Genomic Considerations in the Treatment of Thyroid Carcinoma

Highlighting genomically driven targeted therapies to improve outcomes in advanced thyroid carcinoma.

Resilience strengthening in youth with a chronic medical condition: a randomized controlled feasibility trial of a combined app and coaching program

Youth with a chronic medical condition (CMC) are often affected by comorbid mental disorders. Resilience-strengthening interventions can protect youth's mental health, yet evidence-based programs remain scarce. To address this lack, this study aimed to evaluate the feasibility of a dual approach combining app-based resilience training and cognitive behavioral group coaching. Fifty-one youths with CMC treated at a German university children's hospital aged 12-16 years were recruited. They were randomly assigned to a combined app game and coaching intervention or sole app gameplay. At pre-, post-intervention, and at a 2-month follow-up resilience, automatic negative thoughts and an app and coaching evaluation were assessed. Feasibility was defined as a recruitment rate of 70%, an 85% adherence rate for the REThink game, and 70% participation in both coaching sessions. Feasibility criteria were reached for coaching participation but not for recruitment or app adherence. While both the REThink game app and coaching intervention had high acceptance rates among youth with CMC, participants receiving additional coaching sessions showed higher satisfaction and adherence rates. Participants preferred remote to in-person meetings. The findings support a combination of a gamification app approach with online group coaching. Group coaching can improve adherence while online options increase accessibility. Future research should focus on testing in diverse participant samples, language, and age-adapted updates of the REThink game app. These findings provide guidance for increasing adherence in future intervention studies in youth with CMC cohorts.

Tooth-composite bond failure with a universal and an etch-and-rinse adhesive depending on mode and frequency of application

OBJECTIVES

To evaluate the effect of an additional layer of universal adhesive on the interfacial enamel/dentin-composite gap formation in relation to application mode and aging, via spectral domain optical coherence tomography (SD-OCT) and scanning electron microscopy (SEM).

METHODS

In vitro class V cavities in 114 caries-free premolars were restored by applying one or two layers of a universal adhesive (Scotchbond Universal, SBU) in self-etch (se) and etch-and-rinse (er) mode or the reference adhesive OptiBond FL (OFL-er). The restorations were imaged by SD-OCT (six groups, n = 8) and SEM (n = 3) directly after filling (t1), water storage (t2, 24 h), embedding (t3), and thermo-mechanical loading (t4, TCML). The interfacial gaps were quantified using 26 parameters and analyzed using principal component analysis and linear mixed effect models.

RESULTS

Gap formation at enamel and dentin was significantly influenced by the adhesive, the application mode and number of layers (p < 0.001). This was due to the influence of the SBU-er mode (p < 1e-05), which showed significantly more gap formation and a greater range of variation with double application when compared to SBU-se and OFL. The fewest interfacial gaps occurred with one or two applications of OFL-er and one layer of SBU-er.

SIGNIFICANCE

Adhesive application mode and the number of adhesive layers are relevant factors in the tooth-composite bond failure. Double application worsened the adaptation of SBU to freshly prepared dentin conditioned with phosphoric acid.

A phase 1 evaluation of the safety and tolerability of niraparib in combination with everolimus in advanced ovarian and breast cancers

OBJECTIVES

Phase 1 trial to determine the safety and tolerability of everolimus and niraparib in patients with advanced ovarian and breast malignancies.

RESULTS

Fourteen heavily pretreated patients were enrolled (12 high-grade serous ovarian cancer, 1 clear cell ovarian cancer, and 1 triple negative breast cancer). All patients were PARP naïve and received comprehensive genomic profiling prior to enrollment. Two DLTs were experienced in cohort 2 (niraparib 200 mg daily and everolimus 5 mg 3 days per week) with one patient experiencing prolonged thrombocytopenia and the other experiencing severe hypertension. Four additional patients were enrolled after dose de-escalation with one patient again experiencing severe hypertension leading to conclusion of the study. The most frequent grade 3 or greater adverse events were thrombocytopenia, hypertension, anemia, fatigue, neutropenia, and elevated alkaline phosphatase. Two patients had a PR and five patients had SD. ORR was 18% and the CBR was 45% in 11 evaluable patients. Median PFS was 6 months, and median OS is approximately 18 months with three patients still alive at the data cutoff.

CONCLUSIONS

The combination of everolimus and niraparib demonstrated significant toxicity at lower doses and is not feasible due to rapid onset and severe hypertension. This limitation possibly blunted the efficacy of the combination as PFS was modest, but OS was surprisingly robust due to three patients with ovarian cancer remaining alive with platinum refractory disease. Further investigation of multiagent blockade of the PI3K pathway combined with PARP is warranted.

Evaluation of anti-Xa levels in patients with venous thromboembolism within the first 48 h of anticoagulation with unfractionated heparin

Background: A 2019 study by Prucnal and colleagues found that the majority of patients treated with unfractionated heparin for pulmonary embolism did not maintain therapeutic activated partial thromboplastin time levels during the first 48 h of therapy. Objective: The purpose of this study was to evaluate the ability of an institution's unfractionated heparin dosing protocol to achieve and maintain therapeutic anti-Xa levels within the first 48 h of therapy in patients with venous thromboembolism. Methods: This retrospective study included 205 patients from May 2016 through September 2020. Patients were divided into two cohorts: bolus plus infusion (N = 89) and infusion only (N = 116). The primary objective was to determine the number of patients who achieved at least one therapeutic level. Results: Overall, 200 patients (97.6%) had at least one therapeutic level with no statistically significant difference between cohorts (p = 0.65). No more than 60% of patients achieved a therapeutic level at any of the 6-h intervals throughout the timeframe. The median time to the first therapeutic level in the overall group was 12.8 h with no statistically significant difference between the bolus plus infusion and infusion-only cohorts (13.3 h versus 12.7 h, respectively, p = 0.48). Conclusions: Most patients were able to achieve at least one therapeutic level within the first 48 h, but fewer were able to maintain therapeutic levels. Further studies are warranted to determine whether alternative dosing strategies would yield consistent achievement of therapeutic levels and affect patient-oriented outcomes.

Combining Solid and Liquid Biopsy for Therapy Monitoring in Esophageal Cancer

Esophageal cancer (EC) has one of the highest mortality rates among cancers, making it imperative that therapies are optimized and dynamically adapted to individuals. In this regard, liquid biopsy is an increasingly important method for residual disease monitoring. However, conflicting detection rates (14% versus 60%) and varying cell-free circulating tumor DNA (ctDNA) levels (0.07% versus 0.5%) have been observed in previous studies. Here, we aim to resolve this discrepancy. For 19 EC patients, a complete set of cell-free DNA (cfDNA), formalin-fixed paraffin-embedded tumor tissue (TT) DNA and leukocyte DNA was sequenced (139 libraries). cfDNA was examined in biological duplicates and/or longitudinally, and TT DNA was examined in technical duplicates. In baseline cfDNA, mutations were detected in 12 out of 19 patients (63%); the median ctDNA level was 0.4%. Longitudinal ctDNA changes were consistent with clinical presentation. Considerable mutational diversity was observed in TT, with fewer mutations in cfDNA. The most recurrently mutated genes in TT were TP53, SMAD4, TSHZ3, and SETBP1, with SETBP1 being reported for the first time. ctDNA in blood can be used for therapy monitoring of EC patients. However, a combination of solid and liquid samples should be used to help guide individualized EC therapy.

Prevalence trends of type 1 and type 2 diabetes in children and adolescents in North Rhine-Westphalia, the most populous federal state in Germany, 2002-2020

AIMS

To estimate the prevalence and temporal trends of type 1 and type 2 diabetes mellitus in children and adolescents (type 1 diabetes: 0-19 years, type 2 diabetes: 10-19 years) in North Rhine-Westphalia (NRW), Germany, from 2002 to 2020.

METHODS

The NRW Diabetes Registry records new cases based on three data sources (median completeness of ascertainment 99% for type 1 diabetes, 94% for type 2 diabetes). We determined age- and/or sex-standardized prevalence estimates (95% confidence intervals) per 100,000 individuals. Differences in age and sex, as well as time trends, were examined by Poisson regression. Furthermore, joinpoint regression was used to evaluate changes in prevalence trends over time.

RESULTS

At the end of 2020, the estimated type 1 diabetes prevalence was 247.1 (240.3; 253.9) with an annual increase of 2.9% (2.7%; 3.1%). The type 2 diabetes prevalence was 12.7 (10.6; 14.9) and increased by 6.4% (5.6%; 7.3%) per year. The prevalence trends were not uniform over the total period and flattened considerably in recent years.

CONCLUSIONS

The prevalence of type 1 and type 2 diabetes has increased significantly but at a lower rate in recent years. Continued surveillance of the prevalence is essential for the planning of health care resources and prevention measures.

Phase I dose escalation study of dual PI3K/mTOR inhibition by Sapanisertib and Serabelisib in combination with paclitaxel in patients with advanced solid tumors

BACKGROUND

Phase I trial to determine the safety and efficacy of paclitaxel, sapanisertib, and serabelisib.

PATIENTS AND METHODS

Patients with previously treated advanced solid tumors were eligible for this open label, cohort study of sapanisertib (TAK-228) and serabelisib (TAK-117) with weekly paclitaxel. A traditional 3 + 3 dose escalation design with 5 dosing cohorts was used. Patient reported outcomes were also evaluated.

RESULTS

19 heavily pretreated patients were enrolled (10 ovarian, 3 breast, and 6 endometrial cancers). All patients received comprehensive genomic profiling prior to enrollment. RP2D is sapanisertib 3 or 4 mg, serabelisib 200 mg on days 2-4, 9-11, 16-18 and 23-25 with paclitaxel 80 mg/m2 on days 1, 8 and 15 every 28 days. All patients in Cohort 5 required dose reductions and one patient experienced a DLT. The most frequent grade 3 or 4 adverse events were decreased WBCs (20%), nonfebrile neutropenia (12%), anemia (9%), elevated liver enzymes (4%), and hyperglycemia (11%). 3 patients had a CR, 4 had a PR, and 4 patients had SD > six months. ORR was 47% and CBR was 73% in 15 evaluable patients. Including all 19 enrolled patients, the PFS was 11 months and OS is still ongoing at 17 months.

CONCLUSIONS

The combination of sapanisertib, serabelisib, and paclitaxel was safe and generally well tolerated. Preliminary efficacy was remarkable in an area of unmet need, especially for patient with PI3K/AKT/mTOR pathway aberrations. Positive effects and sustained clinical benefit were even seen in patients that were refractory to platinum and had failed taxane, everolimus, or temsirolimus.

CLINICAL TRIAL NUMBER

ClinicalTrials.gov, NCT03154294.

Abstract 4095: Development of a molecular and clinical evidence-based algorithm for selecting optimal precision therapeutic strategy for patients with metastatic breast cancer

Background: Tumor complexity and heterogeneity require matching of actionable genomic alterations with available therapy to increase response rates and prolong survival in patients with cancer. It has been a long-standing challenge for treating oncologists to select an effective patient-specific therapeutic strategy due to the molecular rationale, disease relevance, patient-specific issues, including patient access to treatments. We have developed a set of molecular and clinical evidence-based criteria as an algorithm for ranking therapeutic strategies in order to deliver optimal care and improve outcomes in patients with metastatic malignancies.

Methods: Patients included in the analysis received comprehensive genomic profiling (CGP) for selected biomarkers. CGP results of 50 patients with stage IV tumors were reviewed by our multidisciplinary Molecular Tumor Board (MTB), after which treatment recommendations were generated based on molecular matching only (Cohort 1). CGP results of the other current 29 patients with stage IV breast cancer were reviewed by MTB, and therapeutic recommendations were provided with ranking scores calculated by our molecular and clinical evidence-based algorithm with the criteria not only focusing on molecular matching, but also including disease relevance, patient-specific clinical considerations and treatment availability as weighting factors (Cohort 2). The matching rates from recommendations and treatment outcomes of the two cohorts were then assessed.

Results: In Cohort 1, of the 50 patients, 34 patients (68%) were initiated with personalized therapeutic plans based on molecular matching that were recommended by our MTB. The other 16 patients were not treated with molecular matching therapeutic plans recommended by MTB, as the results of treating oncologists’ choices, treatment availability or patient preference. Patients were followed and outcomes were then evaluated. Thirteen patients (38.2% of 34 patients) achieved progression-free survival (PFS) at 12-week time point, and 6 patients achieved PFS (including stable disease, N=4 and partial response, N=2) at 6-month time point. The other 21 patients (61.8% of 34 patients) could not be assessed due to disease progression, treatment termination per drug toxicity or death before the follow-up time point. Cohort 2 is ongoing, the results of which will be presented in the meeting.

Conclusion: Our novel molecular and clinical evidence-based algorithm may be used to support oncologists decision-making to utilize the most clinically appropriate and effective therapeutic options. Additional studies with larger sample sizes in different type of solid tumors are planned in order to determine a clinically and statistically relevant range of score for the treatment recommendations with optimal clinical outcomes.

Citation Format: Yuliang Sun, Tobias Meissner, Rachel Elsey, Leah Theisen, Jason Jones, Casey Williams. Development of a molecular and clinical evidence-based algorithm for selecting optimal precision therapeutic strategy for patients with metastatic breast 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 4095.

Abstract 2271: Patient-specific visualization of cancer pathways

​Introduction: Analysis of whole transcriptomics datasets to quantify gene expression and determine differentially expressed genes has provided valuable information for precision medicine. Evaluating enrichment of specific gene groups and pathways, and visualizing these results is an important step to obtain inferences about patient treatment outcomes, overall survival, drug resistance and therapeutic targets.

However, pathway analysis of cancer patient samples in a N-of-1 setting without their respective control (normal) samples remains to be challenging. There is a crucial need for methods and tools to conduct and visualize pathway analysis results in this setting.

Methods and Results: Our method focuses on a visualization technique showing patient-specific pathway activation relative to reference populations from The Cancer Genome Atlas (TCGA) and The Genotype-Tissue Expression (GTEX). Patient-specific pathway activity scores are displayed within the respective percentiles and averages of the TCGA and GTEX cohorts to visualize a patient's individual pathway activation profile within the TCGA tumor and GTEX normal reference population. Patient-specific pathway scores are derived from an individual patient's transcriptomic profile and transformed into activity scores for each of 14 cancer pathways. This allows for the comparison of an individual patient’s pathway activation profile with reference samples from TCGA and GTEX. We used PROGENy (Pathway RespOnsive GENes for activity inference) to calculate activity scores for the 14 cancer related pathways.

The pathway activity scores of each new tumor sample are scaled using the parameters of scaled pathway activity scores obtained from TCGA and GTEX gene expression data of all cancer tissue types. Finally we visualized the pathway activity scores of each patient sample.

Conclusion: Our visualization method is expected to unravel the activation patterns of each of the 14 cancer pathways in our patient samples. Specific pathway genes can then be evaluated in the patient samples to identify causal mutations and their associations with the pathway activity scores hence aid in treatment selection and in the further development of precision medicine therapeutic solutions.

Citation Format: Padmapriya Swaminathan, Casey B. Williams, Tobias Meissner. Patient-specific visualization of cancer pathways [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 2271.

Abstract 1899: TrialMatch: A computational resource for the management of biomarker-based clinical trials at a precision oncology center

Introduction: The adoption of routine tumor sequencing, and the incorporation of biomarker-based clinical trials in the treatment of cancer has been steadily rising over the past few years. Access and ability to participate in clinical trials is a key element in providing therapeutic options for cancer patients.At the Avera Cancer Institute, options of biomarker-based clinical trials are routinely presented to the treating clinicians at the molecular tumor board (MTB). With everincreasing numbers of trials, a systematic method for keepingtrack of available trials andevaluating patients for trial options was needed. A search for solutions led to only one open-source tool, MatchMiner, but it did not meet our needs.

Methods and Results: We developed an open-source web application, TrialMatch, that has the ability to (i) add trials through a semi-automated curation interface, (ii) browse and search trials, (iii) and match patients to biomarker-based trials.TrialMatch is an R Shiny application that uses a mongo database to store the trial data. Software installation and application instantiation is managed through Docker. Curate This section has fields for a user to enter trial name and a NCT ID from clinicaltrials.gov. It then queries the clinicaltrials.gov API and fetches data about the sponsor, treatment, etc.Although disease and biomarker data are available on clinicaltrials.gov, they are not stored as discrete fields that can be queried, and hence require manual input. The user provides disease type based on the OncoTree classification, as well as biomarker information for mutations, copy numbers, fusions, TMB, MSI status, PD-L1 status, RNA expression, and disease specific markers such as ER/PR/HER2 status.All information for a particular trial is entered in a mongo database collection, with each trial stored as a document. The ability to add and edit data fields can be restricted to specific users. Browse This section allows the user to browse through all trials with key information such as NCT ID, trial name, disease, and biomarkers. Each row represents one trial and can be expanded to show more detailed information. This is useful to keep track of trials, and to quickly filter trials to a specific disease or biomarker. Match This section displays a patient-centric view of the trials that each patients’ age, sex, disease, and biomarkers have matched to. The matching can be automated for scheduled recurrentruns. At Avera, this is used during MTB to evaluate treatment options, but can also be used by clinicians to get a sense of the trials available for their patients, while awaiting formal review.

Conclusion: We believe that this computational tool fulfills a crucial need in the clinical application of precision oncology, and will ultimately increase clinical trial enrollment for patients.

Citation Format: Anu Amallraja, Shivani Kapadia, Padmadpriya Swaminathan, Casey Williams, Tobias Meissner. TrialMatch: A computational resource for the management of biomarker-based clinical trials at a precision oncology center [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 1899.

Implementation of the Avera/Sema4 oncology and analytics protocol (ASAP)

TPS6605

Background: Precision medicine represents a new era in oncology and population health. Comprehensive molecular profiling and hereditary cancer testing are increasingly important in the routine management of many malignancies, yet may not be widely adopted in many practices and leads to patients not consistently receiving care recommended by current national guidelines such as NCCN and ASCO. In addition, available targeted DNA sequencing panels may be limited to only defined drivers and lack detection in precancerous conditions. Whole exome sequencing (WES) combined with whole transcriptome sequencing (WTS) represent an expanded testing approach that identifies additional genetic changes beyond standard commercial panel tests. Current evidence suggests that WES/WTS is feasible to carry out in routine clinical practice, with improved detection of somatic alterations compared to smaller panels, and the promise to enhance access to targeted therapies and clinical trials. The primary purpose of the ASAP study is to understand the breadth of molecular characteristics present in participants cared for in a large integrated community-based health system, by linking comprehensive molecular profiles with clinical data extracted and curated from the electronic medical record. Methods: Avera Health is a large, Midwestern, predominantly rural vertically integrated health system with six regional cancer centers and over 40 oncology outreach sites across South Dakota and surrounding states. The ASAP study was initiated in November 2021 in GYN and as of February, the study is enrolling in the Otolaryngology clinic and expected to open in medical oncology and hematology in March/April 2022. The study will expand to include additional cancer centers outside of Sioux Falls later in 2022 and is anticipated to be open for accrual for 5 years. Enrolled participants are expected to receive WES/WTS and proteomics on their primary tumor and metastatic sites were feasible as well as hereditary testing, pharmacogenomics (PGx) and microbiome profiling. Liquid biopsies will be performed every 3 months while on treatment or when treatment is changed, in follow up to coincide with scheduled radiographic testing, and as part of annual routine surveillance. For participants not diagnosed with cancer, each participant will receive hereditary testing, PGx, microbiome, and a liquid biopsy at least annually. Participants also consent to sharing their electronic health information. Future stages of this work will employ natural language processing (NLP) methods to develop algorithms to help identify opportunities to improve patient outcomes. Projected enrollment is 1000 participants in year 1, 1500 participants in year 2, and up to 3000 annually thereafter. Approximately 50 patients have consented as of February 1 2022. Clinical trial information: NCT05142033.

Feasibility and potential efficacy of a guided internet- and mobile-based CBT for adolescents and young adults with chronic medical conditions and comorbid depression or anxiety symptoms (youthCOACHCD): a randomized controlled pilot trial

Background

Adolescents and young adults (AYA) with a chronic medical condition show an increased risk for developing mental comorbidities compared to their healthy peers. Internet- and mobile-based cognitive behavioral therapy (iCBT) might be a low-threshold treatment to support affected AYA. In this randomized controlled pilot trial, the feasibility and potential efficacy of youthCOACH_CD, an iCBT targeting symptoms of anxiety and depression in AYA with chronic medical conditions, was evaluated.

Methods

A total of 30 AYA (M_age 16.13; SD= 2.34; 73% female), aged 12-21 years either suffering from cystic fibrosis, juvenile idiopathic arthritis or type 1 diabetes, were randomly assigned to either a guided version of the iCBT youthCOACH_CD (IG, n=15) or to a waitlist control group (CG, n=15), receiving an unguided version of the iCBT six months post-randomization. Participants of the IG and the CG were assessed before (t0), twelve weeks after (t1) and six months after (t2) randomization. Primary outcome was the feasibility of the iCBT. Different parameters of feasibility e.g. acceptance, client satisfaction or potential side effects were evaluated. First indications of the possible efficacy with regard to the primary efficacy outcome, the Patient Health Questionnaire Anxiety and Depression Scale, and further outcome variables were evaluated using linear regression models, adjusting for baseline values.

Results

Regarding feasibility, intervention completion was 60%; intervention satisfaction (M = 25.42, SD = 5.85) and perceived therapeutic alliance (M = 2.83, SD = 1.25) were moderate and comparable to other iCBTs. No patterns emerged regarding subjective and objective negative side effects due to participation in youthCOACH_CD. Estimates of potential efficacy showed between group differences, with a potential medium-term benefit of youthCOACH_CD (β = -0.55, 95%CI: -1.17; 0.07), but probably not short-term (β = 0.20, 95%CI: -0.47; 0.88).

Conclusions

Our results point to the feasibility of youthCOACH_CD and the implementation of a future definitive randomized controlled trial addressing its effectiveness and cost-effectiveness. Due to the small sample size, conclusions are premature, however, further strategies to foster treatment adherence should be considered.

Trial registration

The trial was registered at the WHO International Clinical Trials Registry Platform via the German Clinical Trials Register (ID: DRKS00016714, 25/03/2019).

Supplementary Information

The online version contains supplementary material available at 10.1186/s12887-022-03134-3.

Abstract 1385: Clinical outcomes between obese and non-obese breast and gynecological cancer patients with alterations in the PI3K/AKT/mTOR pathway

Purpose Obesity has been shown to be strongly associated with the development of breast and gynecologic cancers. PIK3CA is one of the most commonly altered genes in solid tumors, and patients who have alterations are routinely initiated on therapies that target this pathway. However, response can vary greatly between patients, and the reason for differences in response has yet to be completely understood. Obesity has been shown to alter cancer metabolism and further dysregulate the PI3K/AKT/mTOR pathway which may affect response to target therapy. L. Cantley and colleagues suggest that the state of consistent hyperinsulinemia, which is common in obesity, can compromise the clinical benefit of PI3K-pathway targeted therapy, as insulin is a known potent stimulator of this pathway. Therefore, the purpose of this study was to compare clinical outcomes between obese and non-obese patients on pathway-directed therapy.

Methods A retrospective analysis was performed on 140 patients with breast, ovarian, cervical, or endometrial malignancies at Avera Cancer Institute. Female patients with a documented oncogenic PIK3CA alteration were included in the study. Overall survival (OS) and progression free survival (PFS) were the primary endpoints. BMI groups were determined by using existing clinical categories of obesity as defined by the CDC. Patients were stratified into 2 BMI groups: Group A 25 kg/m2 and Group B 25 kg/m2. The Kaplan-Meier method was used to derive time-to-event estimates and test for significance. A cox proportional-hazard model was utilized to determine the association between survival time for patients with BMI being the predictor variable.

Results Of the 140 patients, 106 patients had breast cancer, 21 patients had endometrial cancer, 9 patients had ovarian cancer, 3 patients had cervical cancer, and 1 patient had vaginal melanoma. There were 52 patients in Group A and 88 patients in Group B. 25 of the 140 patients had documented PIK3CA alterations but were never initiated on targeted therapy. Group B was found to reduce the hazard by a factor of 0.63 (p=0.09). The subset of Group B with PI3K/mTOR targeted therapy was found to reduce the hazard by a factor of 0.43 (p=0.008). Among the 43 patients who were included in PFS analysis, it was found that there was no statistically significant (p=0.6) improved PFS between the two groups.

Conclusion In this analysis, patients with a PIK3CA mutation and who had a higher BMI had an improved response rate from targeted therapy and overall survival than compared to patients with a lower BMI. Treatment lines prior to initiation of targeted therapy varied greatly, and differences in the multiple types of malignancies studied in this analysis was a limitation. More prospective studies that are statistically powered are warranted in order to assess the true impact of obesity on improved OS compared to patients with a BMI 25.

Citation Format: Diana Kim, Bing Xu, Rachel Elsey, Tobias Meissner, Casey Williams. Clinical outcomes between obese and non-obese breast and gynecological cancer patients with alterations in the PI3K/AKT/mTOR pathway [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 1385.

Abstract 371: A single-center retrospective review assessing the use of tumor mutation burden as a predictor of therapeutic success in patients receiving immunotherapy

Background

Cancer is a genetic disease in which cells may accumulate somatic mutations. The measurement of the frequency these somatic mutations occur is referred to as tumor mutational burden or TMB. A minority of these mutations may give rise to neoantigens that could in turn be recognized and targeted by the immune system. The more somatic mutations a tumor develops, the more likely these neoantigens are to form. Recent studies, namely KEYNOTE-158, found high TMB status to be associated with improved outcomes in patients receiving pembrolizumab monotherapy.

Materials and Methods

This was a single-center retrospective study that analyzed 73 patients who received cancer treatment at Avera Cancer Institute between June 2016 and July 2019. Patients were included/excluded from the final analysis based on having received at least one dose of pembrolizumab, ipilimumab, and/or nivolumab. Information was collected on patient characteristics, treatment, and clinical outcomes. The primary outcomes were complete and partial response rates and were assessed objectively based on a composite of radiographic reports, physician documentation, and treatment course. Secondary outcomes were clinical outcomes in patients with PD-1 and/or PD-L1 expression, clinical outcomes in patients receiving mono-immunotherapy vs combination therapy, and clinical outcomes based on the line of treatment in which immunotherapy was utilized.

Results

A total of 34 patients met the inclusion criteria of having a high TMB value (10 mutations/megabase) and having received one dose of pembrolizumab, ipilimumab, or nivolumab.

Primary Outcomes•16 patients experienced a partial response (AR = 0.47) and 6 of these patients experienced a complete response (AR = 0.17)

Secondary Outcomes•Absolute risk with prior TMB information (PR 0.43, CR: 0.17)•Absolute risks for monotherapy (PR: 0.375, CR: 0.125) vs combination therapy (PR: 0.556, CR: 0.375)•Average line of treatment for TF, PR, and CR were 2.24, 2, and 1.83 respectively.

Discussion

Studies like KEYNOTE-158 found a significant correlation between high TMB and improved clinical outcomes in patients receiving checkpoint inhibitors. However, in this cohort of patients high TMB status was not a good predictor of therapeutic success compared to the data presented in KEYNOTE-001, CHECKMATE-057, OAK, or PACIFIC. While there are limitations associated with the sample size, the data support that checkpoint therapy benefits patients when it is used earlier in their treatment course and combined with other treatments. Further exploration is required to determine the most appropriate cut point for calling a patient TMB high as well as how TMB and PD-L1 predict response to specific therapies.

Citation Format: Khai Nguyen, Bing Xu, Rachel Elsey, Tobias Meissner, Casey Williams. A single-center retrospective review assessing the use of tumor mutation burden as a predictor of therapeutic success in patients receiving immunotherapy [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 371.

The Effect of Solutions Containing Extracts of Vochysia tucanorum Mart., Myrcia bellaCambess., Matricaria chamomilla L. and Malva sylvestris L. on Cariogenic Bacterial Species and Enamel Caries Development

This study evaluated the effect of experimental solutions containing plant extracts on bacterial species and enamel caries prevention. Microcosm biofilm was produced from human saliva mixed with McBain saliva (0.2% sucrose) on bovine enamel for 5 days (3 days under anaerobiosis and 2 days under aerobiosis) at 37°C. From the 2nd day, the following treatments were applied (1 × 60 s/day): Vochysia tucanorum (10 mg/mL); Myrcia bella (5 mg/mL); Matricaria chamomilla (80 mg/mL); Malva sylvestris, fluoride, and xylitol (Malvatricin Plus®); 0.12% chlorhexidine (CHX, PerioGard®); and PBS (negative control). The medium pH was measured. Quantitative polymerase chain reaction was performed for the detection of Streptococcus mutans and Lactobacillus spp. Enamel demineralization was measured by spectral-domain optical coherence tomography. The data were compared by means of the Kruskal-Wallis/Dunn, two-way ANOVA/Bonferroni, and ANOVA/Tukey tests (p < 0.05). The pH decreased after sucrose exposure; only CHX reestablished pH >5.5 by the last day. CHX also eliminated Lactobacillusspp., but the other treatments did not differ significantly from PBS. Malvatricin Plus® and CHX eliminated S. mutans, but the other treatments did not differ from PBS. Similar results were seen concerning the reduction of lesion depth and reflectivity. The experimental natural-extract solutions were ineffective against cariogenic bacteria and in preventing the development of enamel caries.

Abstract P4-05-20: Case report - 16 year life history and genomic evolution of an ER+ HER2- breast cancer

Introduction

Metastasis is the primary cause of cancer-related death, with genomic evolution between primary and metastatic breast cancer only recently being studied in smaller numbers. We reconstructed the tumor evolution of a female patient originally diagnosed with localized ER+ HER2- disease to investigate the molecular changes that triggered relapse after long term aromatase inhibitor (AI) therapy and tracked them during subsequent treatments. The patient was diagnosed in 2002, relapsed in 2012 (regional lymph node), progressed in 2015 (liver metastasis), and passed away in 2018. We performed DNA- and RNA-sequencing on FFPE tumor samples and multiple liquid biopsies. The patient underwent eight lines of therapy including genome guided targeted therapy.

Materials and Methods

Whole exome and transcriptome sequencing was performed on the patient's primary tumor site at diagnosis (T1) and a metastatic lymph node (M1). Targeted DNA sequencing was performed on a metastatic liver sample (M2, 315 genes) and on liquid biopsies (n=11, 70 genes) every 2-3 months from 2015-2018.

Results

The mutational landscape between timepoints T1, M1 and M2 revealed low mutational burden at diagnosis which ultimately doubled at progression with active mutational processes (APOBEC, POLE) showing concordance between timepoints. DNA-based analysis revealed multiple mutations in the PI3K-Akt signaling pathway. Two mutations were shared between the samples: a clonal PIK3CA Q546R and a TP53 E180K mutation detected as clonal in M1/M2 and subclonal in T1. Individual samples carried private driver mutations, ranging from n=4 in T1, n=7 in M1 to n=16 in M2. While T1 harbored a single clonal driver mutation, with additional driver mutations being subclonal, M1 and M2 harbored multiple clonal driver mutations and a smaller percentage of subclonal driver mutations. A phylogenetic tree showed branching off between T1 and M1/M2. Liquid biopsies, while initially negative, started to detect mutations found among T1, M1 and M2, with increasing allele frequency (AF) throughout time. By the end of 2016, an ESR1 E380Q mutation not previously detected was found at a low AF that had rapidly increased by the end of 2017. RNA-Seq analysis revealed 908 (209 up, 699 down) genes to be differentially expressed between T1 and M1. Most significantly downregulated genes in M1 were TFF1 and PGR indicating loss-of-sensitivity / resistance to AI therapy. Most upregulated genes in M1 included PTHLH, S100P, and SOX2 which have been implicated in promoting tumor growth and metastasis. Pathway analysis between T1 and M1 showed enrichment for the hallmark gene sets ‘Estrogen Response early and late’ and ‘Epithelial mesenchymal transition’.

Conclusions

This phylogenetic reconstruction of the life history of a single patient's cancer revealed an increased mutational rate over time between the patient's primary tumor at diagnosis and samples taken at relapse; and a high level of heterogeneity with metastatic sites sharing only one driver mutation with the primary tumor at diagnosis and having acquired multiple de-novo driver mutations. Transcriptome profiling aided in uncovering the mechanisms that lead to the patient's initial relapse, indicating expression profile changes that promote tumor progression and metastasis as well as reduced sensitivity / resistance to the patients AI based therapy. Monitoring tumor progression through frequent liquid biopsies allowed for the detection of mutations from multiple metastatic sites, in addition to the detection and growth of an AI resistant clone harboring an ESR1 E380Q mutation that was not present in any of the solid tissue samples.

Citation Format: Bing Xu, Anu Amallraja, Padmapriya Swaminathan, Rachel Elsey, Christel Davis, Stephanie Theel, Sarah Viet, Jason Petersen, Amy Krie, Gareth E Davies, Casey B Williams, Erik Ehli, Tobias Meissner. Case report - 16 year life history and genomic evolution of an ER+ HER2- breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-05-20.

A Small Hypoxia Signature Predicted pCR Response to Bevacizumab in the Neoadjuvant GeparQuinto Breast Cancer Trial

PURPOSE

In breast cancer, bevacizumab increased pCR rate but not long-term survival and no predictive markers are available to identify patients with long-term benefit from the drug.

EXPERIMENTAL DESIGN

We profiled 289 pretherapeutic formalin-fixed, paraffin-embedded (FFPE) biopsies of HER2-negative patients from the GeparQuinto trial of neoadjuvant chemotherapy ± bevacizumab by exome-capture RNA-sequencing (RNA-seq). In a prospectively planned study, we tested molecular signatures for response prediction. IHC validation was performed using tissue microarrays.

RESULTS

We found strong agreement of molecular and pathologic parameters as hormone receptors, grading, and lymphocyte infiltration in 221 high-quality samples. Response rates (49.3% pCR overall) were higher in basal-like (68.9%) and HER2-enriched (45.5%) than in luminal B (35.7%), luminal A (17.9%), and normal-like (20.0%) subtypes. T-cell (OR = 1.60; 95% confidence interval, 1.21-2.12; P = 0.001), proliferation (OR = 2.88; 95% CI, 2.00-4.15; P < 0.001), and hypoxia signatures (OR = 1.92; 95% CI, 1.41-2.60; P < 0.001) significantly predicted pCR in univariate analysis. In a prespecified multivariate logistic regression, a small hypoxia signature predicted pCR (OR = 2.40; 95% CI, 1.28-4.51; P = 0.006) with a significant interaction with bevacizumab treatment (P = 0.020). IHC validation using NDRG1 as marker revealed highly heterogenous expression within tissue leading to profound loss of sensitivity in TMA analysis, still a significant predictive value for pCR was detected (P = 0.025).

CONCLUSIONS

Exome-capture RNA-seq characterizes small FFPE core biopsies by reliably detecting factors as for example ER status, grade, and tumor-infiltrating lymphocytes levels. Beside molecular subtypes and immune signatures, a small hypoxia signature predicted pCR to bevacizumab, which could be validated by IHC. The signature can have important applications for bevacizumab treatment in different cancer types and might also have a role for novel combination therapies of bevacizumab with immune checkpoint inhibition.

Evaluation of lipoprotein-associated phospholipase A2 as a marker for renal microvasculopathy in adolescents with Type 1 diabetes

AIM

To assess the relevance of lipoprotein-associated phospholipase A2 activity as a diagnostic and prognostic marker for renal microvascular diseases.

METHODS

We analysed lipoprotein-associated phospholipase A2 activity and lysophosphatidylcholine levels (as a surrogate marker of oxidative stress) in 165 adolescents (aged 17.0 ± 2.3 years) with a history of Type 1 diabetes greater than 10 years. Clinical data were obtained from the German/Austrian nationwide Diabetes-Patients Follow-up (DPV) registry at blood collection and on average 2.4 ± 1.3 years later at follow-up. Relationships between lipoprotein-associated phospholipase A2 activity and clinical, demographic and laboratory variables, lysophosphatidylcholine levels and presence of albuminuria were evaluated by multivariable linear and logistic regression.

RESULTS

Lipoprotein-associated phospholipase A2 activity was higher in male than female adolescents (P = 0.002). Albuminuria was present in 14% (22/158) of participants at baseline, and 5% (4/86) of participants without albuminuria at baseline developed albuminuria until follow-up. Lipoprotein-associated phospholipase A2 activity was associated neither with present nor with incident albuminuria. Lysophosphatidylcholine did not correlate with lipoprotein-associated phospholipase A2 activity. Cross-sectional bivariate correlation as well as multivariable linear regression analysis revealed a negative correlation of lipoprotein-associated phospholipase A2 activity with HbA_1c and HDL-cholesterol.

CONCLUSIONS

Lipoprotein-associated phospholipase activity was not associated with surrogate markers for oxidative stress and early diabetic nephropathy. The association of decreased lipoprotein-associated phospholipase A2 activity with poor glucose control might limit its function as a predictor of micro- and macrovascular diseases in Type 1 diabetes.

Abstract 5147: Clinical benefit of molecularly-guided treatment strategies on progression free survival in patients with advanced gastrointestinal malignancies

Introduction: Despite many advances, the treatment for most patients with advanced solid tumors in the abdomen continues to be a clinical challenge. The purpose of our study was to evaluate the clinical benefit of molecularly-guided treatment strategies on progression free survival in patients with advanced gastrointestinal malignancies.

Materials and Methods: We performed a retrospective chart review of 112 patients with advanced (&gt;90% stage IV) gastrointestinal cancer (n=60 colon, n=21 pancreas, n=10 cholangio, n=8 esophageal, n=13 others) that underwent targeted DNA sequencing of 343 genes and assessed mutations, treatments and outcomes. We compared evidence-based standard of care therapy to molecularly-guided treatment on progression free survival time pre- and post-sequencing. We further assessed KRAS mutational status on patient outcomes, as well as potential correlation between time to molecularly-guided treatment and patient outcomes.

Results: Out of 112 patients sequenced and presented to our molecular tumor board, 50% received molecularly-guided treatment. Most frequent molecularly-guided regimens included the addition of either a MEK and/or an mTOR inhibitor. The MEK inhibitor Trametinib was recommended for 58/112 patients, due to activating mutations in the RAS-MAPK pathway (46 of all patients were KRAS mutated), and 27/58 patients received Trametinib. The mTOR inhibitor Everolimus was recommended for 32/112 patients due to PI3K-mTOR pathway activating mutations, with 18/32 patients receiving Everolimus. Doublet therapy of Trametinib and Everolimus was given to n=13 patients, with n=5 patients receiving Everolimus only and n=14 patients receiving Trametinib only as targeted therapy. Comparing patients for whom either Trametinib and/or Everolimus was given after recommendation with patients who did not receive the recommendation, we did not find a difference in outcome. However, overall progression free survival (PFS) increased for patients receiving molecularly-guided treatment after sequencing compared to patients who received standard treatment, by an average PFS of 9 months. Patients who did not receive molecularly-guided therapy until later in their disease course had poorer outcomes compared to those who received it earlier in their treatment.

Conclusions: Molecularly-guided therapy is an emerging treatment strategy for patients with gastrointestinal cancers. Our work showed that progression free survival was increased in patients who received molecularly-guided therapy compared to standard treatment. More research is needed to assess any direct correlations between most genetic mutations and clinical outcomes.

Citation Format: Blake Buzard, Tyler Gonser, Melissa Hinrichsen, Anu Amallraja, Kirstin Williams, Pradip De, Brian Leyland-Jones, Rachel Elsey, Tobias Meissner, Casey Williams. Clinical benefit of molecularly-guided treatment strategies on progression free survival in patients with advanced gastrointestinal malignancies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5147.

Abstract P3-10-01: Single-cell profiling identifies hypoxic carcinoma cells as source of an immunosuppressive VEGFA metagene

Background:

We have previously shown that expression of the IL8/VEGFA-metagene eliminates the good prognostic effect of TILs in TNBC (PMID 21978456, 28750120). We also showed that the VEGFA metagene predicted response to neoadjuvant bevacizumab in the GeparQuinto trial (Karn 2017 SABCS #851166). The main cellular sources of the transcripts that comprise the VEGFA metagene are unknown since mRNA profiling of bulk biopsies contains signals from different cell types.

Methods:

Individual genes that comprise the VEGFA metagene were measured in bulk tissue- and single cell-RNA-Seq from breast cancer subtypes and normal cells on different platforms (Affymetrix n=4915, Agilent n=597, Illumina n=2433, RNA-Seq n=1215, Exome Capture RNA-Seq n=226, HTG-Seq n=243, sc-RNA-Seq n=24710). For blinded, orthogonal validation we performed immunohistochemistry. Effect of neoadjuvant chemotherapy with or without bevacizumab was studied by RNA-Seq and IHC on samples from GeparQuinto trial. SWOG S0800 (GSE114403), PROMIX (GSE87455), and GeparSixto trials were used for validation. TCGA was mined for mutations and somatic CNA. RNA-Seq from GeparNuevo was used for correlation with checkpoint inhibitor treatment.

Results:

We identified a stable core of six genes (VEGFA, ANGPTL4, ADM, NDRG1, DDIT4, CSTB) in different cohorts. Strong expression of this signature was mainly restricted to TNBC subtype and associated with poor prognosis within this subgroup. Single cell RNA-Seq of breast epithelial cells from 4 reduction mammoplasties and 4 TNBC revealed that these genes are coexpressed in individual epithelial cells and not associated with endothelial cells. In line with their presumed functions in cellular stress and hypoxia, immunohistochemistry revealed strong para-necrotic expression in TNBC. Moreover, high gene expression in TNBC was associated with mutations in DNA damage control pathways, somatic copy number alterations, and lower TILs. While chemotherapy led to downregulation, bevacizumab increased expression. In multivariate analysis, high pretreatment values predict pCR to both bevacizumab and chemotherapy (OR 2.40, P=0.006), which may be explained by sensitivity of tumors which are already under cellular stress. On the other hand, expression of the VEGFA metagene seems to create an immunosuppressive environment that counteracts the positive prognostic effect of TILs. In pre-treatment biopsies from the GeparNuevo checkpoint inhibitor trial we found a negative correlation of VEGFA metagene expression with the amount of the recently identified tissue-resident memory T cell subset (CD8TRM, PMID 29942092; P=0.002), while the subsequent increase of CD8TRM during treatment was larger in tumors with high VEGFA (P=0.019).

Conclusions:

Perinecrotic carcinoma cells under stress from hypoxia and or chromosomal instability are the source of the VEGFA metagene signature. Its predictive value in TNBC suggests estimating and reporting the amount of necrosis in the pathology report may be helpful in predicting response to preoperative chemotherapy, and could be used as stratification factor in clinical trials. The signature indicates an immunosuppressive environment and should be further studied in the context of immune therapies in combinations with anti-angiogenic treatment.

Citation Format: Karn T, Denkert C, Sinn BV, Weber K, Nekljudova V, Rody A, Meissner T, Hatzis C, El-Balat A, Becker S, Solbach C, Untch M, Schneeweiss A, von Minckwitz G, Loibl S, Pusztai L, Holtrich U. Single-cell profiling identifies hypoxic carcinoma cells as source of an immunosuppressive VEGFA metagene [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-10-01.

The multiple myeloma risk allele at 5q15 lowers ELL2 expression and increases ribosomal gene expression

Recently, we identified ELL2 as a susceptibility gene for multiple myeloma (MM). To understand its mechanism of action, we performed expression quantitative trait locus analysis in CD138⁺ plasma cells from 1630 MM patients from four populations. We show that the MM risk allele lowers ELL2 expression in these cells (P_combined = 2.5 × 10⁻²⁷; β_combined = −0.24 SD), but not in peripheral blood or other tissues. Consistent with this, several variants representing the MM risk allele map to regulatory genomic regions, and three yield reduced transcriptional activity in plasmocytoma cell lines. One of these (rs3777189-C) co-locates with the best-supported lead variants for ELL2 expression and MM risk, and reduces binding of MAFF/G/K family transcription factors. Moreover, further analysis reveals that the MM risk allele associates with upregulation of gene sets related to ribosome biogenesis, and knockout/knockdown and rescue experiments in plasmocytoma cell lines support a cause–effect relationship. Our results provide mechanistic insight into MM predisposition.

ELL2 was recently discovered as a susceptibility gene for multiple myeloma (MM). Here, they show that the MM risk allele lowers ELL2 expression in plasma cells, that it also upregulates gene sets related to ribosome biogenesis, and that one of the linked variants reduces binding of MAFF/G/K family transcription factors.

Abstract P2-09-02: Blinded molecular subtyping analysis from RNA-Seq of FFPE samples in the GeparQuinto trial reveals predictive value of VEGFA metagene for bevacizumab treatment

Background:

RNA-Seq from total RNA in FFPE tissue can be more challenging due to limited capture of partially degraded RNA. Exome-capture based RNA-Seq may circumvent such problems and allow reproducible complete molecular characterization of low-quality RNA from small clinical samples.

Methods:

HER2 negative patients within the GeparQuinto trial were treated with neoadjuvant anthracycline-taxane-based chemotherapy +/- bevacizumab. Patients with bevacizumab therapy had a significantly higher pCR rate, especially within the triple negative subgroup. We performed exome-capture RNA-Seq on 5µm FFPE sections from pre-therapeutic cores of 400 HER2 negative samples from this trial. In a prospectively planned, blinded study we correlated molecular subtypes and metagenes for proliferation, stroma, MHC2, and VEGFA with clinical and histopathological data. Molecular subtypes were defined using the AIMS methods. Metagenes were calculated as mean values corresponding to previously described gene clusters after platform transfer (Rody et al. 2011 PMID 21978456, Hu et al. 2009 PMID 19291283) and then z-transformed.

Results:

296 samples with RNA-Seq data were classified as either of high (n=226) or of limited quality (n=70). For 22 samples RNA yield was insufficient and 82 did not pass initial QC. 121 (41%), 63 (21%), 34 (11.5%), 46 (15.5%), and 32 (11%) samples were defined as basal-like, HER2-enriched, luminal A, luminal B, and normal-like, respectively. Subtyping was robust with regard to gene filtering, normalization, and sample quality. ER and PR status from local IHC strongly correlated with gene expression (overall correctness 84% and 80% for ER, and 85% and 74% for PR, in samples with high and limited quality, respectively) and luminal subtypes (95% ER positive). Proliferation metagene correlated with histological grade (median -0.73, -0.39, and 0.53 in G1, G2, and G3, respectively; P&lt;0.001) and MHC2 metagene correlated strongly with TIL counts (Rho=0.53, P&lt;0.001). Among the high quality samples response rates (49.3% pCR overall) differed significantly by subtype, with higher pCR rates in basal-like (68.9%) and HER2-enriched (45.5%) than in luminal B (35.7%), luminal A (17.9%), and normal-like (20.0%). MHC2- (OR 1.60, 95%CI 1.21-2.12, P=0.001), proliferation- (OR 2.88, 95%CI 2.00-4.16, P&lt;0.001), and VEGFA-metagenes (OR 1.92, 95%CI 1.41-2.60, P&lt;0.001) were significant predictors for pCR. In a multivariate logistic regression (adjusted for bevacizumab treatment and hormone receptor status) both VEGFA metagene (OR 2.59, 95%CI 1.40-4.77, P=0.002) and the interaction between the VEGFA-metagene and bevacizumab treatment arm (P=0.023) significantly predicted pCR.

Conclusions:

Exome-capture RNA-Seq allows robust genomic characterization of clinical samples with limited FFPE material from core biopsies, and molecular subtypes and immune metagenes are predictive for pCR. The VEGFA metagene is a specific predictor for response to neoadjuvant bevacizumab treatment.

Citation Format: Karn T, Meissner T, Weber K, Sinn B, Denkert C, Budczies J, Nekljudova V, Fasching PA, Holtrich U, Schem C, Solbach C, Hartmann A, Röcken C, Untch M, Young BM, Willis S, Leyland-Jones B, von Minckwitz G, Loibl S. Blinded molecular subtyping analysis from RNA-Seq of FFPE samples in the GeparQuinto trial reveals predictive value of VEGFA metagene for bevacizumab treatment [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-09-02.

Abstract PD8-10: APOBEC mutation signature in breast cancer correlates with tumor mutation burden and poor responses to therapy

Introduction

Mutational processes can be characterized by unique combinations of mutation types in the form of mutational signatures and have been associated with age, known mutagenic exposures, defects in DNA maintenance, or the APOBEC family of cytidine deaminases. We asked whether mutation signatures could be extracted from DNA sequence information in a targeted 434 gene panel covering 297 breast cancer specimens.

Materials and Methods

Targeted whole exome sequencing (Illumina, 2x50bp) of a 434 gene panel was performed on a set of 297 primary and metastatic breast tumor samples. Tissue of origin included breast (56%), liver (15%), lymph node (10%), lung (3%) and others (16%). Alignment was done with BWA against the human reference hg19 and variant calling was performed using VarDict. Germline variants were filtered based on allele frequencies, cohort specific population frequencies, as well as using 1000 Genomes and ExAC population frequencies. For somatic signature inference, only single nucleotide variants were retained. Panel specific trinucleotide frequencies were computed and normalized towards whole genome frequencies and somatic signatures were inferred using deconstructSigs method.

Results

We identified a total of 26 signatures from the set of 30 known signatures in our patient samples. Due to the small panel size, there was only a limited number of mutations available per patient to infer somatic signatures. On average, we identified two somatic signatures per sample. Most common mutation signatures identified were: Signature 1 (90.8%) - result of an endogenous mutational process initiated by spontaneous deamination of 5-methylcytosine; Signature 6 (21.8%) - defective DNA mismatch repair; Signature 15 (15.6%) - defective DNA mismatch repair; Signatue 7 (9.9%) - ultraviolet light exposure; and Signature 10 (6.5%) - altered activity of POLE. An APOBEC specific signature was identified in 20 (7%) samples. APOBEC positive samples showed significantly higher tumor mutational burden (10.7 vs. 5.7 mutations/mb) as compared to APOBEC negative samples (p&lt;=0.001). PIK3CA was found to be mutated in 80% of APOBEC positive samples, compared to 36% of APOBEC negative samples. In addition, we found higher rates of mutations in TP53 (70% vs. 50%), MLL3 (50% vs. 19%) and MLL2 (25% vs 14%) of APOBEC positive patients. Response rates of APOBEC positive patients were significantly worse than of APOBEC negative patients, with 50 percent of patients having progressive disease compared to 25 percent of APOBEC negative patients(p=0.07, borderline).

Conclusions

We demonstrate the feasibility of a targeted sequencing approach to extract somatic mutation signatures from breast tumor samples, and we highlight the potential of using the APOBEC signature to predict therapeutic responses.

Citation Format: Meissner T, Amallraja A, Willis S, Harris R, Leyland-Jones B, Williams C. APOBEC mutation signature in breast cancer correlates with tumor mutation burden and poor responses to therapy [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr PD8-10.

Abstract 5355: PANCeq - Development and validation of a targeted sequencing assay for detection of mutations and copy number changes in most recurrently mutated driver genes

Next generation sequencing is becoming increasingly prevalent as a tool for the identification of genetic variation to aid diagnosis and support therapy decisions in routine clinical care. It has been shown that tumors are comprised of subpopulations of cells with distinct genomic alterations, and hence tumor heterogeneity is becoming an important factor in deciding treatment. Deep sequencing of tumor samples allows for the determination of number and proportions of low variant allele frequency tumor subclones. Currently, high costs for whole-exome deep sequencing (&gt; 250X) limit its application in routine clinical care, and there is a need for more affordable targeted approaches. Here we present PAN Cancer Sequencing (PANCeq), a targeted deep sequencing panel for the detection of mutations and copy number variants (CNVs) in most recurrently mutated cancer driver genes. A platform-independent computational Docker-based pipeline for data analysis and automatic report generation was developed. PANCeq uses customized targeted enrichment, followed by next-generation sequencing of (FFPE) tumor and matched germline samples.

We included 12 patient samples (breast, ovarian, kidney and prostate) as well as triplicates of 3 reference standards (HD200, HD753, HD733 - Horizon). These were sequenced on Illumina NextSeq o an average depth of 1000X. Sequencing data was aligned using BWA to hg19 human reference. Somatic variants and CNVs were identified using VarDict and CNVkit respectively.

We mined TCGA data across 26 tumor types, and selected known mutations from the most recurrently mutated genes, yielding 2849 mutations across 467 genes. In addition, we included 79 pharmacogenomic relevant and 218 sample tracking SNPs as well as 80 cancer relevant CNVs (whole exon), and designed a custom panel based on their genomic locations, resulting in a panel size of 708kb. To assess performance, we sequenced reference standards with known variants spiked-in at varying VAF (1 - 41.5%). Somatic variant calling was performed against a wildtype sample. For HD200, out of 21 covered mutations, 14 were correctly classified as germline, and 7 as somatic. For HD733, out of 21 mutations, 3 were correctly identified as germline, 18 as somatic. For HD753, all 6 germline and somatic mutations were correctly identified. The 2 CNVs spiked-in were also correctly identified. In all cases we found a good agreement between observed and expected VAF. Somatic variant results for 12 patient samples were compared with variants reported by a private vendor. While we found good agreement at VAF &gt; 20%, our panel detected on average 7 additional clinically relevant mutations at &lt; 20%.

We demonstrate that PANCeq is an accurate and sensitive method for timely identification of clinically actionable mutations and copy number variations across multiple cancer types.

Citation Format: Tobias Meissner, Anu Amallraja, Brandon Michael Young, Adam Mark, Cayce Conolly, Amanda Andrews, Casey Williams, Brian Leyland-Jones. PANCeq - Development and validation of a targeted sequencing assay for detection of mutations and copy number changes in most recurrently mutated driver genes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5355. doi:10.1158/1538-7445.AM2017-5355

Abstract P1-05-23: Utilities and challenges of RNA-Seq based expression and variant calling in a clinical setting

Introduction

Variant calling based on DNA samples has been the gold standard of clinical testing since the advent of Sanger sequencing. The use of DNA variants has proved a great value to guide treatment in cancer patients. However, DNA based analysis will not inform about expression status of the gene harboring a particular variant. RNA has long been used to monitor expression. To this point RNA assays and analysis are confined to the research laboratory and rarely used clinically except in specifically defined gene signatures such as PAM50 and OncoType Dx. Beyond expression, RNA has the ability to confirm expression of DNA variants and identify fusion events. We hypothesize that the combination of DNA and RNA based data will allow the determination of variant specific expression status and improve clinical diagnostics. It has been previously shown that RNA sequencing (RNA-Seq) based variant calls are highly accurate and confirm DNA based variant calls. In this study we investigated the utility of RNA-Seq as a diagnostic assay integrated with DNA based sequencing data.

Materials and Methods

Targeted DNA sequencing of 321 genes was performed on 37 patient samples (FFPE), including 22 breast cancer samples by a commercial vendor. RNA-Seq on the same patient samples was performed using 100ng of total RNA. Libraries were run on the Illumina NextSeq 500 with a minimum of 75M paired 75bp reads. To evaluate RNA-seq expression reproducibility, replicates of 6 normal ovarian tissue samples (min. 50M reads) were run in sets of triplicates. STAR was used for alignment (hg19) and gene expression quantification (RefSeq). RNA-Seq based variant calling was performed using the SNPiR pipeline. Based on the results of the commercial assay, DNA based variants were examined for expression of the corresponding genes and ability to confirm variants in the RNA-Seq data.

Results

RNA expression data showed no corresponding gene expression for at least one single nucleotide variant (SNV) in 9/37 patients analyzed (24.3%). In 18/37 patients (48.6%) SNV corresponding expression was in the lowest quartile of expression values. Variant calls could be confirmed by RNA-Seq for 95/455 SNVs, with adequate coverage in 263 of the remaining 360 variant locations (median coverage: 34). Of these, a homozygous reference call was made in 166/263 SNVs. Concordance for RNA-Seq gene level expression data between replicates was &gt; 0.995.

Conclusions

These findings suggest that RNA-Seq based data can provide clinical value when using gene expression values in combination with DNA based variant calls. We found gene level expression to be highly reproducible and will further investigate the use of spike in controls to determine clinically usable expression ranges and lower limit of expression values. To our knowledge, it has not been shown that RNA-Seq based variant calls are reproducible which is the focus of our current research as this will be one requirement for usage in a regulated environment. While our use of RNA Seq is currently limited to gene expression level data, we have demonstrated a clinically relevant benefit to using RNA Seq data as an additive feature to the current standard of DNA variant calling.

Citation Format: Young B, Mark A, Meissner T, Amallraja A, Andrews A, Connolly C, Williams C, Leyland-Jones B. Utilities and challenges of RNA-Seq based expression and variant calling in a clinical setting [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-05-23.

Abstract P1-05-22: The value of RNA-Seq for the detection of clinically actionable targets in breast cancer - A small cohort analysis

Introduction

Next generation sequencing has facilitated the understanding of pathogenesis and molecular heterogeneity of breast cancer (BC) as well as accelerated the path towards precision medicine. DNA sequencing (DNA-Seq) based assays for the detection of mutations and alterations in solid and hematologic cancers are finding their way into clinical practice and are readily available as clinical products. RNA sequencing (RNA-Seq), so far being vastly applied in the research context, promises to expand the diagnostic, prognostic and therapeutic use of this technology in cancer. Beyond mutational status, RNA-Seq enables the detection of fusions, quantification of gene expression level, detection of differentially expressed genes, molecular based subtyping, and risk-stratification. In this study we analyzed RNA-Seq and copy number data from BC patients that had undergone DNA-Seq based diagnostics through commercial providers with the goal to detect additional actionable targets.

Materials and Methods

We included 18 BC patients (5/18 triple negative) that had previously undergone DNA-based targeted (321 genes) sequencing. RNA-Seq to a minimum of 75M reads (75pb) was performed using 100 ng of total RNA on the Illumina NextSeq 500 platform. STAR was used for alignment (hg19) and gene expression quantification (RefSeq). Fusions were detected using STAR-Fusion. DESeq2 was utilized to identify patient specific differentially expressed genes by analyzing samples individually against a set of 13 controls from healthy breast tissue generated in-house. Copy number variations (CNVs) were detected using the Nanostring CNV Cancer panel (89 genes) on the Nanostring nCounter platform. Differentially upregulated or amplified genes were queried against DGIdb and Gene Drug Knowledge database for suitable drug matches, limiting the queries to clinically actionable antineoplastic drugs.

Results

Analyzing the cohort of 18 BC patients, we detected on average 26 BC relevant genes (526 total, log2 FC &gt; 2) to be upregulated per patient. Querying the upregulated genes against DGIdb, we found a total of 18 genes that had drug matches and fulfilled the criteria of being actionable antineoplastic drugs, with 17/18 samples having a minimum of two gene targets (avg: 4). Most frequent upregulated genes were TOP2A (83%), AURKA (61%), AURKB (56%), RET (39%)and FGFR3 (28%). In the case of CNVs, 12/18 patients showed at least one gene target with clinically actionable drugs associated. This was observed across 12 gene targets that were amplified (avg: 3) and 4 gene targets that underwent deletions (avg: 1). Most frequent CNVs included MYC (14%) and CCND1 (12%). 4/7 patients having an AURKA overexpression also showed an AURKA amplification on the CNV assay. 10/18 patients had fusions events, with an average of three fusions per patient, including GAB2-WNT11, PAK1-TENM4 and FGFR2-CEP55 fusions.

Conclusions

We show that RNA-Seq and copy number assays provide additional clinical value by detecting suitable drug targets beyond traditional DNA-based approaches. We are conducting further analysis on how these additionally derived drug targets could improve the current treatment schedule of those patients.

Citation Format: Meissner T, Amallraja A, Mark A, Andrews A, Connolly C, Young B, De P, Williams C, Leyland-Jones B. The value of RNA-Seq for the detection of clinically actionable targets in breast cancer - A small cohort analysis [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-05-22.

Need for Better Diabetes Treatment: The Therapeutic Potential of NMDA Receptor Antagonists

Diabetes mellitus is the most common metabolic disorder in children and adolescents. Optimal control of blood glucose concentration is essential to prevent acute and diabetic long-term complications. The options to treat diabetes have clearly improved over the last decades, however, to date neither type 1 diabetes nor type 2 diabetes mellitus can be cured. Therefore, diabetes research aims at developing β-cell protective agents that prevent or even reverse diabetes onset. N-methyl-D-aspartate receptors (NMDARs) are glutamate-gated ion channels that are widely expressed in the central nervous system (CNS) where they hold central roles in CNS function. NMDAR dysfunction is associated with several neurological and psychiatric disorders and therefore NMDAR modulators have several potential therapeutic indications. Only little is known about the role of pancreatic NMDA receptors. Our data provide evidence that inhibition of pancreatic NMDARs, either genetically or pharmacologically with the over-the-counter drug dextromethorphan, increases glucose-stimulated insulin secretion from mouse and human pancreatic islets, improves glucose tolerance in mice and individuals with diabetes and promotes islet cell survival under diabetogenic conditions. Thus, our data indicate for the first time that NMDAR antagonists could serve as adjunct treatment for diabetes mellitus. The development of a safe, blood glucose lowering and particularly β-cell protective medication would significantly enhance current diabetes treatment.

Effects of dextromethorphan as add-on to sitagliptin on blood glucose and serum insulin concentrations in individuals with type 2 diabetes mellitus: a randomized, placebo-controlled, double-blinded, multiple crossover, single-dose clinical trial

In this clinical trial, we investigated the blood glucose (BG)-lowering effects of 30, 60 and 90 mg dextromethorphan (DXM) as well as 100 mg sitagliptin alone versus combinations of DXM and sitagliptin during an oral glucose tolerance test (OGTT) in 20 men with T2DM. The combination of 60 mg DXM plus 100 mg sitagliptin was observed to have the strongest effect in the OGTT. It lowered maximum BG concentrations and increased the baseline-adjusted area under the curve for serum insulin concentrations in the first 30 min of the OGTT (mean ± standard deviation 240 ± 47 mg/dl and 8.1 ± 6.1 mU/l/h, respectively) to a significantly larger extent than did 100 mg sitagliptin alone (254 ± 50 mg/dl and 5.8 ± 2.5 mU/l/h, respectively; p < 0.05) and placebo (272 ± 49 mg/dl and 3.9 ± 3.0 mU/l/h, respectively; p < 0.001). All study drugs were well tolerated, alone and in combination, without serious adverse events or hypoglycaemia. Long-term clinical trials are now warranted to investigate the potential of the combination of 30 or 60 mg DXM and dipeptidyl peptidase-4 inhibitors in the treatment of individuals with T2DM, in particular as preclinical studies have identified the β-cell protective properties of DXM.

A Furan-Based Lewis-Y-(CD174)-Saccharide Mimetic Inhibits Endothelial Functions and In Vitro Angiogenesis

BACKGROUND

Angiogenesis is a fundamental process underlying cancer progression and autoimmune disease. Lewis Y is known as a regulated glycan-structure supporting human endothelial function and angiogenesis.

OBJECTIVES

We hypothesize that Lewis Y based analogues interfere with Lewis Y mediated endothelial functions and angiogenesis. We therefore evaluated the ability of 3, 4-bis [(b-D-galactopyranosyl)osy]-methyl-furan (BGF) a furan-based Lewis-Y saccharide mimetic to inhibit human endothelial adhesion, migration and in vitro angiogenesis.

MATERIAL AND METHODS

The ability of BGF and additional furan-based saccharide-mimetics was investigated to inhibit adhesion and migration of human bone marrow endothelial cells (HBMEC). Influence of BGF was tested on a multicelluar in vitro - angiogenesis assay in the presence of VEGF.

RESULTS

BGF significantly inhibited HBMEC adhesion and migration stimulated by TNF-alpha by up to 70%. The anti-adhesive effect of BGF was particularly evident when HBMEC adhesion and migration was tested on collagen as extracellular matrix with weaker effect when laminin and fibronectin were used as an extracellular matrix. BGF was ineffective when HBMEC were stimulated with VEGF. The inhibition of endothelial function translated into a significant inhibitory effect of BGF in the multicellular in vitro angiogenesis-assay. BGF reduced the angiogenesis index compared to the positive controls by 32%.

CONCLUSIONS

We identified the ability of the furan-based Lewis Y saccharide mimetic BGF as a specific modulator of TNF-alpha activated endothelial function and in vitro angiogenesis. BGF and other related glycan analogues should further be explored for their ability to down modulate endothelial activation in TNF-alpha driven pathophysiologic conditions in autoimmune disease and cancer indications.

Impact of regular physical activity on blood glucose control and cardiovascular risk factors in adolescents with type 2 diabetes mellitus--a multicenter study of 578 patients from 225 centres

INTRODUCTION

Regular physical activity (RPA) is a major therapeutic recommendation in children and adolescents with type 2 diabetes mellitus (T2DM). We evaluated the association between frequency of RPA and metabolic control, cardiovascular risk factors, and treatment regimes.

METHODS

The Pediatric Quality Initiative (DPV), including data from 225 centers in Germany and Austria, provided anonymous data of 578 patients (10-20 yr; mean 15.7 ± 2.1 yr; 61.9% girls) with T2DM. Patients were grouped by the frequency of their self-reported RPA per week: RPA 0, none; RPA 1, 1-2×/wk; RPA 2, >2×/wk.

RESULTS

The frequency of RPA ranged from 0 to 9×/wk (mean 1.1×/wk ±1.5). 55.7% of the patients reported no RPA (58.1% of the girls). Hemoglobin A1c (HbA1c) differed significantly among RPA groups (p < 0.002), being approximately 0.8 percentage points lower in RPA 2 compared to RPA 0. Body mass index (BMI-SDS) was higher in the groups with less frequent RPA (p < 0.00001). Multiple regression analysis revealed a negative association between RPA and HbA1c (p < 0.0001) and between RPA and BMI-SDS (p < 0.01). The association between RPA and high density lipoprotein (HDL)-cholesterol was positive (p < 0.05), while there was no association to total cholesterol, low density lipoprotein (LDL)-cholesterol or triglycerides. Approximately 80% of the patients received pharmacological treatment (oral antidiabetic drugs and/or insulin) without differences between RPA groups.

CONCLUSION

More than half of the adolescents with T2DM did not perform RPA. Increasing physical activity was associated with a lower HbA1c, a lower BMI-SDS, a higher HDL-cholesterol, but not with a difference in treatment regime. These results suggest that regular exercise is a justified therapeutic recommendation for children and adolescents with T2DM.

Treatment of young patients with HNF1A mutations (HNF1A-MODY)

AIM

Children and adolescents with a molecular diagnosis of HNF1A-MODY should be treated with oral sulfonylurea according to current International Society for Pediatric and Adolescent Diabetes (ISPAD) guidelines.

METHODS

We surveyed the German-Austrian DPV database of 50 043 people and included 114 patients with a confirmed molecular-genetic diagnosis of HNF1A mutation and diabetes onset at below age 18 years. We analysed hypoglycaemic episodes, metabolic control (HbA1c ) and other clinical variables according to treatment groups.

RESULTS

People with HNF1A-MODY were included and analysed according to treatment with insulin alone (n = 34), sulfonylurea (n = 30), meglitinides (n = 22) or lifestyle (n = 28). In those receiving any drug treatment (n = 86), severe hypoglycaemia did not occur with meglitinide and was highest (at 3.6 events per 100 patient-years) with insulin. HbA1c was highest with insulin treatment (insulin = 58 mmol/mol, 7.5%; sulfonylurea = 55 mmol/mol, 7.2%; meglitinides = 52 mmol/mol, 6.9%; P = 0.008), whereas weight (BMI SD score), serum lipids and blood pressure were not different.

CONCLUSIONS

Of note, 40% of people with HNF1A-MODY and medical treatment were receiving insulin alone and thus were not being treated in line with up-to-date International Society for Pediatric and Adolescent Diabetes/International Diabetes Federation guidelines, despite insulin treatment being associated with worse metabolic control and the risk of hypoglycaemia. The unlicensed use of oral drugs in patients below age 18 years and adherence by both doctors and patients to the initial insulin treatment might contribute to this finding.

Overweight and Obesity Based on Four Reference Systems in 18,382 Paediatric Patients with Type 1 Diabetes from Germany and Austria

AIM

To evaluate the prevalence of overweight and obesity in paediatric type 1 diabetes (T1D) subjects, based on four commonly used reference populations.

METHODS

Using WHO, IOTF, AGA (German pediatric obesity), and KiGGS (German Health Interview and Examination Survey for Children and Adolescents) reference populations, prevalence of overweight (≥90th percentile) and obesity (≥97th percentile) and time trend between 2000 (n = 9,461) and 2013 (n = 18,382) were determined in 2-18-year-old T1D patients documented in the German/Austrian DPV database.

RESULTS

In 2000, the overweight prevalence was the highest according to IOTF (22.3%), followed by WHO (20.8%), AGA (15.5%), and KiGGS (9.4%). The respective rates in 2013 were IOTF (24.8%), WHO (22.9%), AGA (18.2%), and KiGGS (11.7%). Obesity prevalence in 2000 was the highest according to WHO (7.9%), followed by AGA (4.5%), IOTF (3.1%), and KiGGS (1.8%). In 2013, the respective rates were WHO (9.6%), AGA (6.2%), IOTF (4.5%), and KiGGS (2.6%). Overall, the prevalence of overweight and obesity increased from 2000 to 2006 (p < 0.001) but showed stabilization thereafter in girls and overweight in boys.

CONCLUSION

Overweight and obesity prevalence in T1D subjects differs significantly if it is assessed by four separate reference populations. More detailed assessment of each child is required to determine obesity-related risks.

Functional expression of dental plaque microbiota

Dental caries remains a significant public health problem and is considered pandemic worldwide. The prediction of dental caries based on profiling of microbial species involved in disease and equally important, the identification of species conferring dental health has proven more difficult than anticipated due to high interpersonal and geographical variability of dental plaque microbiota. We have used RNA-Seq to perform global gene expression analysis of dental plaque microbiota derived from 19 twin pairs that were either concordant (caries-active or caries-free) or discordant for dental caries. The transcription profiling allowed us to define a functional core microbiota consisting of nearly 60 species. Similarities in gene expression patterns allowed a preliminary assessment of the relative contribution of human genetics, environmental factors and caries phenotype on the microbiota's transcriptome. Correlation analysis of transcription allowed the identification of numerous functional networks, suggesting that inter-personal environmental variables may co-select for groups of genera and species. Analysis of functional role categories allowed the identification of dominant functions expressed by dental plaque biofilm communities, that highlight the biochemical priorities of dental plaque microbes to metabolize diverse sugars and cope with the acid and oxidative stress resulting from sugar fermentation. The wealth of data generated by deep sequencing of expressed transcripts enables a greatly expanded perspective concerning the functional expression of dental plaque microbiota.

Role of Growth arrest-specific gene 6-Mer axis in multiple myeloma

Multiple myeloma is a mostly incurable malignancy characterized by the expansion of a malignant plasma cell (PC) clone in the human bone marrow (BM). Myeloma cells closely interact with the BM stroma, which secretes soluble factors that foster myeloma progression and therapy resistance. Growth arrest-specific gene 6 (Gas6) is produced by BM-derived stroma cells and can promote malignancy. However, the role of Gas6 and its receptors Axl, Tyro3 and Mer (TAM receptors) in myeloma is unknown. We therefore investigated their expression in myeloma cell lines and in the BM of myeloma patients and healthy donors. Gas6 showed increased expression in sorted BMPCs of myeloma patients compared with healthy controls. The fraction of Mer(+) BMPCs was increased in myeloma patients in comparison with healthy controls whereas Axl and Tyro3 were not expressed by BMPCs in the majority of patients. Downregulation of Gas6 and Mer inhibited the proliferation of different myeloma cell lines, whereas knocking down Axl or Tyro3 had no effect. Inhibition of the Gas6 receptor Mer or therapeutic targeting of Gas6 by warfarin reduced myeloma burden and improved survival in a systemic model of myeloma. Thus, the Gas6-Mer axis represents a novel candidate for therapeutic intervention in this incurable malignancy.