Molecular Biomarkers Of Response Research Articles

TRLS-10. CLINICAL TRIAL IN PROGRESS - CONNECT2007: PHASE I/II STUDY OF LUTATHERA IN PATIENTS WITH RECURRENT AND/OR PROGRESSIVE HIGH-GRADE CENTRAL NERVOUS SYSTEM (CNS) TUMORS AND MENINGIOMAS THAT DEMONSTRATE UPTAKE ON DOTATATE PET

Abstract BACKGROUND Somatostatin type-2A receptors (SST2A) regulate cell growth through complex downstream modulation of proliferation and apoptosis signaling, thereby representing a potential therapeutic target. Lutetium (177Lu-DOTATATE), a radionuclide therapy which binds SST2A and delivers local radiation via beta particle emission, gained FDA approval for gastroenteropancreatic neuroendocrine tumors, a disease characterized by SST2A expression. Potential expansion of Lutathera into pediatric neuro-oncology is supported by evidence that medulloblastoma, other embryonal tumors, and meningiomas consistently express membranous SST2A, exhibit corresponding uptake on SST2A-radiolabeled nuclear imaging (DOTATATE PET), and have demonstrated radiographic response to SST2A-targeted therapy, suggesting sufficient CNS penetration to achieve therapeutic benefit. METHODS CONNECT2007 (NCT05278208) is an international, multicenter phase I/II study investigating safety and efficacy of Lutathera in children and adults with SST2A-expressing CNS tumors. Patients with recurrent/progressive high-grade CNS tumors and meningiomas can undergo screening, consisting of DOTATATE PET imaging for functional confirmation of SST2A expression, requiring adequate uptake (Krenning score ≥2) by central review. The phase I cohort will enroll patients aged 4-<12 years to determine the pediatric recommended phase II dose (RP2D) following a Rolling Six design, with three potential dose levels, starting at the adult RP2D (200mCi), scaled by body surface area. The phase II cohort will enroll patients aged ≥12 years to assess anti-tumor activity through evaluation of 6-month progression-free survival in medulloblastoma/embryonal tumors (descriptive in other histologies). Lutathera is administered intravenously, with concurrent amino acids for nephroprotection, dosed every 8 weeks for up to 4 cycles. Longitudinal correlative studies include 1) evaluating prevalence, heterogeneity, and clinical, histologic molecular, and radiographic predictors of SST2A expression, 2) characterizing radiation dosimetry of Lutathera in organs at risk of toxicity and within CNS to assess tumor penetration, and 3) identifying imaging and molecular biomarkers of response. Enrollment began in January 2023; both cohorts remain open to accrual.

Predictive genomic biomarkers of therapeutic effects in renal cell carcinoma.

In recent years, there have been great improvements in the therapy of renal cell carcinoma. Nevertheless, the therapeutic effect varies significantly from person to person. To discern the effective treatment for different populations, predictive molecular biomarkers in response to target, immunological, and combined therapies are widely studied. This review summarized those studies from three perspectives (SNPs, mutation, and expression level) and listed the relationship between biomarkers and therapeutic effect, highlighting the great potential of predictive molecular biomarkers in metastatic RCC therapy. However, due to a series of reasons, most of these findings require further validation.

Defining Clinical and Molecular Biomarkers for Venetoclax-Based Drug Combinations to Augment AML Therapy

Background: The combination of the BCL2 inhibitor venetoclax with azacytidine (Ven+Aza) is efficacious for elderly patients with acute myeloid leukemia (AML) who are unfit for standard chemotherapy. However, the overall and progression-free survival of these patients after 1 year of therapy is approximately 30-40%, and resistance to Ven+Aza, either primary or adaptive through clonal evolution, limits its durability. Therefore, we evaluated new venetoclax combinations to elucidate mechanisms and biomarkers of response and resistance. Methods: We tested a set of 31 venetoclax (Ven) combinations using an ex vivo assay on primary AML patient specimens (n=433, though not all combinations were screened for all samples). Enhanced efficacy was determined using a combination ratio (CR), defined as the sensitivity of the combination (by AUC) divided by the sensitivity of the most potent single agent AUC. Drug combination synergy was evaluated using the highest single agent (HSA) method. Clinical, genetic, and disease status information were collated, and ex vivo combination sensitivities were compared to matched single-agent data by Friedman test, across groups by Wilcoxon rank sum or Kruskal-Wallis test, and with continuous variables by Spearman rank correlation. For patient specimens with RNAseq data collected (n=279 patients), transcriptomic gene signatures of AML tumor cell state (van Galen, Cell 2019) were correlated with combination sensitivity by Spearman rank. Uni- and multi-variate analyses were applied to the full dataset to identify biomarkers of differential sensitivity to each combination. For one combination, Ven plus the JAK1/2 inhibitor ruxolitinib (Rux), additional genome wide CRISPR screens and follow up in vivo patient xenograft and mechanistic validation experiments using AML cell line models were performed. Results: Using Ven+Aza as a benchmark, we found several venetoclax combinations that exceeded both the ex vivo activity and enhanced efficacy observed with Ven+Aza in primary AML patient samples (Fig. 1A), while showing limited to no effect on stromal cell controls. Evaluation of clinical and genetic data with combination sensitivity revealed many significant transcriptomic, genetic, and immunophenotypic associations. The strong bias in sensitivity of Ven with respect to transcriptomic signatures of primitive tumor cell states compared to more mature, monocytic tumor states was unchanged with Ven+Aza and select other combinations. Importantly, this differential sensitivity was overcome when pairing Ven with several new drug partners such as Rux or the p38 MAPK inhibitor doramapimod (Fig. 1B). Uni- and multi-variate analyses further revealed an array of different biomarkers involving clinical and genetic features that correlated with significant differential sensitivity to each combination. Many of these likewise involved markers of cell differentiation state, such as CD14. To elucidate the mechanisms of enhanced efficacy of the Ven+Rux combination, which is currently under phase 1 clinical investigation, in vivo murine patient xenograft models and genome-wide CRISPR screens in OCI-AML2 cells were performed. Ven+Rux demonstrated superior inhibition of tumor growth in an AML xenograft model compared to either single-agent. The Ven+Rux CRISPR screen identified many genes whose knockdown was enriched in combination-resistant cells, including three (MDM2, MED13L, MEIS2) that were confirmed to confer resistance in subsequent immunoblotting and drug sensitivity validation experiments. In comparison, analysis of a control CRISPR screen using Ven alone revealed numerous gene hits in the JAK/STAT signaling pathway as enhancing the sensitivity of Ven. Conclusion: To expand the utility of venetoclax-inclusive combinations, we prospectively profiled a set of drug combinations and identified several with activity that exceeds Ven+Aza in ex vivo assays. Associations of clinical features with sensitivities to these drug combinations provide insight into their effectiveness which may be used to align the most promising combinations with translation to treatment of discrete subsets of AML patients. Together, these findings support opportunities for expanding the impact of Ven-based drug combinations in AML by leveraging clinical and molecular biomarkers of response. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Abstract OT-35-01: Solti-1507 A phase ib study of ipatasertib and anti-her2 therapy in her2-positive advanced breast cancer with pik3ca mutation (ipather)

Abstract Background The combination of trastuzumab, pertuzumab (HP) and a taxane increases progression-free survival (PFS) and overall survival (OS) in patients with HER2-positive (HER2+) advanced breast cancer (BC). PIK3CA mutations can occur in 30-35% of HER2+ tumors, independently of hormone receptor (HR) status. In an exploratory analysis from CLEOPATRA, patients with a tumor harboring a PIK3CA mutation (mut) had a shorter PFS. The AKT inhibitor ipatasertib (IPAT) blocks the PI3K/AKT pathway and has activity in PI3K/AKT-altered tumors. We hypothesize that ipatasertib + HP is safe and can be beneficial in patients with PIK3CAmut HER2+ BC. Trial design This is an open-label, single arm, phase Ib study to evaluate the safety and preliminary efficacy of IPAT plus HP (+/- endocrine therapy [ET]) in patients with PIK3CA mut HER2+ BC. Key inclusion criteria include the presence of locally advanced/unresectable or metastatic HER2+ BC with a PIK3CA mut (detected in tissue or plasma ctDNA); candidates to receive maintenance HP (+/- ET) after taxane discontinuation in first line setting for a reason different to progressive disease; male and female (pre and postmenopausal status); adequate performance status (ECOG 0-1); and adequate bone marrow, cardiac and hepatic function. Key exclusion criteria include: active or progressive brain metastases; diabetes mellitus requiring insulin, and prior exposure to an AKT inhibitor. The primary endpoint is to define the maximum tolerated dose (MTD) and the recommended phase 2 dose of the combination. MTD is defined as the highest dose level at which ≤1 of 6 subjects experience a dose-limiting toxicity (DLT) during the first 28 days of treatment. Grade ≥3 diarrhea for more than 72 hours or Grade ≥2 diarrhea for more than 5 days are considered DLTs amongst others. Secondary endpoints include objective response rate, duration of response, clinical benefit rate and PFS. Exploratory objectives include identification of molecular biomarkers of response to treatment both in ctDNA (Amplicon-seq) and tumor tissue (Breast Cancer 360 panel), as well as to characterize the pharmacokinetics of study drugs. Given the low risk for overlapping toxicities, full doses of IPAT (400mg orally once daily D1-21 q28d) and standard dose HP will be used in the first cohort. Dose reductions of IPAT (300mg and 200mg) are allowed if the full dose exceeds MTD. Loperamide is given as prophylaxis for diarrhea. In HR-positive tumors, ET may be started after the DLT period. Approximately 25 evaluable patients in a given dose level will be required to assess the safety of the combination of IPAT plus HP. Patients are currently being screened for PIK3CA mutations at 7 sites in Spain. The first patient was enrolled in March 2020 and the recruitment is ongoing. This study is sponsored by SOLTI and financially supported by Roche. For further information on this trial, visit ClinicalTrials.gov (NCT04253561) Citation Format: Mafalda Oliveira, Patricia Villagrasa, Eva Ciruelos, Joaquín Gavilá, Alexandra Cortegoso, Fernando Henao, Estela Vega, Javier S. Bofill, Vanesa Quiroga, Laura García-Estevez, Serafín Morales, Pablo Tolosa, Pamela Céliz, Xavier Gonzalez Farré, Cristina Saura. Solti-1507 A phase ib study of ipatasertib and anti-her2 therapy in her2-positive advanced breast cancer with pik3ca mutation (ipather) [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr OT-35-01.

Effects of paralytic shellfish poisoning toxin-producing dinoflagellate Gymnodinium catenatum on the marine copepod Tigriopus japonicus

To understand how the marine copepod Tigriopus japonicus responds to the toxic marine dinoflagellate Gymnodinium catenatum, we assessed acute toxicity and investigated swimming behavior parameters (e.g., swimming speed, swimming path trajectory, and swimming distance) in response to G. catenatum exposure. In addition, the mRNA expression levels of detoxification-related genes (e.g., phase I cytochrome P450 [CYP] and phase II glutathione-S transferase [GST]) were measured in G. catenatum-exposed copepods. No significant change in survival was observed in response to G. catenatum, but swimming speed was significantly decreased (P<0.05) at a high concentration of G. catenatum (600cells/mL). Furthermore, the swimming distance was significantly decreased (P<0.05) compared to that of the control at 600 cells/mLG. catenatum, while no significant change in swimming path trajectory was observed, suggesting that G. catenatum potentially has adverse effects on the swimming behavior of T. japonicus. In addition, the transcriptional regulation of T. japonicus CYPs and -GSTs were significantly upregulated and downregulated (P<0.05), respectively, in response to G. catenatum. In particular, certain genes (e.g., CYPs [CYP307E1, CYP3041A1, and CYP3024A2] and GSTs [GST-kappa, GST-mu5, and GST-omega]) were significantly induced (P<0.05) by G. catenatum, suggesting that these genes likely play a critical role in detoxification mechanisms and might be useful as potential molecular biomarkers in response to G. catenatum exposure. Overall, these results elucidate the potential impacts of the dinoflagellate G. catenatum on the swimming behavior and detoxification system of the marine copepod T. japonicus.

Abstract 4280: Potential molecular biomarkers of response to eribulin in patients with leiomyosarcoma

Abstract Background. The recent randomized phase 3 trial Eisai Study 309 evaluated efficacy of eribulin (ERI) compared to dacarbazine (DTIC) in advanced liposarcoma (LPS) and leiomyosarcoma (LMS). Improved overall survival (OS) in ERI-treated patients led to US and EU regulatory approval of ERI for LPS, but not in LMS where DTIC has clinically relevant activity. As part of the translational effort in this trial we have now explored the molecular profile of LMS tumors from North American study sites, in order to identify potential predictive molecular factors for treatment with ERI. Material and Methods. From 82 archival primary tumor or metastatic LMS samples collected prior to study entry, 78 specimens were available for low-coverage whole genome sequencing. We analyzed copy number alterations (CNAs) and performed whole exome sequencing (WES) for mutational profiling. Forty patients received experimental treatment with ERI, while 38 were treated with DTIC. Treatment response was evaluated using RECIST v1.1; disease control was defined as complete/partial response and stable disease. Results. Overall 111 focal CNAs were observed in the entire group of LMS, including 55 gains and 56 loses. Gain of 17q12 was the most common CNA (43/78 cases; 55.1%) observed in the entire group analyzed, with 26 samples showing high level amplification. MYOCD is a suggested target of 17q12 gains in LMS, encodes myocardin which induces smooth muscle differentiation and promotes cell migration. In the ERI-treated group, gains of 4q26, 20p12.2, 13q13.3, 8q22.2, 8q13.2 and loss of 1q44 had a negative impact on progression-free survival (PFS) (p&amp;lt;0.05; log rank test), while loss of 2p12 was a positive prognosticator. Gains of 4q22.1 and losses of 3q14.2, 2q14.1 and 11q25 had a negative impact on OS in ERI-treated patients. Using WES we detected an average of 266.1 (143-626) nonsynonymous substitutions and 4.7 indels (0-16) per sample, with an average of 11.5 (0-28) variants affecting Cancer Consensus Genes. The most commonly mutated genes in analyzed samples were TP53 (38%), MUC16 (31%) and ATRX (17%). In ERI-treated patients, the presence of ATRX mutations was more frequently observed in patients progressing on ERI (7/20 in patients with PD vs. 1/20 in group with disease control; p=0.0435). The presence of ATRX mutation had a negative impact on both PFS and OS. TP53 mutations were associated with longer PFS, and these mutations were more frequently observed in patients achieving disease control, although this was not statistically significant (11/20 vs. 5/20). ATRX andTP53 mutations were not linked with clinical benefit/response to DTIC. Conclusions. LMS has a complex genetic background, with multiple CNAs and mutations affecting genes implicated in tumorigenesis. We identified several molecular changes with potential impact on disease control and survival of LMS patients treated with ERI. These observations require further prospective validation. Citation Format: Agnieszka Wozniak, Bram Boecks, Elodie Modave, Amy Weaver, Diether Lambrechts, Bruce A. Littlefield, Patrick Schöffski. Potential molecular biomarkers of response to eribulin in patients with leiomyosarcoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4280.

Clinical and molecular markers of immune checkpoint inhibitor (ICI) response in dMMR colorectal cancer (CRC) patients (pts).

225 Background: ICIs induce durable responses in dMMR CRC patients. However, clinical and molecular biomarkers of response to ICIs have not been well-established. In this study, we investigated impact of specific MMR gene loss, BRAF V600E mutation and clinical characteristics of pts on clinical outcomes of ICIs. Methods: Pts were eligible if they had confirmed dMMR CRC by IHC or MSI-H by PCR and received ICIs between 01/01/2012 and 05/01/2019 at Winship Cancer Institute of Emory University, Mayo Clinic, Vanderbilt or Stanford University. Due to the functional dependency, the groups were categorized as protein loss of MLH1+PMS2 vs MSH2+MSH6. Log-rank test, Cox hazard model and Fisher’s exact test were used for survival outcomes, the best response and the distribution of variables among the subgroups. Results: A total of 66 pts with dMMR CRC were identified and BRAF status was available for 41 pts. ORRs in MLH1+PMS2 and MSH2+MSH6 groups were 72.9% and 56.5% respectively (P = 0.189). At 2 years, PFS rates were 55.6% and 78.2% for MLH1+PMS2 and MSH2+MSH6 groups respectively (P &lt; 0.001). Pts with BRAF V600E mutations had significantly worse outcomes as compared to pts with wild-type BRAF (2-year PFS rate of 35.0% and 73.3% respectively; P &lt; 0.001). Notably pts &lt; 65 had better 2-year disease control rates when compared to &gt; 65 (71.1% and 41.5% respectively; P &lt; 0.001). We also observed worse 2-year PFS rates in pts with liver metastases (P = 0.014). CRC side and tumor volume did not impact 2-year PFS rates in our cohort. Conclusions: Our data suggest that pts with loss of function in MSH2+MSH6 may have better 2 year-PFS rates compared pts with MLH1+PMS2 even though ORR favored MLH1+PMS2 group suggesting that ORR may not reflect the durability of ICI response in dMMR CRC patients. Consistently, pts with BRAF V600E mutation which is associated with MLH1 promoter methylation had significantly worse 2-year PFS rates. Overall, our findings suggest that BRAFV600E mutation, the affected MMR proteins, pt age, and site of metastasis may impact durability of ICI response in dMMR CRC patients.

Patient-Derived Xenografts and Matched Cell Lines Identify Pharmacogenomic Vulnerabilities in Colorectal Cancer.

Patient-derived xenograft (PDX) models accurately recapitulate the tumor of origin in terms of histopathology, genomic landscape, and therapeutic response, but some limitations due to costs associated with their maintenance and restricted amenability for large-scale screenings still exist. To overcome these issues, we established a platform of 2D cell lines (xeno-cell lines, XL), derived from PDXs of colorectal cancer with matched patient germline gDNA available. Whole-exome and transcriptome sequencing analyses were performed. Biomarkers of response and resistance to anti-HER therapy were annotated. Dependency on the WRN helicase gene was assessed in MSS, MSI-H, and MSI-like XLs using a reverse genetics functional approach. XLs recapitulated the entire spectrum of colorectal cancer transcriptional subtypes. Exome and RNA-seq analyses delineated several molecular biomarkers of response and resistance to EGFR and HER2 blockade. Genotype-driven responses observed in vitro in XLs were confirmed in vivo in the matched PDXs. MSI-H models were dependent upon WRN gene expression, while loss of WRN did not affect MSS XLs growth. Interestingly, one MSS XL with transcriptional MSI-like traits was sensitive to WRN depletion. The XL platform represents a preclinical tool for functional gene validation and proof-of-concept studies to identify novel druggable vulnerabilities in colorectal cancer.

Abstract LB-299: A comprehensive platform of patient-derived xenografts and matched cell lines mirrors the genomic landscape of colorectal cancer

Abstract Preclinical models that accurately reflect patients’ tumor with regards to histopathology, genomics, and therapeutic response represent a compelling need to fuel the progress of effective cancer treatments. Patient-derived tumor xenografts (PDXs) have significantly accelerated this process, but, although they closely mirror structural and molecular features of the tumor of origin, they still retain important restrictions related to maintenance costs and large-scale screening. To overcome this issue, we have established a novel platform of 2D-cell lines (xeno-cell lines, XL) derived from PDXs of colorectal cancer (CRC) from which patient’s germline gDNA was available. We have characterized XL-cells at multiple levels to confirm their proximity to the PDXs of origin and to assess their suitability as patient avatars in vitro to interrogate functional networks in colorectal cancer. All XL-cells showed an epithelial-like morphology and phenotype, as also confirmed by EMT biomarker transcriptomic analysis. Whole exome and RNA-seq analyses showed that genomic features were consistently preserved between PDXs and matched cell models. Expression analysis revealed the XL-line collection as a significant representative of all CRC subtypes (CMS and CRIS subgroups). Furthermore, genomic analysis allowed the identification of molecular biomarkers of response and resistance to targeted therapies, including EGFR and HER2 blockade. In particular, molecular determinants of resistance to dual-HER2 blockade previously reported in the Heracles-A trial were validated in XL-cells. In conclusion, the XL-cell line and PDX platform represents a unique and comprehensive preclinical tool to validate gene function e to identify novel pharmacological vulnerabilities in colorectal cancer. Citation Format: Luca Lazzari, Giorgio Corti, Claudio Isella, Monica Montone, Pamela Arcella, Eugenia Zanella, Luca Novara, Fabiane Barbosa, Andrea Cassingena, Carlotta Cancelliere, Enzo Medico, Andrea Sartore-Bianchi, Salvatore Siena, Andrea Bertotti, Livio Trusolino, Federica Di Nicolantonio, Michael Linnebacher, Alberto Bardelli, Sabrina Arena. A comprehensive platform of patient-derived xenografts and matched cell lines mirrors the genomic landscape of colorectal cancer [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 LB-299.

Abstract PL08-04: High-throughput drug screens in cancer cell models to enable precision cancer medicine

Abstract Alterations in cancer genomes strongly influence clinical responses to therapy and can be used as molecular biomarkers of response to targeted agents. However, the identification of biomarkers for effective patient stratification remains a considerable challenge for the development of effective therapies. We are performing large-scale drug sensitivity screens using genetically characterised in vitro cellular models of human cancer. Cancer cells are profiled for differential sensitivity to clinical, pre-clinical and experimental anti-cancer compounds and drug response is linked with genomic features. We aim to identify the molecular features of cancer cells which impact on drug sensitivity and resistance, and investigate the molecular rationale for the observed sensitivity. This provides insights into mechanism of drug action, identifies opportunities for re-purposing existing drugs for new indications, and enables the identification of biomarkers to facilitate the development of targeted cancer therapies. I will describe results from our recent analysis of how cancer-driving alterations identified from the analysis of 11,000 patient tumours correlate with response to 265 compounds profiled in a panel of 1,000 human cancer cell-lines. This comprehensive analysis provides an initial glimpse of the landscape of pharmacogenomic interactions operative in human cancer, and is a resource to identify novel therapeutic possibilities for selected cancer sub-populations. Citation Format: Mathew Garnett. High-throughput drug screens in cancer cell models to enable precision cancer medicine. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr PL08-04.

Identification of potential molecular biomarkers in response to thioredoxin reductase 1 deficiency under nickel exposure

Nickel (II) is a ubiquitous environmental contaminant and it is known to be a highly toxic metal. The level of nickel in the environment has been raised with advances in industrialization and the role of nickel in human diseases is of increasing concern. Thioredoxin reductase 1 (Trr 1) is one of major redox factors having a potential role in cellular defense system against exposure to environmental toxicants. In this study, we investigated the protective roles of the Trr 1 against nickel-induced DNA damage. We found significantly higher amounts of DNA strand break in Trr 1 silencing cells compared to Trr 1 wild-type cells under nickel exposure, using γ-H2AX immunofluorescence staining. We also identified the potential molecular biomarkers that participated in gene-environment interaction between Trr 1 deficiency and nickel exposure via microarray analysis. In particular, seven upregulated genes (AHNAK, FZR1, LGALS7, PLD1, PPM1F, RHOB and SFRP1) and three down-regulated genes (IFITM1, MAPK8 and RCN1), whose functions are principally in toxicity-prone as well as cytoprotection processes, including cell proliferation, cell survival, apoptosis, inflammation and DNA repair. Our findings demonstrate gene-environment interaction between Trr 1 deficiency and nickel-induced toxicity, as evidence that insufficient of redox factor Trr 1 accelerated DNA lesions caused by nickel exposure. These results suggest that the candidate genes might be further useful in the establishment of Trr 1-mediated strategies by which modulate cellular defense against environmental toxicants, nickel.