></p><p>H S Teh, P P Oosthuizen</p><p><strong>56. Mental disorders in HIV-infected indivat various HIV Treatment sites in South Africa</strong></p><p>Rita Thom</p><p><strong>57. Attendanc ile of long-term mental health care users at ocupational therapy group sessions at Weskoppies Hospital</strong></p><p>Ronel van der Westhuizen, Christa Kruger</p><p><strong>58. Epidemiological patterns of extra-medical drug use in South Africa: Results from the South African stress and health study</strong></p><p>Margaretha S van Heerden, Anna Grimsrud, David Williams, Dan  Stein</p><p><strong>59. Persocentred diagnosis: Where d ps and mental disorders fit in the International classificaton of diseases (ICD)?</strong></p><p>Werdie van Staden</p><p><strong>60. What every psychiatrist needs to know about scans</strong></p><p>Herman van Vuuren</p><p><strong>61. Psychiatric morbidity in health care workers withle drug-resistant erulosis (MDR-TB) A case series</strong></p><p>Urvashi Vasant, Dinesh Singh</p><p><strong>62. Association between uetrine artery pulsatility index and antenatal maternal psychological stress</strong></p><p>Bavanisha Vythilingum, Lut Geerts, Annerine Roos, Sheila Faure, Dan J Stein</p><p><strong>63. Approaching the dual diagnosis dilemma</strong></p><p>Lize Weich</p><p><strong>64. Women's mental health: Onset of mood disturbance in midlife - Fact or fiction</strong></p><p>Denise White</p><p><strong>65. Failing or faking: Isses in the fiagnosis and treatment of adult ADHD</strong></p><p>Dora Wynchank</p>

Exchange bias as a probe of the incommensurate spin-density wave in epitaxial Fe/Cr(001)

We report clear multiple period oscillations in the temperature dependence of exchange bias in an Fe thin film exchange coupled to a neighboring Cr film. The oscillations arise due to an incommensurate spin-density wave in the Cr, with wave vector perpendicular to the Fe/Cr(001) interface. The exchange bias and coercivity allow for a determination of the extent of the thermally driven wavelength expansion, the (strain-suppressed) spin-flip transition temperature, and the Cr Néel temperature, which show a crossover from bulklike to finite-size behavior at a Cr thickness of approximately 1100 A. The data are consistent with a transition from a transverse to longitudinal wave on cooling.

High-energy cutoff in the spectrum of strong-field nonsequential double ionization

Electron energy distributions of singly and doubly ionized helium in an intense 390 nm laser field have been measured at two intensities (0.8 PW/cm2 and 1.1 PW/cm2, where PW is defined as 10(15) W/cm2). Numerical solutions of the full-dimensional time-dependent helium Schrödinger equation show excellent agreement with the experimental measurements. The high-energy portion of the two-electron energy distributions reveals an unexpected 5U(p) cutoff for the double ionization (DI) process and leads to a proposed model for DI below the quasiclassical threshold.

Molecular mechanism of target RNA transcript recognition by Argonaute-guide complexes

Argonaute proteins participate in conferring all known functions of RNA-mediated gene silencing phenomena. However, prior to structural investigations of this evolutionarily conserved family of proteins, there was little information concerning their mechanisms of action. Here, we describe our crystallographic analysis of the PIWI domain of an archaeal Argonaute homolog, AfPiwi. Our structural analysis revealed that the Argonaute PIWI fold incorporates both an RNase-H-like catalytic domain and an anchor site for the obligatory 5' phosphate of the RNA guide strand. RNA-AfPiwi binding assays combined with crystallographic studies demonstrated that AfPiwi interacts with RNA via a conserved region centered on the carboxyl terminus of the protein, utilizing a novel metal-binding site. A model of the PIWI domain of Argonaute in complex with a small interfering RNA (siRNA)-like duplex is consistent with much of the existing biochemical and genetic data, explaining the specificity of the RNA-directed RNA endonuclease reaction and the importance of the 5' region of microRNAs (miRNAs) (the "seed") to nucleate target RNA recognition and provide high-affinity guide-target interactions.