Characterisation of seven medications approved for attention-deficit/hyperactivity disorder using in vitro models of hepatic metabolism

The metabolism of most medications approved for the treatment of attention deficit/hyperactivity disorder (ADHD) is not fully understood.In vitro studies using cryopreserved, plated human hepatocytes (cPHHs) and pooled human liver microsomes (HLMs) were performed to more thoroughly characterise the metabolism of several ADHD medications.The use of enzyme-specific chemical inhibitors indicated a role for CYP2D6 in atomoxetine (ATX) metabolism, and roles for CYP3A4/5 in guanfacine (GUA) metabolism.The 4-hydroxy-atomoxetine and N-desmethyl-atomoxetine pathways represented 98.4% and 1.5% of ATX metabolism in cPHHs, respectively. The 3-OH-guanfacine pathway represented at least 2.6% of GUA metabolism in cPHHs, and 71% in HLMs.The major metabolising enzyme for methylphenidate (MPH) and dexmethylphenidate (dMPH) could not be identified using these methods because these compounds were too unstable. Hydrolysis of these medications was spontaneous and did not require the presence of protein to occur.Clonidine (CLD), amphetamine (AMPH), and dextroamphetamine (dAMPH) did not deplete substantially in cPHHs nor HLMs, suggesting that these compounds may not undergo considerable hepatic metabolism. The major circulating metabolites of AMPH and dAMPH (benzoic acid and hippuric acid) were not observed in either system, and therefore could not be characterised. Additionally, inhibition experiments suggested a very minimal role for CYP2D6 in CLD and AMPH metabolism.

A breast cancer (BC) risk model incorporating Tyrer-Cuzick version 8 (TCv8) and a polygenic risk score (PRS) for diverse ancestries

557

Background: BC risk assessment is important for guiding personalized screening and risk-reducing interventions. TCv8 is used to estimate BC risk based on age, breast density, family cancer history and other clinical factors. Accuracy may be improved by combining TCv8 with a PRS. We developed and validated a PRS for diverse ancestries based on 149 common genetic variants (PRS-149) comprised of 56 ancestry-informative and 93 BC-associated variants. Here, we describe a BC risk model that combines PRS-149 with TCv8. Methods: Subjects had multigene panel testing for hereditary cancer and were negative for pathogenic variants in known BC susceptibility genes. A combined risk score (CRS), incorporating PRS-149 and TCv8, was developed based on 189,230 women, including 43,444 (23%) with a history of BC. Breast Imaging Reporting and Data System (BI-RADS) breast density measurements were available for 12,363 women. We used multivariable logistic regression to test breast density and PRS-149 for association with risk of BC. An independent test cohort of 6,030 BC-unaffected women with BI-RADS assessment was used to evaluate the effect of PRS-149 on risk stratification. Relative contributions of family history, breast density, other clinical factors in TCv8 and PRS-149 were examined by adding terms sequentially to an ANOVA model. We compared differences in classification of women as high (20%) or low/moderate (20%) remaining lifetime risk according to TCv8 versus CRS. Results: In the development cohort, increased breast density was significantly associated with higher risk of BC (p=3.0x10-6) with an effect size consistent with TCv8. PRS-149 improved BC risk prediction over age, breast density and family history (OR per unit standard deviation: 1.41, 95% CI: 1.37 – 1.46; p: 1.8x10-105). PRS-149 was weakly but significantly correlated with both family history (r=0.09) and breast density (r=0.01). After adjusting for multiple testing, no other factors were correlated with PRS-149. In the independent test cohort, PRS-149 explained 27% of CRS variability after accounting for family history, breast density and other clinical factors. Adding PRS-149 to TCv8 significantly altered risk estimates, with 16.3% (983/6,030) of patients classified differently by CRS versus TCv8. By TCv8 alone, 38.0% (2,289/6,030) of patients were classified as high-risk. Among patients who were high-risk by TCv8, 25.2% (576/2,289) were downgraded by CRS. Conclusions: This is the first BC risk model that includes breast density, family history, and a PRS based on genetically determined ancestry that is validated for diverse populations. Addition of PRS-149 improved risk prediction and substantially modified risk stratification compared to TCv8 alone. Implementation of CRS may therefore lead to improved identification of women who are likely to benefit from increased surveillance and preventive medications.

Analysis of mutation status and homologous recombination deficiency in tumors of patients with germline BRCA1 or BRCA2 mutations and metastatic breast cancer: OlympiAD

BACKGROUND

Presence of a germline BRCA1 and/or BRCA2 mutation (gBRCAm) may sensitize tumors to poly(ADP-ribose) polymerase (PARP) inhibition via inactivation of the second allele, resulting in gene-specific loss of heterozygosity (gsLOH) and homologous recombination deficiency (HRD). Here we explore whether tissue sample testing provides an additional route to germline testing to inform treatment selection for PARP inhibition.

PATIENTS AND METHODS

In this prespecified exploratory analysis, BRCA1 and/or BRCA2 mutations in blood samples (gBRCAm) and tumor tissue (tBRCAm) were analyzed from patients with human epidermal growth factor receptor 2 (HER2)-negative metastatic breast cancer and known gBRCAm, enrolled in the phase III OlympiAD trial. The frequency and nature of tBRCAm, HRD score status [HRD-positive (score ≥42) versus HRD-negative (score <42) using the Myriad myChoice® CDx test] and rates of gsLOH were determined, and their impact on clinical efficacy (objective response rate and progression-free survival) was explored.

RESULTS

Tissue samples from 161/302 patients yielded tBRCAm, HRD and gsLOH data for 143 (47%), 129 (43%) and 125 (41%) patients, respectively. Concordance between gBRCAm and tBRCAm was 99%. gsLOH was observed in 118/125 (94%) patients [BRCA1m, 73/76 (96%); BRCA2m, 45/49 (92%)]. A second mutation event was recorded for two of the three BRCA1m patients without gsLOH. The incidence of HRD-negative was 16% (21/129) and was more common for BRCA2m (versus BRCA1m) and/or for hormone receptor-positive (versus triple-negative) disease. Olaparib antitumor activity was observed irrespective of HRD score.

CONCLUSIONS

gBRCAm identified in patients with HER2-negative metastatic breast cancer by germline testing in blood was also identified by tumor tissue testing. gsLOH was common, indicating a high rate of biallelic inactivation in metastatic breast cancer. Olaparib activity was seen regardless of gsLOH status or HRD score. Thus, additional tumor testing to inform PARP inhibitor treatment selection may not be supported for these patients.

POS0456 EXTERNAL VALIDATION OF A MULTI-BIOMARKER-BASED CARDIOVASCULAR DISEASE RISK PREDICTION SCORE FOR RHEUMATOID ARTHRITIS PATIENTS

Background:

A novel score for predicting 3-year risk for CVD events in RA patients combines age, four traditional CVD risk factors (diabetes, hypertension, smoking, history of high-risk CVD event), a personalized assessment of RA-related inflammation based on the multi-biomarker disease activity (MBDA) score and, individually, 3 of its 12 biomarkers, TNF-R1, MMP-3 and leptin (log-transformed). This score was developed and internally validated using patient data from the Medicare database.

Objectives:

The purpose of this analysis was to externally validate the MBDA-based CVD risk prediction score in a younger cohort from the Symphony claims database.

Methods:

A cohort of patients greater than or equal to 18 years old with RA diagnosis from a rheumatologist and evidence of an RA-specific treatment, excluding patients with malignancy, past myocardial infarction (MI) or stroke, was created by a third party (Symphony) by matching medical and pharmaceutical claims and linking them to MBDA scores from a database of tests done for routine care. Medicare patients were excluded to avoid overlap with the internal validation cohort. Only the first MBDA test was used for each patient. The study endpoint was time from MBDA testing to first CVD event within a 3-year time horizon. CVD event was defined as MI or stroke, based on ICD-9 or ICD-10 diagnosis codes in hospital claims. Analyses focused on relative risk, not absolute risk, because CVD event data in Symphony may be incomplete. A univariate Cox proportional hazards regression model was fit with the MBDA-based CVD risk score as the sole predictor of time to CVD event to obtain a hazard ratio (HR) estimate (95% CI) and p-values from a likelihood ratio test (LRT). Sensitivity analyses determined HR for patient subgroups, with p-values determined for the interaction between subgroups and the MBDA-based CVD risk score. Using a multivariate Cox proportional hazard regression model, the MBDA-based CVD risk score was compared to a simpler model that included only age, sex, diabetes, hypertension, history of other CVD, smoking and CRP (log-transformed) for ability to predict time to a CVD event.

Results:

48,868 patients with 337 CVD events met eligibility criteria and had linked biomarker data. Mean age was 54.4 years. 81.7% were female (Table 1). Mean follow-up was 24.4 months. The MBDA-based CVD risk score (mean 3.3, IQR 2.8–3.8) was highly significant in univariate analysis, with HR = 3.99 (95% CI: 3.52-4.51, p = 4.4×10-95); i.e., for every 1-unit increase in risk score, the CVD event rate in this cohort was ~4 times as high. Similar results were seen in the subset of 44,379 patients <65 years old, with HR=4.26 (95% CI: 3.53-5.14, p = 1.2×10-47). In sensitivity analyses, after adjusting for multiple comparisons, there were no significant differences between HR of complementary subgroups (Figure 1). The MBDA-based CVD risk score added significant prognostic information to a simpler, clinical model (HR=2.28 [95% CI: 1.69-3.08, p = 1.6×10-7] after accounting for all other factors).

Conclusion:

The MBDA-based CVD risk prediction score has been externally validated in a cohort that is younger than and independent of the Medicare cohort used previously for test development and internal validation.

Table 1.

Cohort characteristics of RA patients with linked biomarker data and at risk for CVD events.

VariableMedian (IQR) or N (%)Total patients48,868()Age, years54 (46-60)Sex, male8,940 (18.3%)Diabetes7,974 (16.3%)Hypertension19,132 (39.2%)History of high-risk CVD event6,713 (13.7%)Smoking7,487 (15.3%)CRP, mg/L4.1 (1.4-11.5)Leptin, ng/mL24.3 (10.6-47.1)MMP-3, ng/mL21.1 (14.3-36.2)TNF-RI, ng/mL1.4 (1.1-1.7)MBDA score40 (31-48)MBDA-based CVD risk score3.3 (2.8-3.8)

Disclosure of Interests:

Jeffrey Curtis Grant/research support from: Abbvie, Amgen, BMS, Corrona, Eli Lilly, Jannsen, Myriad Genetics, Inc., Pfizer, Regeneron, Roche, and UCB., Eric Sasso Shareholder of: Myriad Genetics, Inc., Employee of: Myriad Autoimmune, Elena Hitraya Shareholder of: Myriad Genetics, Inc., Employee of: Myriad Autoimmune, Cheryl Chin Shareholder of: Myriad Genetics, Inc., Employee of: Myriad Autoimmune, Richard Bamford Shareholder of: Myriad Genetics, Inc., Employee of: Myriad Autoimmune, Rotem Ben-Shachar Shareholder of: Myriad Genetics, Inc., Employee of: Myriad Genetics, Inc., Alexander Gutin Shareholder of: Myriad Genetics, Inc., Employee of: Myriad Genetics, Inc., Darl Flake Shareholder of: Myriad Genetics, Inc., Employee of: Myriad Genetics, Inc., Brent Mabey Shareholder of: Myriad Genetics, Inc., Employee of: Myriad Genetics, Inc., Jerry Lanchbury Shareholder of: Myriad Genetics, Inc., Employee of: Myriad Genetics, Inc.

Clinical validation of EndoPredict in premenopausal women with estrogen receptor-positive (ER+), human epidermal growth factor receptor 2-negative (HER2-) primary breast cancer

537

Background: The EndoPredict 12-gene prognostic assay is validated to predict distant recurrence-free survival (DRFS) and response to chemotherapy in post-menopausal women with ER+, HER2- breast cancer. This study evaluated the performance of EndoPredict in pre-menopausal women. Methods: Stored tumor samples from women with ER+, HER2- primary breast cancer who were pre-menopausal at the time of diagnosis and were systemically treated with endocrine therapy alone were obtained from two sites (University of Nottingham and University of Cyprus). These samples were tested with EndoPredict to produce a 12-gene molecular score (EP). Pathologic tumor size and nodal status were algorithmically combined with the EP score to produce the clinicomolecular EPclin score. Cases with tumors > pT3, which were treated with chemotherapy, or for whom the EPclin score was missing or invalid were excluded. Associations of EP and EPclin with 10-year DRFS were evaluated in terms of hazard ratios (HRs) from Cox proportional hazards models stratified by cohort. 10-year DRFS was estimated for EPclin high-risk and low-risk women by Kaplan-Meier analysis. Results: Out of 411 eligible cases, 385 had a valid EPclin score and were included in the analysis. Mean age at breast cancer diagnosis was 46.5 years (standard deviation 4.7). Most women (N = 239, 62.6%) had grade II tumors and 16.1% (N = 62) had node-positive disease. Over the observation period (median 9.7 years, interquartile range 6.6-13.9 years), 35 women had a distant recurrence within 10 years. Both the molecular EP score and the molecular-clinicopathologic EPclin score were associated with increased risk of distant recurrence [HR 1.3, 95% confidence interval (CI) 1.2-1.5; p < 0.001 and HR 3.6, 95% CI 2.3-5.7; p < 0.001, respectively]. Of these patients, 249 (64.7%) were categorized as low risk by EPclin score while the remaining 136 (35.3%) were categorized as high risk. Compared to EPclin low-risk women, EPclin high-risk patients were more likely to experience distant recurrence (HR 4.6, 95% CI 1.4-15.2; p = 0.004). At 10 years post-diagnosis, EPclin low-risk women who received endocrine therapy alone had a DRFS of 97% (95% CI 93-99%). Conversely, EPclin high-risk women had a DRFS of only 76% (95% CI 67-82%). Conclusions: The EPclin score is highly associated with DRFS in pre-menopausal women who received adjuvant endocrine therapy alone. Based on these data, pre-menopausal women with EPclin low-risk breast cancer may safely forgo adjuvant chemotherapy in addition to endocrine therapy.

Ancestrally unbiased polygenic breast cancer (BC) risk assessment

10502

Background: BC risk is influenced by single-nucleotide polymorphisms (SNPs) with small effects that can be aggregated into polygenic risk scores (PRSs). PRSs have primarily been developed and validated for populations of European descent. To make a PRS available for all women, we developed and validated a novel global PRS (gPRS) that utilizes individual ancestral genetic composition. Methods: Ancestry-specific PRSs corresponding to 3 continental ancestries were developed from 149 SNPs (93 BC and 56 ancestry-informative): an African PRS was developed using a cohort of 31,126 self-reported African American patients referred for hereditary cancer testing; an East Asian PRS was developed based on published data from the Asia Breast Cancer Consortium; and a European PRS was developed using data from the Breast Cancer Association Consortium and 24,259 European hereditary cancer testing patients. For each patient, ancestry-informative SNPs were used to calculate the fractional ancestry attributable to each of the 3 continents. The gPRS was the sum of ancestry specific PRSs weighted according to genetic ancestral composition. In an independent validation cohort (N = 62,707), we evaluated discrimination and calibration of gPRS, and compared performance against a previously described 86-SNP PRS for women of European ancestry. Associations of SNPs and PRSs with BC were analyzed using logistic regression adjusted for personal and family cancer history, age, and ancestry. Odds ratios (ORs) are reported per standard deviation within the corresponding patient population. P-values are reported as two-sided. Results: The gPRS was strongly associated with BC in the full validation cohort and in sub-cohorts defined by self-reported ancestry (Table). 95% (88/93) of BC SNPs had ≥1% frequency of risk alleles within each of the self-reported populations. Compared to the aforementioned 86-SNP PRS, the gPRS showed improved discrimination overall, and within each sub-cohort, with the exception of the Asian population where the sample size was too small to show superiority of either score. The 86-SNP PRS was calibrated for white non-Hispanic women but mis-calibrated for non-European ancestries. The gPRS was properly calibrated for all women. Conclusions: The 149-SNP gPRS is validated and calibrated for women of all ancestries. Combined with clinical and biological risk factors, this approach may offer improved risk stratification for all women, regardless of ancestry.[Table: see text]

Abstract 3536: Genetic validation of an ATM immunohistochemistry assay for genomic and clinical-pathologic characterization of primary prostate cancers with ATM loss

Background: ATM, a protein kinase involved in double-strand DNA break repair, is mutated in a significant fraction of prostate cancers, and targeted therapies such as ATR inhibitors appear promising for ATM-deficient tumors. However, few ATM-deficient primary prostate cancers have been clinically and genomically characterized.

Design: We validated an automated and dichotomously-scored clinical-grade immunohistochemistry (IHC) assay to detect ATM protein loss using prostate cancer cell lines and 52 very high-grade prostate tumors (Gleason score 5+4=9 or 5+5=10) with known ATM genomic status. We examined the frequency of ATM protein loss among 29 tumors with known pathogenic germline ATM mutations or variants of unknown significance (VUS). Finally, we screened more than 800 additional primary prostate carcinomas using tissue microarrays (TMA) for ATM protein loss. Targeted somatic genomic sequencing using HRD Plus (Myriad Genetics) or UW-OncoPlex was conducted in a subset of immunostained tumors in each cohort.

Results: ATM protein loss by IHC was found in 13% (7/52) of very high-grade (primary Gleason pattern 5) tumors with somatic genomic sequencing data. Of 7 cases with ATM protein loss, 4 had a deleterious ATM mutation and 3 had apparent single copy ATM genomic loss. Of the remaining 45 cases without ATM protein loss, none had ATM genomic alterations. In the cohort of tumors with pathogenic germline ATM mutations, 74% (17/23) had ATM protein loss, but only 45% (9/20) with evaluable sequencing had a second pathogenic alteration in ATM detected (all of these had protein loss). Of those with germline mutations and ATM protein loss, the majority (76% or 13/17) had an apparent clonal alteration with homogeneous protein loss in all tumor cells sampled. In contrast, among 6 cases with germline ATM VUS, only one had protein loss. On TMA analysis, ATM loss was present in 3% (25/824) of evaluable tumors overall, and was significantly more common in tumors from Grade Group 5 (12/130; 9.2%) compared to all other Grade Groups (13/694; 1.9%) (P&lt;0.0001). Of tumors found by TMA screening with available sequencing, 80% (4/5) with homogeneous ATM protein loss and 58% (7/12) with heterogeneous ATM protein loss had detectable pathogenic alterations in ATM. Of these, 82% (9/11) were inferred to have somatic ATM variants.

Conclusions: Validated ATM IHC is a sensitive assay for detecting underlying ATM alterations and may be useful to evaluate VUS in ATM. However, not all tumors with ATM protein loss have detectable genomic alterations. ATM protein loss is likely an early clonal event in tumors with germline mutations and is significantly enriched in high-grade prostate cancers.

Citation Format: Harsimar Kaur, Jessica Hicks, Colin Pritchard, Angelo De Marzo, William Isaacs, Jerry Lanchbury, Kirsten Timms, Emmanuel Antonarakis, Tamara L. Lotan. Genetic validation of an ATM immunohistochemistry assay for genomic and clinical-pathologic characterization of primary prostate cancers with ATM loss [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3536.

FRI0553 DEVELOPMENT AND VALIDATION OF A BIOMARKER-BASED CARDIOVASCULAR RISK PREDICTION SCORE IN RHEUMATOID ARTHRITIS

Background:

Rheumatoid arthritis (RA) patients are at elevated risk for cardiovascular (CV) events, but risk stratification based on CV prediction models is not part of routine rheumatology practice.

Objectives:

To develop and validate a biomarker-based CV risk prediction model and compare it to alternative risk prediction models.

Methods:

We constructed a cohort of RA patients - age ≥40 with ≥1 RA diagnosis from a rheumatologist, excluding patients with malignancy, past myocardial infarction (MI) or stroke - by linking Medicare administrative data from 2006-2016 to multi-biomarker disease activity (MBDA) test results obtained as part of routine care. The cohort was split 2:1 to create training and internal validation datasets. The composite CV outcome was MI, stroke or CV death occurring within 3 years. Clinical predictors examined were: age, sex, race, traditional CV risk factors (e.g. diabetes, hypertension, hyperlipidemia, high-risk CV conditions [e.g. angina]), RA-related factors (e.g. glucocorticoid use, MTX, number of prior biologics), adjusted MBDA score1and its 12 biomarkers, log-transformed. Backward elimination was used to remove predictors with p ≥0.05. The resulting CV risk score was compared to four prediction models (age+sex; age+sex+CRP; age+sex+diabetes+hypertension+ smoking+high risk CV [±CRP]) in the validation dataset. We evaluated: 1) incremental improvement in the likelihood ratio test (LRT) statistic, 2) discrimination (AUROC), and 3) goodness-of-fit (predicted vs. observed, based on Kaplan-Meier estimates). Validation analyses were prespecified.

Results:

30,751 RA patients with 904 CV events were linked to MBDA test results and eligible for analysis. Patient characteristics were mean (SD) age 68.7 (9.5) years; 23.4% age <65; 82% women. Comorbidities included diabetes (39%), hypertension (78%), smoking (24%) and history of high-risk CV condition (37%). RA-related features included use of glucocorticoids (58%), MTX (60%), TNFi (33%) and other biologics (16%). Mean (SD) MBDA score was 41 (14). The final covariates included in the MBDA-based CV risk score were age, diabetes, hypertension, smoking, history of high-risk CV conditions, adjusted MBDA score, leptin, TNFRI and MMP-3. Median (IQR) of the predicted 3-year CV risk was 3.4% (2.1%, 5.6%). Based on extrapolation to 10-year risk, 9.4% of patients would be considered low, 10.2% borderline, 52.2% intermediate, and 28.2% high risk per 2019 ACC/AHA guidelines.

Compared to four simpler CV prediction models, significant improvement in the LRT statistic was observed with the addition of the biomarker-based CV risk score (Figure 1). Model fit was good across deciles (Figure 2). The AUROC was 0.70. The MBDA-based model reclassified 28.5% of patients vs. the model based on age+sex+diabetes+hypertension +smoking+high risk CV+CRP.

Figure 1.

Incremental Improvement of MBDA-based CV Risk Score Compared to Other CV Risk Prediction Models

Figure 2.

MBDA-Based CV Risk Score Calibration for Composite CV Outcome at 3 Years

Conclusion:

A biomarker-based prediction score incorporating a few clinical risk factors appears to have good accuracy to predict CV risk in RA. Additional validation in independent cohorts will help verify its performance characteristics.

References:

[1] Curtis et al.,Rheumatology2018;58:874.

Disclosure of Interests:

Jeffrey Curtis Grant/research support from: AbbVie, Amgen, Bristol-Myers Squibb, Corrona, Janssen, Lilly, Myriad, Pfizer, Regeneron, Roche, UCB, Consultant of: AbbVie, Amgen, Bristol-Myers Squibb, Corrona, Janssen, Lilly, Myriad, Pfizer, Regeneron, Roche, UCB, Fenglong Xie: None declared, Cynthia S. Crowson Grant/research support from: Pfizer research grant, Brent Mabey Shareholder of: Myriad Genetics, Inc., Employee of: Myriad Genetics, Inc., Darl Flake Shareholder of: Myriad Genetics, Inc., Employee of: Myriad Genetics, Inc., Richard Bamford Shareholder of: Myriad Genetics, Inc., Employee of: Myriad Genetics, Inc., Cheryl Chin Shareholder of: Myriad Genetics, Inc., Employee of: Myriad Genetics, Inc., Eric Sasso Shareholder of: Myriad Genetics, Inc., Employee of: Myriad Genetics, Inc., Elena Hitraya Shareholder of: Myriad Genetics, Inc., Employee of: Myriad Genetics, Inc., Rotem Ben-Shachar Shareholder of: Myriad Genetics, Inc., Employee of: Myriad Genetics, Inc., Alexander Gutin Shareholder of: Myriad Genetics, Inc., Employee of: Myriad Genetics, Inc., Jerry Lanchbury Shareholder of: Myriad Genetics, Inc., Employee of: Myriad Genetics, Inc.

AB1243 TRAINING AND VALIDATION OF A MULTIVARIATE PREDICTOR OF RISK OF RADIOGRAPHIC PROGRESSION FOR PATIENTS WITH RHEUMATOID ARTHRITIS

Background:

The multi-biomarker disease activity (MBDA) score, adjusted for age, sex and adiposity (MBDAadj), has been shown to be better than several conventional disease activity measures for predicting risk for radiographic progression (RP) in patients with rheumatoid arthritis (RA).1Serologic status and other non-disease activity measures are also predictive of RP risk. Combining them with the MBDAadjshould result in a stronger prognostic test for RP than any one measure alone.

Objectives:

Develop a multivariate model for predicting risk for RP that includes the adjusted MBDA score and other known predictors of RP.

Methods:

Four RA cohorts were used, two for training (OPERA and BRASS, n=555) and two for validation (SWEFOT and Leiden, n=397). Each pair of cohorts was heterogeneous in disease duration and treatment history. BMI data were not available for one validation cohort, so a BMI surrogate was modeled using forward selection with the two training cohorts and 3 others (CERTAIN, InFoRM, RACER) (N=1411). An RP risk score was then trained using forward selection in a linear mixed-effects regression, considering disease-related and demographic variables as predictors of change in modified total Sharp score over one year (ΔmTSS), with a random effect on cohort. The RP risk score was validated as a predictor of RP with two cutoffs (ΔmTSS >3 and >5) using logistic mixed-effects regression. Odds ratios (OR) and 95% profile likelihood-based confidence intervals (CI) were calculated from the models and significance was assessed by likelihood ratio tests. Risk curves were generated to show probability of RP as a function of the RP risk score.

Results:

The BMI surrogate included leptin, sex, age and age2and correlated well with BMI (ρ = 0.76). In training, the most significant independent predictors of RP were MBDAadj(p = 0.00020), seropositivity (p = 9.3 x 10-5), BMI surrogate score (p = 0.013) and use of targeted therapy (p = 0.0026). The final model was: RP risk score = 0.024 x MBDAadj+ 0.093 if seropositive – 0.063 x BMI surrogate score – 0.61 if using a targeted therapy. In validation, the OR (95% CI) of the RP risk score for predicting ΔTSS >3 or >5 were 2.2 (1.6, 3.2) (p = 2.6 × 10-6) and 3.1 (2.0, 5.0) (p = 5.7 × 10-8), respectively (Figure 1). The odds of a patient having RP increases by 50% for each 21-unit or 15-unit increase in MBDAadj, for RP defined as ΔTSS >3 or >5, respectively.

Figure 1.

Conclusion:

A multivariate model containing adjusted MBDA score, seropositivity, a BMI surrogate and use of targeted therapy has been trained and validated as a prognostic test for radiographic progression in RA.

References:

[1]Curtis, et al.Rheumatology [Oxford].2018;58:874

Disclosure of Interests:

Thomas Huizinga Grant/research support from: Ablynx, Bristol-Myers Squibb, Roche, Sanofi, Consultant of: Ablynx, Bristol-Myers Squibb, Roche, Sanofi, Michael E. Weinblatt Grant/research support from: BMS, Amgen, Lilly, Crescendo and Sonofi-Regeneron, Consultant of: Horizon Therapeutics, Bristol-Myers Squibb, Amgen, Abbvie, Crescendo, Lilly, Pfizer, Roche, Gilead, Nancy Shadick Grant/research support from: Mallinckrodt, BMS, Lilly, Amgen, Crescendo Biosciences, and Sanofi-Regeneron, Consultant of: BMS, Cecilie Heegaard Brahe: None declared, Mikkel Ǿstergaard Grant/research support from: AbbVie, Bristol-Myers Squibb, Celgene, Merck, and Novartis, Consultant of: AbbVie, Bristol-Myers Squibb, Boehringer Ingelheim, Celgene, Eli Lilly, Hospira, Janssen, Merck, Novartis, Novo Nordisk, Orion, Pfizer, Regeneron, Roche, Sandoz, Sanofi, and UCB, Speakers bureau: AbbVie, Bristol-Myers Squibb, Boehringer Ingelheim, Celgene, Eli Lilly, Hospira, Janssen, Merck, Novartis, Novo Nordisk, Orion, Pfizer, Regeneron, Roche, Sandoz, Sanofi, and UCB, Merete L. Hetland Grant/research support from: BMS, MSD, AbbVie, Roche, Novartis, Biogen and Pfizer, Consultant of: Eli Lilly, Speakers bureau: Orion Pharma, Biogen, Pfizer, CellTrion, Merck and Samsung Bioepis, Saedis Saevarsdottir Employee of: Part-time at deCODE Genetics/Amgen Inc, working on genetic research unrelated to this project, Megan Horton Shareholder of: Myriad Genetics, Inc., Employee of: Myriad Genetics, Inc., Brent Mabey Shareholder of: Myriad Genetics, Inc., Employee of: Myriad Genetics, Inc., Darl Flake Shareholder of: Myriad Genetics, Inc., Employee of: Myriad Genetics, Inc., Rotem Ben-Shachar Shareholder of: Myriad Genetics, Inc., Employee of: Myriad Genetics, Inc., Eric Sasso Shareholder of: Myriad Genetics, Inc., Employee of: Myriad Genetics, Inc., Alexander Gutin Shareholder of: Myriad Genetics, Inc., Employee of: Myriad Genetics, Inc., Elena Hitraya Shareholder of: Myriad Genetics, Inc., Employee of: Myriad Genetics, Inc., Jerry Lanchbury Shareholder of: Myriad Genetics, Inc., Employee of: Myriad Genetics, Inc., Jeffrey Curtis Grant/research support from: AbbVie, Amgen, Bristol-Myers Squibb, Corrona, Janssen, Lilly, Myriad, Pfizer, Regeneron, Roche, UCB, Consultant of: AbbVie, Amgen, Bristol-Myers Squibb, Corrona, Janssen, Lilly, Myriad, Pfizer, Regeneron, Roche, UCB

Comprehensive breast cancer (BC) risk assessment for CHEK2 carriers incorporating a polygenic risk score (PRS) and the Tyrer-Cuzick (TC) model

1504

Background: Women with pathogenic variants in the moderate penetrance CHEK2 gene have on average an estimated > 20% lifetime risk for breast cancer, thereby meeting an established threshold for more aggressive screening, including consideration of breast magnetic resonance imaging (MRI). However, we previously showed that CHEK2 penetrance is modified by an 86-SNP PRS. CHEK2 risk is further modified by family history (FH) and other TC model variables. Here, we describe development of a comprehensive risk prediction model for women of European ancestry to more precisely estimate risk by incorporating CHEK2, PRS and TC V7.02. The number of CHEK2 carriers with low ( < 20%), moderate (20%-50%) and high ( > 50%) remaining lifetime risk based on the combined model was examined in an independent study cohort. Methods: This IRB-approved study included de-identified clinical records from 358,471 women of European ancestry who were tested clinically for hereditary cancer risk with a multi-gene panel. Model development was based on analysis of CHEK2 PV carriers ( N= 4,331) and women negative for BC gene PV ( N =353,681) who were tested between September 2013 and July 2019. Risk estimates incorporating CHEK2, PRS and TC were calculated using a fixed-stratified (FS) method that accounts for correlations between risk factors in a manner equivalent to multivariable co-estimation. Risk stratification was assessed in an independent cohort of CHEK2 carriers ( N= 459) who were tested after July 2019 and not included in model development. Results: We detected significant correlation of CHEK2 status with FH ( p= 4.1 × 10−17) and of PRS with FH among CHEK2 carriers ( p= 1.7× 10−5). For these factors, joint effects were co-estimated using the FS method. In an independent cohort, 24.0% of CHEK2 carriers were categorized as low risk ( < 20%), and 62.6% were categorized as moderate risk (20-50%). For 13.4% of CHEK2 carriers, risk estimation incorporating PRS and TC generated BC risks of greater than 50%, consistent with genes recognized as highly penetrant. Conclusions: In CHEK2 PV carriers, comprehensive risk assessment could inform individualized decision-making and may lead to improved targeting of screening and prevention strategies.

Performance of the IBIS/Tyrer-Cuzick (TC) Model by race/ethnicity in the Women’s Health Initiative

1503

Background: The TC model, a breast cancer (BC) risk assessment tool based on family cancer history, reproductive and lifestyle factors is used to guide BC screening and prevention. TC was developed and validated largely in non-Hispanic White (NHW) women. We evaluated the calibration and discrimination of TC version 7.02 among racially/ethnically diverse post-menopausal women enrolled in the Women’s Health Initiative (WHI) clinical trials or observational study. Methods: WHI enrolled post-menopausal women from 1993-1998 and followed them prospectively for BC incidence. We included women aged ≤80 years at enrollment with no prior BC or mastectomy and with data required for TC, including weight, height, ages at menarche, first birth and menopause, menopausal hormone therapy use and family history of breast or ovarian cancer in first or second-degree relatives. Calibration was assessed by the ratio of observed BC cases to the number expected by TC (O/E), with expected cases calculated as the sum of cumulative hazards. We tested for differential discrimination by race/ethnicity (NHW, African American, Hispanic, Asian/Pacific Islander, Native American, other) using Cox regression. Time to BC was modeled using age, race/ethnicity, TC estimate (transformed by log of relative lifetime risk), and a term for interaction between race/ethnicity and TC estimate. Results: During the follow-up period (median 18.9 years, maximum 23.4 years), 6,836 new BC cases were diagnosed among 91,893 women. TC was well-calibrated overall (O/E 0.95) in NHW and African Americans, but over-estimated risk for Hispanics (O/E 0.75, Table). Results suggested good calibration for Asian/Pacific Islanders and Native Americans, but sample sizes were small. Discrimination did not differ significantly by race/ethnicity (two-sided p-value for interaction = 0.33). Conclusions: TC provided similar risk discrimination among post-menopausal women of different racial/ethnic groups over nearly 20 years of follow-up; however, it overestimated risk for Hispanics. Future studies in diverse populations are warranted, with need for a more accurate breast cancer risk assessment tool for Hispanics. [Table: see text]

Comparison of genomic instability test scores used for predicting PARP activity in ovarian cancer

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Background: Clinical trials have explored the utility of various genomic instability (GI) scores or gene panels to assess deficiencies in the homologous recombination (HR) DNA repair pathway and support PARP inhibitor use in ovarian cancer; however, these methods of assessing homologous recombination deficiency (HRD) may not be equivalent. The myChoice HRD test is the only analytically and clinically validated, FDA-approved HRD test that includes BRCA1/2 mutation status and three measures of GI. We compared the proportion of patients identified as candidates for PARP inhibitor use by two measures of HRD [percent loss of heterozygosity (%LOH), 11-gene panel] to myChoice HRD. Methods: Whole-genome SNP analysis was used to reconstruct ovarian tumor genomic profiles to calculate the myChoice HRD score and %LOH in 2 cohorts (clinical laboratory cohort, N = 3,278; SCOTROC4 trial, N = 248). Mutation screening for a set of 11 genes in the HR pathway ( ATM, BARD1, BRCA1, BRCA2, BRIP1, CHEK2, MRE11A, NBN, PALB2, RAD51C, RAD51D) was performed for a subset of tumors from the SCOTROC trial (n = 187). Samples were considered positive if the myChoice HRD score was above the threshold (threshold scores of 42 and 33 were assessed), %LOH above the threshold (16%), or a pathogenic variant in one of the 11 HR genes. The correlation between positive results from %LOH and the 11-gene panel were compared to myChoice HRD. Percent positive agreement (PPA) was the proportion of positive test results from myChoice HRD that were also positive by %LOH or the 11-gene panel. Results: The table shows the correlation and PPA between myChoice HRD, %LOH, and the 11-gene panel. Overall, 19%-61% of patients identified as positive by myChoice HRD would have been missed by %LOH or the 11-gene panel in these two cohorts. Conclusions: These data show that HRD tests used in published and ongoing clinical trials are not equivalent, and they should not be considered interchangeable in predicting PARP inhibitor response in clinical practice. [Table: see text]

Comparison between whole exome sequencing (WES) and single nucleotide polymorphism (SNP)-based tumor mutation burden analysis

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Background: Immune checkpoint inhibitors (ICI) block proteins which enable cancer cells to evade the immune system. Recent studies have shown that the higher the tumor mutation burden (TMB) the greater the likelihood of response to ICI therapy. Analysis of TMB has focused on WES of paired tumor and normal samples. This study tests the feasibility of measuring TMB from a SNP-based resequencing assay (myChoice HRD Plus). Methods: WES and myChoice HRD Plus were performed on matched tumor and normal DNA from 44 breast and 12 colon tumors. myChoice HRD Plus combines homologous recombination deficiency analysis with resequencing of 108 genes and microsatellite instability analysis. WES-based TMB was calculated by identifying all variants in paired samples, and subtracting germline variants. Two SNP-based TMB (SbTMB) methods were utilized to calculate TMB. The first used germline subtraction similar to the WES-based method. The second utilized an algorithm which removed background germline variants. Median sequence length to calculate TMB was 9.7 Mb for WES, 4.6 Mb for SbTMB (germline subtraction), and 1.9 Mb for SbTMB (algorithm). Results: Correlation coefficients for WES vs. SbTMB (germline subtraction) and SbTMB (algorithm) were 0.895 and 0.908, respectively. The two SbTMB methods had a correlation coefficient of 0.834. SbTMB measures of TMB were generally higher than WES-based TMB with a mean increase in score of 1.6 variants/Mb for SbTMB (germline subtraction; p = 4.6x10-6) and 1.5 variants/MB for SbTMB (algorithm; p = 1.2x10-5). No significant difference in magnitude of TMB score between the SbTMB measures was observed (0.04 variants/Mb; p = 0.88). Conclusions: SNP-based methods for calculating TMB produced highly concordant scores compared to WES-based methods. SbTMB assays produced elevated TMB scores, consistent with selective pressure against mutations in coding regions of genes, necessitating a higher score threshold for when using a SbTMB assay. This SbTMB analysis expands the utility of myChoice HRD Plus, and provides a method for calculation of TMB without sequencing a germline comparator.

Abstract C53: Homologous recombination deficiency (HRD) of high grade serous ovarian tumors from the NOVA Phase III clinical study

Background: Genome-wide analysis was conducted on tumors obtained from patients enrolled in the NOVA study, a Phase 3 clinical trial evaluating the PARP inhibitor niraparib as a maintenance treatment in patients with platinum-sensitive ovarian cancer. Homologous recombination deficiency (HRD) and mutations in DNA damage repair genes were evaluated.

Material and methods: DNA was extracted from formalin-fixed paraffin-embedded (FFPE) tumor tissue and used to create libraries that were hybridized to a custom Agilent SureSelect capture array carrying probes for 54,091 single nucleotide polymorphism sites distributed across the human genome, as well as probes targeting 43 genes involved in DNA repair, including BRCA1 and BRCA2. The captured and enriched DNA was sequenced on an Illumina HiSeq 2500 sequencer. Sequences covering SNP positions were used to generate allelic imbalance profiles. Measures of genomic instability, including determination of an HRD score (integer value of 0-100), were calculated using allelic imbalance profiles and determination of loss of heterozygosity (LOH) by allele-specific copy number (ASCN). A previously identified HRD threshold score of 42 was used to define HRD positivity in the absence of a BRCA mutation.

Results: The NOVA study is a Phase 3, multicenter, randomized, double-blind, placebo-controlled study of niraparib as maintenance therapy in ovarian cancer patients who have either gBRCAmut or a tumor with high-grade serous histology and who have responded to their most recent chemotherapy containing a platinum agent. Tumor BRCA mutational status, HRD score and genomic sequencing of 43 DNA repair genes were obtained from tumor samples from both gBRCAmut and non-gBRCAmut cohorts. In the gBRCAmut cohort, HRD analysis of the tumor confirmed the presence of a deleterious or suspected deleterious mutation in all cases. In addition, an HRD score ≥ 42 and the presence of a deleterious mutation in TP53 with loss of heterozygosity (LOH) were observed in nearly all tumors. In the non-gBRCA cohort, somatic BRCA mutations were observed in approximately 13% of tumors, and approximately half of tumors with no evidence of a BRCA mutation had a high HRD score. In both cohorts, the use of three scoring algorithms (LOH, telomeric allelic imbalance [TAI], large-scale state transitions [LST]), was more predictive of BRCA mutational status than LOH alone. Additional genomic sequencing identified deleterious mutations with LOH in DNA repair genes, such as BRIP1, CDK12, RAD51C, PTEN, and RAD51D, with many tumors exhibiting multiple deleterious mutations.

Conclusions: High grade serous ovarian cancer is characterized by a high degree of genomic instability. Genomic analysis in the clinical setting is able to identify patients with both germline and somatic BRCA mutations, in addition to BRCAwt tumors with other genetic defects that may be sensitive to agents exploiting deficiencies in HR.

Citation Format: Keith Wilcoxen, Christopher Neff, Victor Abkevich, Joshua Timothy Jones, Kathryn Kolquist, Michael Mirza, Jerry Lanchbury, Keith Mikule, Shefali Agarwal, Anne-Renee Hartman, Alexander Gutin, Kirsten Timms. Homologous recombination deficiency (HRD) of high grade serous ovarian tumors from the NOVA Phase III clinical study. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr C53.

Abstract P4-11-15: Risk stratification within luminal B breast cancer using a second generation prognostic RNA signature

Background: Indication to adjuvant chemotherapy in early stage ER-positive breast cancer is usually based on clinico-pathological parameters, and has been recently improved by the introduction of prognostic expression profiles. Clinical or molecular features are efficient in identifying low-risk (pT1, histological grade 1, pN0, low RS, Luminal A subtype) and high-risk patients (&gt;pT1, grade 3, N2, high RS). However, a large group of patients with intermediate clinical or molecular characteristic (grade 2, intermediate RS, luminal B) fall into the category between distinctly low and distinctly high risk and receive no treatment guidance from current decision tools.

Methods: From a population of 1929 chemo-naïve, hormone treated, luminal B (Her-2 negative), pT1-pT3, pN0-N1a breast cancer patients diagnosed and treated at the European Institute of Oncology from 1997 to 2005, we selected a random subcohort of 555 cases, in a case-cohort design. All the patients with local or distant metastasis which were not already included were added to the subcohort, leading to a total of 704 patients (208 with local or distant recurrences and 496 random controls). Luminal B status was determined by the immunohistochemical analysis of ER, PgR, HER2 and Ki-67, according to the 2011 St. Gallen criteria. FFPE sections of the primary tumor were analyzed for the mRNA expression of 43 genes by multiplex quantitative PCR. A molecular score (MS) was calculated from the average expression of 23 cell cycle progression genes, the average expression of seven lymphocyte specific genes and the expression of PR and ABCC5, based on a model derived from an independent training cohort. A combined score of MS and the clinical variables of tumor size, grade and node status was modeled in the training cohort and applied to the Luminal B set. The association between MS and the risk of distant metastasis was evaluated in a weighted multivariable Cox regression model, adjusted for traditional clinical factors and Ki-67 labeling index (LI).

Results: 640 samples, including 102 distant metastasis, had full clinical and expression data. In the 500 samples from the subcohort, median Ki67 LI was 21% (IQR=11%, Q1=16%, Q3=27%). Either one unit increase of Ki-67 LI (HR 1.06, 95%CI (1.04-1.08), p&lt;0.0001) and of MS (HR 3.4, 95%CI (2.5-4.6), p&lt;0.0001) were highly significant predictors of distant recurrence in univariable analysis. In multivariable analysis, the MS provided independent significant prognostic information after adjustment for Ki-67 LI, tumor size, grade and node status (HR 4.3, 95%CI (2.5-7.3), p=&lt;0.0001). Using the combined score of MS and clinical variables, 383 patients or 77% of the subcohort had an estimated 10 year risk of distant recurrence of ≤10%. Similar results were obtained when samples were re-defined according to 2013 St. Gallen guidelines.

Conclusions: The MS provides important prognostic discrimination beyond traditional clinico-pathological characteristics, including Ki-67 LI, in Luminal B breast cancer, and contributes in identifying a subset of patients which may be successfully treated with endocrine therapy only.

Citation Format: Giancarlo Pruneri, Vincenzo Bagnardi, Davide Disalvatore, Giuseppe Curigliano, Nicole Rotmensz, Carmen Criscitiello, Darl D Flake II, Susanne Wagner, Alexander Gutin, Jerry Lanchbury, Massimo Barberis, Francesca Lombardi, Giuseppe Viale. Risk stratification within luminal B breast cancer using a second generation prognostic RNA signature [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P4-11-15.

Abstract P5-06-04: The PARP inhibitor niraparib demonstrated activity in patient-derived triple-negative breast cancer xenograft models with high homologous recombination deficiency (HRD) score

Triple negative breast cancer (TNBC), which comprises 15% of all breast cancers, has a poor prognosis and currently lacks effective treatment. TNBCs are highly proliferative, genomically unstable and share molecular characteristics with that of BRCA1/2 mutation driven breast cancer. Poly(ADP-ribose) polymerase-1 (PARP) is a key DNA repair enzyme that mediates single strand break (SSB) repair through the base excision repair (BER) pathway. PARP inhibitors have been demonstrated to selectively kill tumor cells that harbor BRCA1 and BRCA2 mutations. In addition, pre-clinical and preliminary clinical data suggest that PARP inhibitors are selectively cytotoxic for tumors with homologous recombination repair deficiency caused by dysfunction of genes other than BRCA1 or BRCA2.

Niraparib is a potent, orally active PARP inhibitor that is being evaluated in Phase 3 clinical studies for ovarian cancer and BRCA related breast cancer. Previously, we demonstrated that a subset of basal breast cancer (BBC) patient-derived xenograft (PDX) models responded robustly to single agent niraparib treatment. To understand the selectivity observed, the samples from a collection of 37 BBC PDX models have been subjected to homologous recombination deficiency (HRD) analysis. HRD analysis is a DNA-based assay that is capable of detecting homologous recombination deficiency independent of its etiology. Genome-wide SNP data was generated from a custom Agilent SureSelect XT capture followed by sequencing on an Illumina HiSeq2500. SNP data was analyzed using three algorithms (LOH, TAI and LST scores), and the final HRD score is the sum of the LOH+TAI+LAST scores.

Niraparib’s antitumor activity was investigated in patient derived BBC models with various HRD scores. The correlation between niraparib efficacy, HRD score and BRCA deficiency will be discussed.

Citation Format: Yan Wang, Stefano Cairo, Olivier Deas, Anne-Renee Hartman, Joshua Jones, Alexander Gutin, Jerry Lanchbury, Zaina Sangale, Cara Solimeno, Jean-Gabriel Judde, Kirsten Timms, Keith Wilcoxen. The PARP inhibitor niraparib demonstrated activity in patient-derived triple-negative breast cancer xenograft models with high homologous recombination deficiency (HRD) score [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P5-06-04.

Abstract 1763: Frequency of homologous recombination repair defects across breast cancer subtypes

Introduction: Defects in homologous recombination (HR) repair have potential therapeutic relevance, and current clinical studies are focused on examining the efficacy of agents that exploit HR deficiency in triple negative breast cancer. A homologous recombination deficiency (HRD) score based on whole genome tumor LOH profiles has been developed that is highly correlated with defects in BRCA1/2, and other HR pathway genes, in ovarian cancer(1), and which predicts response to platinum-based neoadjuvant therapy in triple negative breast cancer(2). This study examines the frequency of BRCA1/2 defects and elevated HRD score across breast cancer subtypes as defined by IHC hormone receptor status.

Methods: A targeted custom hybridization panel was developed targeting BRCA1, BRCA2, and 50,000 selected SNPs across the entire human genome. This panel, in combination with sequencing on the Illumina HiSeq, was used to analyze approximately 50 randomly ascertained tumors from each of 4 breast cancer subtypes (triple negative, ER+/Her2-, ER-/Her2+, ER+/Her2+) for BRCA1/2 somatic and germline mutations, and SNP allele frequencies. HRD scores were calculated using LOH profiles reconstructed from the SNP analysis. A BRCA1 promoter methylation assay was also performed on all samples.

Results: BRCA1/2 somatic and germline mutations were detected in all breast cancer subtypes. BRCA1/2 mutations were observed most frequently in triple negative and ER+/Her2+ tumors. BRCA1 promoter methylation was confined almost exclusively to triple negative tumors. Association between elevated HRD score and BRCA defects was observed regardless of tumor type, and BRCA1/2 intact tumors with elevated HRD scores were observed in all breast cancer subtypes.

Conclusions: Elevated HRD score is significantly associated with BRCA1/2 defects in breast cancer. BRCA1/2 defects and elevated HRD scores were observed in all subtypes of breast cancer, suggesting the presence of HR defects in genes other than BRCA1/2 are present in all breast cancer subtypes. HRD score could potentially be used to facilitate the expansion of platinum or PARP inhibitor therapy beyond triple negative breast cancer into other subtypes.

Citation Format: Kirsten M. Timms, Victor Abkevich, Chris Neff, Brian Morris, Jennifer Potter, Thanh V. Tran, Jian Chen, Zaina Sangale, Eliso Tikishvili, Andrey Zharkikh, Michael Perry, Alexander Gutin, Jerry Lanchbury. Frequency of homologous recombination repair defects across breast cancer subtypes. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1763. doi:10.1158/1538-7445.AM2013-1763

Abstract 3116: Patterns of genomic loss of heterozygosity predict homologous recombination repair defects in ovarian cancer

Introduction: BRCA1 and BRCA2 are key members of the homologous recombination (HR) pathway. Mutations in these genes and other HR pathway defects have potential therapeutic relevance when used to support agents that introduce or exploit double-strand DNA breaks. This study examines the association between HR deficiency and genomic patterns of loss of heterozygosity (LOH). Methods: Ovarian tumors from two independent datasets were characterized for germline and somatic defects in BRCA1 and BRCA2. Whole genome LOH profiles were generated using Affymetrix SNP arrays. Publically available data was downloaded from the TCGA website for a third independent ovarian cancer dataset. RAD51C promoter methylation was assayed in two of the datasets. Comprehensive profiling of BRCA1 and BRCA2 defects, and genome wide LOH was also performed on approximately 70 breast, ovarian, colon and pancreatic cell lines. Results: Examination of the pattern of LOH within ovarian tumors with BRCA1, BRCA2, or RAD51C defects compared to tumors without defects in these genes has resulted in the development of a homologous recombination deficiency (HRD) score that has highly significant association with HRD (p=9*10-11). An intermediate class of LOH sizes (&gt;15 Mb but less than a whole chromosome) is highly positive correlated with defective HR, suggesting this class of LOH exists due to double strand DNA break formation and requires repair by HR. The HRD score was validated in two independent ovarian cancer datasets (p=2*10-7 and 9*10-29), and successfully identified breast and pancreatic cell lines with BRCA defects, suggesting it will be effective across multiple tumor types. Conclusions: BRCA1 or BRCA2 mutation carriers have improved outcomes following treatment with DNA damaging agents such as platinum salts, and preclinical studies have demonstrated PARP inhibitor efficacy in BRCA1 or BRCA2 deficient cells. HR deficiency in ovarian cancer is not solely due to germline BRCA1 and BRCA2 mutations, and HR deficiency is not unique to ovarian tumors. Each type of cancer is likely to have a unique spectrum of genetic variants resulting in HRD. The HRD score appears capable of detecting HRD regardless of etiology or mechanism. This score could have clinical utility in breast and ovarian cancer, and could be used to target the use of PARP inhibitors and platinum salts in other cancers.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3116. doi:1538-7445.AM2012-3116

Abstract IA6: Cell cycle progression genes differentiate indolent from aggressive prostate cancer

Background: In cancers with variable natural history, prognostic biomarkers are needed for selecting patients for therapeutic intervention. This is particularly true for prostate cancer, where many screen-detected cases are indolent and predicting adverse outcomes is difficult. Therefore, we developed an expression signature composed of genes involved in cell cycle progression (CCP) and tested its utility in prostate cancer.

Methods: We developed a 46-gene prognostic RNA signature that is based on measuring the expression of CCP genes. The expression score (CCP score) is derived as the normalized mean expression all CCP genes in the signature.

Results: The prognostic utility of the CCP score has been tested in both multiple clinical settings and patient populations. First, it was tested in a post-prostatectomy cohort from the U.S. where the CCP score predicted biochemical recurrence in univariate (χ2 = 34.0, 1df, p = 5·6 × 10-9) and multivariate analysis (χ2 = 21.65, 1df, p = 3.3 × 10-6). CCP score and PSA were the dominant variables in the best predictive model and were much more significant than any other clinical measure. Second, it was tested in a conservatively managed TURP cohort from the UK where the CCP score was the dominant variable for predicting death from prostate cancer in both univariate (χ2 = 92.7, 1df, p = 6.1 × 10-22) and multivariate analyses (χ2 = 42.2, p = 8.2 × 10-11). Third, it was tested in a conservatively managed needle biopsy cohort from the UK where the CCP score was a better univariate predictor of prostate cancer death than any other variable (χ2 = 37·6, 1df, p = 8.6 × 10-10). The best multivariate model from this study included Gleason and PSA, but CCP dominated (HR for one unit increase = 1.65, 95% CI (1.31, 2.09) χ2 = 17.7, P = 3 × 10-5) with Gleason score (χ2 = 12.1, P = 5 × 10-4) and baseline PSA (χ2 = 5.7, P = 0.017) providing significant, but smaller additional contributions.

Conclusions: A CCP expression signature is prognostic in prostate cancer patients at diagnosis and after prostatectomy. It consistently provides information beyond clinical and pathological variables to help differentiate aggressive from indolent disease. Studies aimed at expanding the clinical utility of this signature are warranted and ongoing.

Citation Format: Steven Stone, On behalf of the Transatlantic Prostate Group, Jack Cuzick, Dan Berney, Julia Reid, Gabrielle Fisher, Jerry Lanchbury, Alexander Gutin, Greg Swanson. Cell cycle progression genes differentiate indolent from aggressive prostate cancer [abstract]. In: Proceedings of the AACR Special Conference on Advances in Prostate Cancer Research; 2012 Feb 6-9; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(4 Suppl):Abstract nr IA6.

Somatic BRCA status in ovarian tumors

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Background: The combined prevalence of BRCA1/2 mutations in germline DNA derived from a population of invasive ovarian cancer patients is up to 15.3%. PARP inhibitor trials are ongoing in patients who carry germline BRCA1/2 mutations. It is important to know whether somatic (non-germline) BRCA changes are present in ovarian tumors, given the predicted sensitivity of BRCA mutation-carrying tumors to PARP inhibitors and other DNA damaging agents. However, a large cohort of ovarian tumor tissues has not been studied to determine the frequency of BRCA deficiency due to additional somatic changes. Methods: BRCA1/2 exons/flanking regions were sequenced in 235 high-grade ovarian cancers and 38 ovarian cancer cell lines. In 112 tumors, we also performed gene expression analysis and copy number arrays with ultradense probe tiling throughout both BRCA genes. Results: For BRCA1, 31 tumors (13.2%) harbored mutations: 23 known deleterious mutations, 1 suspected deleterious mutation, 3 novel indels, 1 novel mis-sense and 3 novel nonsense mutations. For BRCA2, 12/178 sequenced tumors (6.7%) harbored mutations: 8 known deleterious mutations, 1 suspected deleterious mutation and 3 novel indels. Only 3 BRCA1 mutations were detected in 2 cell lines, two known deleterious and 1 a novel 29 base pair deletion. One cell line thus appears to have both a germline and a somatic mutation. BRCA mutation status was associated with a trend to improved progression-free survival (PFS) in univariate analysis (p = 0.17). However, BRCA deficiency (defined by BRCA1/2 gene expression loss (4 tumors) and homozygous deletion (1 tumor) in addition to mutations) was associated with improved PFS in univariate (p = 0.04) and multivariate (p = 0.03) analyses. Conclusions: The frequency of BRCA1/2 mutations in ovarian tumors detected by sequencing regardless of family history is ≈20%, higher than the expected prevalence of germline mutations. In both BRCA1/2 genes, almost 25% of mutations in tumor tissue were novel and not previously seen in germline DNA. We are now sequencing corresponding germline DNA to determine the exact number of these novel mutations that are somatic. Direct analysis of ovarian tumor tissue is likely to expand the number of women with BRCA-deficient tumors beyond that detectable by germline sequencing.

[Table: see text]

Genome-wide association scan identifies a prostaglandin-endoperoxide synthase 2 variant involved in risk of knee osteoarthritis

Osteoarthritis (OA), the most prevalent form of arthritis in the elderly, is characterized by the degradation of articular cartilage and has a strong genetic component. Our aim was to identify genetic variants involved in risk of knee OA in women. A pooled genome-wide association scan with the Illumina550 Duo array was performed in 255 controls and 387 cases. Twenty-eight variants with p < 1 x 10(-5) were estimated to have probabilities of being false positives <or=0.5 and were genotyped individually in the original samples and in replication cohorts from the UK and the U.S. (599 and 272 cases, 1530 and 258 controls, respectively). The top seven associations were subsequently tested in samples from the Netherlands (306 cases and 584 controls). rs4140564 on chromosome 1 mapping 5' to both the PTGS2 and PLA2G4A genes was associated with risk of knee OA in all the cohorts studied (overall odds ratio OR(mh) = 1.55 95% C.I. 1.30-1.85, p < 6.9 x 10(-7)). Differential allelic expression analysis of PTGS2 with mRNA extracted from the cartilage of joint-replacement surgery OA patients revealed a significant difference in allelic expression (p < 1.0 x 10(-6)). These results suggest the existence of cis-acting regulatory polymorphisms that are in, or near to, PTGS2 and in modest linkage disequilibrium with rs4140564. Our results and previous studies on the role of the cyclooxygenase 2 enzyme encoded by PTGS2 underscore the importance of this signaling pathway in the pathogenesis of knee OA.

Identification of ZNF313/RNF114 as a novel psoriasis susceptibility gene

Psoriasis is an immune-mediated skin disorder that is inherited as a multifactorial trait. Linkage studies have clearly identified a primary disease susceptibility locus lying within the major histocompatibility complex (MHC), but have generated conflicting results for other genomic regions. To overcome this difficulty, we have carried out a genome-wide association scan, where we analyzed more than 408,000 SNPs in an initial sample of 318 cases and 288 controls. Outside of the MHC, we observed a single cluster of disease-associated markers, spanning 47 kb on chromosome 20q13. The analysis of two replication data sets confirmed this association, with SNP rs495337 yielding a combined P-value of 1.4 x 10(-8) in an overall sample of 2679 cases and 2215 controls. Rs495337 maps to the SPATA2 transcript and is in absolute linkage disequilibrium with five SNPs lying in the adjacent ZNF313 gene (also known as RNF114). Real-time PCR experiments showed that, unlike SPATA2, ZNF313 is abundantly expressed in skin, T-lymphocytes and dendritic cells. Furthermore, an analysis of the expression data available from the Genevar database indicated that rs495337 is associated with increased ZNF313 transcripts levels (P = 0.003), suggesting that the disease susceptibility allele may be a ZNF313 regulatory variant tagged by rs495337. Homology searches indicated that ZNF313 is a paralogue of TRAC-1, an ubiquitin ligase regulating T-cell activation. We performed cell-free assays and confirmed that like TRAC-1, ZNF313 binds ubiquitin via an ubiquitin-interaction motif (UIM). These findings collectively identify a novel psoriasis susceptibility gene, with a putative role in the regulation of immune responses.

A high quality draft consensus sequence of the genome of a heterozygous grapevine variety

Background

Worldwide, grapes and their derived products have a large market. The cultivated grape species Vitis vinifera has potential to become a model for fruit trees genetics. Like many plant species, it is highly heterozygous, which is an additional challenge to modern whole genome shotgun sequencing. In this paper a high quality draft genome sequence of a cultivated clone of V. vinifera Pinot Noir is presented.

Principal Findings

We estimate the genome size of V. vinifera to be 504.6 Mb. Genomic sequences corresponding to 477.1 Mb were assembled in 2,093 metacontigs and 435.1 Mb were anchored to the 19 linkage groups (LGs). The number of predicted genes is 29,585, of which 96.1% were assigned to LGs. This assembly of the grape genome provides candidate genes implicated in traits relevant to grapevine cultivation, such as those influencing wine quality, via secondary metabolites, and those connected with the extreme susceptibility of grape to pathogens. Single nucleotide polymorphism (SNP) distribution was consistent with a diffuse haplotype structure across the genome. Of around 2,000,000 SNPs, 1,751,176 were mapped to chromosomes and one or more of them were identified in 86.7% of anchored genes. The relative age of grape duplicated genes was estimated and this made possible to reveal a relatively recent Vitis-specific large scale duplication event concerning at least 10 chromosomes (duplication not reported before).

Conclusions

Sanger shotgun sequencing and highly efficient sequencing by synthesis (SBS), together with dedicated assembly programs, resolved a complex heterozygous genome. A consensus sequence of the genome and a set of mapped marker loci were generated. Homologous chromosomes of Pinot Noir differ by 11.2% of their DNA (hemizygous DNA plus chromosomal gaps). SNP markers are offered as a tool with the potential of introducing a new era in the molecular breeding of grape.

Sequence variants in the genes for the interleukin-23 receptor (IL23R) and its ligand (IL12B) confer protection against psoriasis

Psoriasis is an inflammatory skin disorder that is inherited as a multifactorial trait. Genetic analyses have repeatedly identified a primary disease susceptibility locus lying within the major histocompatibility complex (MHC), on chromosome 6p21. A small number of non-MHC susceptibility loci have also been identified. These regions tend to overlap with susceptibility intervals for Crohn's disease and atopic dermatitis, suggesting the possibility that genetic variants affecting inflammatory pathways may contribute to the pathogenesis of multiple disorders. Here, we report a genetic analysis of the interleukin 23 receptor gene (IL23R), which was recently identified as a susceptibility determinant for Crohn's disease. We initially examined the results of a whole-genome association scan, carried out on 318 cases and 288 controls. We observed a significant increase of a non-synonymous substitution (p.Arg381Gln) among controls (P = 0.00036). We validated this finding by extending our cohort to include a further 519 cases and 528 controls. In the overall sample, the frequency of the 381Gln allele was 3.6% in cases and 7% in controls, yielding a P value of 0.00014. Next, we examined genetic variation at the IL12RB1, IL23A and IL12B genes, respectively, encoding the second subunit of the IL23R receptor and the two subunits of its ligand. This analysis identified independent associations for IL12B SNPs rs10045431 (P value for the extended dataset = 0.0001) and rs3212227 (P = 0.036). Altogether, these findings indicate that genes participating in IL23 signalling play a significant role in the pathogenesis of chronic epithelial inflammation.

Association of familial and sporadic rheumatoid arthritis with a single corticotropin-releasing hormone genomic region (8q12.3) haplotype

OBJECTIVE

Rheumatoid arthritis (RA) is a common disabling autoimmune disease with a complex genetic component. We have previously described linkage of a region of chromosome 8q12.3 with RA and association of the microsatellite marker CRHRA1 with RA in 295 affected sibling-pair families. In the current study we aimed to physically link the RA-associated marker with the corticotropin-releasing hormone (CRH) candidate gene, and to examine the genomic region for additional short tandem repeat (STR) genetic markers in order to clarify the association with RA.

METHODS

We examined the association of 2 STR markers with disease in the original 295 multicase families and in a cohort of 131 simplex families to refine our understanding of this genetic region in disease susceptibility in sporadic and familial RA. Genomic library screening and sequencing were used to generate physical sequences in the CRH genomic region. Bioinformatic analysis of the sequence flanking the CRH structural gene was used to screen for additional STRs and other genetic features. Genotyping was carried out using a standard fluorescence approach. Estimations of haplotype frequencies were performed to assess linkage disequilibrium. The transmission disequilibrium test was performed using TRANSMIT.

RESULTS

Physical cloning and sequencing analyses identified the genomic region linking the CRHRA1 marker and the CRH structural locus. Moreover, we identified a further STR, CRHRA2, which was in strong linkage disequilibrium with CRHRA1 (P = 4.0 x 10(-14)). A haplotype, CRHRA1*10;CRHRA2*14, was preferentially carried by unaffected parents at a frequency of 8.6% compared with the expected frequency of 3.1%. This haplotype was overtransmitted in the multiply affected families (P = 0.0077) and, similarly, in the simplex families (P = 0.024). Combined analysis of both family cohorts confirmed significant evidence for linkage (P = 4.9 x 10(-4)) and association (P = 5.5 x 10(-3)) for this haplotype with RA.

CONCLUSION

In demonstrating significant linkage disequilibrium between these 2 markers, we have refined the disease-associated region to a single haplotype and confirmed the significance of this region in our understanding of the genetics of RA.

The glucocorticoid inhibition of LFA-1 and CD2 expression by human mononuclear cells is reversed by IL-2, IL-7 and IL-15

Glucocorticoids are agents endowed with powerful immunosuppressive and anti-inflammatory properties partially related to the inhibition of adhesion-related processes. We have previously demonstrated that glucocorticoids inhibit LFA-1 and CD2 expression in human peripheral blood mononuclear cells (PBMC) by down-regulating mRNA steady-state levels. In this study, we investigated whether glucocorticoids could also act indirectly by modulating the effect/function of cytokines whose expression are known to inhibit. To test this hypothesis, we replenished the following cytokines IL-2, IL-7, IL-15, TNF-alpha, IL-1beta, IL-4 and IL-10, in an in vitro PBMC culture system. Our results indicate that only the IL-2Rgamma-chain-dependent cytokines IL-2, IL-7 and IL-15, among the cytokines of this panel, could reverse the inhibition of glucocorticoids on PBMC adhesion molecule expression and the related functions of intercellular aggregation and proliferation. Furthermore, we also demonstrated that IL-2, IL-7 and IL-15 could induce de novo the synthesis of LFA-1 and CD2. Taken together, these data suggest that glucocorticoids inhibit PBMC LFA-1 and CD2 expression not only directly by modulating transcriptional events, but also indirectly through the inhibition of IL-2Rgamma-dependent cytokines.

Are differences in interleukin 10 production associated with joint damage?

OBJECTIVE

Constitutive differences between individuals in cytokine production may determine the variation in the course of inflammatory arthritis.

METHODS

The association between interleukin 10 (IL-10) production and joint destruction was studied by comparing IL-10 mRNA content in synovial biopsies from seven patients with destructive joint disease and six patients with non-destructive joint disease. The IL-10 mRNA content was 0.4 +/- 0.6 arbitrary units in erosive joints compared with 2.3 +/- 1.2 arbitrary units in non-erosive joints (P: < 0.03, Mann-Whitney U:-test). As this difference suggested that IL-10 production was associated with joint destruction, we tested whether the IL-10 locus determined the extent of joint damage.

RESULTS

Innate differences in IL-10 production are locus-dependent. In line with these data, we showed that innate differences in IL-10 protein production were also present as differences in IL-10 mRNA levels. We tested if polymorphisms in the promoter of IL-10 were associated with the extent of joint damage.

DISCUSSION

In a cohort study of female rheumatoid arthritis patients followed for 12 yr, the extent of joint destruction differed significantly between patients with different IL-10 genotypes. In patients with the -1082AA genotype who were studied prospectively, the mean increase in radiographic damage score (modified Sharp score of X-rays of hands and feet) during the first 6 yr was 9 +/- 9 per yr vs 19 +/- 16 per yr for patients with the genotype -1082GG (P: < 0.02). In line with these data, cultures of endotoxin-stimulated whole blood from 158 donors showed that the presence of the allele associated with less joint destruction correlated with slightly higher IL-10 production.

CONCLUSIONS

Both the immunogenetic and the synovial biopsies suggest that a variation in IL-10 production is associated with joint destruction.

Analysis of T cell receptor V alpha polymorphisms in rheumatoid arthritis

OBJECTIVE

To test for association of T cell receptor (TCR) V alpha polymorphisms and rheumatoid arthritis (RA) in British and Swiss white populations.

METHODS

TCRAV polymorphisms were analysed in RA patients and controls by single strand conformational polymorphism (SSCP) analysis. Associations were sought between defined genotypes and RA, and the effect of HLA-DR4 status analysed. Putative associations were then retested further in new groups of patients and controls. Overall, 360 RA patients and 197 controls were studied.

RESULTS

No association between TCRAV5S1, V6S1, V8S1, V17S1 or V21S1 polymorphisms and RA were observed in the initial population screened. Stratification for DR4 status showed an increase of V5S1*01/*01 in DR4 positive versus DR4 negative patients (chi 2 = 7.19, p = 0.028 (2df), p = 0.14 after correction for multiple comparisons). This putative association was tested in three further patient groups, none of which showed significant increase of V5S1*01/*01 in DR4 positive patients, although an overall trend towards an increase in V5S1*01/*01 was observed.

CONCLUSION

No evidence was found for a strong association of TCRAV genes and RA in a white population. However, these results suggest a weak association of V5S1*01/*01 with DR4 positive RA, although this requires confirmation using larger groups of patients and controls.

Corticosteroids inhibit lymphocyte binding to endothelium and intercellular adhesion: an additional mechanism for their anti-inflammatory and immunosuppressive effect

Glucocorticosteroids (GCS) are potent anti-inflammatory and immunosuppressive agents widely used in the treatment of many medical conditions, but their mechanism of action is not yet fully understood. Some of the anti-inflammatory effects of GCS have been attributed to the synthesis of lipocortins, whereas the immunosuppressive effects are thought to be mediated through the inhibition of several immune functions through a down-regulation of cytokine gene expression. Another important mechanism of action of GCS may relate to their ability to interfere with the phenomena of adhesion and migration of inflammatory cells. In this study, the direct effects of GCS on lymphocyte adhesion capacity in vitro were investigated. We demonstrate that GCS inhibit lymphocyte adhesion to endothelium through the down-modulation of lymphocyte adhesion molecules. We also provide evidence that GCS inhibit cell aggregate formation induced by TCR ligation, which directly correlates with the down-modulation of LFA-1 and CD2, but not LFA-3 or ICAM-1. Such down-modulation was paralleled by a decrease in the steady state mRNA level of LFA-1 and CD2 gene products, which suggests a direct GCS control of the expression of these genes. Finally, we show that GCS effects are mediated through the GCS receptor, since they can be completely reversed by the GCS-R antagonist RU-486. This study supports the concept that some of the immunosuppressive and anti-inflammatory effects of GCS are likely to be exerted by the inhibition of adhesion-dependent lymphocyte functions.

Corticosteroids inhibit lymphocyte binding to endothelium and intercellular adhesion: an additional mechanism for their anti-inflammatory and immunosuppressive effect

Glucocorticosteroids (GCS) are potent anti-inflammatory and immunosuppressive agents widely used in the treatment of many medical conditions, but their mechanism of action is not yet fully understood. Some of the anti-inflammatory effects of GCS have been attributed to the synthesis of lipocortins, whereas the immunosuppressive effects are thought to be mediated through the inhibition of several immune functions through a down-regulation of cytokine gene expression. Another important mechanism of action of GCS may relate to their ability to interfere with the phenomena of adhesion and migration of inflammatory cells. In this study, the direct effects of GCS on lymphocyte adhesion capacity in vitro were investigated. We demonstrate that GCS inhibit lymphocyte adhesion to endothelium through the down-modulation of lymphocyte adhesion molecules. We also provide evidence that GCS inhibit cell aggregate formation induced by TCR ligation, which directly correlates with the down-modulation of LFA-1 and CD2, but not LFA-3 or ICAM-1. Such down-modulation was paralleled by a decrease in the steady state mRNA level of LFA-1 and CD2 gene products, which suggests a direct GCS control of the expression of these genes. Finally, we show that GCS effects are mediated through the GCS receptor, since they can be completely reversed by the GCS-R antagonist RU-486. This study supports the concept that some of the immunosuppressive and anti-inflammatory effects of GCS are likely to be exerted by the inhibition of adhesion-dependent lymphocyte functions.

Antigen-specific T cell recognition of affinity-purified and recombinant thyroid peroxidase in autoimmune thyroid disease

The T cell proliferative responses of peripheral blood lymphocytes from 20 patients with autoimmune thyroid disease (AITD) and 20 healthy controls were analysed to immunoaffinity-purified thyroid peroxidase (TPO) and recombinant antigen preparations generated in Escherichia coli as glutathione-s-transferase fusion proteins. The epitope specificity of the T cell response was investigated using a selection of eight discrete recombinant fragments encompassing the whole of the extracellular region of the TPO molecule. Significant differences in the proliferative responses between patients and controls were observed to the full length, affinity-purified TPO molecule (P less than 0.002) as well as to the recombinant fragments R1c (residues 145-250) (P less than 0.001) and R2b (residues 457-589) (P less than 0.001) suggesting the presence of at least two distinct T cell determinants on this autoantigen. One of these T cell epitopes, localized within the region R1c, has not previously been identified by studies with synthetic peptides.