Abstract P2-08-18: Evaluation of the activity of key actionable oncogenic driving pathways in triple negative breast cancer using OncoSignal™; a novel molecular assay based on transcriptional profile analysis

Introduction: Triple negative breast cancer (TNBC), defined by the absence of expression of estrogen receptor (ER), progesterone receptor, and HER2, is a heterogenous subgroup of breast cancer which currently accounts for a significant proportion of the mortality from the disease. Consequently, there is an urgent need to identify more effective therapy for women with this type of breast cancer. We have recently developed a novel assay, OncoSignal™ which is capable of precisely measuring the activity of seven key signaling pathways through utilizing measurements of mRNA. The assay quantitatively determines the specific activity of ER, androgen receptor, PI3K, MAPK, HedgeHog, Notch, and TGFβ signal pathways via measurement and analysis of mRNA expression from transcriptional targets of these pathways. This approach overcomes some of the limitations of NGS and other methods which analyze only partial components of a complex signaling pathway, producing significant risk of false positive and negative results, and resulting in potentially inaccurate diagnosis and treatment selection. In this study we evaluated oncogenic pathway activation in 88 cases of TNBC using the OncoSignal™ assay. Materials and methods: Samples and pathway scores for TNBC tumors were calculated using a publicly available Affymetrix dataset GSE76275. This study included 88 cases of TNBC obtained at Baylor College of Medicine. OncoSignal™ pathway activity scores (PAS) were calculated from the transcriptional profile for each case. In addition, 10 samples of benign breast tissue were available for analysis of PAS and used as controls for this evaluation. The mean pathway activity scores and ranges were calculated from the benign tissues. The PAS results for each of the 7 oncogenic pathways from the TNBC cases were compared with PAS results from benign tissues. Results: The OncoSignal™ PAS were significantly higher in TNBC compared to benign tissues for MAPK, PI3K, and HH pathways. The PAS of ER and TGFβ pathways were significantly lower in TNBC compared to the benign tissue. MAPK, AR, ER, PI3K, and HH were elevated in 86%, 17%, 8%, 95%, and 94% of TNBC cases respectively. TGFβ pathway, for which oncogenic versus tumor suppressive functionality is contextually determined, showed reduced PAS in 85% of TNBC cases compared to benign tissue controls. Conclusion: OncoSignal™ analysis identifies enhanced targetable oncogenic pathway activity in a majority of TNBC breast cancers. Of interest, 7 of 88 cases (8%) classified as TNBC using IHC methods showed evidence of estrogen receptor signal pathway activation, and 15 (17%) showed elevated AR PAS. PI3K and MAPK had high PAS in over 85% of TNBC cases. Results suggest loss of tumor suppressive function of the TGFβ pathway. We conclude that OncoSignal™ analysis may help identify TNBC tumors with targetable signal transformation pathways.

Citation Format: Genevra Magliocco, Eveline den Biezen, Diederick Keizer, Martijn Akse, Martijn van Zelst, Dianne van Strijp, Saskia Vermeer, Anja van de Stolpe, Anthony Magliocco. Evaluation of the activity of key actionable oncogenic driving pathways in triple negative breast cancer using OncoSignal™; a novel molecular assay based on transcriptional profile analysis [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 P2-08-18.

Abstract 740: A robust rapid mRNA based test to profile simultaneously ER, AR, PI3K and MAPK functional signaling pathway activity for precision oncology

Introduction: OncoSignal test was developed to determine and quantify functional signal transduction pathway activity levels of 4 key oncogenic signaling pathways (ER, AR, PI3K and MAPK), based on the quantitative measurement of mRNA expression levels of the direct target genes. Here we present data of a 4 pathway qPCR test, that can be used in external labs and is able to measure simultaneously the 4 pathway activities in tumor tissue samples possibly providing important information for optimal therapy selection for treatment of breast cancer.

Materials and methods: OncoSignal 4 pathway test was compared between 2 reference laboratories; the Philips service lab in The Netherlands and at Protean BioDiagnostics, a US CAP-certified CLIA service lab. mRNA was isolated from unstained FFPE tissue sections of well characterized breast tissues obtained from 65 patients (retrospective). Annotated areas with at least 50% tumor cells were used (total volume about 0.25mm3). The OncoSignal test was used to measure the signal transduction pathway activity of AR, ER, PI3K and MAPK pathways. IHC staining for ER, PR, Ki67 and HER2 was also available for all samples enabling tumor categorization into conventional breast cancer subtypes.

Results: Excellent inter-lab concordance was found with correlation coefficients of 0.99, 0.99, 0.98 and 0.99 for ER, AR, PI3K and MAPK, respectively. Average absolute difference between pathway activities was 3.6 activity points on a 0-100 activity score scale. All 32 cases passed the criteria set for reproducibility. Of the 65 tested breast cancer samples, 58 could be subtyped based on IHC. Five of the 58 samples failed QC. Of interest, ER IHC positive luminal A (41%) and B (28%) breast cancer showed high variation in ER pathway activity between cases, suggesting that the ER signaling pathway is not the tumor driving pathway in a significant subset of IHC ER positive tumors. As expected the Her2-enriched (17%) and TNBC (17%) sub-groups predominantly had a very low ER pathway activity score. AR pathway activity was most prominent in the HER2 enriched tumor groups, while in TNBC the MAPK pathway was most active.

Conclusion: The OncoSignal 4 pathway test is robust and can be implemented in external (local) labs as shown by the excellent correlation results. The results of the signal pathway activity analysis correlate well with breast subtype classification, however, the assay has the potential to uncover specific pathway activation independent of subtype which may have significant value for precision oncology and targeted therapy selection. The test has potential for wide utilization as it can be performed on conventional FFPE prepared breast specimens, and may be complementary to conventional mutational and IHC analysis for classifying breast cancer and selecting appropriate therapy.

Citation Format: Eveline den Biezen, Saskia Vermeer, Diederick Keizer, Martijn Akse, Martijn van Zelst, Dianne van Strijp, Hannah Park, Anthony Magliocco. A robust rapid mRNA based test to profile simultaneously ER, AR, PI3K and MAPK functional signaling pathway activity for precision oncology [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 740.

Abstract 741: Characterization of high-grade serous ovarian carcinoma by measuring functional signal transduction pathway activity

Introduction: The majority of advanced stage high-grade serous ovarian carcinoma (HGSC), the most common subtype of ovarian cancer, recurs within the first 24 months despite complete remission after initial treatment. Yet there are remarkable differences in disease-free (DFS) and overall survival (OS). We hypothesize that differences in signal transduction pathway (STP) activity may relate to survival and may also improve targeted therapy selection. We investigate the STP activity in relation to survival in patients diagnosed with advanced stage HGSC, as well as identify STPs that may be targeted in alternative treatment strategies.

Methods: We included 85 HGSC patients (DFS <12 months, n=52 and DFS >24 months, n=33) who achieved complete remission after treatment with debulking surgery and chemotherapy. Total mRNA was extracted, and RT-qPCR was performed to determine expression levels of pathway-specific target genes in primary HGSC samples taken prior to start of chemotherapy. OncoSignal pathway assays were used to quantitatively measure functional STP activity of the androgen and estrogen receptor (ER), PI3K, Hedgehog, TGF-β and Wnt pathways. Survival analysis in relation to STP activity was performed by means of Cox regression analysis and differences between groups were analyzed with Mann-Whitney U tests.

Results: Differences in PI3K, Hedgehog and TGF-β pathway activity were observed across the HGSC cohort, suggesting unique tumor activation patterns. Median STP activity was not discernably different between the short and long DFS groups. Significantly higher ER pathway activity was found in premenopausal women (n=16) compared to postmenopausal women (n=67) (p=0.002). Cox regression analysis in postmenopausal women (n=67) showed that ER pathway activity was positively associated with DFS (HR=0.943, p=0.033) and OS (HR=0.930, p=0.041) in univariate analysis. None of the pathways were significantly related to DFS or OS in premenopausal women (n=16).

Conclusion: We observed a positive association between ER pathway activity and survival in postmenopausal women but not in premenopausal women. Also, differences in activation levels of the other STPs were observed in individual patients. STP analysis may be used to aid targeted therapy selection, such as anti-hormonal therapy, in HGSC patients.

Citation Format: Phyllis van der Ploeg, Laura van Lieshout, Yvonne Wesseling-Rozendaal, Anja van de Stolpe, Diederick Keizer, Steven Bosch, Marjolein Lentjes-Beer, Caroline Vos, Joanne de Hullu, Ruud Bekkers, Jurgen Piek. Characterization of high-grade serous ovarian carcinoma by measuring functional signal transduction pathway activity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 741.

Predictive and prognostic biomarker identification in a large cohort of androgen receptor-positive salivary duct carcinoma patients scheduled for combined androgen blockade

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Background: Patients suffering from recurrent or metastatic (R/M) salivary duct carcinoma (SDC) are often treated with combined androgen blockade (CAB). This treatment however frequently fails (response rates: 18-53%), resulting in a worse prognosis. Therefore, biomarkers that have prognostic value and can predict treatment response are urgently needed. Methods: mRNA from 77 R/M androgen receptor (AR) positive SDC patients treated with leuprorelin acetate combined with bicalutamide was extracted from pre-treatment tumor specimens. AR, Notch, Mitogen-Activated Protein Kinase (MAPK), Transforming Growth Factor beta (TGFβ), Estrogen Receptor (ER), Hedgehog (HH) and the Phosphoinositide 3-Kinase (PI3K) signaling pathway activities were calculated based on expression levels of relevant target genes. Besides this, 5-alpha reductase type 1 ( SRD5A1) expression and Human Epidermal growth factor Receptor 2 (HER2) status were determined. Clinical benefit was defined as complete or partial response or stable disease ≥6 months. Results: Of the 7 signaling pathways, AR pathway activity was the best predictor of clinical benefit (AUC 0.67, 95%-CI 0.54-0.80). At a threshold of 47.8, 21% of the patients tested negative, with a negative predictive value of 93%. SRD5A1 expression outperformed the signaling pathways regarding predictive value (AUC 0.78, 95%-CI 0.67-0.88). Fitting of a multivariable model led to the identification of SRD5A1, Notch and TGFβ as most predictive combination (AUC 0.82, 95%-CI 0.72-0.91). AR, Notch, HH and SRD5A1 were also of prognostic importance regarding progression free survival and SRD5A1 expression levels also for overall survival (median of 175.0 weeks for high versus 96.7 weeks for low expression). Conclusions: Our study revealed predictive and/or prognostic value of AR, HH, Notch and TGFβ signaling activities and SRD5A1 expression in SDC patients treated with CAB. AR pathway activity can be used for identifying non-responders. Further clinical validation is required before implementation of these biomarkers in clinical practice. The observed role of SRD5A1 expression in CAB response forms a rational basis for including SRD5A1-inhibitors in the treatment of SDC patients.[Table: see text]

Prediction of clinical benefit from androgen deprivation therapy in salivary duct carcinoma patients

Androgen deprivation therapy (ADT) is first‐line palliative treatment in androgen receptor‐positive (AR+) salivary duct carcinoma (SDC), and response rates are 17.6–50.0%. We investigated potential primary ADT resistance mechanisms for their predictive value of clinical benefit from ADT in a cohort of recurrent/metastatic SDC patients receiving palliative ADT (n = 30). We examined mRNA expression of androgen receptor (AR), AR splice variant‐7, intratumoral androgen synthesis enzyme‐encoding genes AKR1C3, CYP17A1, SRD5A1 and SRD5A2, AR protein expression, ERBB2 (HER2) gene amplification and DNA mutations in driver genes. Furthermore, functional AR pathway activity was determined using a previously reported Bayesian model which infers pathway activity from AR target gene expression levels. SRD5A1 expression levels and AR pathway activity scores were significantly higher in patients with clinical benefit from ADT compared to those without benefit. Survival analysis showed a trend toward a longer median progression‐free survival for patients with high SRD5A1 expression levels and high AR pathway activity scores. The AR pathway activity analysis, and not SRD5A1 expression, also showed a trend toward better disease‐free survival in an independent cohort of locally advanced SDC patients receiving adjuvant ADT (n = 14) after surgical tumor resection, and in most cases a neck dissection (13/14 patients) and postoperative radiotherapy (13/14 patients). In conclusion, we are the first to describe that AR pathway activity may predict clinical benefit from ADT in SDC patients, but validation in a prospective study is needed.

What's new?

Androgen deprivation therapy (ADT) is a leading treatment strategy in the palliative care of patients with androgen receptor (AR)‐positive salivary duct carcinoma (SDC). However, while as many as half of patients may respond to ADT, resistance frequently emerges, undermining its use. In this investigation of primary ADT resistance mechanisms, expression of the androgen synthesis enzyme‐encoding gene SRD5A1 and functional activity of the AR pathway were found to predict clinical benefit from ADT in SDC patients. High AR pathway activity scores were further linked to improved disease‐free survival in SDC patients with locally advanced disease who received adjuvant ADT.

Analytical evaluation of a new point of care system for measuring cardiac Troponin I

OBJECTIVES

Point-of-care cardiac troponin testing with adequate analytical performances has the potential to improve chest pain patients flow in the emergency department. We present the analytical evaluation of the newly developed Philips Minicare cTnI point-of-care immunoassay.

DESIGN & METHODS

Li-heparin whole blood and plasma were used to perform analytical studies. The sample type comparison study was performed at 4 different hospitals. The 99th percentile upper reference limit (URL) study was performed using Li-heparin plasma, Li-heparin whole blood and capillary blood samples from 750 healthy adults, aging from 18 to 86years.

RESULTS

Limit of the blank, limit of detection and limit of quantitation at 20% coefficient of variation (CV) were determined to be 8.5ng/L, 18ng/L and 38ng/L respectively without significant differences between whole blood and plasma for LoQ. Cross-reactivity and interferences were minimal and no high-dose hook was observed. Total CV was found to be from 7.3% to 12% for cTnI concentrations between 109.6 and 6135.4ng/L. CV at the 99th percentile URL was 18.6%. The sample type comparison study between capillary blood, Li-heparin whole blood and Li-heparin plasma samples demonstrated correlation coefficients between 0.99 and 1.00 with slopes between 1.03 and 1.08. The method comparison between Minicare cTnI and Beckman Coulter Access, AccuTnI+3 demonstrated a correlation coefficient of 0.973 with a slope of 1.09. The 99th percentile URL of a healthy population was calculated to be 43ng/L with no significant difference between genders or sample types.

CONCLUSIONS

The Minicare cTnI assay is a sensitive and precise, clinical usable test for determination of cTnI concentration that can be used in a near-patient setting as an aid in the diagnosis of acute myocardial infarction.

Single Pulse Electrical Stimulation to identify epileptogenic cortex: Clinical information obtained from early evoked responses

OBJECTIVE

Single Pulse Electrical Stimulation (SPES) probes epileptogenic cortex during electrocorticography. Two SPES responses are described: pathological delayed responses (DR, >100 ms) associated with the seizure onset zone (SOZ) and physiological early responses (ER, <100 ms) that map cortical connectivity. We analyzed properties of ERs, including frequencies >80 Hz, in the SOZ and seizure propagation areas.

METHODS

We used data from 12 refractory epilepsy patients. SPES consisted of 10 pulses of 1 ms, 4-8 mA and 5s interval on adjacent electrodes pairs. Data were available at 2048 samples/s for six and 512 samples/s (22 bits) for eight patients and analyzed in the time-frequency (TF) and time-domain (TD).

RESULTS

Electrodes with ERs were stronger associated with SOZ than non-SOZ electrodes. ERs with frequency content >80 Hz exist and are specific for SOZ channels. ERs evoked by stimulation of seizure onset electrodes were associated with electrodes involved in seizure propagation.

CONCLUSION

Analysis of ERs can reveal aspects of pathology, manifested by association with seizure propagation and areas with high ER numbers that coincide with the SOZ.

SIGNIFICANCE

Not only DRs, but also ERs could have clinical value for mapping epileptogenic cortex and help to unravel aspects of the epileptic network.

Assessment of the clinical relevance of quantitative sensory testing with Von Frey monofilaments in patients with allodynia and neuropathic pain. A pilot study

BACKGROUND

Allodynia is a common and disabling symptom in many patients with neuropathic pain. Whereas quantification of pain mostly depends on subjective pain reports, allodynia can also be measured objectively with quantitative sensory testing. In this pilot study, we investigated the clinical relevance of quantitative sensory testing with Von Frey monofilaments in patients with allodynia as a consequence of a neuropathic pain syndrome, by means of correlating subjective pain scores with pain thresholds obtained with quantitative sensory testing.

METHODS

During a 4-week trial, we administered a cannabis extract to 17 patients with allodynia. We quantified the severity of the allodynia with Von Frey monofilaments before, during and after the patients finished the trial. We also asked the patients to rate their pain on a numeric rating scale at these three moments.

RESULTS

We found that most of the effect of the cannabis occurred in the last 2 weeks of the trial. In this phase, we observed that the pain thresholds, as measured with Von Frey monofilaments, were inversely correlated with a decrease of the perceived pain intensity.

CONCLUSION

These preliminary findings indicate clinical relevance of quantitative sensory testing with Von Frey monofilaments in the quantification of allodynia in patients with neuropathic pain, although confirmation of our data is still required in further studies to position this method of quantitative sensory testing as a valuable tool, for example, in the evaluation of therapeutic interventions for neuropathic pain.

[The sensitization model: a method to explain chronic pain to a patient]

Chronic pain is pain without a clear somatic substrate. As a result, patients with chronic pain often do not receive a clear diagnosis following a medical examination. In many patients, having pain without a proper explanation or diagnosis induces stress and the urge to search elsewhere for explanations and treatments. There is growing evidence that many chronic-pain syndromes, such as chronic low-back pain, whiplash and fibromyalgia, share the same pathogenesis: sensitisation of pain-modulating systems in the central nervous system at both spinal and supraspinal level. This central sensitisation is facilitated by numerous factors that contribute to the maintenance of pain in a way that differs from individual to individual. How sensitisation may develop and persist as a result of medical, psychological and social factors calls for research from the perspective of a bio-psycho-social model. If sensitisation is used to explain chronic pain to a patient and the patient understands the relation beween pain and the factors that play a role in the maintenance of the pain, this can lead to acceptation of a treatment learning to cope with these factors.