Abstract P5-02-46: Targeted capture sequencing allows sensitive genomic profiling of circulating tumor DNA in advanced HR+/HER- breast cancer patients

Introduction: CDK4/6 inhibitors provide substantial benefits as 1st or 2nd line treatments and are now the standard of care for patients with advanced HR-positive, HER2-negative breast cancer. Recently, we demonstrated that a high-resolution SiMSen-seq assay (SSS) provides a sensitive and robust method for detecting 11 PIK3CA hotspot mutations in cell-free circulating DNA, allowing the identification of patients eligible for alpelisib treatment. Unfortunately, all patients progress at some time point due to intrinsic or acquired resistance. Therefore, detecting additional genomic biomarkers for treatment resistance beyond PIK3CA mutations is crucial. Targeted panel sequencing offers a promising strategy to profile circulating tumor DNA (ctDNA) for genetic alterations in multiple genes associated with treatment response and disease progression. This ongoing study aims to show that a commercial NGS assay (AVENIO ctDNA Expanded Kit, Roche Diagnostics) can (1) detect PIK3CA mutations with similar sensitivity as our high-resolution SSS assay and can (2) simultaneously identify additional genetic alterations in multiple genes, possibly associated with treatment resistance or disease progression. Material and Methods: To this end, we collected plasma samples from 46 metastatic HR+/HER2- breast cancer patients before starting 1st (32 patients) or 2nd (14 patients) line treatment. Samples were analyzed using SSS and the AVENIO ctDNA Expanded Kit, enriching for 77 clinically relevant cancer genes. PIK3CA mutation detection and variant allele frequencies (VAF) were compared between the two methods. Additionally, mFAST-SeqS was used to estimate the tumor fractions in plasma samples. Results: The median z-score from mFAST-SeqS analyses was 2.38 [25–75th percentile: 1.23–4.5], and 17/46 (37%) patients had z-scores 3, indicating elevated tumor fractions (>5%). Patients starting 2nd line treatment had significantly higher z-scores than those starting 1st line treatment (median 2.2 vs. 3.8, rank-sum p-value 0.042). One sample repeatedly failed with the SSS assay, leaving 45 samples for a head-to-head comparison. Considering only PIK3CA hotspot mutations covered by both assays, 16 alterations were detected in 14 patients (31%) by the SSS assay and 19 alterations in 17 patients (38%) by the AVENIO ctDNA Expanded Kit. Both assays detected the identical co-occurrence of two PIK3CA mutations in two samples. Two of three mutations only detected with the AVENIO ctDNA Expanded Kit were also observed with the SSS assay but below the pre-defined detection limit. One mutation was only detected by the AVENIO ctDNA Expanded Kit. Overall, we found an excellent concordance rate of 94% between the two assays, confirming the high sensitivity of the panel sequencing assay. Moreover, the VAF of SSS and AVENIO kit were highly correlated (Spearman’s rho = 0.97, p < 0.001). Using the AVENIO kit, a large number of additional mutations in 40 genes could be identified in 42/46 (91%) patients with a median of 2.0 variants (range 1-13) per sample. The most frequently mutated genes included PIK3CA (43%), followed by ESR1 (20%), TP53 (20%), MET (17%), SMAD4 (17%), ERBB2 (11%), and BRCA2 (11%). The median VAF was 0.64% (range 0.1-29.8). Further analyses are still ongoing. Conclusion: The AVENIO ctDNA Expanded Kit revealed a high sensitivity and concordance rate for detecting PIK3CA hotspot mutations in plasma samples compared with the high-resolution SSS assay. A major advantage of panel sequencing over a single gene approach is that the interrogation of multiple genes can indicate a true negative PIK3CA result if other variants are present with a high VAF. Moreover, other actionable targets or mechanisms of resistance can be captured simultaneously, thus improving the effective precision treatment of metastatic breast cancer patients.

Citation Format: Nadia Dandachi, Ricarda Graf, Nina Potocnik, Lara Pancheri, Eva Klocker, Christoph Suppan, Philipp Jost, Hanno Gerritsmann, Ellen Heitzer, Marija Balic. Targeted capture sequencing allows sensitive genomic profiling of circulating tumor DNA in advanced HR+/HER- breast cancer patients [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-02-46.

Comprehensive surgical treatment strategy for spinal metastases

The management of patients with spinal metastases (SM) requires a multidisciplinary team of specialists involved in oncological care. Surgical management has evolved significantly over the recent years, which warrants reevaluation of its role in the oncological treatment concept. Any patient with a SM was screened for study inclusion. We report baseline characteristics, surgical procedures, complication rates, functional status and outcome of a large consecutive cohort undergoing surgical treatment according to an algorithm. 667 patients underwent 989 surgeries with a mean age of 65 years (min/max 20–94) between 2007 and 2018. The primary cancers mostly originated from the prostate (21.7%), breast (15.9%) and lung (10.0%). Surgical treatment consisted of dorsoventral stabilization in 69.5%, decompression without instrumentation in 12.5% and kyphoplasty in 18.0%. Overall survival reached 18.4 months (95% CI 9.8–26.9) and the median KPS increased by 10 within hospital stay. Surgical management of SMs should generally represent the first step of a conclusive treatment algorithm. The need to preserve long-term symptom control and biomechanical stability requires a surgical strategy currently not supported by level I evidence.

Next-generation diagnostics for precision oncology: Preanalytical considerations, technical challenges, and available technologies

Molecular diagnostics as the centrepiece of precision oncology has gone through revolutionary developments over the last decade, becoming tremendously broad, deep and precise with still ongoing advancements. In the majority of scenarios, treatment selection for cancer patients without any type of molecular characterization is no longer conceivable. Considering the impact of sample quality on the reliability of molecular analyses and the importance of the results for the fate of an individual patient, it is surprising how sparsely preanalytical and analytical requirements are addressed scientifically. Standardization and rigorous quality assessment continue to play only a marginal role in the field. Within this review, we will systematically discuss influencing preanalytic parameters and technology setups affecting molecular test results. We will shed light on the specifics of different analytes, technical modalities, and analysis pipelines. The review will have a certain focus on broad molecular genetic tumour testing with next generation sequencing but will go beyond that including other molecular diagnostic modalities and will give a glimpse into the future of molecular testing.

Three versus one year of adjuvant imatinib for high-risk gastrointestinal stromal tumor (GIST): Survival analysis of a randomized trial after 10 years of follow-up

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Background: Adjuvant imatinib improves recurrence-free survival (RFS) when administered after surgery to selected patients with operable gastrointestinal stromal tumor (GIST). It is uncertain whether overall survival (OS) improves, since imatinib improved OS in only one of the 3 large randomized trials conducted, and in this trial (the Scandinavian Sarcoma Group XVIII/German trial; SSGXVIII/AIO; NCT00116935) the statistical significance for OS remained borderline. The objective of the present analysis was to evaluate long-term OS of patients who participated in the SSGXVIII/AIO trial. Methods: SSGXVIII/AIO is an open-label, randomized (1:1), multicenter phase 3 trial. Four hundred patients who underwent macroscopically complete surgery for GIST with a high estimated risk for recurrence according to the modified National Institutes of Health Consensus Criteria were accrued between February 2004 and September 2008. Imatinib was scheduled to be administered 400 mg/day orally for either 12 months or 36 months after surgery. The patients were scheduled to be followed up for 10 years after study entry. Imaging of the abdomen was carried out periodically. The primary end point was RFS; the secondary objectives included OS and treatment safety. Results: The median follow-up time was 119 months. In the Intention-To-Treat Population 194 RFS events and 96 OS events were recorded. In the 36-month group, 5-year and 10-year RFS was 71.4% and 52.5%, and in the 12-month group, 53.0% and 41.8%, respectively (HR 0.66, 95% CI 0.49-0.87; P = .003). In the 36-month group, the 5-year and 10-year OS rates were 92.0% and 79.0%, and in the 12-month group, 85.5% and 65.3%, respectively (HR 0.55, 95% CI 0.37-0.83; P = .004). In the Efficacy Population, from which 15 patients who did not have GIST in central pathology review and 24 patients who had intra-abdominal metastases removed at surgery were excluded, 10-year OS was 81.6% in the 36-month group and 66.8% in the 12-month group (HR, 0.50, 95% CI 0.32-0.80; P = .003). No new safety signals were detected. Conclusions: About 50% of deaths can be avoided during the first decade of follow-up after surgery with 3-year imatinib treatment as compared to 1-year treatment. Clinical trial information: NCT00116935 .

The concept of hybrid molecules of tacrine and benzyl quinolone carboxylic acid (BQCA) as multifunctional agents for Alzheimer's disease

Novel tacrine-benzyl quinolone carboxylic acid (tacrine-BQCA) hybrids were designed based on multi-target directed ligands (MTLDs) paradigm, synthesized and evaluated in vitro as inhibitors of human acetylcholinesterase (hAChE) and human butyrylcholinesterase (hBChE). Tacrine moiety is represented herein as 7-methoxytacrine, 6-chlorotacrine or unsubstituted tacrine forming three different families of seven members, i.e. 21 compounds in overall. Introducing BQCA, a positive modulator of M1 muscarinic acetylcholine receptors (mAChRs), the action of novel compounds on M1 mAChRs was evaluated via Fluo-4 NW assay on the Chinese hamster ovarian (CHO-M1WT2) cell line. All the novel tacrine-BQCA hybrids were able to block the action of hAChE and hBChE in micromolar to nanomolar range. The hAChE kinetic profile of 5p was found to be mixed-type which is consistent with our docking experiments. Moreover, selected ligands were assessed for their potential hepatotoxicity on HepG2 cell line and presumable permeation through the blood-brain barrier by PAMPA assay. Expected agonistic profile towards M1 mAChRs delivered by BQCA moiety was not confirmed. From all the hybrids, 5o can be highlighted as non-selective cholinesterase inhibitor (hAChE IC₅₀ = 74.5 nM; hBChE IC₅₀ = 83.3 nM) with micromolar antagonistic activity towards M1 mAChR (IC₅₀ = 4.23 μM). A non-selective pattern of cholinesterase inhibition is likely to be valuable during the onset as well as later stages of AD.

A 7-methoxytacrine-4-pyridinealdoxime hybrid as a novel prophylactic agent with reactivation properties in organophosphate intoxication

Chemical warfare agents constitute an increasing threat to both military and civilian populations. Therefore, effective prophylactic approaches are urgently needed. Herein, we present a novel hybrid compound which is able not only to keep acetylcholinesterase resistant to organophosphate (OP) inhibitors, but also to serve as an enzyme reactivator in the case of OP intoxication.

Detection of mutant free circulating tumor DNA in the plasma of patients with gastrointestinal stromal tumor harboring activating mutations of CKIT or PDGFRA

PURPOSE

In gastrointestinal stromal tumor (GIST), there is no biomarker available that indicates success or failure of therapy. We hypothesized that tumor-specific v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog (CKIT)- or platelet-derived growth factor receptor-α (PDGFRA)-mutant DNA fragments can be detected and quantified in plasma samples of patients with GIST.

EXPERIMENTAL DESIGN

We prospectively collected 291 plasma samples from 38 subjects with GIST harboring activating mutations of CKIT or PDGFRA detected in tumor tissue, irrespective of current disease status or treatment. We used allele-specific ligation PCR to detect mutant free circulating DNA (fcDNA).

RESULTS

We were able to detect fcDNA harboring the tumor mutation in 15 of 38 patients. Patients with active disease displayed significantly higher amounts of mutant fcDNA compared with patients in complete remission (CR). The amount of mutant fcDNA correlated with disease course. We observed repeated positive test results or an increase of mutant fcDNA in five patients with progressive disease or relapse. A decline of tumor fcDNA or conversion from positive to negative was seen in five patients responding to treatment. A negative to positive conversion was seen in two patients with relapse and one patient with progression. In two cases, we aimed to identify additional mutations and found four additional exchanges, including mutations not known from sequentially conducted tumor biopsies.

CONCLUSIONS

Our results indicate that fcDNA harboring tumor-specific mutations in the plasma of patients with GIST can be used as tumor-specific biomarker. The detection of resistance mutations in plasma samples might allow earlier treatment changes and obviates the need for repeated tumor biopsies.

Detection of mutant-free circulating tumor DNA in the plasma of patients with gastrointestinal stromal tumor (GIST) harboring activating mutations of C-Kit or PDGFRA

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Background: In gastrointestinal stromal tumor (GIST), there is no biomarker available that indicates success or failure of therapy. We hypothesized that tumor specific CKIT or PDGFRA mutant DNA fragments can be detected and quantified in plasma samples of GIST patients. Methods: We prospectively collected 291 plasma samples from 38 subjects with GIST harbouring activating mutations of CKIT or PDGFRA detected in tumor tissue, irrespective of current disease status or treatment. We used allele-specific Ligation PCR to detect mutant free circulating (fc)DNA. Results: We were able to detect fcDNA harbouring the tumor mutation in 15 out of 38 patients. Patients with active disease displayed significantly higher amounts of mutant fcDNA compared to patients in CR. The amount of mutant fcDNA correlated with disease course. We observed repeated positive test results or an increase of mutant fcDNA in five patients with progressive disease or relapse. A decline of tumor fcDNA or conversion from positive to negative was seen in five patients responding to treatment. A negative to positive conversion was seen in two patients with relapse and one patient with progression. In two cases, we aimed to identify additional mutations, and found four additional exchanges, including mutations not known from sequentially performed tumor biopsies. Conclusions: Our results indicate that free circulating DNA harbouring tumor specific mutations in the plasma of patients with GIST can be used as tumor-specific biomarker. The detection of resistance mutations in plasma samples might allow earlier treatment changes and obviates the need for repeated tumor biopsies. Clinical trial information: NCT01462994.

Disorder-induced localization in crystalline phase-change materials

Localization of charge carriers in crystalline solids has been the subject of numerous investigations over more than half a century. Materials that show a metal-insulator transition without a structural change are therefore of interest. Mechanisms leading to metal-insulator transition include electron correlation (Mott transition) or disorder (Anderson localization), but a clear distinction is difficult. Here we report on a metal-insulator transition on increasing annealing temperature for a group of crystalline phase-change materials, where the metal-insulator transition is due to strong disorder usually associated only with amorphous solids. With pronounced disorder but weak electron correlation, these phase-change materials form an unparalleled quantum state of matter. Their universal electronic behaviour seems to be at the origin of the remarkable reproducibility of the resistance switching that is crucial to their applications in non-volatile-memory devices. Controlling the degree of disorder in crystalline phase-change materials might enable multilevel resistance states in upcoming storage devices.

Extracellular matrix metalloproteinase inducer (CD147) is a novel receptor on platelets, activates platelets, and augments nuclear factor kappaB-dependent inflammation in monocytes

In atherosclerosis, circulating platelets interact with endothelial cells and monocytes, leading to cell activation and enhanced recruitment of leukocytes into the vascular wall. The invasion of monocytes is accompanied by overexpression of matrix metalloproteinases (MMPs), which are thought to promote atherosclerosis and trigger plaque rupture. Following interaction with itself, the extracellular matrix metalloproteinase inducer (EMMPRIN) induces MMP synthesis via a little-known intracellular pathway. Recently, we showed upregulation of EMMPRIN on monocytes during acute myocardial infarction. EMMPRIN also stimulates secretion of MMP-9 by monocytes and of MMP-2 by smooth muscle cells, indicating that it may be an important regulator of MMP activity. Expression of EMMPRIN on platelets has not been described until now. Here, we demonstrate that resting platelets show low surface expression of EMMPRIN, which is upregulated by various platelet stimulators (flow cytometry). EMMPRIN is located in the open canalicular system and in alpha granules of platelets (according to electron microscopy and sucrose gradient ultracentrifugation). Platelet stimulation with recombinant EMMPRIN-Fc induced surface expression of CD40L and P-selectin (according to flow cytometry), suggesting that EMMPRIN-EMMPRIN interaction activates platelets. Coincubation of platelets with monocytes induced EMMPRIN-mediated nuclear factor kappaB activation (according to Western blot) in monocytes with increased MMP-9 (zymography), interleukin-6, and tumor necrosis factor-alpha secretion (according to ELISA) by monocytes. In conclusion, EMMPRIN displays a new platelet receptor that is upregulated on activated platelets. Binding of EMMPRIN to platelets fosters platelet degranulation. Platelet-monocyte interactions via EMMPRIN stimulate nuclear factor kappaB-driven inflammatory pathways in monocytes, such as MMP and cytokine induction. Thus, EMMPRIN may represent a novel target to diminish the burden of protease activity and inflammation in atherosclerosis.

The Bcl10 / Malt1 Signaling Pathway as a Drug Target in Lymphoma

The development of lymphomas and leukemias is frequently caused by chromosomal translocations that deregulate cellular pathways of differentiation, proliferation or survival. The molecules that are involved in these aberrations provide rational targets for selective drug therapies. Recently, several disease specific translocations have been identified in human MALT lymphoma. These aberrations either upregulate the expression of BCL10 or MALT1 or induce the formation of API2-MALT1 fusion proteins. Genetic and biochemical experiments identified BCL10 and MALT1 as central components of an oligomerization-ubiquitinylation-phosphorylation cascade that activates the transcription factor NF-kappaB in response to antigen receptor ligation. Deregulation of the signaling cascade is directly associated with antigen independent MALT lymphoma growth. Here we provide an overview of the physiological and pathological functions of BCL10/MALT1 signal transduction and discuss the potential of this pathway as a drug target.

The beta3-adrenergic agonist CL316,243 inhibits insulin signaling but not glucose uptake in primary human adipocytes

Insulin resistance and obesity are central components of the metabolic syndrome which has become the leading cause of cardiovascular morbidity and mortality worldwide. Direct interactions of the beta (3)-adrenoceptor system with adipocyte signaling and function in humans remain poorly understood. However, this might have important consequences for the regulation of energy homeostasis and insulin resistance in states of hyperinsulinemia and sympatho-adrenergic overactivity. We therefore investigated beta (3)-adrenoceptor-mediated effects on insulin signaling and glucose uptake in mammary adipocytes of healthy women that underwent breast reduction surgery. Glucose uptake was strongly induced by insulin stimulation. This was paralleled by robust induction of insulin receptor kinase activity, insulin receptor substrate-1-associated phosphatidylinositol-3 kinase activity, and protein kinase B phosphorylation. Treatment with the beta (3)-adrenoceptor-selective agonist CL316,243 alone, neither induced alterations in the early insulin signaling cascade nor changed the basal level of glucose uptake. By contrast, pretreatment with the beta (3)-adrenoceptor agonist inhibited the insulin-induced insulin receptor substrate-1-associated phosphatidylinositol-3 kinase activity by 50 % and protein kinase B phosphorylation by 40 % without affecting insulin receptor kinase activity upstream. However, on the functional level insulin-induced glucose uptake remained unchanged by beta (3)-adrenoceptor stimulation. Our data demonstrate an insulin receptor-independent negative influence of beta (3)-adrenoceptor stimulation on proximal insulin signaling. This inhibition is apparently dissociated from glucose uptake in human adipocytes.

Halide anion recognition in water by a hexaprotonated octaaza-cryptand: a molecular dynamics investigation

Based on molecular dynamics simulations, we describe the F- versus Cl- complexation by an hexaprotonated cryptand L6+ in aqueous solution, in order to elucidate their structures, solvation properties and the status of external halide counterions. In water, F- and Cl- simulated inclusive complexes adopt a structure somewhat different from the solid state structure of the F- complex: The anion binding involves two diammonium bridges only, and the accompanying counterions are dissociated from the +5 charged complex. A remarkable result is obtained for the dissociated L6+,3F- ,3Cl- system, where spontaneous complexation of F- (the anion which forms the most stable complex with L6+) takes place during the dynamics. The resulting complex is of facial type; this suggests that the equilibrium involves multiple binding modes and structures in aqueous solution. The question of F-/Cl- binding selectivity is investigated by free energy perturbations simulations which nicely reproduce the spectacular preference for F- over Cl-. Two different methodologies used for the treatment of electrostatics (standard versus Ewald calculations) yield similar conclusions.

Targeted gene delivery into alpha9beta1-integrin-displaying cells by a synthetic peptide

We have investigated the usefulness of two small synthetic peptides comprising either a linear or a cyclic PLAEIDGIEL domain and a DNA-binding moiety of 16 lysine residues to mediate gene transfer selectively into alpha9beta1-integrin-displaying cells. Such specific gene delivery could only be achieved with the peptide containing the cyclic PLAEIDGIEL domain. However, inclusion of the cationic liposome Lipofect-AMINE into the peptide/DNA complexes resulted for both peptides in efficient gene transfer with significant targeting specificity. Naturally, the integrin alpha9beta1 is present only in a few highly specialised tissues and abundant throughout the human airway epithelia in vivo. Targeting gene vectors to this integrin therefore appears a useful approach to gene therapy of lung diseases such as cystic fibrosis. As the integrin alpha9beta1 is associated with tissue differentiation during foetal development and may cause resurgence of the foetal phenotype in colon cancers, such vectors may also be applicable for prenatal and cancer gene therapy.

Photosuicide inactivation of acetylcholinesterase by nitrosamine derivatives

Methyl(acetoxymethyl)nitrosamine and methyl-(butyroxymethyl)nitrosamine are respectively substrate (KM - 10(-2) M) and competitive inhibitor (Ki = 2 x 10(-3) M) of electric eel acetylcholinesterase (EC 3.1.1.7). Irradiation of an incubation mixture of this enzyme with either nitrosamine leads to an irreversible loss of enzyme activity. The inactivation rates are dependent on photolysis wavelength, light intensity, and inhibitor concentration. Experiments where acetylcholinesterase was radioactively labeled by [14C]-methyl(acetoxymethyl)nitrosamine show that the incorporation of 1 mol of radioactive label per active site is sufficient to cause complete enzyme inactivation irrespective of the reaction conditions used. Methyl(acetoxymethyl)nitrosamine shows no affinity for horse serum butyrylcholinesterase (EC 3.1.1.8) while methyl(butyroxymethyl)nitrosamine is a competitive inhibitor (Ki = 2 x 10(-3) M), but no irreversible inhibition is induced by the action of light. We propose that a suicide type of inhibition [Bloch, K. (1969) Acc. Chem. Res. 2, 193-198] is responsible for the inactivation of acetylcholinesterase, based on photoactivation of nitrosamines only when associated with an acidic hydrogen of the active site.