Endocrine Therapy Synergizes with SMAC Mimetics to Potentiate Antigen Presentation and Tumor Regression in Hormone Receptor-Positive Breast Cancer

Immunotherapies have yet to demonstrate significant efficacy in the treatment of hormone receptor-positive (HR+) breast cancer. Given that endocrine therapy (ET) is the primary approach for treating HR+ breast cancer, we investigated the effects of ET on the tumor immune microenvironment (TME) in HR+ breast cancer. Spatial proteomics of primary HR+ breast cancer samples obtained at baseline and after ET from patients enrolled in a neoadjuvant clinical trial (NCT02764541) indicated that ET upregulated β2-microglobulin and influenced the TME in a manner that promotes enhanced immunogenicity. To gain a deeper understanding of the underlying mechanisms, the intrinsic effects of ET on cancer cells were explored, which revealed that ET plays a crucial role in facilitating the chromatin binding of RelA, a key component of the NF-κB complex. Consequently, heightened NF-κB signaling enhanced the response to interferon-gamma, leading to the upregulation of β2-microglobulin and other antigen presentation-related genes. Further, modulation of NF-κB signaling using a SMAC mimetic in conjunction with ET augmented T-cell migration and enhanced MHC-I-specific T-cell-mediated cytotoxicity. Remarkably, the combination of ET and SMAC mimetics, which also blocks prosurvival effects of NF-κB signaling through the degradation of inhibitors of apoptosis proteins, elicited tumor regression through cell autonomous mechanisms, providing additional support for their combined use in HR+ breast cancer.

SIGNIFICANCE

Adding SMAC mimetics to endocrine therapy enhances tumor regression in a cell autonomous manner while increasing tumor immunogenicity, indicating that this combination could be an effective treatment for HR+ patients with breast cancer.

Molecular profiling of aromatase inhibitor sensitive and resistant ER+HER2- postmenopausal breast cancers

Aromatase inhibitors (AIs) reduce recurrences and mortality in postmenopausal patients with oestrogen receptor positive (ER+) breast cancer (BC), but >20% of patients will eventually relapse. Given the limited understanding of intrinsic resistance in these tumours, here we conduct a large-scale molecular analysis to identify features that impact on the response of ER + HER2- BC to AI. We compare the 15% of poorest responders (PRs, n = 177) as measured by proportional Ki67 changes after 2 weeks of neoadjuvant AI to good responders (GRs, n = 190) selected from the top 50% responders in the POETIC trial and matched for baseline Ki67 categories. In this work, low ESR1 levels are associated with poor response, high proliferation, high expression of growth factor pathways and non-luminal subtypes. PRs having high ESR1 expression have similar proportions of luminal subtypes to GRs but lower plasma estradiol levels, lower expression of estrogen response genes, higher levels of tumor infiltrating lymphocytes and immune markers, and more TP53 mutations.

The proteomic landscape of soft tissue sarcomas

Soft tissue sarcomas (STS) are rare and diverse mesenchymal cancers with limited treatment options. Here we undertake comprehensive proteomic profiling of tumour specimens from 321 STS patients representing 11 histological subtypes. Within leiomyosarcomas, we identify three proteomic subtypes with distinct myogenesis and immune features, anatomical site distribution and survival outcomes. Characterisation of undifferentiated pleomorphic sarcomas and dedifferentiated liposarcomas with low infiltrating CD3 + T-lymphocyte levels nominates the complement cascade as a candidate immunotherapeutic target. Comparative analysis of proteomic and transcriptomic profiles highlights the proteomic-specific features for optimal risk stratification in angiosarcomas. Finally, we define functional signatures termed Sarcoma Proteomic Modules which transcend histological subtype classification and show that a vesicle transport protein signature is an independent prognostic factor for distant metastasis. Our study highlights the utility of proteomics for identifying molecular subgroups with implications for risk stratification and therapy selection and provides a rich resource for future sarcoma research.

Abstract PD10-07: PD10-07 Low plasma estradiol, low expression of estrogen responsive genes and TP53 mutations are associated with poor anti-proliferative response to aromatase inhibitors

Background: Aromatase inhibitors (AIs) are highly effective at reducing recurrences and mortality in postmenopausal patients with estrogen receptor positive breast cancer (ER+ BC). Poor anti-proliferative (Ki67) response or ER+ BCs to AIs after 2 weeks is associated with worse long-term outcomes. Factors that relate to the degree of the response may identify markers and/or mechansims of resistance. Methods: The PeriOperative Endocrine Therapy for Individualizing Care (POETIC) trial randomized 4,480 with ER+ BC to 2 weeks’ AI before surgery or no presurgical treatment. All patients within the bottom 15% of Ki67 responders to AI (poor responders [PRs]; n=177 with RNA extracted) were selected from and matched to good responders (GRs) within the 50% showing the best response (n=190). Matching was based on baseline Ki67 levels as measured by immunohistochemistry (IHC). Response to AI was measured by the percentage change in Ki67 after 2 weeks’ treatment. PRs were further divided into groups expressing high ESR1 (PRs ESR1HIGH; n=119) and low ESR1 (PRs ESR1LOW; n=58) levels since there were very few GRs with low ESR1. RNAseq, targeted exome DNA sequencing of 87 BC/resistance related genes and measurement of plasma estradiol levels by mass spectrometry were performed to understand mechanisms of de novo resistance. Intrinsic subtypes were estimated from RNAseq data. Results: More than 90% of PRs ESR1LOW were non-luminal subtypes with low expression of estrogen-responsive genes. In contrast, 11% of PRs ESR1HIGH were non-luminal compared to 4% of GRs but only HER2-enriched subtypes were significantly higher in PR ESR1HIGH (p=0.05, Fisher exact). While AI treatment had limited impact on Ki67 IHC values in PRs ESR1HIGH, PGR expression was more than 2-fold lower after 2 weeks of AI. Gene-set enrichment analysis showed significantly lower expression of estrogen-response genes in PRs ESR1HIGH compared to GRs (FDR< 10-9) at baseline despite similar percentage of Luminal subtypes in PRs ESR1HIGH and GRs. Plasma estradiol levels were correlated with expression of estrogen-response genes (FDR=0.01) and levels were significantly lower in PRs ESR1HIGH compared to GRs (p=0.003, Mann Whitney). PRs ESR1HIGH had significantly more mutations in RB1, TP53, ARID1B and DNAH11 genes (p< 0.05, Fisher exact). TP53 mutations were significantly enriched in Luminal-A PRs ESR1HIGH compared to GRs (22% and 3% respectively; p=0.003, Fisher exact), but not in Luminal-B tumors (23% and 15% mutated respectively). Discussion and conclusions: In approximately 33% of PRs, de novo AI resistance was associated with and most likely due to low expression of ER/ESR1 and estrogen-responsive genes in non-luminal tumors. In the remaining tumors, AI treatment still impacted some estrogen responsive genes but had limited downstream impact on suppressing proliferation. This might be due to mutations including in TP53 that limit suppression of proliferation downstream of estrogen signaling. The proportion of Luminal tumors in GRs and PRs ESR1HIGH was similar, suggesting better outcome of Luminal-A tumors on AI is likely due to their better intrinsic prognosis rather than better response to endocrine therapy.

Citation Format: Eugene F. Schuster, Elena López-Knowles, Anastasia Alataki, Lila Zabaglo, Elizabeth Folkerd, David Evans, Kally Sidhu, Holly Tovey, Perry Maxwell, Nicholas Turner, Stephen Johnston, Manuel Salto-Tellez, Maggie Chon U Cheang, John Robertson, Ian Smith, Judith Bliss, Mitch Dowsett. PD10-07 Low plasma estradiol, low expression of estrogen responsive genes and TP53 mutations are associated with poor anti-proliferative response to aromatase inhibitors [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD10-07.

Relationship between ER expression by IHC or mRNA with Ki67 response to aromatase inhibition: a POETIC study

BACKGROUND

In clinical practice, oestrogen receptor (ER) analysis is almost entirely by immunohistochemistry (IHC). ASCO/CAP recommends cut-offs of < 1% (negative) and 1-10% (low) cells positive. There is uncertainty whether patients with ER low tumours benefit from endocrine therapy. We aimed to assess IHC and mRNA cut-points for ER versus biological response of primary breast cancer to 2 weeks' aromatase inhibitor treatment as measured by change in Ki67.

METHODS

Cases were selected from the aromatase inhibitor treatment group of POETIC. We selected the 15% with the poorest Ki67 response (PR, < 40% Ki67 suppression, n = 230) and a random 30% of the remainder categorised as intermediate (IR, 40-79% Ki67 suppression, n = 150) and good-responders (GR, ≥ 80% Ki67 suppression, n = 230) from HER2 - group. All HER2 + cases available were selected irrespective of their response category (n = 317). ER expression was measured by IHC and qPCR.

RESULTS

ER IHC was available from 515 HER2 - and 186 HER2 + tumours and ER qPCR from 367 HER2 - and 171 HER2 + tumours. Ninety-one percentage of patients with ER IHC < 10% were PRs with similar rates in HER2 - and HER2 + cases. At or above ER IHC 10% substantial numbers of patients showed IR or GR. Similar proportions of patients were defined by cut-points of ER IHC < 10% and ER mRNA < 5 units. In addition, loss of PgR expression altered ER anti-proliferation response with 92% of PgR - cases with ER IHC < 40% being PRs.

CONCLUSIONS

There was little responsiveness at IHC < 10% and no distinction between < 1% and 1-10% cells positive. Similar separation of PRs from IR/GRs was achieved by IHC and mRNA.

HER2-enriched subtype and novel molecular subgroups drive aromatase inhibitor resistance and an increased risk of relapse in early ER+/HER2+ breast cancer

BACKGROUND

Oestrogen receptor positive/ human epidermal growth factor receptor positive (ER+/HER2+) breast cancers (BCs) are less responsive to endocrine therapy than ER+/HER2- tumours. Mechanisms underpinning the differential behaviour of ER+HER2+ tumours are poorly characterised. Our aim was to identify biomarkers of response to 2 weeks' presurgical AI treatment in ER+/HER2+ BCs.

METHODS

All available ER+/HER2+ BC baseline tumours (n=342) in the POETIC trial were gene expression profiled using BC360™ (NanoString) covering intrinsic subtypes and 46 key biological signatures. Early response to AI was assessed by changes in Ki67 expression and residual Ki67 at 2 weeks (Ki672wk). Time-To-Recurrence (TTR) was estimated using Kaplan-Meier methods and Cox models adjusted for standard clinicopathological variables. New molecular subgroups (MS) were identified using consensus clustering.

FINDINGS

HER2-enriched (HER2-E) subtype BCs (44.7% of the total) showed poorer Ki67 response and higher Ki672wk (p<0.0001) than non-HER2-E BCs. High expression of ERBB2 expression, homologous recombination deficiency (HRD) and TP53 mutational score were associated with poor response and immune-related signatures with High Ki672wk. Five new MS that were associated with differential response to AI were identified. HER2-E had significantly poorer TTR compared to Luminal BCs (HR 2.55, 95% CI 1.14-5.69; p=0.0222). The new MS were independent predictors of TTR, adding significant value beyond intrinsic subtypes.

INTERPRETATION

Our results show HER2-E as a standardised biomarker associated with poor response to AI and worse outcome in ER+/HER2+. HRD, TP53 mutational score and immune-tumour tolerance are predictive biomarkers for poor response to AI. Lastly, novel MS identify additional non-HER2-E tumours not responding to AI with an increased risk of relapse.

FUNDING

Cancer Research UK (CRUK/07/015).

Impact of Duration of Neoadjuvant Aromatase Inhibitors on Molecular Expression Profiles in Estrogen Receptor-positive Breast Cancers

PURPOSE

Aromatase inhibitor (AI) treatment is the standard of care for postmenopausal women with primary estrogen receptor-positive breast cancer. The impact of duration of neoadjuvant endocrine therapy (NET) on molecular characteristics is still unknown. We evaluated and compared changes of gene expression profiles under short-term (2-week) versus longer-term neoadjuvant AIs.

EXPERIMENTAL DESIGN

Global gene expression profiles from the PeriOperative Endocrine Therapy for Individualised Care (POETIC) trial (137 received 2 weeks of AIs and 47 received no treatment) and targeted gene expression from 80 patients with breast cancer treated with NET for more than 1 month (NeoAI) were assessed. Intrinsic subtyping, module scores covering different cancer pathways and immune-related genes were calculated for pretreated and posttreated tumors.

RESULTS

The differences in intrinsic subtypes after NET were comparable between the two cohorts, with most Luminal B (90.0% in the POETIC trial and 76.3% in NeoAI) and 50.0% of HER2 enriched at baseline reclassified as Luminal A or normal-like after NET. Downregulation of proliferative-related pathways was observed after 2 weeks of AIs. However, more changes in genes from cancer-signaling pathways such as MAPK and PI3K/AKT/mTOR and immune response/immune-checkpoint components that were associated with AI-resistant tumors and differential outcome were observed in the NeoAI study.

CONCLUSIONS

Tumor transcriptional profiles undergo bigger changes in response to longer NET. Changes in HER2-enriched and Luminal B subtypes are similar between the two cohorts, thus AI-sensitive intrinsic subtype tumors associated with good survival might be identified after 2 weeks of AI. The changes of immune-checkpoint component expression in early AI resistance and its impact on survival outcome warrants careful investigation in clinical trials.

Abstract PD15-03: Overlapping molecular features (proliferation, immune signatures andTP53mutations) associated with palbociclib resistance inER+HER2- primary breast cancer

Background: Cyclin-dependent kinase 4/6 (CDK4/6) inhibitors in combination with anti-hormone therapy are highly effective treatments for oestrogen receptor positive (ER+) and HER2 negative (HER2-) advanced breast cancer. Pre-clinical and clinical studies have reported mechanisms of resistance to CDK4/6 inhibitors to include interferon signalling, high CCNE1 expression and loss of RB1 expression. The PALLET phase II randomized neoadjuvant trial of letrozole (LET) ± palbociclib (PALBO) in postmenopausal ER+HER2- primary breast cancer showed that suppression of proliferation as measured by Ki67 was significantly greater with addition of PALBO to LET but did not result in all patients achieving complete cell-cycle arrest, indicating intrinsic resistance in some patients. We report phenotypes/genotypes associated with that resistance. Methods: In the PALLET trial, 307 patients were randomized to LET+PALBO (n=204) or LET (n=103) for 14wks. For the first 2wks of LET+PALBO patients were randomised to LET, PALBO or LET+PALBO. RNA-seq of baseline samples from consented patients was performed on fresh frozen biopsies for 224 patients (LET-only n=77; LET+PALBO n=147); whole exome sequencing was performed on 188 tumors and matched blood samples (LET-only n=61; LET+PALBO n=127). After 14wks of treatment, those patients with Ki67% &lt; 2.7% were classified as having complete cell-cycle arrest (CCCA). Differentially expressed genes (DEGs) were identified between patients sensitive (CCCA) and resistant (non-CCCA) to treatments with or without PALBO at 14wks by DESeq2. Mutect2 and VarScan was used to identify somatic mutations and CNVkit was used to identify copy number alterations in whole exome sequencing (WES). Results: In LET+PALBO treated patients, higher expression of E2F targets, interferon gamma response and mTORC1 signalling genes were observed in baseline gene expression of non-CCCA patients at 14wks (FDR&lt;0.05, GSEA). Similar results were also observed if using 2wk Ki67 data. In LET-only non-CCCA patients, higher expression of mTORC1 signalling and lower expression of oestrogen response genes (FDR&lt;0.05, GSEA) were observed. Additional analysis of baseline gene expression for non-CCCA at 14wks LET+PALBO patients showed higher expression of immune checkpoint inhibition associated genes including IFNG, IDO1, PD-L1 (FDR&lt;0.05, DESeq2), higher expression of genes expressed only in immune cells and two gene signatures related to interferon signalling and immune checkpoint blockade (FDR&lt;0.05, GSEA). Somatic mutation analysis showed a trend for enrichment of mutations in TP53 for both LET-only and LET+PALBO non-CCCA patients (p=0.02 and p=0.06, respectively, Fisher-exact) and significant enrichment of MAP3K1 mutations in LET-only CCCA patients (p&lt;0.05, Fisher-exact). TP53 mutations were also associated with higher proliferation, mTORC1 and immune related signatures (all p&lt;0.01, Mann-Whitney). Change at 14wks Ki67 was significantly different (p=0.02, Mann-Whitney) between TP53wt and TP53MUT for LET-only patients (median WT = -92%, MUT = -66%, p=0.02, Mann-Whitney ) but not for LET+PALBO (median WT = -99% MUT = -95%, p=0.13, Mann-Whitney). No copy number alterations were significantly enriched in LET+PALBO non-CCCA patients. Conclusion: We observe, confirming previous studies, an association of CDK4/6 inhibitor resistance, high expression of CCNE1 and genes related to interferon gamma signalling. We show that there is an overlap between resistance mechanisms and TP53 mutations. However, ER+HER2- patients with TP53 mutations may still benefit from PALBO adding to suppression of proliferation compared to LET-only treatment.

Citation Format: Eugene F Schuster, Hui Xiao, Maggie Cheang, Elena Lopez-Knowles, Lucy Kilburn, Viktoriya Korchina, Sejal Salvi, Samuel A Jacobs, Melanie Finnigan, David A Wheeler, Shannon Puhalla, Donna Muzny, Harsha Doddapaneni, Katherine Pogue-Geile, Yuan Liu, Judith Bliss, Stephen Johnston, Mitch Dowsett, Mothaffar Rimawi, On behalf of the PALLET Trialists. Overlapping molecular features (proliferation, immune signatures andTP53mutations) associated with palbociclib resistance inER+HER2- primary breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr PD15-03.

Abstract PD2-07: Impact of using cross-platform gene expression profiling technologies and computational methods for intrinsic breast cancer subtyping in PALOMA-2 and PALLET

Background Intrinsic breast cancer molecular subtyping (IBCMS) provides significant prognostic information for patients (pts) with breast cancer (BC) treated with chemotherapy, human epidermal growth factor receptor 2 (HER2) targeted therapies, and endocrine therapies (ETs). Classifying tumors into intrinsic subtypes to determine optimal treatment is often applied using PAM50, commercially known as Prosigna. Meanwhile, Absolute Assignment of Breast Cancer Intrinsic Molecular Subtypes (AIMS) computational method was trained to predict PAM50-based IBCMS. As the PAM50 algorithm was developed to capture the major subtypes in a general pt population, clinicopathologic distribution of the study cohort and technology platform calibration should be considered in IBCMS analyses. This study compared different next-generation sequencing technologies and methodologic approaches of PAM50 on tumor samples from 2 randomized trials of postmenopausal women with estrogen receptor-positive (ER+)/HER2-negative (HER2-) BC. Methods PALOMA-2 is a double-blind, randomized study of first-line palbociclib (PAL) + letrozole (LET) for ER+/HER2- advanced BC (ABC). Tumor samples from consented pts were subtyped using the validated RUO PAM50 assay (ruoProsigna, NanoString); results were compared with published subtype results using AIMS on EdgeSeq Oncology Biomarker Panel (HTG Molecular Diagnostics). PALLET is a phase 2, randomized trial of PAL+LET as neoadjuvant therapy in pts with ER+ HER2- BC. Baseline frozen tumor biopsies underwent whole transcriptome mRNA-sequencing (mRNA-seq). IBCMS was performed using AIMS; PAM50 subtyping was performed on data normalised with subgroup-specific gene centering and microarray-RNA-sequencing calibration. Results In PALOMA-2, 222 pts had both ruoProsigna and AIMS data; an overall 54% agreement rate between methods was observed, with 46% (56/121) of Luminal B (LumB) subtype by ruoProsigna assigned as Luminal A (LumA) by AIMS and 67% (6/9) of basal-like by ruoProsigna as HER2-enriched (HER2-E) by AIMS (Table 1). In PALLET, 224 pts had mRNA-seq data; a 69% agreement between the two approaches (AIMS and PAM50) was observed, with only 4% (2/49) of LumB assigned as LumA by AIMS but 17% (26/156) and 16% (25/156) of LumA considered LumB or normal-like by AIMS, respectively. Progression-free survival (PFS) by ruoProsigna-derived subtype in PALOMA-2 showed that PAL+LET benefited all pts but those with a basal-like subtype (Table 2). With AIMS, PAL+LET provided a PFS benefit in pts with LumA and LumB subtypes, but was less effective in the HER2-E subtype. Conclusion Intrinsic subtyping has potential clinical utility. PAL+ET should be considered for ER+/HER2- ABC, except possibly in pts with a basal-like tumor, consistent with previous reports. A standardized clinical PAM50 assay and bioinformatics approach should be used as discrepancies in gene expression platforms and algorithms lead to different results and could misguide treatment decisions. Clinical trial identification: Pfizer (NCT01740427)

Table 1.Intrinsic Subtyping by IBCMS MethodsPALOMA-2PALLETMethodruoProsignaPAM50 mRNAseqAIMS BasalHER2LumALumBGrand TotalBasalHER2LumALumBNormalGrand TotalBasal-like, n (%)1 (11)NANANA13 (75)0001 (8)4HER2-E, n (%)6 (67)6 (30)6 (8)13 (10)311 (25)3 (100)8 (5)6 (12)1 (8)19LumA, n (%)NA2 (10)60 (83)56 (46)1180097 (62)2 (4)099LumB, n (%)2 (22)12 (60)3 (4)52 (43)690026 (17)41 (84)067Normal-like, n (%)NANA3 (4)NA30025 (16)010 (83)35Grand Total9 (100)20 (100)72 (100)121 (100)2224 (100)3 (100)156 (100)49 (100)12 (100)224NA=Not available

Table 2.Median PFS statistics by subtype in PALOMA-2PAL+LET PFS, monthsPBO+LET PFS, monthsHazard Ratio(95% CI)P ValueruoProsignaBasal-like8.2 (n=5)3.6 (n=4)0.39 (0.09-1.77)0.206HER2-E11.0 (n=12)5.1 (n=8)0.41 (0.15-1.11)0.071LumA37.2 (n=52)13.6 (n=20)0.42 (0.21-0.84)0.011LumB27.6 (n=79)13.8 (n=42)0.63 (0.40-1.00)0.049AIMSBasal-likeNANANANAHER2-E16.4 (n=21)8.4 (n=10)0.82 (0.32-2.1)0.684LumA30.6 (n=84)16.5 (n=34)0.56 (0.33-0.95)0.029LumB19.3 (n=41)8.8 (n=28)0.39 (0.23-0.67)&lt;0.001NA=Not available; PBO=placebo

Citation Format: Maggie Cheang, Mitch Dowsett, Mothaffar Rimawi, Stephen Johnston, Samuel Jacobs, Judith Bliss, Katherine Pogue-Geile, Lucy Kilburn, Zhou Zhu, Eugene F. Schuster, Hui Xiao, Lisa Swaim, Shibing Deng, Dongrui R. Lu, Eric Gauthier, Jennifer Tursi, Dennis J. Slamon, Hope S. Rugo, Richard S. Finn, Yuan Liu. Impact of using cross-platform gene expression profiling technologies and computational methods for intrinsic breast cancer subtyping in PALOMA-2 and PALLET [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr PD2-07.

Abstract PS5-01: Biomarkers of resistance to palbociclib in ER+ primary breast cancer in the PALLET trial

Background: CDK4/6 inhibitors are being used in combination with aromatase inhibitors as therapy for advanced ER+ breast cancer (BC) and are being explored for use in primary BC. Few mechanisms driving resistance to added CDK4/6 inhibitors have been defined. The PALLET phase II randomized neoadjuvant trial of letrozole (LET) ± palbociclib (PALBO) in postmenopausal ER+HER2- primary BC reported that clinical response rate over 14wks was not significantly increased by adding PALBO to LET but suppression of Ki67 was significantly increased (Johnston et al, JCO 2018, 37, 178): after 14wks complete cell cycle arrest (CCCA, Ki67&lt;2.7%) was present in 59% on LET and 90% on LET+PALBO. Here we sought to identify biomarkers of de novo resistance to allow selection of patients most likely to benefit from added PALBO.

Methods: 307 patients were randomized to LET (n=103) or LET+PALBO (n=204) for 14 wks. The first 2wks of LET+PALBO patients were randomised to LET, PALBO, or LET+PALBO. Biopsies were taken at baseline, 2wks and 14wks. Biomarker data are presented here for baseline only, other than Ki67 at both baseline and 14wks. IHC analyses were conducted on FFPE biopsies for ER, PgR, RB1, cyclin-E1, and cyclin-D1 (also FISH). RNA-seq was performed on fresh frozen biopsies. Association of each biomarker with CCCA was determined by logistic regression. Differentially expressed genes (DEGs) were identified between patients sensitive (CCCA) (n=94) and resistant (non-CCCA) (n=10) to treatments with or without PALBO at 14wks by DESeq2. Fifty hallmark gene sets were tested for significant enrichment with DEGs and differential gene sets were identified by using Gene Set Enrichment Analysis (GSEA).

Results: The association of IHC biomarkers with CCCA is shown in the table. Lower levels of ER, higher levels of cyclin-E1, and amplification of cyclin-D1 were each significantly associated with a greater chance of non-CCCA with LET+PALBO. High cyclin-E1 levels were also associated with reduced chance of CCCA with LET only. Patients with high baseline Ki67 also exhibited higher non-CCCA with LET+PALBO at 14wks (p=0.0002). In the RNAseq data we identified 1973 DEGs between the 14wk CCCA and non-CCCA patients for LET+PALBO. E2F and MYC targets, PI3K/AKT/MTOR signalling and interferon response gene sets were among the hallmark gene sets enriched for genes with higher expression in non-CCCA patients at 14wks for LET+PALBO (FDR&lt;0.05). For LET-only, 311 DEGs were identified and the “Estrogen Response Early” gene set was significantly enriched in genes with higher expression in CCCA samples. At the individual gene level, genes significantly associated with non-CCCA after 14wks LET+PALBO included CCNE1, CDK2 and several E2F-related genes (p&lt;0.05). Their expression was not significantly different between non-CCCA and CCCA patients with LET alone.

Conclusion: Biomarkers associated with response/resistance to added PALBO were different from LET only. PALBO resistance was associated with higher baseline expression of cyclin-E1 (both IHC and RNA), CDK2, and genes related to E2F, MYC, interferon and MTOR signalling. These results suggest that multiple identifiable mechanisms of de novo resistance to PALBO are likely to exist in primary ER+ BC. On-going WES analyses will allow the significance of alterations at the DNA level to be presented.

Table 1.Continuous measurement in a logistic regression for CCCA at 14 weeks; Oddsratio calculated separately for group A and groups B,C,D and were adjusted forregion (UK vs NA); * amplified vsnon-amplifiedContinuous measurement in a logistic regression for CCCA at 14 weeksBiomarkerLET LET+PALBOOdds ratio95% CIpOdds ratio95% CIpER1.120.36, 3.480.844.471.62, 12.380.004PgR4.381.03, 18.580.053.050.50, 18.560.23RB13.010.24, 38.560.400.420.05, 38.490.83Cyclin-E10.100.01, 0.840.030.020.00, 0.200.001Cyclin-D1 IHC3.090.51, 18.490.222.560.28, 23.330.40CyclinD1 FISH*1.470.43, 4.990.530.280.06, 0.860.03

Citation Format: Eugene F Schuster, Hui Xiao, Elena Lopez-Knowles, Lucy Kilburn, Mothaffar Rimawi, David A Wheeler, Katherine Pogue-Geile, Yuan Lui, Samuel A Jacobs, Chet Cornman, Shannon Puhalla, Maggie Cheang, Judith Bliss, Stephen Johnston, Mitch Dowsett, On behalf of the PALLET Trialists. Biomarkers of resistance to palbociclib in ER+ primary breast cancer in the PALLET trial [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS5-01.

Development and validation for research assessment of Oncotype DX® Breast Recurrence Score, EndoPredict® and Prosigna®

Multi-gene prognostic signatures including the Oncotype® DX Recurrence Score (RS), EndoPredict® (EP) and Prosigna® (Risk Of Recurrence, ROR) are widely used to predict the likelihood of distant recurrence in patients with oestrogen-receptor-positive (ER+), HER2-negative breast cancer. Here, we describe the development and validation of methods to recapitulate RS, EP and ROR scores from NanoString expression data. RNA was available from 107 tumours from postmenopausal women with early-stage, ER+, HER2- breast cancer from the translational Arimidex, Tamoxifen, Alone or in Combination study (TransATAC) where previously these signatures had been assessed with commercial methodology. Gene expression was measured using NanoString nCounter. For RS and EP, conversion factors to adjust for cross-platform variation were estimated using linear regression. For ROR, the steps to perform subgroup-specific normalisation of the gene expression data and calibration factors to calculate the 46-gene ROR score were assessed and verified. Training with bootstrapping (n = 59) was followed by validation (n = 48) using adjusted, research use only (RUO) NanoString-based algorithms. In the validation set, there was excellent concordance between the RUO scores and their commercial counterparts (rc(RS) = 0.96, 95% CI 0.93-0.97 with level of agreement (LoA) of -7.69 to 8.12; rc(EP) = 0.97, 95% CI 0.96-0.98 with LoA of -0.64 to 1.26 and rc(ROR) = 0.97 (95% CI 0.94-0.98) with LoA of -8.65 to 10.54). There was also a strong agreement in risk stratification: (RS: κ = 0.86, p < 0.0001; EP: κ = 0.87, p < 0.0001; ROR: κ = 0.92, p < 0.001). In conclusion, the calibrated algorithms recapitulate the commercial RS and EP scores on individual biopsies and ROR scores on samples based on subgroup-centreing method using NanoString expression data.

Abstract P4-06-02: Multi-parameter FACS sorting identifies higher mutational burden in aromatase inhibitor resistant subclones in estrogen positive breast cancer at diagnosis

Background: In many cancers, intratumor heterogeneity is associated with poor outcomes and resistance to treatment but datasets and techniques to identify genomic differences between the resistant and sensitive subclones in primary tumors have been limited. Short-term presurgical treatment of estrogen positive (ER+) breast cancer with aromatase inhibitors (AIs) leads to marked reduction in proliferation in most tumours. However, some proliferating cells remain in most ER+ cancers after treatment and these cells may be responsible for the outgrowth of resistant clones. We provide data from a novel approach that may allow a better understanding of the molecular drivers of the de novo endocrine resistant cells that may underpin the eventual emergence of clinical resistance and allow early intervention to avoid this.

Methods: Twenty-six FFPE ER+ breast cancer excision biopsies that showed partial Ki67 suppression after 2-weeks neoadjuvant AI treatment were studied. Single cell suspensions were obtained by enzymatic dispersion of 50-µm thick sections using a collagenase/dispase digestion method and were simultaneously stained for cytokeratin (Alexa Fluor 488), vimentin (Alexa Fluor 647), and DNA (DAPI). The stained suspensions were analysed using BD FACSAria II flow cytometer, and cytokeratin positive (epithelial) cells were separated from vimentin positive (stromal) cells by gating on a dot plot showing green (Alexa Fluor 488) versus far red (Alexa Fluor 647) fluorescence. Epithelial cells were further subdivided according to cell cycle into G0/G1 (mainly non-proliferating) and S/G2M (proliferating) populations using DNA histogram gating based on DAPI staining. Cells were sorted until ~90,000 cells or all cells if &lt;90,000 were collected for each sub-population and DNA was extracted for whole exome sequencing. Consensus calls from multiple software packages were used to detect somatic mutations in epithelial cells using the vimentin positive cells as normal controls.

Results: Twenty-six samples were FACS sorted into the 3 populations (non-proliferating and proliferating epithelial cells and stromal cells). Vimentin/stromal populations were almost all diploid and most epithelial populations were aneuploid. Two samples had more than 2 epithelial peaks suggesting multiple tumor subclones. The mean coverage for all samples was 52x and mean number of mutations per sorted sample was 418 (missense, nonsense, splicing, frame shift and non-stop mutations). Two samples had low coverage and were removed for further analysis, and in the remaining 24 FACS sorted samples, mean somatic mutational burden was significantly greater in proliferating cells compared to non-proliferation cells (mean 474 vs. 372, p=0.008 Wilcoxon signed rank test) with 5 tumors showing gross increases. There was no significant difference between the percent of the genome with copy number gains or losses between proliferating and non-proliferating cells. There were no individual genes that had significantly higher mutation rates in proliferating cells after correction for multiple testing.

Conclusions: FACS sorting of neoadjuvant AI treated samples allows the separation of de novo AI-resistant from sensitive cell populations and revealed higher mutational burden in the AI resistant populations at the time of disease presentation. Interrogation of the mutational differences between the proliferative and non-proliferative cells may allow identification of putative drivers of resistance in individual tumours. Additional samples are under analysis to determine whether common drivers can be identified.

Citation Format: Eugene F Schuster, Lila Zabalgo, Charles M Perou, Mitch Dowsett. Multi-parameter FACS sorting identifies higher mutational burden in aromatase inhibitor resistant subclones in estrogen positive breast cancer at diagnosis [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-06-02.

Common and unique transcriptional responses to dietary restriction and loss of insulin receptor substrate 1 (IRS1) in mice

Dietary restriction (DR) is the most widely studied non-genetic intervention capable of extending lifespan across multiple taxa. Modulation of genes, primarily within the insulin/insulin-like growth factor signalling (IIS) and the mechanistic target of rapamycin (mTOR) signalling pathways also act to extend lifespan in model organisms. For example, mice lacking insulin receptor substrate-1 (IRS1) are long-lived and protected against several age-associated pathologies. However, it remains unclear how these particular interventions act mechanistically to produce their beneficial effects. Here, we investigated transcriptional responses in wild-type and IRS1 null mice fed an ad libitum diet (WT^AL and KO^AL) or fed a 30% DR diet (WT^DR or KO^DR). Using an RNAseq approach we noted a high correlation coefficient of differentially expressed genes existed within the same tissue across WT^DR and KO^AL mice and many metabolic features were shared between these mice. Overall, we report that significant overlap exists in the tissue-specific transcriptional response between long-lived DR mice and IRS1 null mice. However, there was evidence of disconnect between transcriptional signatures and certain phenotypic measures between KO^AL and KO^DR, in that additive effects on body mass were observed but at the transcriptional level DR induced a unique set of genes in these already long-lived mice.

Abstract P2-05-02: Age-related genetic and epigenetic changes in estrogen-receptor positive breast cancer

Background:

Age is the main risk factor for developing breast cancer (BC) in women. The increase in incidence with age is dominated by estrogen receptor positive (ER+) BC despite the &gt;90% reduction of estrogen levels during menopause and later life. Recent models suggest the lifetime risk of BC is correlated with the number of stem cell divisions with random mutations arising during each division and driving cancer development. However, only two genes are mutated in more than 20% of BC while several recurrent copy number alterations (CNAs) occur in more than 50%. New models of age-related risk factors need to be developed that incorporate mutations, CNAs, epigenetics, and other biological factors. As data of this type is limited in normal breast tissue, factors correlated with age of diagnosis in ER+ BC were identified to understand which variables changed with age and might impact risk of developing BC.

Methods:

In silico analysis of public databases was used to identify factors in ER+ primary BC and normal adjacent tissue (NT) that are correlated with age of diagnosis including DNA mutations, CNAs, DNA methylation and gene/protein expression (TCGA n=599ER+,113NT; METABRIC n=1435ER+,144NT).

Results:

DNA mutations accumulated with age in ER+ BC with the median mutation count below 28 in primary tumors diagnosis in patients &lt;50yr and rising to more than 43 in patients &gt;80yr. However, the two most frequently mutated genes (PIK3CA and TP53) showed no significant correlation with age. As previously reported, GATA3 mutation rate was nearly twice as high in younger patients (&lt;50yr=0.25,&gt;80yr=0.12). There was little evidence of a general accumulation of CNAs with age, but there were higher rates of gain in 16p (&lt;50yr=0.42,&gt;80yr=0.51) and loss of 1p (&lt;50yr=0.18,&gt;80yr=0.37) in older patients and lower rates of loss in 6q (&lt;50yr=0.34,&gt;80yr=0.24). The most significant correlations with age related to ESR1 including expression of ESR1 mRNA (rho=0.39,P=1.2e-23 Spearman), ERα protein (rho=0.35,P=1.7e-15 Spearman), and demethylation of ESR1 promoter (rho=-0.36,P=1.6e-13 Spearman). The levels of the activated form of ERα (pS118) also correlated with age but to a much lesser extent than total ERα (rho=0.12,P=0.01 Spearman). Demethylation and expression of ESR1 were highly correlated (rho=-0.50,P&lt;1e-16 Spearman). Analysis of data from NT revealed correlation of age of diagnosis, expression of ESR1 (rho=0.34,P=0.001 Spearman) and demethylation of the ESR1 promoter (rho=-0.22,P=0.03 Spearman) but not with ERα expression (rho=0.32,P=0.19 Spearman) although only 19 NT had protein data.

Conclusions:

Analysis of DNA mutations and CNAs fit previous theoretical models with both the result of stochastic processes. In these models, the low impact on fitness from individual mutations allows the accumulation over time while the high fitness costs of CNAs prevent accumulation and are likely acquired in a single catastrophic event. The ability of ER+ BC to progress in the presence of very low postmenopausal estrogen levels may be partly explained by demethylation leading to higher ESR1 expression and maintenance of ERα activation. In theory, changes in expression and demethylation can be targeted to reduce the age-related increase in risk for developing BC.

Citation Format: Schuster EF, Dowsett M. Age-related genetic and epigenetic changes in estrogen-receptor 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 P2-05-02.

Genomic Instability and TP53 Genomic Alterations Associate With Poor Antiproliferative Response and Intrinsic Resistance to Aromatase Inhibitor Treatment

PURPOSE

Although aromatase inhibitor (AI) treatment is effective in estrogen receptor-positive postmenopausal breast cancer, resistance is common and incompletely explained. Genomic instability, as measured by somatic copy number alterations (SCNAs), is important in breast cancer development and prognosis. SCNAs to specific genes may drive intrinsic resistance, or high genomic instability may drive tumor heterogeneity, which allows differential response across tumors and surviving cells to evolve resistance to treatment rapidly. We therefore evaluated the relationship between SCNAs and intrinsic resistance to treatment as measured by a poor antiproliferative response.

PATIENTS AND METHODS

SCNAs were determined by single nucleotide polymorphism array in baseline and surgery core-cuts from 73 postmenopausal patients randomly assigned to receive 2 weeks of preoperative AI or no AI in the Perioperative Endocrine Therapy-Individualizing Care (POETIC) trial. Fifty-six samples from the AI group included 28 poor responders (PrRs, less than 60% reduction in protein encoded by the MKI67 gene [Ki-67]) and 28 good responders (GdRs, greater than 75% reduction in Ki-67). Exome sequencing was available for 72 pairs of samples.

RESULTS

Genomic instability correlated with Ki-67 expression at both baseline (P < .001) and surgery (P < .001) and was higher in PrRs (P = .048). The SCNA with the largest difference between GdRs and PrRs was loss of heterozygosity observed at 17p (false discovery rate, 0.08), which includes TP53. Nine of 28 PrRs had loss of wild-type TP53 as a result of mutations and loss of heterozygosity compared with three of 28 GdRs. In PrRs, somatic alterations of TP53 were associated with higher genomic instability, higher baseline Ki-67, and greater resistance to AI treatment compared with wild-type TP53.

CONCLUSION

We observed that primary tumors with high genomic instability have an intrinsic resistance to AI treatment and do not require additional evolution to develop resistance to estrogen deprivation therapy.

Abstract PD5-05: Genomic instability and poor antiproliferative response to aromatase inhibitor treatment: A POETIC study

Background:

More than 20% of early-stage patients with estrogen positive (ER+) disease relapse. Higher levels of the proliferation marker Ki67, and lack of reduction of Ki67 in response to AI indicate poorer prognosis. Somatic mutations have been the focus of research in treatment resistance. However, recurrent somatic copy number alterations (SCNAs) are more common and affect more genes in primary breast cancer (BC) than somatic mutations. Previous studies have suggested an increased risk of recurrence for patients with high genomic instability and for patients with loss of heterozygosity (LOH) at the TP53 locus, but it is unknown if these SCNA events impact response to AI treatment. In addition, LOH and mutations at the TP53 locus had a higher risk of recurrence than LOH or mutations at TP53 alone. We hypothesised that genomic instability and SCNAs at particular loci would be increased in early BC patients with high baseline Ki67, and particularly in patients with high Ki67 despite pre-operative AI therapy.

Methods:

In a substudy of POETIC (UK-wide, phase III, randomised trial with 4483 women testing perioperative AI in postmenopausal women with early BC), SNParray technology was used to determine SCNAs in baseline and surgical tumour core-cuts and blood from 76 patients (59 AI-treated, 17 controls). Proliferation rate was estimated as percentage (%) of cancer cells staining for Ki67 by IHC. Poor AI responders (PR, &lt;60% reduction in Ki67 between baseline and surgery, n=31) and good AI responders (GR, &gt; 75% reduction in Ki67, n=28) were selected from POETIC samples. Mutation data from exome sequencing was available for tumours from 75 of the patients.

Results:

The fraction of the genome with SCNAs correlated with Ki67 expression in both baseline and surgical samples (baseline Spearman rho=0.5, p &lt; 10-5; surgical Spearman rho=0.44, p &lt; 10-3). In paired baseline vs surgical samples, 24% of samples showed discordance in SCNAs that covered &gt; 10% of the genome. The samples showing the highest discordance were from PRs.

The fraction of the genome with LOH was greater in PR (median PR 20%, GR 10%, p = .065), and the best SCNA to predict the fraction of the genome altered in a sample were segments with LOH at Chr17p13.3 (adjusted p &lt; .001, logistic regression). There was a higher percentage of patients with LOH at Chr17p13.3 that contains the TP53 gene in the PR compared to GR group (PR 71%, GR 39%, p = .029), and integration of previously generated mutation data with SCNA showed that 9 out of 31 PRs have mutations and LOH at the TP53 locus compared to 3 out of 28 GRs (p = 0.16).

Conclusions:

There is discordance between the observed SCNAs in paired samples with high genomic instability and multiple biopsies may be needed to confidently assess all SCNAs. However, LOH at Chr17p13.3 is a biomarker for genomic instability and frequency of LOH is significantly greater in patients that show a poor response to AI treatment. Finally, high genomic instability is associated with high proliferation rates at baseline and surgery after 2 weeks of AI treatment suggesting de novo resistance in tumours with high instability that may lead to a higher rate of recurrence seen in these patients.

Citation Format: Schuster EF, Gellert P, Segal CV, López-Knowles E, Buus R, Morden J, Robertson J, Bliss J, Smith I, Dowsett M, POETIC Trial Management Group and Trialists P. Genomic instability and poor antiproliferative response to aromatase inhibitor treatment: A POETIC study [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr PD5-05.

Dysregulation of Alternative Poly-adenylation as a Potential Player in Autism Spectrum Disorder

We present here the hypothesis that alternative poly-adenylation (APA) is dysregulated in the brains of individuals affected by Autism Spectrum Disorder (ASD), due to disruptions in the calcium signaling networks. APA, the process of selecting different poly-adenylation sites on the same gene, yielding transcripts with different-length 3′ untranslated regions (UTRs), has been documented in different tissues, stages of development and pathologic conditions. Differential use of poly-adenylation sites has been shown to regulate the function, stability, localization and translation efficiency of target RNAs. However, the role of APA remains rather unexplored in neurodevelopmental conditions. In the human brain, where transcripts have the longest 3′ UTRs and are thus likely to be under more complex post-transcriptional regulation, erratic APA could be particularly detrimental. In the context of ASD, a condition that affects individuals in markedly different ways and whose symptoms exhibit a spectrum of severity, APA dysregulation could be amplified or dampened depending on the individual and the extent of the effect on specific genes would likely vary with genetic and environmental factors. If this hypothesis is correct, dysregulated APA events might be responsible for certain aspects of the phenotypes associated with ASD. Evidence supporting our hypothesis is derived from standard RNA-seq transcriptomic data but we suggest that future experiments should focus on techniques that probe the actual poly-adenylation site (3′ sequencing). To address issues arising from the use of post-mortem tissue and low numbers of heterogeneous samples affected by confounding factors (such as the age, gender and health of the individuals), carefully controlled in vitro systems will be required to model the effect of calcium signaling dysregulation in the ASD brain.

Recent insights into Groucho co-repressor recruitment and function

Gene expression is often controlled by transcriptional repressors during development. Many transcription factors lack intrinsic repressive activity but recruit co-factors that inhibit productive transcription. Here we discuss new insights and models for repression mediated by the Groucho/Transducin-Like Enhancer of split (Gro/TLE) family of co-repressor proteins.

DAF-16/FoxO directly regulates an atypical AMP-activated protein kinase gamma isoform to mediate the effects of insulin/IGF-1 signaling on aging in Caenorhabditis elegans

The DAF-16/FoxO transcription factor controls growth, metabolism and aging in Caenorhabditis elegans. The large number of genes that it regulates has been an obstacle to understanding its function. However, recent analysis of transcript and chromatin profiling implies that DAF-16 regulates relatively few genes directly, and that many of these encode other regulatory proteins. We have investigated the regulation by DAF-16 of genes encoding the AMP-activated protein kinase (AMPK), which has α, β and γ subunits. C. elegans has 5 genes encoding putative AMP-binding regulatory γ subunits, aakg-1-5. aakg-4 and aakg-5 are closely related, atypical isoforms, with orthologs throughout the Chromadorea class of nematodes. We report that ∼75% of total γ subunit mRNA encodes these 2 divergent isoforms, which lack consensus AMP-binding residues, suggesting AMP-independent kinase activity. DAF-16 directly activates expression of aakg-4, reduction of which suppresses longevity in daf-2 insulin/IGF-1 receptor mutants. This implies that an increase in the activity of AMPK containing the AAKG-4 γ subunit caused by direct activation by DAF-16 slows aging in daf-2 mutants. Knock down of aakg-4 expression caused a transient decrease in activation of expression in multiple DAF-16 target genes. This, taken together with previous evidence that AMPK promotes DAF-16 activity, implies the action of these two metabolic regulators in a positive feedback loop that accelerates the induction of DAF-16 target gene expression. The AMPK β subunit, aakb-1, also proved to be up-regulated by DAF-16, but had no effect on lifespan. These findings reveal key features of the architecture of the gene-regulatory network centered on DAF-16, and raise the possibility that activation of AMP-independent AMPK in nutritionally replete daf-2 mutant adults slows aging in C. elegans. Evidence of activation of AMPK subunits in mammals suggests that such FoxO-AMPK interactions may be evolutionarily conserved.

Aging is an important problem for human health and is regulated by complex gene regulatory networks. In a simple nematode worm (Caenorhabditis elegans) mutation of the insulin/IGF-1 receptor daf-2 dramatically extends lifespan. This is due to the increased activity of DAF-16, a FoxO transcription factor, leading to altered expression of genes, many encoding other regulatory proteins. We have focused on one such protein, AMP-activated protein kinase (AMPK), that is important for regulating cellular homeostasis under conditions of low energy availability (e.g. starvation). We find that DAF-16 binds to the promoter of aakg-4 (a gene encoding an atypical γ subunit of AMPK) and increases its expression. Inhibition of aakg-4 leads to down-regulation of multiple DAF-16 target genes and shortens the life of daf-2 mutants. Taken together with a previous report showing that AMPK activates DAF-16, this suggests that AAKG-4 and DAF-16 are involved in a positive feedback loop which accelerates effects of DAF-16 on gene expression, and could contribute to longevity. This study defines a new part of the complex gene regulatory network in which DAF-16 acts to control aging. FoxO-AMPK interactions are present in higher animals, where they could potentially also influence aging.

Genome-wide dFOXO targets and topology of the transcriptomic response to stress and insulin signalling

FoxO transcription factors, inhibited by insulin/insulin-like growth factor signalling (IIS), are crucial players in numerous organismal processes including lifespan. Using genomic tools, we uncover over 700 direct dFOXO targets in adult female Drosophila. dFOXO is directly required for transcription of several IIS components and interacting pathways, such as TOR, in the wild-type fly. The genomic locations occupied by dFOXO in adults are different from those observed in larvae or cultured cells. These locations remain unchanged upon activation by stresses or reduced IIS, but the binding is increased and additional targets activated upon genetic reduction in IIS. We identify the part of the IIS transcriptional response directly controlled by dFOXO and the indirect effects and show that parts of the transcriptional response to IIS reduction do not require dfoxo. Promoter analyses revealed GATA and other forkhead factors as candidate mediators of the indirect and dfoxo-independent effects. We demonstrate genome-wide evolutionary conservation of dFOXO targets between the fly and the worm Caenorhabditis elegans, enriched for a second tier of regulators including the dHR96/daf-12 nuclear hormone receptor.

Estimation and correction of non-specific binding in a large-scale spike-in experiment

A combined statistical analysis using the MAS5 PM-MM, GC-NSB and PDNN methods to generate probeset values from microarray data results in an improved ability to detect differential expression and estimates of false discovery rates compared with the individual methods.

Background

The availability of a recently published large-scale spike-in microarray dataset helps us to understand the influence of probe sequence in non-specific binding (NSB) signal and enables the benchmarking of several models for the estimation of NSB. In a typical microarray experiment using Affymetrix whole genome chips, 30% to 50% of the probes will apparently have absent target transcripts and show only NSB signal, and these probes can have significant repercussions for normalization and the statistical analysis of the data if NSB is not estimated correctly.

Results

We have found that the MAS5 perfect match-mismatch (PM-MM) model is a poor model for estimation of NSB, and that the Naef and Zhang sequence-based models can reasonably estimate NSB. In general, using the GC robust multi-array average, which uses Naef binding affinities, to calculate NSB (GC-NSB) outperforms other methods for detecting differential expression. However, there is an intensity dependence of the best performing methods for generating probeset expression values. At low intensity, methods using GC-NSB outperform other methods, but at medium intensity, MAS5 PM-MM methods perform best, and at high intensity, MAS5 PM-MM and Zhang's position-dependent nearest-neighbor (PDNN) methods perform best.

Conclusion

A combined statistical analysis using the MAS5 PM-MM, GC-NSB and PDNN methods to generate probeset values results in an improved ability to detect differential expression and estimates of false discovery rates compared with the individual methods. Additional improvements in detecting differential expression can be achieved by a strict elimination of empty probesets before normalization. However, there are still large gaps in our understanding of the Affymetrix GeneChip technology, and additional large-scale datasets, in which the concentration of each transcript is known, need to be produced before better models of specific binding can be created.

Correcting for sequence biases in present/absent calls

The probe sequence of short oligonucleotides in Affymetrix microarray experiments can have a significant influence on present/absent calls of probesets with absent target transcripts. Probesets enriched for central Ts and depleted of central As in the perfect-match probes tend to be falsely classified as having present transcripts. Correction of non-specific binding for both perfect-match and mismatch probes using probe-sequence models can partially remove the probe-sequence bias and result in better performance of the MAS 5.0 algorithm.

Coordinated multitissue transcriptional and plasma metabonomic profiles following acute caloric restriction in mice

Caloric restriction (CR) increases healthy life span in a range of organisms. The underlying mechanisms are not understood but appear to include changes in gene expression, protein function, and metabolism. Recent studies demonstrate that acute CR alters mortality rates within days in flies. Multitissue transcriptional changes and concomitant metabolic responses to acute CR have not been described. We generated whole genome RNA transcript profiles in liver, skeletal muscle, colon, and hypothalamus and simultaneously measured plasma metabolites using proton nuclear magnetic resonance in mice subjected to acute CR. Liver and muscle showed increased gene expressions associated with fatty acid metabolism and a reduction in those involved in hepatic lipid biosynthesis. Glucogenic amino acids increased in plasma, and gene expression for hepatic gluconeogenesis was enhanced. Increased expression of genes for hormone-mediated signaling and decreased expression of genes involved in protein binding and development occurred in hypothalamus. Cell proliferation genes were decreased and cellular transport genes increased in colon. Acute CR captured many, but not all, hepatic transcriptional changes of long-term CR. Our findings demonstrate a clear transcriptional response across multiple tissues during acute CR, with congruent plasma metabolite changes. Liver and muscle switched gene expression away from energetically expensive biosynthetic processes toward energy conservation and utilization processes, including fatty acid metabolism and gluconeogenesis. Both muscle and colon switched gene expression away from cellular proliferation. Mice undergoing acute CR rapidly adopt many transcriptional and metabolic changes of long-term CR, suggesting that the beneficial effects of CR may require only a short-term reduction in caloric intake.

A novel variant of Inpp5f is imprinted in brain, and its expression is correlated with differential methylation of an internal CpG island

Using a tissue-specific microarray screen in combination with chromosome anomalies in the mouse, we identified a novel imprinted gene, Inpp5f_v2 on mouse chromosome 7. Characterization of this gene reveals a 3.2-kb transcript that is paternally expressed in the brain. Inpp5f_v2 is a variant of the related 4.7-kb transcript, Inpp5f, an inositol phosphatase gene that is biallelically expressed in the mouse. Inpp5f_v2 uses an alternative transcriptional start site within an intron of Inpp5f and thus has a unique alternative first exon. Whereas other imprinted transcripts have a unique first exon located within intron 1 of a longer transcript variant (such as at the Gnas and WT1 loci), Inpp5f_v2 is the first example of which we are aware in which the alternative first exon of an imprinted gene is embedded in a downstream intron (intron 15) of a transcript variant. The CpG island associated with the non-imprinted Inpp5f gene is hypomethylated on both alleles, a finding consistent with biallelic expression, whereas the CpG island present 5' of Inpp5f_v2 is differentially methylated on the maternal versus paternal alleles consistent with its imprinting status.

Genetic linkage analysis of prostate cancer families to Xq27-28

OBJECTIVES

A recent linkage analysis of 360 families at high risk for prostate cancer identified the q27-28 region on chromosome X as the potential location of a gene involved in prostate cancer susceptibility. Here we report on linkage analysis at this putative HPCX locus in an independent set of 186 prostate cancer families participating in the Prostate Cancer Genetic Research Study (PROGRESS).

METHODS

DNA samples from these families were genotyped at 8 polymorphic markers spanning 14.3 cM of the HPCX region.

RESULTS

Two-point parametric analysis of the total data set resulted in positive lod scores at only two markers, DXS984 and DXS1193, with scores of 0.628 at a recombination fraction (theta) of 0.36 and 0.012 at theta = 0.48, respectively. The stratification of pedigrees according to the assumed mode of transmission increased the evidence of linkage at DXS984 in 81 families with no evidence of male-to-male transmission (lod = 1.062 at theta = 0.28).

CONCLUSIONS

Although this analysis did not show statistically significant evidence for the linkage of prostate cancer susceptibility to Xq27-28, the results are consistent with a small percentage of families being linked to this region. The analysis further highlights difficulties in replicating linkage results in an etiologically heterogeneous, complexly inherited disease.

Linkage analysis of 150 high-risk prostate cancer families at 1q24-25

Confirmation of linkage and estimation of the proportion of families who are linked in large independent datasets is essential to understanding the significance of cancer susceptibility genes. We report here on an analysis of 150 high-risk prostate cancer families (2,176 individuals) for potential linkage to the HPC1 prostate cancer susceptibility locus at 1q24-25. This dataset includes 640 affected men with an average age at prostate cancer diagnosis of 66. 8 years (range, 39-94), representing the largest collection of high-risk families analyzed for linkage in this region to date. Linkage to multiple 1q24-25 markers was strongly rejected for the sample as a whole (lod scores at theta = 0 ranged from -30.83 to -18. 42). Assuming heterogeneity, the estimated proportion of families linked (alpha) at HPC1 in the entire dataset was 2.6%, using multipoint analysis. Because locus heterogeneity may lead to false rejection of linkage, data were stratified based on homogeneous subsets. When restricted to 21 Caucasian families with five or more affected family members and mean age at diagnosis < = 65 years, the lod scores at theta = 0 remained less than -4.0. These results indicate that the overall portion of hereditary prostate cancer families whose disease is due to inherited variation in HPC1 may be less than originally estimated.

Analysis of chromosome 1q42.2-43 in 152 families with high risk of prostate cancer

One hundred fifty-two families with prostate cancer were analyzed for linkage to markers spanning a 20-cM region of 1q42.2-43, the location of a putative prostate cancer-susceptibility locus (PCAP). No significant evidence for linkage was found, by use of both parametric and nonparametric tests, in our total data set, which included 522 genotyped affected men. Rejection of linkage may reflect locus heterogeneity or the confounding effects of sporadic disease in older-onset cases; therefore, pedigrees were stratified into homogeneous subsets based on mean age at diagnosis of prostate cancer and number of affected men. Analyses of these subsets also detected no significant evidence for linkage, although LOD scores were positive at higher recombination fractions, which is consistent with the presence of a small proportion of families with linkage. The most suggestive evidence of linkage was in families with at least five affected men (nonparametric linkage score of 1.2; P=.1). If heterogeneity is assumed, an estimated 4%-9% of these 152 families may show linkage in this region. We conclude that the putative PCAP locus does not account for a large proportion of these families with prostate cancer, although the linkage of a small subset is compatible with these data.

Evidence for a rare prostate cancer-susceptibility locus at chromosome 1p36

Combining data from a genomic screen in 70 families with a high risk for prostate cancer (PC) with data from candidate-region mapping in these families and an additional 71 families, we have localized a potential hereditary PC-susceptibility locus to chromosome 1p36. Because an excess of cases of primary brain cancer (BC) have been observed in some studies of families with a high risk for PC, and because loss of heterozygosity at 1p36 is frequently observed in BC, we further evaluated 12 families with both a history of PC and a blood relative with primary BC. The overall LOD score in these 12 families was 3.22 at a recombination fraction (theta) of .06, with marker D1S507. On the basis of an a priori hypothesis, this group was stratified by age at diagnosis of PC. In the younger age group (mean age at diagnosis <66 years), a maximum two-point LOD score of 3.65 at straight theta = .0 was observed, with D1S407. This linkage was rejected in both early- and late-onset families without a history of BC (LOD scores -7.12 and -6.03, respectively, at straight theta = .0). After exclusion of 3 of the 12 families that had better evidence of linkage to previously described PC-susceptibility loci, linkage to the 1p36 region was suggested by a two-point LOD score of 4.74 at straight theta = .0, with marker D1S407. We conclude that a significant proportion of these families with both a high risk for PC and a family member with BC show linkage to the 1p36 region.