Myeloid-derived suppressor cells and tolerogenic dendritic cells are distinctively induced by PI3K and Wnt signaling pathways

Imbalanced immune responses are a prominent hallmark of cancer and autoimmunity. Myeloid cells can be overly suppressive, inhibiting protective immune responses or inactive not controlling autoreactive immune cells. Understanding the mechanisms that induce suppressive myeloid cells, such as myeloid-derived suppressor cells (MDSCs) and tolerogenic dendritic cells (TolDCs), can facilitate the development of immune-restoring therapeutic approaches. MDSCs are a major barrier for effective cancer immunotherapy by suppressing antitumor immune responses in cancer patients. TolDCs are administered to patients to promote immune tolerance with the intent to control autoimmune disease. Here, we investigated the development and suppressive/tolerogenic activity of human MDSCs and TolDCs to gain insight into signaling pathways that drive immunosuppression in these different myeloid subsets. Moreover, monocyte-derived MDSCs (M-MDSCs) generated in vitro were compared to M-MDSCs isolated from head-and-neck squamous cell carcinoma patients. PI3K-AKT signaling was identified as being crucial for the induction of human M-MDSCs. PI3K inhibition prevented the downregulation of HLA-DR and the upregulation of reactive oxygen species and MerTK. In addition, we show that the suppressive activity of dexamethasone-induced TolDCs is induced by β-catenin-dependent Wnt signaling. The identification of PI3K-AKT and Wnt signal transduction pathways as respective inducers of the immunomodulatory capacity of M-MDSCs and TolDCs provides opportunities to overcome suppressive myeloid cells in cancer patients and optimize therapeutic application of TolDCs. Lastly, the observed similarities between generated- and patient-derived M-MDSCs support the use of in vitro-generated M-MDSCs as powerful model to investigate the functionality of human MDSCs.

Functional estrogen receptor signal transduction pathway activity and antihormonal therapy response in low-grade ovarian carcinoma

BACKGROUND

Advanced low-grade ovarian carcinoma (LGOC) is difficult to treat. In several studies, high estrogen receptor (ER) protein expression was observed in patients with LGOC, which suggests that antihormonal therapy (AHT) is a treatment option. However, only a subgroup of patients respond to AHT, and this response cannot be adequately predicted by currently used immunohistochemistry (IHC). A possible explanation is that IHC only takes the ligand, but not the activity, of the whole signal transduction pathway (STP) into account. Therefore, in this study, the authors assessed whether functional STP activity can be an alternative tool to predict response to AHT in LGOC.

METHODS

Tumor tissue samples were obtained from patients with primary or recurrent LGOC who subsequently received AHT. Histoscores of ER and progesterone receptor (PR) were determined. In addition, STP activity of the ER STP and of six other STPs known to play a role in ovarian cancer was assessed and compared with the STP activity of healthy postmenopausal fallopian tube epithelium.

RESULTS

Patients who had normal ER STP activity had a progression-free survival (PFS) of 16.1 months. This was significantly shorter in patients who had low and very high ER STP activity, with a median PFS of 6.0 and 2.1 months, respectively (p < .001). Unlike ER histoscores, PR histoscores were strongly correlated to the ER STP activity and thus to PFS.

CONCLUSIONS

Aberrant low and very high functional ER STP activity and low PR histoscores in patients with LGOC indicate decreased response to AHT. ER IHC is not representative of functional ER STP activity and is not related to PFS.

Corrigendum: Improved diagnosis of inflammatory bowel disease and prediction and monitoring of response to anti-TNF alpha treatment based on measurement of signal transduction pathway activity

[This corrects the article DOI: 10.3389/fphar.2022.1008976.].

Improved diagnosis of inflammatory bowel disease and prediction and monitoring of response to anti-TNF alpha treatment based on measurement of signal transduction pathway activity

Objective: Ulcerative colitis (UC) and Crohn’s disease (CD) are two subtypes of chronic inflammatory bowel disease (IBD). Differential diagnosis remains a challenge. Anti-TNFα treatment is an important treatment for IBD, yet resistance frequently occurs and cannot be predicted. Consequently, many patients receive ineffective therapy with potentially adverse effects. Novel assays are needed to improve diagnosis, and predict and monitor response to anti-TNF-α compounds.

Design: Signal transduction pathway (STP) technology was used to quantify activity of STPs (androgen and estrogen receptor, PI3K, MAPK, TGFβ, Notch, Hedgehog, Wnt, NFκB, JAK-STAT1/2, and JAK-STAT3 pathways) in colon mucosa samples of CD and UC patients, based on transcriptome analysis. Previously described STP assay technology is based on computational inference of STP activity from mRNA levels of target genes of the STP transcription factor.

Results: Results show that NFκB, JAK-STAT3, Wnt, MAPK, and androgen receptor pathways were abnormally active in CD and UC. Colon and ileum-localized CD differed with respect to STP activity, the JAK-STAT1/2 pathway being abnormally active in ileal CD. High activity of NFκB, JAK-STAT3, and TGFβ pathways was associated with resistance to anti-TNFα treatment in UC and colon-located CD, but not in ileal CD. Abnormal STP activity decreased with successful treatment.

Conclusion: We believe that measuring mucosal STP activity provides clinically relevant information to improve differential diagnosis of IBD and prediction of resistance to anti-TNFα treatment in patients with colon-localized IBD, and provides new targets for treatment and overcoming anti-TNFα resistance.

Abstract 1962: The relevance of estrogen driven tumor growth within the molecular subgroups of endometrial cancer

Introduction: Immunohistochemical expression (IHC) of estrogen receptor (ER) and progesterone receptor (PR) are biomarkers for prognosis and response to hormonal therapy in endometrial cancer (EC). However, the presence of ER/PR is not inherently reflective of estrogen driven tumor growth. Previously, ER pathway activity score (ERPAS), a test to asses ER pathway, was shown to reflect estrogen driven tumor growth and to have additional prognostic and predictive value over ER and PR-IHC. Within the four molecular subgroups of EC, ER and PR-IHC are present in all subgroups. Yet, the relation of ERPAS with molecular subgroups is unclear. In this study we aim to identify estrogen driven tumor growth by application of ERPAS in the molecular subgroups.

Methods: ER and PR-IHC expression, ERPAS testing and molecular analysis was available in 72 endometrial cancer cases. ER and PR-IHC expression was analyzed from formalin-fixed paraffin-embedded (FFPE) tumor sections using standard procedures. A cut-off value of 10% was defined as positive. ERPAS was performed using RT-qPCR analysis of the most relevant ER-related genes (www.philips.com/oncosignal). A Bayesian computational model was used to infer ERPAS that were normalized on a scale from 0 to 100. The cut-off value for an active ER pathway was 29.7, as previously defined. Molecular analysis was performed using Next Generation Sequencing with single-molecule Molecular Inversion Probes (smMIPs). Accordingly patients were grouped in the POLE-mutant, MSI high, TP53-mutant or no specific molecular profile, NSMP group.

Results: The TP53-mutant-group had a worse outcome compared to other groups. ER pathway was active in 75% of POLE-mutant, 83.3% of MSI-high, 87.5% of NSMP and 38.9% of TP53-mutant cases. Similarly, PR-IHC expression was present in 100% of POLE-mutant, 72.2% of MSI-high, 81.3% of NSMP and 27.8% of TP53-mutant cases. The mean ERPAS was significantly higher in MSI-high and NSMP groups compared to the TP53-mutant group. Within the NSMP subgroup, an active ER pathway was significantly associated with improved disease-free survival and disease-specific survival in Kaplan-Meier analysis. Analysis in other subgroups was not possible due to limited number of cases.

Conclusions: The majority of POLE-mutant, MSI-high and NSMP tumors showed an active ER pathway, indicating relevance of estrogen driven tumor growth in these groups. In the NSMP subgroup, ERPAS can be used to stratify patients for prognosis. Whether ER pathway is prognostic in the MSI-high and TP53-mutant subgroups needs to be evaluated in larger cohorts. If hormonal therapy is applied, we suggest to tailor it to patient with an active ER pathway.

Citation Format: Willem Jan van Weelden, Stephanie Vrede, Louis van der Putten, Hans Bulten, Marc Snijders, Sanne Sweegers, Andrea Romano, Astrid Eijkelenboom, Anja van de Stolpe, Johanna Pijnenborg. The relevance of estrogen driven tumor growth within the molecular subgroups of endometrial cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1962.

Measurement of activity of developmental signal transduction pathways to quantify stem cell pluripotency and phenotypically characterize differentiated cells

Important challenges in stem cell research and regenerative medicine are reliable assessment of pluripotency state and purity of differentiated cell populations. Pluripotency and differentiation are regulated and determined by activity of developmental signal transduction pathways (STPs). To date activity of these STPs could not be directly measured on a cell sample. Here we validate a novel assay platform for measurement of activity of developmental STPs (STP) for use in stem cells and stem cell derivatives. In addition to previously developed STP assays, we report development of an additional STP assay for the MAPK-AP1 pathway. Subsequently, activity of Notch, Hedgehog, TGFβ, Wnt, PI3K, MAPK-AP1, and NFκB signaling pathways was calculated from Affymetrix transcriptome data of human pluripotent embryonic (hES) and iPS cell lines under different culture conditions, organ-derived multipotent stem cells, and differentiated cell types, to generate quantitative STP activity profiles. Results show that the STP assay technology enables reliable and quantitative measurement of multiple STP activities simultaneously on any individual cell sample. Using the technology, we found that culture conditions dominantly influence the pluripotent stem cell STP activity profile, while the origin of the stem cell line was a minor variable. A pluripotency STP activity profile (Pluripotency qPAP) was defined (active PI3K, MAPK, Hedgehog, Notch, TGFβ, and NFκB pathway, inactive Wnt pathway). Differentiation of hES cells to intestinal progenitor cells resulted in an STP activity profile characterized by active PI3K, Wnt and Notch pathways, comparable to the STP activity profile measured on primary intestinal crypt stem cells. Quantitative STP activity measurement is expected to improve experimental reproducibility and standardization of pluripotent and multipotent stem cell culture/differentiation, and enable controlled manipulation of pluripotency/differentiation state using pathway targeting compounds.

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.

A Microfluidic Cancer-on-Chip Platform Predicts Drug Response Using Organotypic Tumor Slice Culture

Optimal treatment of cancer requires diagnostic methods to facilitate therapy choice and prevent ineffective treatments. Direct assessment of therapy response in viable tumor specimens could fill this diagnostic gap. Therefore, we designed a microfluidic platform for assessment of patient treatment response using tumor tissue slices under precisely controlled growth conditions. The optimized Cancer-on-Chip (CoC) platform maintained viability and sustained proliferation of breast and prostate tumor slices for 7 days. No major changes in tissue morphology or gene expression patterns were observed within this time frame, suggesting that the CoC system provides a reliable and effective way to probe intrinsic chemotherapeutic sensitivity of tumors. The customized CoC platform accurately predicted cisplatin and apalutamide treatment response in breast and prostate tumor xenograft models, respectively. The culture period for breast cancer could be extended up to 14 days without major changes in tissue morphology and viability. These culture characteristics enable assessment of treatment outcomes and open possibilities for detailed mechanistic studies. SIGNIFICANCE: The Cancer-on-Chip platform with a 6-well plate design incorporating silicon-based microfluidics can enable optimal patient-specific treatment strategies through parallel culture of multiple tumor slices and diagnostic assays using primary tumor material.

Characterization of Immunoactive and Immunotolerant CD4+ T Cells in Breast Cancer by Measuring Activity of Signaling Pathways That Determine Immune Cell Function

Simple Summary

Immunotherapy enhances the immune response against cancer and is potentially curative. Unfortunately, few patients with breast cancer benefit from this therapy. It is not possible to predict which patients will benefit. A blood cell, called CD4+ T-cell, plays a role in the immune response and in resistance to immunotherapy. Its function is determined by activity of biochemical processes, called signal transduction pathways (STPs). We developed a new technology to measure activity of these STPs, which was used to investigate whether CD4+ T cells function abnormally in breast cancer patients. We show that in CD4+ T-cells from most of the investigated breast cancer patients a number of these STPs are overactive. The abnormal activity of a few notable STPs (Notch and TGFβ) suggests that CD4+ T-cells have changed into regulatory T-cells, which inhibit the immune response against cancer and have been associated with resistance to immunotherapy. We also provide evidence that this change in the CD4+ T- cells is caused by a factor produced by breast cancer cells. We conclude that this new technology can be used to measure STP activity in blood of patients with cancer and has the potential to better identify patients who will benefit from immunotherapy.

Abstract

Cancer immunotolerance may be reversed by checkpoint inhibitor immunotherapy; however, only a subset of patients responds to immunotherapy. The prediction of clinical response in the individual patient remains a challenge. CD4+ T cells play a role in activating adaptive immune responses against cancer, while the conversion to immunosuppression is mainly caused by CD4+ regulatory T cell (Treg) cells. Signal transduction pathways (STPs) control the main functions of immune cells. A novel previously described assay technology enables the quantitative measurement of activity of multiple STPs in individual cell and tissue samples. The activities of the TGFβ, NFκB, PI3K-FOXO, JAK-STAT1/2, JAK-STAT3, and Notch STPs were measured in CD4+ T cell subsets and used to investigate cellular mechanisms underlying breast cancer-induced immunotolerance. Methods: STP activity scores were measured on Affymetrix expression microarray data of the following: (1) resting and immune-activated CD4+ T cells; (2) CD4+ T-helper 1 (Th1) and T-helper 2 (Th2) cells; (3) CD4+ Treg cells; (4) immune-activated CD4+ T cells incubated with breast cancer tissue supernatants; and (5) CD4+ T cells from blood, lymph nodes, and cancer tissue of 10 primary breast cancer patients. Results: CD4+ T cell activation induced PI3K, NFκB, JAK-STAT1/2, and JAK-STAT3 STP activities. Th1, Th2, and Treg cells each showed a typical pathway activity profile. The incubation of activated CD4+ T cells with cancer supernatants reduced the PI3K, NFκB, and JAK-STAT3 pathway activities and increased the TGFβ pathway activity, characteristic of an immunotolerant state. Immunosuppressive Treg cells were characterized by high NFκB, JAK-STAT3, TGFβ, and Notch pathway activity scores. An immunotolerant pathway activity profile was identified in CD4+ T cells from tumor infiltrate and blood of a subset of primary breast cancer patients, which was most similar to the pathway activity profile in immunosuppressive Treg cells. Conclusion: Signaling pathway assays can be used to quantitatively measure the functional immune response state of lymphocyte subsets in vitro and in vivo. Clinical results suggest that, in primary breast cancer, the adaptive immune response of CD4+ T cells may be frequently replaced by immunosuppressive Treg cells, potentially causing resistance to checkpoint inhibition. In vitro study results suggest that this is mediated by soluble factors from cancer tissue. Signaling pathway activity analysis on TIL and/or blood samples may improve response prediction and monitoring response to checkpoint inhibitors and may provide new therapeutic targets (e.g., the Notch pathway) to reduce resistance to immunotherapy.

Cyclic activity of signal transduction pathways in fimbrial epithelium of the human fallopian tube

INTRODUCTION

The local environment of the fallopian tube represents the optimal conditions for reproductive processes. To maintain tissue homeostasis, signal transduction pathways are thought to play a pivotal role. Enhancing our understanding of functional signal transduction pathway activity is important to be able to clarify the role of aberrant signal transduction pathway activity leading to female subfertility and other tubal diseases. Therefore, in this study we investigate the influence of the hormonal cycle on the activity of key signal transduction pathways in the fimbrial epithelium of morphologically normal fallopian tubes.

MATERIAL AND METHODS

We included healthy pre- (n = 17) and postmenopausal (n = 8) patients who had surgical interventions for benign gynecologic conditions. Histologic sections of the fallopian tubes were reviewed by two pathologists and, for the premenopausal patients, hormone serum levels and sections of the endometrium were examined to determine the hormonal phase (early follicular [n = 4], late follicular [n = 3], early luteal [n = 5], late luteal [n = 5]). After laser capture microdissection, total mRNA was extracted from the fimbrial epithelium and real-time quantitative reverse transcription-PCR was performed to determine functional signal transduction pathway activity of the androgen receptor (AR), estrogen receptor (ER), phosphoinositide-3-kinase (PI3K), Hedgehog (HH), transforming growth factor-beta (TGF-β) and canonical wingless-type MMTV integration site (Wnt) pathways.

RESULTS

The early luteal phase demonstrated high AR and ER pathway activity in comparison with the late luteal phase (p = 0.016 and p = 0.032, respectively) and low PI3K activity compared with the late follicular phase (p = 0.036), whereas the late luteal phase showed low activity of HH and Wnt compared with the early follicular phase (both p = 0.016). Signal transduction pathway activity in fimbrial epithelium from postmenopausal patients was most similar to the early follicular and/or late luteal phase with regard to the AR, ER and PI3K pathways. Wnt pathway activity in postmenopausal patients was comparable to the late follicular and early luteal phase. We observed no differences in HH and TGF-β pathway activity between pre- and postmenopausal samples. The cyclic changes in signal transduction pathway activity suggest a stage-specific function which may affect the morphology and physiology of the human fallopian tube.

CONCLUSIONS

We demonstrated cyclic changes in activity of the AR, ER, PI3K, HH and Wnt pathways throughout the hormonal cycle.

Androgen Receptor Pathway Activity Assay for Sepsis Diagnosis and Prediction of Favorable Prognosis

Introduction: Sepsis is a life-threatening complication of a bacterial infection. It is hard to predict which patients with a bacterial infection will develop sepsis, and accurate and timely diagnosis as well as assessment of prognosis is difficult. Aside from antibiotics-based treatment of the causative infection and supportive measures, treatment options have remained limited. Better understanding of the immuno-pathophysiology of sepsis is expected to lead to improved diagnostic and therapeutic solutions. Functional activity of the innate (inflammatory) and adaptive immune response is controlled by a dedicated set of cellular signal transduction pathways, that are active in the various immune cell types. To develop an immune response-based diagnostic assay for sepsis and provide novel therapeutic targets, signal transduction pathway activities have been analyzed in whole blood samples from patients with sepsis. Methods: A validated and previously published set of signal transduction pathway (STP) assays, enabling determination of immune cell function, was used to analyze public Affymetrix expression microarray data from clinical studies containing data from pediatric and adult patients with sepsis. STP assays enable quantitative measurement of STP activity on individual patient sample data, and were used to calculate activity of androgen receptor (AR), estrogen receptor (ER), JAK-STAT1/2, JAK-STAT3, Notch, Hedgehog, TGFβ, FOXO-PI3K, MAPK-AP1, and NFκB signal transduction pathways. Results: Activity of AR and TGFβ pathways was increased in children and adults with sepsis. Using the mean plus two standard deviations of normal pathway activity (in healthy individuals) as threshold for abnormal STP activity, diagnostic assay parameters were determined. For diagnosis of pediatric sepsis, the AR pathway assay showed high sensitivity (77%) and specificity (97%), with a positive prediction value (PPV) of 99% and negative prediction value (NPV) of 50%. For prediction of favorable prognosis (survival), PPV was 95%, NPV was 21%. The TGFβ pathway activity assay performed slightly less for diagnosing sepsis, with a sensitivity of 64% and specificity of 98% (PPV 99%, NPV 39%). Conclusion: The AR and TGFβ pathways have an immunosuppressive role, suggesting a causal relation between increased pathway activity and sepsis immunopathology. STP assays have been converted to qPCR assays for further evaluation of clinical utility for sepsis diagnosis and prediction of prognosis, as well as for prediction of risk at developing sepsis in patients with a bacterial infection. STPs may present novel therapeutic targets in sepsis.

Survival Is Related to Estrogen Signal Transduction Pathway Activity in Postmenopausal Women Diagnosed with High-Grade Serous Ovarian Carcinoma

High-grade serous ovarian carcinoma (HGSC), the most common subtype of ovarian cancer, has a high mortality rate. Although there are some factors associated with survival, such as stage of disease, there are remarkable differences in survival among women diagnosed with advanced stage disease. In this study, we investigate possible relations between survival and signal transduction pathway (STP) activity. We assessed the functional activity of the androgen receptor (AR), estrogen receptor (ER), phosphoinositide-3-kinase (PI3K), Hedgehog (HH), transforming growth factor beta (TGF-β) and canonical wingless-type MMTV integration site (Wnt) pathway in 85 primary tumor samples of patients with FIGO stage IIIC to IVB HGSC and disease-free survival (DFS) below 12 (n = 52) or over 24 months (n = 33). There were no significant differences in median pathway activity between patients with a short and long DFS. In univariate Cox proportional hazards analysis, ER pathway activity was related to a favorable DFS and overall survival (OS) in postmenopausal women (p = 0.033 and p = 0.041, respectively), but not in premenopausal women. We divided the postmenopausal group into subgroups based on ER pathway activity quartiles. Survival analysis revealed that postmenopausal women in the lowest ER quartile had a shorter DFS and OS (log-rank p = 0.006 and p < 0.001, respectively). Furthermore, we were able to form subgroups of patients based on an inverse relation between ER and PI3K pathway activity. In conclusion, in postmenopausal patients with advanced stage HGSC, a poorer survival outcome was associated with low functional ER pathway activity.

Impact of hormonal biomarkers on response to hormonal therapy in advanced and recurrent endometrial cancer

BACKGROUND

Approximately 20% of women with endometrial cancer have advanced-stage disease or suffer from a recurrence. For these women, prognosis is poor, and palliative treatment options include hormonal therapy and chemotherapy. Lack of predictive biomarkers and suboptimal use of existing markers for response to hormonal therapy have resulted in overall limited efficacy.

OBJECTIVE

This study aimed to improve the efficacy of hormonal therapy by relating immunohistochemical expression of estrogen and progesterone receptors and estrogen receptor pathway activity scores to response to hormonal therapy.

STUDY DESIGN

Patients with advanced or recurrent endometrial cancer and available biopsies taken before the start of hormonal therapy were identified in 16 centers within the European Network for Individualized Treatment in Endometrial Cancer and the Dutch Gynecologic Oncology Group. Tumor tissue was analyzed for estrogen and progesterone receptor expressions and estrogen receptor pathway activity using a quantitative polymerase chain reaction-based messenger RNA model to measure the activity of estrogen receptor-related target genes in tumor RNA. The primary endpoint was response rate defined as complete and partial response using the Response Evaluation Criteria in Solid Tumors. The secondary endpoints were clinical benefit rate and progression-free survival.

RESULTS

Pretreatment biopsies with sufficient endometrial cancer tissue and complete response evaluation were available in 81 of 105 eligible cases. Here, 22 of 81 patients (27.2%) with a response had estrogen and progesterone receptor expressions of >50%, resulting in a response rate of 32.3% (95% confidence interval, 20.9-43.7) for an estrogen receptor expression of >50% and 50.0% (95% confidence interval, 35.2-64.8) for a progesterone receptor expression of >50%. Clinical benefit rate was 56.9% for an estrogen receptor expression of >50% (95% confidence interval, 44.9-68.9) and 75.0% (95% confidence interval, 62.2-87.8) for a progesterone receptor expression of >50%. The application of the estrogen receptor pathway test to cases with a progesterone receptor expression of >50% resulted in a response rate of 57.6% (95% confidence interval, 42.1-73.1). After 2 years of follow-up, 34.3% of cases (95% confidence interval, 20-48) with a progesterone receptor expression of >50% and 35.8% of cases (95% confidence interval, 20-52) with an estrogen receptor pathway activity score of >15 had not progressed.

CONCLUSION

The prediction of response to hormonal treatment in endometrial cancer improves substantially with a 50% cutoff level for progesterone receptor immunohistochemical expression and by applying a sequential test algorithm using progesterone receptor immunohistochemical expression and estrogen receptor pathway activity scores. However, results need to be validated in the prospective Prediction of Response to Hormonal Therapy in Advanced and Recurrent Endometrial Cancer (PROMOTE) study.

Multiple Myeloma Relapse Is Associated with Increased NFκB Pathway Activity and Upregulation of the Pro-Survival BCL-2 Protein BFL-1

Multiple myeloma (MM) is a hematological malignancy that is still considered incurable due to the development of therapy resistance and subsequent relapse of disease. MM plasma cells (PC) use NFκB signaling to stimulate cell growth and disease progression, and for protection against therapy-induced apoptosis. Amongst its diverse array of target genes, NFκB regulates the expression of pro-survival BCL-2 proteins BCL-XL, BFL-1, and BCL-2. A possible role for BFL-1 in MM is controversial, since BFL-1, encoded by BCL2A1, is downregulated when mature B cells differentiate into antibody-secreting PC. NFκB signaling can be activated by many factors in the bone marrow microenvironment and/or induced by genetic lesions in MM PC. We used the novel signal transduction pathway activity (STA) computational model to quantify the functional NFκB pathway output in primary MM PC from diverse patient subsets at multiple stages of disease. We found that NFκB pathway activity is not altered during disease development, is irrespective of patient prognosis, and does not predict therapy outcome. However, disease relapse after treatment resulted in increased NFκB pathway activity in surviving MM PC, which correlated with increased BCL2A1 expression in a subset of patients. This suggests that BFL-1 upregulation, in addition to BCL-XL and BCL-2, may render MM PC resistant to therapy-induced apoptosis, and that BFL-1 targeting could provide a new approach to reduce therapy resistance in a subset of relapsed/refractory MM patients.

The effectiveness of monotherapy with PI3K/AKT/mTOR pathway inhibitors in ovarian cancer: A meta-analysis

OBJECTIVE

To determine the clinical benefit of monotherapy with PI3K/AKT/mTOR inhibitors in patients diagnosed with advanced or recurrent ovarian cancer and to investigate the predictive value of current PI3K/AKT/mTOR biomarkers on therapy response.

METHODS

A systematic search was conducted in PubMed, Embase and the Cochrane Library for articles reporting on treatment with PI3K/AKT/mTOR inhibitors in ovarian cancer. The primary endpoint was defined as the clinical benefit rate (CBR), including the proportion of patients with complete (CR) and partial response (PR) and stable disease (SD). Secondary endpoints included the overall response rate (ORR, including CR and PR) and drug-related grade 3 and 4 adverse events.

RESULTS

We included 233 patients from 19 studies and observed a pooled CBR of 32% (95% CI 20-44%) and ORR of 3% (95% CI 0-6%) in advanced or recurrent ovarian cancer patients treated with PI3K/AKT/mTOR inhibitors. Subgroup analysis tended to favor the studies who selected patients based on current PI3K/AKT/mTOR biomarker criteria (e.g. genomic alterations or loss of PTEN protein expression), but the difference in CBR was not statistically significant from studies with unselected populations (respectively, CBR of 42% (95% CI 23-62%) and 27% (95% CI 14-42%), P = 0.217). To better reflect true patient benefit, we excluded SD <6 months as a beneficial outcome which resulted in a pooled CBR of 7% (95% CI 2-13%). The overall proportion of patients with drug-related grade 3 and 4 adverse events was 36%.

CONCLUSIONS

The efficacy of monotherapy with PI3K/AKT/mTOR inhibitors in advanced recurrent ovarian cancer patients is limited to a small subgroup and selection of patients with the use of current biomarkers did not improved the CBR significantly. Given the toxicity profile, we suggest that current treatment with PI3K/AKT/mTOR inhibitors should not be initiated unless in clinical trials. Furthermore, improved biomarkers to measure functional PI3K/AKT/mTOR pathway activity are needed to optimize patient selection.

Abstract 533: Breast cancer IHC subtypes display heterogenous and independent targetable signaling pathway activity profiles

Background: Primary breast cancer is routinely subtyped using immunohistochemistry (IHC) staining and treatment choice is guided by the subtype. Targeted treatment requires the targeted signaling pathway to be active and tumor driving. IHC staining does not provide reliable information on active signaling pathways, and we reported before that clinical response of ER positive breast cancer patients to neoadjuvant aromatase inhibitor therapy appears to be more closely related to ER pathway activity rather than ER/PR IHC staining. To better understand the role of tumor driving signaling pathways within breast cancer subtypes and potentially improve precision medicine we evaluated signaling pathway activity profiles per IHC subtype, using novel assays to quantitatively measure activity of multiple main tumor driving signal transduction pathways, within tissue samples.

Methods: mRNA-based estrogen (ER) and androgen (AR) receptor, MAPK, PI3K, Hedgehog (HH), TGFβ, Notch, Wnt signal transduction pathway assays have been previously described. Pathway activity scores (PAS) were measured on primary untreated breast cancer samples, and compared to normal breast epithelium, using Affymetrix expression dataset GSE65194 (Institut Marie Curie), excluding the duplicate measures, containing 29 Luminal A, 30 Luminal B, 30 HER2, 41 triple negative (TN) breast cancer and 6 normal breast tissue sample data. Pathway activity scores exceeding the 95th percentile of normal were considered highly active.

Results: PAS thresholds for defining highly active pathway activity were for MAPK 23, AR 29, ER 34, PI3K 42, HH 34, Notch 65, TGFβ 48, Wnt 29. Luminal A was characterized by high ER pathway activity (n=25, 86%, mean PAS 45, SD 10); luminal B by high ER (n=10, 33%; mean PAS 32, SD 11) increased PI3K pathway activity (n=27, 90%; mean PAS 53, SD 10) and increased HH pathway activity (n=23, 77% mean PAS 29, SD 7); HER2 by high AR (n=18, 60%; mean PAS 30, SD 6) increased PI3K pathway activity (n=19, 63%; mean PAS 48, SD8) and increased HH pathway activity (n=27, 90% mean PAS 30 SD 7) ; TNBC by high PI3K (n=37, 90%; mean PAS 53, SD 7) plus high developmental pathway activity (Notch, n=6, 15%; mean PAS 53, SD 12; Wnt, n=28, 68%; mean PAS 31, SD 6). All subtypes had elevated MAPK pathway activity.

Discussion: Each breast cancer subtype based on IHC, had in the overall population a typical pathway activity profile. However within each IHC subtype, a substantial range of pathway activities between patients is observed, suggesting that within same IHC subtypes, clear differences in signal pathway activation can be measured that may provide a novel approach to more effectively select patients for specific precision oncology targeted therapy treatments.

Citation Format: Anthony M. Magliocco, Anja van de Stolpe, Martijn Akse, Eveline den Biezen, Laurent Holtzer. Breast cancer IHC subtypes display heterogenous and independent targetable signaling pathway activity profiles [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 533.

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 &lt;12 months, n=52 and DFS &gt;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.

Heterogeneity in Signaling Pathway Activity within Primary and between Primary and Metastatic Breast Cancer

Targeted therapy aims to block tumor-driving signaling pathways and is generally based on analysis of one primary tumor (PT) biopsy. Tumor heterogeneity within PT and between PT and metastatic breast lesions may, however, impact the effect of a chosen therapy. Whereas studies are available that investigate genetic heterogeneity, we present results on phenotypic heterogeneity by analyzing the variation in the functional activity of signal transduction pathways, using an earlier developed platform to measure such activity from mRNA measurements of pathways' direct target genes. Statistical analysis comparing macro-scale variation in pathway activity on up to five spatially distributed PT tissue blocks (n = 35), to micro-scale variation in activity on four adjacent samples of a single PT tissue block (n = 17), showed that macro-scale variation was not larger than micro-scale variation, except possibly for the PI3K pathway. Simulations using a "checkerboard clone-size" model showed that multiple small clones could explain the higher micro-scale variation in activity found for the TGFβ and Hedgehog pathways, and that intermediate/large clones could explain the possibly higher macro-scale variation of the PI3K pathway. While within PT, pathway activities presented a highly positive correlation, correlations weakened between PT and lymph node metastases (n = 9), becoming even worse for PT and distant metastases (n = 9), including a negative correlation for the ER pathway. While analysis of multiple sub-samples of a single biopsy may be sufficient to predict PT response to targeted therapies, metastatic breast cancer treatment prediction requires analysis of metastatic biopsies. Our findings on phenotypic intra-tumor heterogeneity are compatible with emerging ideas on a Big Bang type of cancer evolution in which macro-scale heterogeneity appears not dominant.

RNA Based Approaches to Profile Oncogenic Pathways From Low Quantity Samples to Drive Precision Oncology Strategies

Precision treatment of cancer requires knowledge on active tumor driving signal transduction pathways to select the optimal effective targeted treatment. Currently only a subset of patients derive clinical benefit from mutation based targeted treatment, due to intrinsic and acquired drug resistance mechanisms. Phenotypic assays to identify the tumor driving pathway based on protein analysis are difficult to multiplex on routine pathology samples. In contrast, the transcriptome contains information on signaling pathway activity and can complement genomic analyses. Here we present the validation and clinical application of a new knowledge-based mRNA-based diagnostic assay platform (OncoSignal) for measuring activity of relevant signaling pathways simultaneously and quantitatively with high resolution in tissue samples and circulating tumor cells, specifically with very small specimen quantities. The approach uses mRNA levels of a pathway's direct target genes, selected based on literature for multiple proof points, and used as evidence that a pathway is functionally activated. Using these validated target genes, a Bayesian network model has been built and calibrated on mRNA measurements of samples with known pathway status, which is used next to calculate a pathway activity score on individual test samples. Translation to RT-qPCR assays enables broad clinical diagnostic applications, including small analytes. A large number of cancer samples have been analyzed across a variety of cancer histologies and benchmarked across normal controls. Assays have been used to characterize cell types in the cancer cell microenvironment, including immune cells in which activated and immunotolerant states can be distinguished. Results support the expectation that the assays provide information on cancer driving signaling pathways which is difficult to derive from next generation DNA sequencing analysis. Current clinical oncology applications have been complementary to genomic mutation analysis to improve precision medicine: (1) prediction of response and resistance to various therapies, especially targeted therapy and immunotherapy; (2) assessment and monitoring of therapy efficacy; (3) prediction of invasive cancer cell behavior and prognosis; (4) measurement of circulating tumor cells. Preclinical oncology applications lie in a better understanding of cancer behavior across cancer types, and in development of a pathophysiology-based cancer classification for development of novel therapies and precision medicine.

A Novel Dual Antibody Staining Assay to Measure Estrogen Receptor Transcriptional Activity

Activity of the canonical estrogen receptor (ER) pathway is equivalent to functional activity of the nuclear ER transcription factor. Monoclonal antibodies (MoAbs) that identify nuclear ER in cells and tissue samples are frequently used to assess ER transcriptional activity, however, it remains unclear if this approach is sufficiently predictive of ER pathway activity. This study uses ER-positive breast cancer cell lines (MCF7 and T47D) in which ER transcriptional activity was quantified using an mRNA-based ER pathway activity assay. The relationship between ER activity and nuclear ER staining with ER MoAbs was then investigated. Confirming earlier findings, the results show that while the presence of ER in the cell nucleus is a prerequisite for ER activity, it is not predictive of ER transcriptional activity. There were remarkable differences in the behaviours of the antibodies used in the study. EP1 and 1D5 showed reduced nuclear staining when ER was transcriptionally active, while staining with H4624 was independent of ER activity. To improve discrimination between active and inactive nuclear ER based on ER staining, a method was developed which consists of dual ER MoAb immunofluorescent staining, followed by generation of a digital image with a standard digital pathology scanner. Then a cell nucleus detection algorithm and per cell calculation of the nuclear H4624/EP1 fluorescence intensity ratio was applied, where a high H4624/EP1 ratio predicts an active ER pathway. With this method, the EP1 and 1D5 antibodies are interchangeable. We hypothesize that the transcriptional activation of ER hides the epitope recognized by MoAbs EP1 and 1D5, while H4624 binds an ER epitope that remains accessible during ER pathway activation. The method described in this study should add substantial value to the assessment of ER pathway activity for biomedical research and diagnostics.

A Molecular Test for Quantifying Functional Notch Signaling Pathway Activity in Human Cancer

Simple Summary

The Notch signal transduction pathway is important for various physiological processes, including immune responses, and plays a role in many diseases, for example cancer. We have developed a new assay to quantitatively measure Notch pathway activity, and we validated it using data from various human cancer cell lines. The assay can be applied across different cell types, and offers numerous possibilities to explore the contribution of the Notch pathway to tumor formation and the stratification of cancer patients. We assessed Notch pathway activity in a cohort of T cell acute lymphoblastic leukemia (T-ALL) patient samples, and found that the pathway activity score more accurately reflects Notch pathway activity than a prediction on the basis of NOTCH1 mutations alone. Finally, we found that patients with low Notch pathway activity had a significantly shorter event-free survival compared to patients who had T-ALL cells with higher activity.

Abstract

Background: The Notch signal transduction pathway is pivotal for various physiological processes, including immune responses, and has been implicated in the pathogenesis of many diseases. The effectiveness of various targeted Notch pathway inhibitors may vary due to variabilities in Notch pathway activity among individual patients. The quantitative measurement of Notch pathway activity is therefore essential to identify patients who could benefit from targeted treatment. Methods: We here describe a new assay that infers a quantitative Notch pathway activity score from the mRNA levels of generally conserved direct NOTCH target genes. Following the calibration and biological validation of our Notch pathway activity model over a wide spectrum of human cancer types, we assessed Notch pathway activity in a cohort of T-ALL patient samples and related it to biological and clinical parameters, including outcome. Results: We developed an assay using 18 select direct target genes and high-grade serous ovarian cancer for calibration. For validation, seven independent human datasets (mostly cancer series) were used to quantify Notch activity in agreement with expectations. For T-ALL, the median Notch pathway activity was highest for samples with strong NOTCH1-activating mutations, and T-ALL patients of the TLX subtype generally had the highest levels of Notch pathway activity. We observed a significant relationship between ICN1 levels and the absence/presence of NOTCH1-activating mutations with Notch pathway activity scores. Patients with the lowest Notch activity scores had the shortest event-free survival compared to other patients. Conclusions: High Notch pathway activity was not limited to T-ALL samples harboring strong NOTCH1 mutations, including juxtamembrane domain mutations or hetero-dimerization combined with PEST-domain or FBXW7 mutations, indicating that additional mechanisms may activate Notch signaling. The measured Notch pathway activity was related to intracellular NOTCH levels, indicating that the pathway activity score more accurately reflects Notch pathway activity than when it is predicted on the basis of NOTCH1 mutations. Importantly, patients with low Notch pathway activity had a significantly shorter event-free survival compared to patients showing higher activity.

Measurement of Cellular Immune Response to Viral Infection and Vaccination

Combined cellular and humoral host immune response determine the clinical course of a viral infection and effectiveness of vaccination, but currently the cellular immune response cannot be measured on simple blood samples. As functional activity of immune cells is determined by coordinated activity of signaling pathways, we developed mRNA-based JAK-STAT signaling pathway activity assays to quantitatively measure the cellular immune response on Affymetrix expression microarray data of various types of blood samples from virally infected patients (influenza, RSV, dengue, yellow fever, rotavirus) or vaccinated individuals, and to determine vaccine immunogenicity. JAK-STAT1/2 pathway activity was increased in blood samples of patients with viral, but not bacterial, infection and was higher in influenza compared to RSV-infected patients, reflecting known differences in immunogenicity. High JAK-STAT3 pathway activity was associated with more severe RSV infection. In contrast to inactivated influenza virus vaccine, live yellow fever vaccine did induce JAK-STAT1/2 pathway activity in blood samples, indicating superior immunogenicity. Normal (healthy) JAK-STAT1/2 pathway activity was established, enabling assay interpretation without the need for a reference sample. The JAK-STAT pathway assays enable measurement of cellular immune response for prognosis, therapy stratification, vaccine development, and clinical testing.

Signal Transduction Pathway Activity in High-Grade, Serous Ovarian Carcinoma Reveals a More Favorable Prognosis in Tumors with Low PI3K and High NF-κB Pathway Activity: A Novel Approach to a Long-Standing Enigma

Simple Summary

All cells have a complex internal network of ‘communication chains’ called signal transduction pathways (STPs). Through interaction of different proteins in STPs, they are partly responsible for the behavior of a cell. In our study, we investigated the activity of eight STPs in datasets with genetic information on 140 cancer samples. These samples were derived from the most common subtype of ovarian cancer: high grade serous ovarian carcinoma (HGSC). With a novel method, we determined which STPs were active and discerned two groups based on activity of the phosphoinositide 3-kinase (PI3K) and nuclear factor-kappa B (NF-kB) pathways. The group with low PI3K and high NF-kB activity had a better progression free and overall survival compared to the group with high PI3K and low NF-kB activity. This difference may indicate that the ‘better prognosis group’ had a more active immune system or that the cells divided at a slower rate.

Abstract

We investigated signal transduction pathway (STP) activity in high-grade serous ovarian carcinoma (HGSC) in relation to progression-free survival (PFS) and overall survival (OS). We made use of signal transduction pathway activity analysis (STA analysis), a novel method to quantify functional STP activity. Activity of the following pathways was measured: androgen receptor (AR), estrogen receptor (ER), phosphoinositide 3-kinase (PI3K), Hedgehog (Hh), Notch, nuclear factor-kappa B (NF-κB), transforming growth factor beta (TGF-β), and Wnt. We selected HGSC samples from publicly available datasets of ovarian cancer tissue, and used repeated k-means clustering to identify pathway activity clusters. PFS and OS of the clusters were analyzed. We used a subset of publicly available dataset GSE9891 (n = 140), where repeated k-means clustering based on PI3K and NF-κB pathway activity in HGSC samples resulted in two stable clusters. The cluster with low PI3K and high NF-κB pathway activity (n = 72) had a more favorable prognosis for both PFS (p = 0.004) and OS (p = 0.001) compared to the high-PI3K and low-NF-κB pathway activity cluster (n = 68). The low PI3K and high NF-κB pathway activity of the favorable prognosis cluster may indicate a more active immune response, while the high PI3K and low NF-κB pathway activity of the unfavorable prognosis cluster may indicate high cell division.

Oestrogen receptor pathway activity is associated with outcome in endometrial cancer

BACKGROUND

Oestrogen receptor (ER) expression is a prognostic biomarker in endometrial cancer (EC). However, expression does not provide information about the functional activity of the ER pathway. We evaluated a model to quantify ER pathway activity in EC, and determined the prognostic relevance of ER pathway activity.

METHODS

ER pathway activity was measured in two publicly available datasets with endometrial and EC tissue, and one clinical cohort with 107 samples from proliferative and hyperplastic endometrium and endometrioid-type EC (EEC) and uterine serous cancer (USC). ER pathway activity scores were inferred from ER target gene mRNA levels from Affymetrix microarray data (public datasets), or measured by qPCR on formalin-fixed paraffin-embedded samples (clinical cohort) and related to ER expression and outcome.

RESULTS

ER pathway activity scores differed significantly throughout the menstrual cycle supporting the validity of the pathway test. The highest ER pathway scores were found in proliferative and hyperplastic endometrium and stage I EEC, whereas stage II-IV EEC and USCs had significantly lower levels. Low ER pathway activity was associated with recurrent disease, and added prognostic value in patients with low ER expression.

CONCLUSION

The ER pathway test reflects activity of the ER pathway, and may improve prediction of outcome in EC patients.

Abstract P5-02-08: Androgen receptor pathway activity and the ratio between androgen and estrogen receptor pathway activity in breast cancer subtypes

Background: Androgen receptor (AR) immunohistochemistry staining in breast cancer has revealed frequent AR expression in all breast cancer subtypes. Activity of the AR signaling pathway can be either tumor suppressive or tumor promoting, depending on tumor context (Pharmacol Ther., In press, https://doi.org/10.1016/j.pharmthera.2019.05.005). For this reason, in an individual patient, AR phenotypic activity needs to be defined in order to choose the proper AR targeted therapy. The AR/ER protein ratio has been suggested as a biomarker to define this AR function and enable the appropriate therapy choice, i.e. androgen therapy in case of a low AR/ER protein expression ratio, and anti-androgen therapy in case of a high ratio. However, AR and ER expression are not necessarily associated with an active signaling pathway. Therefore we investigated the ratio between functional AR and ER pathway activities as this may have an advantage in guiding therapy choice. Methods: AR and ER pathway activity and AR/ER pathway activity ratio were determined on public Affymetrix HG-U133 Plus 2.0 gene expression microarray data of clinical breast cancer studies (available in the GEO database: GSE12276, GSE21653, GSE20685, GSE42568, GSE6532, GSE9195, GSE45827, GSE7307, GSE10780, GSE17907, GSE21422, GSE5764, GSE31192, GSE54002 and Array Express: E-MTAB-365; total n=2090). For this, we used previously described tests that enable quantification of functional pathway activity, based on Bayesian computational model inference of pathway activity from measurements of mRNA levels of target genes of the ER and AR transcription factor (Cancer Res., 2014, vol. 74, no. 11, pp. 2936-2945; Sci Rep., 2019, vol. 9, no. 1, p. 1603). Intrinsic subtyping of all samples has been done using the same methodology as described elsewhere (Am J Pathol, 2018, vol. 188, no. 9, pp 1956-1972).Results: AR pathway activity was increased in all breast cancer subtypes compared to normal breast tissue (p&lt;0.0001); highest AR activity scores were observed in the HER2-enriched subtype. As shown before, ER activity scores were highest in luminal A and B subtypes. The AR/ER pathway activity ratio was low in luminal A and B, and comparable with normal tissue, but high in HER2 and basal breast cancer subtypes (p&lt;0.0001). Discussion: Results are compatible with currently available evidence and show that the AR pathway can be activated in all breast cancer subtypes. We hypothesize that its function depends on the level of co-existent ER pathway activity, i.e. a tumor suppressive function in ER pathway active breast cancer, and a tumor promoting function in ER pathway inactive breast cancer. Upon future clinical conformation, the AR/ER pathway activity ratio as determined on an individual patient tissue sample may be an improved biomarker to guide the choice of (complementary) AR pathway targeted therapy in breast cancer, i.e. androgen receptor pathway inhibitors in case of a high ratio and potential use of androgen receptor modulators in case of a low ratio.

Citation Format: Anja van de Stolpe, Yvonne Wesseling-Rozendaal, Marcia Alves de Inda, Henk van Ooijen, Wim Verhaegh. Androgen receptor pathway activity and the ratio between androgen and estrogen receptor pathway activity in breast cancer subtypes [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 P5-02-08.

Abstract P5-02-14: The MAPK pathway is variably active across breast cancer subtypes, and increased activity may be associated with hormonal therapy resistance

Background: Based on preclinical research, the MAPK growth factor pathway is thought to be an oncogenic pathway driving breast cancer, potentially in association with the ER pathway. In patients it is unclear how functional activity of the MAPK pathway activity relates to activity of the ER pathway to drive cancer growth. We have reported before on the development of assays, e.g. for the ER pathway, that enable quantitative measurement of activity of signal transduction pathways based on Bayesian computational model inference of pathway activity from measurements of mRNA levels of target genes of the ER transcription factor (Cancer Res., 2014, vol. 74, no. 11, pp. 2936-2945). We now present (1) development of the MAPK-AP1 pathway model, (2) MAPK-AP1 pathway activity and its relation to ER pathway activity in breast cancer; (3) emergence of MAPK pathway activity associated with hormonal therapy resistance. Methods: The MAPK-AP1 pathway model was developed and biologically validated on Affymetrix mRNA data from samples (different cell types) with a known MAPK pathway activity. MAPK-AP1 and ER pathway activity scores were measured on Affymetrix expression data of primary untreated breast cancer samples (GSE45827, n=141) and of fulvestrant sensitive and resistant MCF7 cell line clones (GSE74391). Results: In clinical breast cancer samples, average MAPK pathway activity was increased in all subtypes compared to normal breast tissue, with a large dynamic range indicating that in each subtype there are samples with high and with low pathway activity; ER pathway activity in Luminal A and B subtypes ranged from high to low, and was low in all other subtypes. MAPK-AP1 pathway activity did not correlate with ER pathway activity. Fulvestrant-sensitive MCF7 cells had high ER and low MAPK pathway activity scores, while resistant MCF7 clones exhibited increased MAPK pathway activity and complete loss of ER pathway activity, explaining therapy resistance. Discussion: The MAPK-AP1 pathway is frequently activated in all breast cancer subtypes, independent of ER pathway activity. We hypothesize that in case of resistance to hormonal therapy measurement of both pathway activities may be informative as to the underlying resistance mechanism, i.e. loss of ER pathway activity and/or gain of MAPK pathway activity. Future clinical studies are needed to confirm the role of these signaling pathways in hormonal resistance.

Citation Format: Anja van de Stolpe, Laurent Holtzer, Yvonne Wesseling-Rozendaal, Wim Verhaegh. The MAPK pathway is variably active across breast cancer subtypes, and increased activity may be associated with hormonal therapy resistance [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 P5-02-14.

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.

Abstract A131: Fulvestrant resistance in an MCF-7 model for breast cancer is associated with complete loss of ER pathway activity and gain of MAPK-AP1 pathway activity

Background: 10-15 signal transduction pathways govern major cellular processes, e.g. cell division, differentiation and migration, both in physiology and pathophysiology. They are frequently abnormally active in cancer and can drive cancer growth and metastasis. Resistance to targeted drugs directed towards specific signaling pathways like the ER pathway, can be mediated by induction of activity of other signaling pathways. The past decade we developed a new method to quantitatively measure functional activity status of signal transduction pathways in individual cell and tissue samples, based on Bayesian computational model inference of pathway activity from measurements of mRNA levels of target genes of the pathway-associated transcription factor1,2,3. Assays have been developed for androgen (AR) and estrogen receptor (ER), Hedgehog (HH), Wnt, TGFb, Notch, NFkB, PI3K, JAK-STAT 1/2 and 3, and MAPK-AP1 pathways. They can be performed simultaneously on a single cell or tissue sample using Affymetrix HG-U133 Plus 2.0 microarray or qPCR, and provide quantitative pathway activity scores expressed on a log2odds scale. Method. Pathway analysis using these assays was performed on public Affymetrix expression microarray data (GSE74391,4) from ER-positive MCF-7 cells that were either sensitive or resistant to fulvestrant (n=26). Results. Resistance to fulvestrant was associated with complete loss of functional ER pathway activity (difference 16 log2odds score, p=0.00029) and gain of MAPK-AP1 pathway activity (difference 5.8 log2odds, p=0.00029) in ER positive MCF-7 cells. In the resistant MCF-7 cells, PI3K and MAPK-AP1 pathway activity were negatively correlated (Pearson 0.652, p=0.002), suggesting mutually exclusive pathway activation. Conclusion. Our pathway assays enabled identification of the previously unidentified mechanism of resistance to fulvestrant in a cell culture model system for breast cancer, demonstrating that: (1) ER positivity is a prerequisite, but not sufficient, for ER pathway activity, in agreement with our earlier clinical studies1,5,6;; (2) MAPK pathway activity may confer resistance to hormonal therapy; (3) in the absence of MAPK-AP1 pathway activity, the PI3K pathway may be an alternative resistance pathway; (3) signalling pathway assays are well suited to (quantitatively) investigate activity of signal transduction pathways which may confer resistance to a (targeted) drug treatment. References 1. Verhaegh, W. et al. SCancer Res. 74, 2936–2945 (2014). 2. van Ooijen, H. et al. Am. J. Pathol. 188, 1956–1972 (2018). 3. Stolpe, A. van de, et al. Sci Rep 9, 1603 (2019). 4. Alves, C. L. et al. Clin. Cancer Res. 22, 5514–5526 (2016). 5. Blok, E. J. et al. Cancer Res 76, P3-07-65-P3-07–65 (2016). 6. Yang, S.-R. et al. Cancer Res 79, P5-11-06-P5-11–06 (2019).

Citation Format: Yvonne Wesseling-Rozendaal, Anja van de Stolpe, Laurent Holtzer, Marcia Alves de Inda, Paul van de Wiel. Fulvestrant resistance in an MCF-7 model for breast cancer is associated with complete loss of ER pathway activity and gain of MAPK-AP1 pathway activity [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr A131. doi:10.1158/1535-7163.TARG-19-A131

Abstract C020: Quantitative measurements of functional activity of the TGFβ and MAPK-AP1 pathways in colon cancer provides information on their role in cancer development and metastasis

Background: The advancement of targeted drugs for blocking tumor driving signaling pathway(s) is expected to lead to improved outcome for cancer patients. However, a critical requirement for that is reliable and accurate diagnostics on activity of oncogenic signaling pathways. A novel analysis method, based on Bayesian network-based inference of signaling pathway activity from levels of target gene mRNAs of the pathway-associated transcription factor, was developed to infer pathway activity from mRNA expression data [1], with which we previously reported that the WNT [1] and PI3K pathway [2] become active in colon carcinomas. Methods. Public datasets from the Gene Expression Omnibus, measured with the Affymetrix U133 Plus 2.0 platform, were analyzed for signaling pathway activity scores, among which are the MAPK-AP1, and TGFβ pathways. Colon tissue samples have been classified using the Consensus Molecular Subtypes of colorectal cancer classification (CMS). [3] Results. WNT and PI3K pathway activity were increased in colon carcinomas as reported before. The signaling pathway activity described by the CMS classification was confirmed using pathway activity analysis, TGFβ pathway activity was highest in the bad prognosis CMS4 subtype. A Kaplan-Meier curve shows higher TGFβ pathway activity to be associated with lower survival chance (p &lt; 0.0001). Higher TGFβ pathway activity is seen in colon cancer metastases compared to primary tumors (p &lt; 1e-13, based on 13 independent datasets). MAPK-AP1 pathway activity was increased (p &lt; 1e-15, based on 18 analyzed datasets) in primary tumor samples compared to normal colon tissue, as demonstrated across multiple datasets, including a dataset with matched primary tumor and normal adjacent samples. Conclusion. MAPK-AP1 pathway activity in colon cancer is in line with frequent KRAS mutations that activate this pathway, while the dynamic range in activity may suggest a variation in sensitivity to targeted therapy. Results suggest that the lower survival associated with the CMS4 subtype is caused by increased TGFβ pathway activity, which is known to play a role in metastatic behavior, especially when activated in the presence of an active MAPK-AP1 signaling pathway, through interaction between the respective associated SMAD and c-Jun transcription factors [4]. Activity of these pathways can be measured simultaneously in a quantitative manner in an individual patient sample. They are clinically actionable and provide targets for drug-based therapy. Further clinical studies will be directed towards confirmation of the results and exploration of the clinical value of potential therapeutic approaches to prevent metastatic behavior in CRC on a personalized basis. References. [1] Cancer Res, vol. 74, no. 11, pp. 2936–2945, Jun. 2014. [2] The American Journal of Pathology, vol. 188, no. 9, pp. 1956–1972, Sep. 2018. [3] Nature Medicine, vol. 21, no. 11, pp. 1350–1356, Nov. 2015. [4] Cell, vol. 134, no. 2, pp. 215–230, Jul. 2008.

Citation Format: Yvonne Wesseling-Rozendaal, Paul van Swinderen, Julie Gil, Sieglinde Neerken, Anja van de Stolpe. Quantitative measurements of functional activity of the TGFβ and MAPK-AP1 pathways in colon cancer provides information on their role in cancer development and metastasis [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr C020. doi:10.1158/1535-7163.TARG-19-C020

Estrogen Receptor Pathway Activity Score to Predict Clinical Response or Resistance to Neoadjuvant Endocrine Therapy in Primary Breast Cancer

Endocrine therapy is important for management of patients with estrogen receptor (ER)-positive breast cancer; however, positive ER staining does not reliably predict therapy response. We assessed the potential to improve prediction of response to endocrine treatment of a novel test that quantifies functional ER pathway activity from mRNA levels of ER pathway-specific target genes. ER pathway activity was assessed on datasets from three neoadjuvant-treated ER-positive breast cancer patient cohorts: Edinburgh: 3-month letrozole, 55 pre-/2-week/posttreatment matched samples; TEAM IIa: 3- to 6-month exemestane, 49 pre-/28 posttreatment paired samples; and NEWEST: 16-week fulvestrant, 39 pretreatment samples. ER target gene mRNA levels were measured in fresh-frozen tissue (Edinburgh, NEWEST) with Affymetrix microarrays, and in formalin-fixed paraffin-embedded samples (TEAM IIa) with qRT-PCR. Approximately one third of ER-positive patients had a functionally inactive ER pathway activity score (ERPAS), which was associated with a nonresponding status. Quantitative ERPAS decreased significantly upon therapy (P < 0.001 Edinburgh and TEAM IIa). Responders had a higher pretreatment ERPAS and a larger 2-week decrease in activity (P = 0.02 Edinburgh). Progressive disease was associated with low baseline ERPAS (P = 0.03 TEAM IIa; P = 0.02 NEWEST), which did not decrease further during treatment (P = 0.003 TEAM IIa). In contrast, the staining-based ER Allred score was not significantly associated with therapy response (P = 0.2). The ERPAS identified a subgroup of ER-positive patients with a functionally inactive ER pathway associated with primary endocrine resistance. Results confirm the potential of measuring functional ER pathway activity to improve prediction of response and resistance to endocrine therapy.

Artificial Intelligence in Clinical Health Care Applications: Viewpoint

The idea of artificial intelligence (AI) has a long history. It turned out, however, that reaching intelligence at human levels is more complicated than originally anticipated. Currently, we are experiencing a renewed interest in AI, fueled by an enormous increase in computing power and an even larger increase in data, in combination with improved AI technologies like deep learning. Healthcare is considered the next domain to be revolutionized by artificial intelligence. While AI approaches are excellently suited to develop certain algorithms, for biomedical applications there are specific challenges. We propose six recommendations—the 6Rs—to improve AI projects in the biomedical space, especially clinical health care, and to facilitate communication between AI scientists and medical doctors: (1) Relevant and well-defined clinical question first; (2) Right data (ie, representative and of good quality); (3) Ratio between number of patients and their variables should fit the AI method; (4) Relationship between data and ground truth should be as direct and causal as possible; (5) Regulatory ready; enabling validation; and (6) Right AI method.

Quantitative Measurement of Functional Activity of the PI3K Signaling Pathway in Cancer

The phosphoinositide 3-kinase (PI3K) growth factor signaling pathway plays an important role in embryonic development and in many physiological processes, for example the generation of an immune response. The pathway is frequently activated in cancer, driving cell division and influencing the activity of other signaling pathways, such as the MAPK, JAK-STAT and TGFβ pathways, to enhance tumor growth, metastasis, and therapy resistance. Drugs that inhibit the pathway at various locations, e.g., receptor tyrosine kinase (RTK), PI3K, AKT and mTOR inhibitors, are clinically available. To predict drug response versus resistance, tests that measure PI3K pathway activity in a patient sample, preferably in combination with measuring the activity of other signaling pathways to identify potential resistance pathways, are needed. However, tests for signaling pathway activity are lacking, hampering optimal clinical application of these drugs. We recently reported the development and biological validation of a test that provides a quantitative PI3K pathway activity score for individual cell and tissue samples across cancer types, based on measuring Forkhead Box O (FOXO) transcription factor target gene mRNA levels in combination with a Bayesian computational interpretation model. A similar approach has been used to develop tests for other signaling pathways (e.g., estrogen and androgen receptor, Hedgehog, TGFβ, Wnt and NFκB pathways). The potential utility of the test is discussed, e.g., to predict response and resistance to targeted drugs, immunotherapy, radiation and chemotherapy, as well as (pre-) clinical research and drug development.

Fibrinogen Binding to ICAM-1 on EA.hy 926 Endothelial Cells Is Dependent on an Intact Cytoskeleton

Fibrinogen is a ligand for Intercellular Adhesion Molecule-1 (ICAM-1), and enhances monocyte-endothelial cell interaction by coupling Mac-1 on monocytes to ICAM-1 on endothelial cells. We investigated the role of the cytoskeleton in fibrinogen binding to the human endothelial cell line EA.hy 926 using immunofluorescence techniques. In this cell line TNFα induced the simultaneous appearance of stress fibers and of ICAM-1, which was clustered predominantly on endothelial cell projections. Incubation of TNFα-stimulated endothelial cells with fibrinogen resulted in binding of fibrinogen to ICAM-1 on these cell projections. Disruption of the cytoskeleton by cytocholasin B abolished fibrinogen binding. Activation of protein kinase C with 12-O-tetradecanoyl phorbol- 13-acetate resulted in simultaneous loss of both stress fibers and fibrinogen binding. These results suggest that a connection between ICAM-1 and the cytoskeleton results in clustering of ICAM-1 on cell projections, which is required for fibrinogen binding.

Assessment of Functional Phosphatidylinositol 3-Kinase Pathway Activity in Cancer Tissue Using Forkhead Box-O Target Gene Expression in a Knowledge-Based Computational Model

The phosphatidylinositol 3-kinase (PI3K) pathway is commonly activated in cancer. Tumors are potentially sensitive to PI3K pathway inhibitors, but reliable diagnostic tests that assess functional PI3K activity are lacking. Because PI3K pathway activity negatively regulates forkhead box-O (FOXO) transcription factor activity, FOXO target gene expression is inversely correlated with PI3K activity. A knowledge-based Bayesian computational model was developed to infer PI3K activity in cancer tissue samples from FOXO target gene mRNA levels and validated in cancer cell lines treated with PI3K inhibitors. However, applied to patient tissue samples, FOXO was often active in cancer types with expected active PI3K. SOD2 was differentially expressed between FOXO-active healthy and cancer tissue samples, indicating that cancer-associated cellular oxidative stress alternatively activated FOXO. To enable correct interpretation of active FOXO in cancer tissue, threshold levels for normal SOD2 expression in healthy tissue were defined above which FOXO activity is oxidative stress induced and below which PI3K regulated. In slow-growing luminal A breast cancer and low Gleason score prostate cancer, FOXO was active in a PI3K-regulated manner, indicating inactive PI3K. In aggressive luminal B, HER2, and basal breast cancer, FOXO was increasingly inactive or actively induced by oxidative stress, indicating PI3K activity. We provide a decision tree that facilitates functional PI3K pathway activity assessment in tissue samples from patients with cancer for therapy response prediction and prognosis.

Abstract 2656: Estrogen receptor pathway activity in endometrial carcinomas and its relation to tumor grade and recurrence

Background

Immunohistochemical (IHC) loss of expression of the estrogen (ER) and progesterone receptor (PR) from endometrial carcinomas is associated with high tumor grade, and with recurrent disease. However, expression of these receptors is not always indicative of functional pathway activity. A novel approach to predict signaling pathway activity, based on Knowledge-based Bayesian computational models interprets quantitative transcriptome data as the functional output of an active signaling pathway by using expression levels of transcriptional target genes. The objectives of this study were to compare ER pathway activity to ER and PR IHC results with respect to endometrial carcinoma grade and disease recurrences.

Materials and Methods

Originally for Affymetrix, the pathway analysis was adapted for RT-qPCR enabling use on FFPE tissue. Calibration and threshold definition was performed using tissue with known pathway activity. Pathway analysis was performed on: (1) A public dataset (GSE56026) containing Affymetrix expression microarray data from 62 patients with grade 1 (n=23),2 (n=17) and 3 (n=11) endometrioid and serous (n=12) carcinomas, and (2) formalin fixed, paraffin embedded (FFPE) tissue from endometrioid (n=70) and serous carcinomas (n=15), treated at the Radboud university medical center, which were immunohistochemically stained for ER and PR, and analyzed for pathway activity using qPCR.

Results

(1)

Analysis of the public dataset showed an inverse relation between ER pathway activity score and cancer grade, with the lowest ER activity in serous carcinomas. The Mann-Whitney U test showed significant differences between grade 1 and 2 (p=0.015), grade 1 and 3 (p=0.004), and grade 1 and serous carcinomas (p&lt;0.0001).

(2)

These results were confirmed in the FFPE tissue. The ER pathway was active in 30% (n=18), and inactive in 70% (n=41) of the samples. In advanced stage endometrioid and all serous carcinomas, ER pathway was active in 8% (n=2) and inactive in 92% (n=24) of the samples (Fisher p=0.03). Endometrial carcinoma related death (ECD) rate was 20% (n=17). While individually, ER pathway activity, ER and PR IHC were all significantly correlated with ECD, (logistic regression odds ratio, OR = 0.53, 0.12, 0.15, and p=0.0004, 0.0005, 0.002, respectively). In a multivariate analysis only ER pathway activity and disease stage remained significantly correlated with ECD (OR=0.52, p=0.03).

Conclusion

In two independent patient cohorts, the ER pathway model analysis, performed on data from Affymetrix microarrays and qPCR measurements showed an inverse relationship between the pathway activity and increasing tumor grade. While ER activity and ER/PR staining were related, only ER activity and cancer stage remained significant in a multivariate analysis with respect to immunohistochemistry alone when trying to predict recurrent disease.

Citation Format: Louis J. van der Putten, Anne van Brussel, Willem Jan van Weelden, Márcia A. de Inda, Leon F. Massuger, Henk van Ooijen, Anja van de Stolpe, Johanna M. Pijnenborg. Estrogen receptor pathway activity in endometrial carcinomas and its relation to tumor grade and recurrence [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2656.

Abstract 1052: Identification of signal transduction pathway activity in patient-derived xenograft models in comparison with their originating clinical samples of a variety of human cancer types

Background. Targeted drugs are directed against cellular signal transduction pathways, such as the PI3K pathway, and efficacy depends on the active pathway in the tumor. Development and clinical application of targeted drugs for personalized cancer treatment require tests which identify pathway activity in cancer cells/tissue. Patient-derived xenograft (PDX) models are becoming the cornerstone of preclinical drug development. Characterization of PDX models and clinical samples for pathway activity is needed for successful preclinical drug testing and patient drug response prediction. Inference of signal transduction pathway activity from cancer genomics information is often unreliable. A novel analysis method has been developed which enables identification and quantification of activity of signal transduction pathways, based on Bayesian reasoning models which infer an activity score from mRNA levels of pathway target genes (Verhaegh et al, Cancer Res 2014:2936-45). For the AR, ER, PI3K, Hedgehog, TGFbeta, Wnt, and NFkB pathways, models have been biologically validated on a number of different cell/tissue types. Methods. For a number of different cancer types (among which colon, breast, lung, ovarian, bladder, osteosarcoma, melanoma, esophagus), AR, ER, PI3K, Hedgehog, TGFbeta, Wnt, and NFkB pathway activity was inferred from Affymetrix HG-U133Plus2.0 microarray data, available from clinical studies (GEO database) and from PDX models (Charles River). Clinical and xenograft pathway activity scores were compared and where possible correlated to genomic datato identify associated pathway driving alterations. Results. Different cancer types were analyzed and compared. Pathway activity patterns for different cancer types in PDX models resemble pathway activity in clinical patient cohorts. Furthermore, known associated cancer mutations are reproduced in PDX models, such as APC mutations in colon PDX and ovary PDX, and an activating beta-catenin mutation in breast PDX, that show an activated Wnt pathway. Conclusion. Signal transduction pathway activity in PDX models resembles pathway activity in patient cohorts with corresponding cancer types and corresponds with known driving mutations. Functional pathway activity testing in PDX models is expected to increase xenograft model utility for (1) further validation of pathway tests for clinical diagnostic use and for (2) preclinical testing of targeted drug efficacy.

Citation Format: Wim Verhaegh, Anja van de Stolpe, Nevisa Caushaj, Manuel Landesfeind, Angelika Zaremba. Identification of signal transduction pathway activity in patient-derived xenograft models in comparison with their originating clinical samples of a variety of human cancer types [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1052.