A non-coding RNA balancing act: miR-346-induced DNA damage is limited by the long non-coding RNA NORAD in prostate cancer

BACKGROUND

miR-346 was identified as an activator of Androgen Receptor (AR) signalling that associates with DNA damage response (DDR)-linked transcripts in prostate cancer (PC). We sought to delineate the impact of miR-346 on DNA damage, and its potential as a therapeutic agent.

METHODS

RNA-IP, RNA-seq, RNA-ISH, DNA fibre assays, in vivo xenograft studies and bioinformatics approaches were used alongside a novel method for amplification-free, single nucleotide-resolution genome-wide mapping of DNA breaks (INDUCE-seq).

RESULTS

miR-346 induces rapid and extensive DNA damage in PC cells - the first report of microRNA-induced DNA damage. Mechanistically, this is achieved through transcriptional hyperactivation, R-loop formation and replication stress, leading to checkpoint activation and cell cycle arrest. miR-346 also interacts with genome-protective lncRNA NORAD to disrupt its interaction with PUM2, leading to PUM2 stabilisation and its increased turnover of DNA damage response (DDR) transcripts. Confirming clinical relevance, NORAD expression and activity strongly correlate with poor PC clinical outcomes and increased DDR in biopsy RNA-seq studies. In contrast, miR-346 is associated with improved PC survival. INDUCE-seq reveals that miR-346-induced DSBs occur preferentially at binding sites of the most highly-transcriptionally active transcription factors in PC cells, including c-Myc, FOXA1, HOXB13, NKX3.1, and importantly, AR, resulting in target transcript downregulation. Further, RNA-seq reveals widespread miR-346 and shNORAD dysregulation of DNA damage, replication and cell cycle processes. NORAD drives target-directed miR decay (TDMD) of miR-346 as a novel genome protection mechanism: NORAD silencing increases mature miR-346 levels by several thousand-fold, and WT but not TDMD-mutant NORAD rescues miR-346-induced DNA damage. Importantly, miR-346 sensitises PC cells to DNA-damaging drugs including PARP inhibitor and chemotherapy, and induces tumour regression as a monotherapy in vivo, indicating that targeting miR-346:NORAD balance is a valid therapeutic strategy.

CONCLUSIONS

A balancing act between miR-346 and NORAD regulates DNA damage and repair in PC. miR-346 may be particularly effective as a therapeutic in the context of decreased NORAD observed in advanced PC, and in transcriptionally-hyperactive cancer cells.

The tumor microenvironment and immune responses in prostate cancer patients

The landscape of cancer treatment has been transformed over the past decade by the success of immune-targeting therapies. However, despite sipuleucel-T being the first-ever approved vaccine for cancer and the first immunotherapy licensed for prostate cancer in 2010, immunotherapy has since seen limited success in the treatment of prostate cancer. The tumour microenvironment of prostate cancer presents particular barriers for immunotherapy. Moreover, prostate cancer is distinguished by being one of only two solid tumours where increased T cell-infiltration correlates with a poorer, rather than improved, outlook. Here, we discuss the specific aspects of the prostate cancer microenvironment that converge to create a challenging microenvironment, including myeloid-derived immune cells and cancer-associated fibroblasts. By exploring the immune microenvironment of defined molecular subgroups of prostate cancer, we propose an immunogenomic subtyping approach to single-agent and combination immune-targeting strategies that could lead to improved outcomes in prostate cancer treatment.

Abstract OT3-02-07: Neo-DDRD: A biomarker-driven neoadjuvant feasibility study in breast cancer

Background

Anthracycline-based chemotherapy reduces the risk of early breast cancer recurrence but to date it has not been possible to predict which patients specifically benefit from this treatment. The Almac DDRD assay, a 44 gene signature, has been developed to detect DNA damage response deficiency (DDRD) within breast and other cancer types. The DDRD assay has been shown to predict benefit from DNA damaging chemotherapy in retrospective analyses in neoadjuvant and adjuvant settings (Mulligan et al, JNCI 2014). This pilot study aims to prospectively evaluate the feasibility and utility of this signature in the neoadjuvant setting in breast cancer. It will inform the design of a phase II randomised study where the DDRD assay will be utilised to guide neoadjuvant chemotherapy selection.

Study design

A single-centre, non-randomised feasibility study of 30 women with a histologically confirmed diagnosis of breast cancer, where neoadjuvant chemotherapy is the treatment modality of choice.

Inclusion criteria:

Age >18 years

Early (T1-2, N0-1), locally advanced or inflammatory breast cancer

Normal left ventricular function, haematological and biochemical parameters

ECOG PS 0-1

Exclusion criteria:

Metastatic disease

Bilateral breast cancer

Pregnancy/breastfeeding

Inability to give informed consent

At diagnosis, patients consented to providing two core needle biopsies in addition to a diagnostic biopsy. Axillary nodal status was determined by axillary ultrasound, fine needle aspiration cytology, and pre-treatment sentinel node biopsy if pre-operative axillary staging was negative.

Chemotherapy was administered as per standard institutional practice: 6 cycles fluourouracil, epirubicin and cyclophosphamide (FEC) in node-negative patients; 3 cycles of FEC followed by 3 cycles of docetaxel in node positive patients. Neoadjuvant trastuzumab was given in Her2 positive patients. Imaging (mammography and ultrasound) was repeated after three cycles, and repeat FFPE and snap frozen core biopsies undertaken. At conclusion of treatment, patients underwent surgery as appropriate (mastectomy or breast conservation at the discretion of the operating surgeon), with axillary node clearance for patients who were node positive at diagnosis. Further biopsies (FFPE and fresh frozen) were taken intra-operatively. Plasma samples were obtained at diagnosis, mid-treatment and surgery. Pathological reporting of the surgical specimen was standardised using the residual cancer burden (RCB) reporting system.

Aims

· To assess the feasibility of carrying out the DDRD assay on diagnostic core biopsy specimens

· To evaluate the turn-around time for the assay to assess feasibility of integration into the breast cancer treatment pathway

· To assess the correlation of DDRD assay scores and pathological tumour response

· Exploratory biomarker analysis will be carried out within Queen's University, Belfast, including:

o correlation of DDRD score with changes in Ki67 protein level after three cycles of chemotherapy

o exploratory analysis of chemokine expression in peripheral plasma samples, and correlation with pathological response to treatment

Accrual

The study opened in April 2014. Accrual to date is 14 patients.

Citation Format: McIntosh SA, Parkes EE, James CR, Lioe T, Lowry K, Keating KE, Khambata-Ford S, Kennedy RD. Neo-DDRD: A biomarker-driven neoadjuvant feasibility study in breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr OT3-02-07.

Abstract P6-07-24: Prognostic Tools in Early Breast Cancer: Predicting benefit of adjuvant chemotherapy

Introduction: Adjuvant chemotherapy (CT) in early breast cancer reduces the risk of mortality. However, absolute reductions in mortality can be small. For patient with low risk disease, prognostic tools such as ‘Adjuvant! Online’ and ‘Predict’ can be used to estimate the benefit of adjuvant chemotherapy. We compare the survival gains estimated using ‘Adjuvant! Online’ and ‘Predict’ in routine clinical practice, assessing the characteristics of patients in which ‘Adjuvant! Online’ and ‘Predict’ disagree.

Methods: In a retrospective study using the hospital electronic database, the clinical and pathological details of all patients with early breast cancer referred for adjuvant therapy at the Northern Ireland Cancer Centre in a 3 month period in 2011 were collected and were entered in to ‘Adjuvant! Online’ and ‘Predict’ to assess percentage benefit (absolute reduction in mortality at 10 years) from CT. We categorised patients into three prognostic groups: those where risk from CT outweighs benefit (<2% predicted benefit), marginal benefit (2 to 5%) and significant benefit from CT (>5%) We excluded patients with metastatic disease at presentation, DCIS, a second primary breast cancer or receiving neo-adjuvant treatment.

Results: Of the 250 patients identified, 61 (24.4%) fell in to different prognostic groups depending on whether ‘Adjuvant! Online’ or ‘Predict’ was used to calculate benefit from CT. In those in whom there was disagreement, ‘Adjuvant! Online’ suggested marginal or significant benefit in 75.4% of patients, compared to 55.7% using ‘Predict’. Nine patients had “major” comorbidities, which is weighted only in ‘Adjuvant! Online’, and were excluded in subsequent analysis. Of those without major comorbidities, ‘Adjuvant! Online’ offered at least 2% benefit in 85% of cases, and ‘Predict’ in only 58.3%. The majority (93.3%) of cases were ER positive, and node negative (85.0%). This difference was notable in women aged 65 or less, with 86.2% with >2% benefit using ‘Adjuvant! Online’, compared to 55.1% using ‘Predict’. ‘Adjuvant! Online’ estimates of benefit were on average 3.7% higher for this age group. HER2 status had little impact, with similar recommendations using either ‘Adjuvant! Online’ or ‘Predict’.

Conclusions: This study highlights lack of concordance between two available online prognostic tools, notably in ER positive, node negative patients. For patients with a marginal benefit from adjuvant chemotherapy, care must be used when making adjuvant treatment decisions as other prognostic tools may be of help in this group of patients.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P6-07-24.

Preparation and characterization of an antiserum to cultured human oat-cell carcinoma cells

Viable cultured oat-cell carcinoma cells were used to immunize a goat. The resulting antiserum contained high titres of anti-normal activity and antibodies to CEA. It was also shown, by indirect immunofluorescence, using fluorescein-conjugated rabbit anti-goat Ig, to localize at high titres on the surface membranes of human lung cancer cells of 4 different histological types. Booster immunizations produced a maximum secondary response one week after 2 weekly injections. The course of each immunization has been monitored for activity against normal human tissues, and the final sera have been absorbed with human spleen cells to remove anti-normal activity. Cross-reactivity with the lung-cancer-cell panel and antibodies to CEA persisted in high titre after absorption of anti-normal antibodies, and were present in the ammonium-sulphate-precipitated globulin fraction. The cells used for immunization did not produce detectable amounts of CEA in culture, and were not known to contain CEA prior to this experiment. Removal of anti-CEA antibodies by absorption with purified CEA has not reduced the cross-reactivity of the absorbed antiserum with the panel of human lung-cancer cells.