PTEN Alterations Research Articles

Histological and molecular glioblastoma, IDH-wildtype: a real-world landscape using the 2021 WHO classification of central nervous system tumors.

Glioblastoma (GBM), the most lethal primary brain malignancy, is divided into histological (hist-GBM) and molecular (mol-GBM) subtypes according to the 2021 World Health Organization classification of central nervous system tumors. This study aimed to characterize the clinical, radiological, molecular, and survival features of GBM under the current classification scheme and explore survival determinants. We re-examined the genetic alterations of IDH-wildtype diffuse gliomas at our institute from 2011 to 2022, and enrolled GBMs for analysis after re-classification. Univariable and multivariable analyses were used to identify survival determinants. Among 209 IDH-wildtype gliomas, 191 were GBMs, including 146 hist-GBMs (76%) and 45 mol-GBMs (24%). Patients with mol-GBMs were younger, less likely to develop preoperative motor dysfunction, and more likely to develop epilepsy than hist-GBMs. Mol-GBMs exhibited lower radiographic incidences of contrast enhancement and intratumoral necrosis. Common molecular features included copy-number changes in chromosomes 1, 7, 9, 10, and 19, as well as alterations in EGFR, TERT, CDKN2A/B, and PTEN, with distinct patterns observed between the two subtypes. The median overall survival (mOS) of GMB was 12.6 months. Mol-GBMs had a higher mOS than hist-GBMs, although not statistically significant (15.6 vs. 11.4 months, p=0.17). Older age, male sex, tumor involvement of deep brain structure or functional area, and genetic alterations in CDK4, CDK6, CIC, FGFR3, KMT5B, and MYB were predictors for a worse prognosis, while MGMT promoter methylation, maximal tumor resection, and treatment based on the Stupp protocol were predictive for better survival. The definition of GBM and its clinical, radiological, molecular, and prognostic characteristics have been altered under the current classification.

Abstract PR003: Convergent evolution in DNA repair-deficient mCRPC in response to targeted therapy

Abstract BACKGROUND: Distinct metastatic prostate cancer lesions within the same patient can show a range of responses to targeted therapy. These variations in response present a challenge for the interpretation of predictive biomarkers derived from a single lesion. The influence of tumor evolution on how lesions respond to Androgen Signaling Inhibitor (ASI) or PARP inhibitor therapy has been difficulty to study, because few autopsy studies have been performed in heavily treated patients with DNA repair defects. METHODS: In this study, we analyzed an autopsy cohort of 54 tumors from six men with DNA repair-deficient metastatic prostate cancer using whole genome, exome, and targeted DNA sequencing as well as RNA-sequencing. Observations were validated in an independent cohort of 135 mCRPC biopsies with whole genome and transcriptome sequencing. To automate the analysis of mutations conferring resistance to PARP inhibitor therapy, we developed a tool (AARDVARK) that detects and annotates PARP inhibitor resistance mutations. RESULTS: Patients harboring germline inactivation of the DNA repair gene BRCA2 showed consistent BRCA2 biallelic inactivation, while somatic BRCA2 inactivation was not always associated with biallelic deletion and genomic scars of DNA repair inactivation. AARDVARK identified numerous identical resistance mutations in physically distinct tumors in the same individual, consistent with dissemination of these mutations prior to later targeted therapy. We identified DNA structural variations linked to extra-chromosomal DNA (ecDNA) in 52% of mCRPC biopsies, and ecDNA amplified an oncogene 28% of the time. Extensive heterogeneity of structural variants was present at the Androgen Receptor locus, which was the most frequent target of ecDNA amplification (15% of tumors). Cyclins CCND1 and CCNE1 were amplified in 3% of cases, and a long tail of oncogenes were also targeted. Phylogenetic analysis was consistent with AR amplification by ecDNA in response to both androgen deprivation therapy and second-generation ASI. The presence of ecDNA was significantly associated with overall genomic instability, aneuploidy, whole genome doubling, chromothripsis, and with inactivating PTEN alterations. CONCLUSIONS: This study demonstrated that mCRPC lesions continue to evolve on therapy, and their varied responses can be influenced by shared genetic backgrounds. Oncogene amplification by ecDNA is common in mCRPC, particularly at the AR locus, and is linked to genomic instability. Alterations conferring resistance to ASI and PARP inhibitor therapy can be present in individual lesions before metastatic dissemination, and the evolutionary history of tumors plays an important role in their tumor response to targeted therapy. Citation Format: Thaidy Moreno, Meng Zhang, Arian Lundberg, Raunak Shrestha, Martin Sjöström, Anu Pasam, Adam Foye, Anna Trigos, Felix Feng, Shahneen Sandhu, David A. Quigley. Convergent evolution in DNA repair-deficient mCRPC in response to targeted therapy [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr PR003.

3D open-top light-sheet microscopy and 3D microdissection of neuoadjuvant-treated primary prostate cancer reveals latent subclonal mutations.

e17109 Background: Intratumoral molecular heterogeneity is a well described phenomenon in primary prostate cancer. Increased genomic heterogeneity is associated with more aggressive clinical behavior, including recurrence and metastasis. However, current methods to characterize heterogeneity suffer from tradeoffs between generating high quality morphologic information, correlating morphology with genomic alterations, and workflow considerations. We describe a technology to image prostate samples in 3D, perform 3D microdissection of regions of interest (ROIs), and preserve nucleic acids for DNA sequencing. Methods: Samples (N = 18) were obtained from patients (N = 12) enrolled in an open-label, single-site, Phase II neoadjuvant trial in men with NCCN high to very-high risk PC. Patients received 12 weeks of apalutamide, abiraterone acetate plus prednisone, degarelix, and indomethacin followed by radical prostatectomy (RP). Fresh frozen prostate samples (~2x2x0.4cm) were obtained from RP specimens. Frozen samples were fixed in an ethanol-based fixative, stained with nuclear (TOPRO-3) and general protein (eosin) fluorescent dyes, cleared with ethyl cinnamate, and imaged using 3D open-top light-sheet (OTLS) fluorescence microscopy. Image-guided 3D microdissection was performed on ROIs with distinct morphologies. Microdissected ROIs measured 0.5x0.5x2mm. Microdissected samples were sent for DNA extraction and sequencing using the comprehensive clinically-validated UW-OncoPlex NGS assay. Results: The tissue from neoadjuvant-treated patients contained sparse carcinoma, with cancer volumes ranging from 0.01-0.3 cm2 and cellularity ranging from 2%-30%. Molecular alterations were detected in a sample with only 0.07 cm2 volume of carcinoma with 5% cellularity. The read depth of 3D microdissected samples was 3.9 times greater than the read depth of FFPE samples from the same patients. At least two morphologically distinct ROIs were 3D microdissected from 11 of 12 patients. Four of the 18 samples had molecular alterations that differed between ROIs, i.e. intra-sample molecular heterogeneity. For example, one sample with three microdissected ROIs had a PTEN alteration exclusive to a single ROI. Conclusions: The findings show the potential for 3D microdissection of morphologically distinct subclones in samples from neoadjuvant-treated patient, to enable sequencing of specific cellular populations. The sparsity of carcinoma necessitated a spatially targeted approach for extracting material for sequencing. The increased yield from avoiding FFPE processing and carcinoma enrichment from targeted 3D microdissection of carcinoma ROIs enabled the detection of spatially distinct molecular subclones. Future work will include the analysis of additional samples and implementation of AI-guided ROI detection to streamline workflows.

Establishment of a novel model of endometriosis-associated ovarian cancer by transplanting uterine tissue from Arid1a/Pten knockout mice

Although endometriosis is primarily benign, it has been identified as a risk factor for endometriosis-associated ovarian cancer (EAOC). Genetic alterations in ARID1A, PTEN, and PIK3CA have been reported in EAOC; however, an appropriate EAOC animal model has yet to be established. Therefore, the present study aimed to create an EAOC mouse model by transplanting uterine pieces from donor mice, in which Arid1a and/or Pten was conditionally knocked out (KO) in Pax8-expressing endometrial cells by the administration of doxycycline (DOX), onto the ovarian surface or peritoneum of recipient mice. Two weeks after transplantation, gene KO was induced by DOX and endometriotic lesions were thereafter removed. The induction of only Arid1a KO did not cause any histological changes in the endometriotic cysts of recipients. In contrast, the induction of only Pten KO evoked a stratified architecture and nuclear atypia in the epithelial lining of all endometriotic cysts, histologically corresponding to atypical endometriosis. The induction of Arid1a; Pten double-KO evoked papillary and cribriform structures with nuclear atypia in the lining of 42 and 50% of peritoneal and ovarian endometriotic cysts, respectively, which were histologically similar to EAOC. These results indicate that this mouse model is useful for investigating the mechanisms underlying the development of EAOC and the related microenvironment.

LncRNA-PVT1 was identified as a key regulator for TMZ resistance and STAT-related pathway in glioma

BackgroundPVT1, a previously uncharacterized lncRNA, was identified as a critical regulator involved in multiple functions in tumor, including cell proliferation, cell motility, angiogenesis and so on. However, the clinical significance and underlying mechanism of PVT1 was not be fully explored in glioma.MethodsIn this study, 1210 glioma samples with transcriptome data from three independent databases (CGGA RNA-seq, TCGA RNA-seq and GSE16011 cohorts) were enrolled in this study. Clinical information and genomic profiles containing somatic mutations and DNA copy numbers were collected from TCGA cohort. The R software was performed for statistical calculations and graphics. Furthermore, we validated the function of PVT1 in vitro.ResultsThe results indicated that higher PVT1 expression was associated with aggressive progression of glioma. Cases with higher PVT1 expression always accompanied by PTEN and EGFR alteration. In addition, functional analyses and western blot results suggested that PVT1 inhibited the sensitivity of TMZ chemotherapy via JAK/STAT signaling. Meanwhile, knockdown of PVT1 increased the sensitivity of TZM chemotherapy in vitro. Finally, high PVT1 expression was associated with reduced survival time and may serve as a strong prognostic indicator for gliomas.ConclusionsThis study demonstrated that PVT1 expression strongly correlated with tumor progression and chemo-resistance. PVT1 may become a potential biomarker for the diagnosis and treatment in glioma.

Abstract 931: Comprehensive analysis of 3,600 small cell lung cancer cases reveals rare genetic subtypes and multiple mechanisms of histological transformation

Abstract Background: Small cell lung cancer (SCLC) is an aggressive neuroendocrine carcinoma with limited treatment options and extremely poor survival outcomes. A major barrier in the field has been the relative paucity of human tumors studied and lack of access to longitudinal samples to understand tumor evolution. Methods: Here we provide a comprehensive analysis of 3,600 patients with SCLC who underwent targeted genomic profiling of at least 324 cancer-related genes as part of routine clinical care, including 678 cases with additional clinical and treatment information obtained from a US-based de-identified SCLC clinico-genomic database that originated from approximately 280 US cancer clinics. This large cohort allowed us to examine for new genetic subtypes, ancestry-associated genomic alterations, biopsy site-specific patterns, survival trends and histological transformation of SCLC from non-small cell lung cancer (NSCLC). Results: Consistent with prior studies, SCLCs were predominantly TP53/RB1 altered. Yet, 5.5% of the cases in our cohort were TP53/RB1 wild-type tumors. These tumors often lacked a tobacco mutational signature, exhibited alternate mechanisms of p53/Rb pathway inactivation (e.g., CDKN2A, CCND1, MDM2), and had a high fraction of human papillomavirus-positive cases (12.7%). Another rare subtype of SCLCs included STK11-altered tumors (1.7%), which were observed more frequently in patients of African ancestry, and were associated with a decreased overall survival (OS) compared with the STK11 wild-type cohort. In our cohort, gene amplifications on 4q12 (KDR, KIT, PDGFRA) were associated with increased OS while CCNE1 amplification was associated with decreased OS. Interestingly, alterations in PTEN were more common in brain metastases compared to lung biopsies and liver metastases, suggesting its potentially unique role in brain metastases of SCLCs. Profiling of over 100 putative transformed SCLCs demonstrated that lineage plasticity may occur at variable lengths of time from the original NSCLC diagnosis and include multiple distinct molecular cohorts of NSCLC, beyond EGFR-mutant NSCLC (e.g., kinase fusion+ tumors: RET, ALK, ROS1, NTRK1). Conclusion: Our work underscores the existence of genetic subtypes in SCLC, including rare subtypes with potential clinical utility. Findings from this study provide an improved understanding of genetic subtypes in SCLC and better inform mechanisms of transformation to SCLC from NSCLC, that may further guide the development of personalized therapies for subsets of patients with this fatal tumor. Citation Format: Smruthy Sivakumar, Jay A. Moore, Meagan Montesion, Douglas I. Lin, Zoe Fleischmann, Ericka M. Ebot, Justin Newberg, Jennifer M. Mills, Priti S. Hegde, Garrett M. Frampton, Julien Sage, Christine M. Lovly. Comprehensive analysis of 3,600 small cell lung cancer cases reveals rare genetic subtypes and multiple mechanisms of histological transformation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 931.

Abstract 3431: Molecular determinants of KRAS p.G12C inhibitor efficacy in advanced NSCLC

Abstract Background: Irreversible allosteric KRAS p.G12C inhibitors (KG12Ci) such as sotorasib and adagrasib have revolutionized the therapeutic landscape of advanced KG12C-mutant NSCLC, however individual responses are heterogeneous and curtailed by innate and adaptive/acquired resistance. Molecular determinants of KG12Ci efficacy in NSCLC are poorly defined. We dissected the impact of major KG12C co-mutations and explored the effects of less prevalent co-alterations on the clinical activity of KG12Ci in the largest treated cohort to date of patients (pts) with advanced NSCLC. Key findings were validated in preclinical KG12C NSCLC models. Methods: Baseline clinico-genomic features and clinical outcome data from pts with stage IV KG12C NSCLC (ECOG PS 0-2) treated with single-agent KG12Ci were collected retrospectively from 20 centers in the US and Europe. The Kaplan-Meier method was used to estimate PFS and OS and differences were assessed with the log-rank test. Hazard ratios (HR) and their 95% CI were estimated using a Cox proportional hazards model stratified for clinical co-variates. The impact of selected co-alterations on sotorasib efficacy was assessed in syngeneic (C57BL/6) KG12C NSCLC models. Results: 411 eligible pts were included in the study. Median age was 68 years, 77% of pts had received both platinum-based chemotherapy and PD-(L)1 inhibitors and 35% had brain metastases. 83% of pts received sotorasib. ORR with KG12Ci was 32.4% (95% CI, 27.9-37.1), PFS was 5.1m (95% CI, 4.5-5.6) and OS was 10.2m (95% CI, 8.4-12.1). Co-alterations in KEAP1, SMARCA4 and CDKN2A/B were each associated with significantly shorter PFS (KEAP1: 2.8m vs 5.5m, HR 2.50, P<0.001; SMARCA4: 1.7m vs 5.5m, HR 2.64, P=0.001; CDKN2A/B: 2.3m vs 5.3m, HR 2.57, P<0.001) and OS with KG12Ci even after adjustment for clinical covariates. STK11 co-mutations without concurrent KEAP1 alterations did not impact clinical outcomes with KG12Ci. In an exploratory analysis, co-mutations in DNA damage repair (DDR) genes and genes encoding components of the ATRX/DAXX/EZH2 pathway were associated with improved KG12Ci efficacy, whereas PI3K/AKT/MTOR/PTEN alterations and missense ROS1/ALK/BRAF/NTRK1-3 mutations resulted in inferior outcomes. The impact of SMARCA4 and DDR gene inactivation was validated in isogenic syngeneic KG12CNSCLC models; additional co-alterations are under evaluation. Integration of KEAP1/SMARCA4/CDKN2A/B co-mutations identified a subgroup (KSCMUT, 37.6% of all pts) with significantly shorter PFS (2.7m vs 6.2m, P<0.001) and OS (6.3m vs 14.6m, P<0.001) that accounted for 57.3% of pts with primary refractory (PFS≤3m) disease. Conclusions: Co-mutations in KEAP1, SMARCA4 and CDKN2A/2B define subgroups of KG12C NSCLC pts with markedly distinct outcomes with KG12Ci monotherapy. Tailoring of KG12C inhibitor-anchored therapeutic strategies and patient stratification should take into account the co-mutation status of individual tumors. Citation Format: Marcelo V. Negrao, Haniel A. Araujo, Giuseppe Lamberti, Alissa J. Cooper, Teng Zhou, Neal Akhave, Lukas Delasos, J Kevin Hicks, Mihaela Aldea, Gabriele Minuti, Jacobi Hines, Jacqueline V. Aredo, Michael J. Dennis, Turja Chakrabarti, Susan Scott, Paolo Bironzo, Matthias Scheffler, Petros Christopoulos, So Yeon Kim, Sarah Goldberg, Ying Ni, Blerina Resuli, Lorenza Landi, Shu-Chi Tseng, Mizuki Nishino, Dwight Owen, Collin Blakely, Giannis Mountzios, Catherine A. Shu, Christine Bestvina, Marina Garassino, Kristen Marrone, Jhanelle Gray, Sandip Pravin Patel, Amy L. Cummings, Heather A. Wakelee, Jurgen Wolf, Giorgio V. Scagliotti, Federico Cappuzzo, Fabrice Barlesi, Pradnya Patil, Don L. Gibbons, Funda Meric-Bernstam, J Jack Lee, John V. Heymach, David S. Hong, Rebecca S. Heist, Mark M. Awad, Ferdinandos Skoulidis. Molecular determinants of KRAS p.G12C inhibitor efficacy in advanced NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3431.

Abstract 5469: Characterization of CCNE1 amplifications and associated genomic features in ovarian and uterine cancers

Abstract Amplification of the Cyclin E1 gene (CCNE1) is a recurrent genetic alteration in ovarian and uterine cancers. Therapeutic approaches to target cancers harboring CCNE1 amplification are being developed (e.g. PKMYT1, WEE1, and CDK2 inhibitors). In this study, we report the genomic landscape and architecture of CCNE1 amplifications using a combination of whole-exome (WES) and whole-genome sequencing (WGS) approaches. WES data from 361 ovarian and 580 uterine cancers was retrieved from TCGA. WGS data from 113 ovarian and 51 uterine cancers was retrieved from PCAWG. For both WES and WGS, amplification was defined as CN minus ploidy (CN-ploidy) >= 4. CCNE1 amplification was detected in up to 21.2% of ovarian and 13.7% of uterine cancers from both methods. A review of the co-alteration landscape using WES revealed that TP53 alterations frequently co-occurred with CCNE1 amplifications in both ovarian and uterine cancers (ovarian: 95.8% vs 87.6%, OR = 3.24, p=0.1; uterine: 89.6% vs 36.0%, OR = 15.2, p =2.14e-13) and BRCA1 alterations were mutually exclusive with CCNE1 amplifications in ovarian cancer (2.1% vs 17.9%, OR=0.2, p = 3.1e-3). In addition, alterations in ARID1A (0% vs 40.5%, OR = 0, p = 1.3e-10) and PTEN (4.2% vs 60.1%, OR = 0.03, p =2.7e-15) were mutually exclusive with CCNE1 amplifications in uterine cancer. The number of CCNE1 copies ranged widely, with median CN-ploidy values of 9.3 (range: 4.0 -35.0) in ovarian and 7.7 (range: 4.0 -40.3) in uterine cancers from the WES cohort, and 7.4 (range: 4.1 -34.3) in ovarian and 11.0 (range: 4.6 - 81.9) in uterine cancers from WGS. We also observed a broad range of CCNE1 amplicon sizes, from highly focal to chromosome arm-level amplifications. WGS data showed frequent loss of heterozygosity (LOH) of chromosome 19 arms and an enrichment of fold-back inversions proximal to the CCNE1 amplicon implicating breakage-fusion-bridge in formation of CCNE1 amplicons. Whole genome duplication (WGD) was detected significantly more frequently in ovarian and uterine cancers with CCNE1 amplification than the wild-type group (ovarian: 90.9% vs 48.3%, p = 6.4e-10; uterine: 78.7% vs 21.9%, p = 7.1e-15). As compared to CCNE1 wild-type cancers, CCNE1-amplified cancers were found to display an enrichment for certain structural variant signatures: RS1, dominated by 100Kb-1Mb duplications (median = 30, p=0.08); RS2, dominated by translocations (median = 16, p=0.001); and RS7, dominated by 100Kb-1Mb deletions (median=23, p=0.0002). In conclusion, CCNE1-amplified ovarian and uterine cancers are enriched for TP53 alterations and display a high degree of genome instability manifested as WGD and characteristic structural variants. Fold-back inversions and LOH were frequently observed at the CCNE1 locus in tumors with CCNE1 amplification, suggesting a potential breakage-fusion-bridge mechanism in the genesis of this amplicon. Citation Format: Sunantha Sethuraman, Dominik Glodzik, Pier Selenica, Adrienne Johnson, Jorge S. Reis-Filho, Artur Veloso, Ian M. Silverman. Characterization of CCNE1 amplifications and associated genomic features in ovarian and uterine cancers. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5469.

Abstract 996: Identification of molecular biomarkers differentiating malignant uterine leiomyosarcoma from benign leiomyoma

Abstract Uterine leiomyosarcomas are rare, aggressive cancers that represent the most common type of uterine sarcomas. They frequently harbor genetic alterations in TP53, RB1, PTEN, and ATRX. Their benign counterpart, uterine leiomyomas (or fibroids) are very common tumors that may significantly affect women’s quality of life. The majority of leiomyomas harbor genetic alterations affecting either MED12, HMGA2, or FH. A third of leiomyosarcomas have been reported to harbor leiomyoma-associated driver mutations, suggesting that some leiomyomas may have undergone malignant transformation. The leiomyoma/leiomyosarcoma diagnosis is largely based on histopathology. This can be specifically challenging in differentiating leiomyosarcomas from a subset of leiomyomas that display histopathological features resembling malignancy. The aim of this study was to identify molecular biomarkers that can accurately differentiate benign and malignant uterine smooth muscle tumors. 3’RNA sequencing of 48 leiomyosarcomas and 44 leiomyomas revealed that leiomyosarcomas are uniquely characterized by dysregulation of the retinoblastoma pathway. We confirmed upregulation of several members of this pathway, including TOP2A and CDK1, in a publicly available transcriptomic dataset of 49 uterine leiomyosarcomas. The second objective of this study was to explore the gene expression profile of leiomyosarcomas carrying leiomyoma-associated driver mutations. This revealed that unlike leiomyomas, leiomyosarcomas do not form distinct gene expression profiles based on the presence of leiomyoma-associated driver mutations such as MED12. However, leiomyosarcomas with a MED12 mutation showed upregulation of RAD51B and ADAM12, which we have previously highlighted as biomarkers of leiomyomas harboring a MED12 mutation. We identified upregulation of IRS4 and characteristic deletions affecting COL4A5 and COL4A6 in four in-house and three additional uterine leiomyosarcomas from The Cancer Genome Atlas (TCGA) collection. Similar driver alterations have previously been reported in a small subset of leiomyomas but not in leiomyosarcomas. In conclusion, leiomyosarcomas display a gene expression profile characterized by dysregulation of genes related to the retinoblastoma pathway. These include potential biomarkers that could be used in a clinical setting to differentiate leiomyosarcomas from leiomyomas. Citation Format: Sara Khamaiseh, Riitta Koivisto-Korander, Terhi Ahvenainen, Ralf Bützow, Miika Mehine, Pia Vahteristo. Identification of molecular biomarkers differentiating malignant uterine leiomyosarcoma from benign leiomyoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 996.

Abstract 1063: Precision medicine and cancer drug repurposing in the management of vascular anomalies

Abstract Vascular anomalies are a heterogeneous group of rare diseases caused by defects in the early stages of vascular development that result in abnormal growth and development of vessels. The treatment typically consists of surgical approaches; unfortunately, many anomalies cannot be cured. Therefore, the goal of the treatment is to control the lesion, and progression or recurrence after an intervention is no exception. In the last 15 years, tremendous progress in understanding the molecular basis of the disease has been made, with alterations in more than 40 genes proven to be causal in the disease pathogenesis. Interestingly, such alterations are also found in many human cancers, which recently raised the question of whether repurposing anti-cancer drugs could be utilized in this setting. Tissue biopsies from 38 patients with vascular anomalies have been analyzed using different approaches ranging from Sanger sequencing to NGS-based detection. In 31 patients, known causal alterations of either germline or somatic origin were found. For the remaining seven patients, sampling issues were considered a cause of the negative result. Given that most patients suffered from a venous type of malformation, most alterations were found in TEK and PIK3CA genes, which are commonly altered in this subgroup. Other findings included alterations of KRAS, GLMN, PTEN, or IDH2 genes. TEK gene mutations were predominantly located in exon 17, which encodes for a part of the tyrosine kinase domain of the protein, with frequent L914F substitution being found in 12 cases. Identified PIK3CA gene mutations were all well-characterized activating alterations described in cancer-related context. Based on an identification of either TEK or PIK3CA mutation, 13 patients were administered targeted treatment using selective PI3K alpha subunit inhibitor alpelisib. For all patients, improvement in quality of life, lesion reduction and normalization of coagulation parameters was achieved. A deeper understanding of the pathophysiology of vascular anomalies can significantly contribute to patient stratification, identification of potential therapeutic targets, and overall better clinical management. At the same time, identifying potential therapeutic targets could lead to the administration of novel anti-cancer drugs within the concept of drug repurposing and better overall disease control compared to routinely used approaches. Supported by the Ministry of Health of the Czech Republic, grant nr. NU20-03-00240 and by the project National Institute for Cancer Research (Programme EXCELES, ID Project No. LX22NPO5102) - Funded by the European Union - Next Generation EU. Citation Format: Petra Pokorna, Renata Faberova, Olga Koskova, Martin Sterba, Hana Palova, Katerina Kozelkova, Robin Jugas, Dagmar Al Tukmachi, Tana Machackova, Jiri Sana, Peter Mudry, Jaroslav Sterba, Ondrej Slaby. Precision medicine and cancer drug repurposing in the management of vascular anomalies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1063.

Impact of T-cell Receptor Status on Mutational Landscape and Outcome in T-ALL.

Impact of T-cell Receptor Status on Mutational Landscape and Outcome in T-ALL.

Targeting the Molecular and Immunologic Features of Leiomyosarcoma.

Leiomyosarcoma (LMS) is a rare, aggressive mesenchymal tumor with smooth muscle differentiation. LMS is one of the most common histologic subtypes of soft tissue sarcoma; it most frequently occurs in the extremities, retroperitoneum, or uterus. LMS often demonstrates aggressive tumor biology, with a higher risk of developing distant metastatic disease than most sarcoma histologic types. The prognosis is poor, particularly in patients with uterine disease, and there is a need for the development of more effective therapies. Genetically, LMS is karyotypically complex and characterized by a low tumor mutational burden, with frequent alterations in TP53, RB1, PTEN, and DNA damage response pathways that may contribute to resistance against immune-checkpoint blockade monotherapy. The LMS immune microenvironment is highly infiltrated with tumor-associated macrophages and tumor-infiltrating lymphocytes, which may represent promising biomarkers. This review provides an overview of the clinical and pathologic behavior of both soft tissue and uterine LMS and summarizes the genomic and immune characteristics of these tumors and how they may provide opportunities for the development of biomarker-based immune therapies.

Landscape of chromatin remodeling gene alterations in endometrial carcinoma

ObjectiveChromatin remodeling genes (CRGs) encode components of epigenetic regulatory mechanisms and alterations in these genes have been identified in several tumor types, including gynecologic cancers. In this study, we sought to investigate the prevalence and clinicopathological associations of CRG alterations in endometrial carcinoma (EC). MethodsWe performed a retrospective analysis of 660 ECs sequenced using a clinical massively parallel sequencing assay targeting up to 468 genes, including 25 CRGs, and defined the presence of somatic CRG alterations. Clinicopathologic features were obtained for all cases. Immunohistochemical interrogation of ARID1A and PTEN proteins was performed in a subset of samples. ResultsOf the 660 ECs sequenced, 438 (66.4%) harbored CRG alterations covered by our panel. The most commonly altered CRG was ARID1A (46%), followed by CTCF (21%), KMT2D (18%), KMT2B (17%), BCOR (16%), ARID1B (12%) and SMARCA4 (11%). We found that ARID1A genetic alterations were preferentially bi-allelic and often corresponded to altered ARID1A protein expression in ECs. We further observed that ARID1A alterations were often subclonal when compared to PTEN alterations, which were primarily clonal in ECs harboring both mutations. Finally, CRG alterations were associated with an increased likelihood of myometrial and lymphovascular invasion in endometrioid ECs. ConclusionCRG alterations are common in EC and are associated with clinicopathologic features and likely play a crucial role in EC.

DICER1-associated central nervous system sarcoma: A comprehensive clinical and genomic characterization of case series of young adult patients.

DICER1 alterations are associated with intracranial tumors in the pediatric population, including pineoblastoma, pituitary blastoma, and the recently described "primary DICER1-associated CNS sarcoma" (DCS). DCS is an extremely aggressive tumor with a distinct methylation signature and a high frequency of co-occurring mutations. However, little is known about its treatment approach and the genomic changes occurring after exposure to chemoradiotherapy. We collected clinical, histological, and molecular data from eight young adults with DCS. Genomic analysis was performed by Next-generation Sequencing (NGS). Subsequently, an additional germline variants analysis was completed. In addition, an NGS analysis on post-progression tumor tissue or liquid biopsy was performed when available. Multiple clinicopathological characteristics, treatment variables, and survival outcomes were assessed. Median age was 20 years. Most lesions were supratentorial. Histology was classified as fusiform cell sarcomas (50%), undifferentiated (unclassified) sarcoma (37.5%), and chondrosarcoma (12.5%). Germline pathogenic DICER1 variants were present in two patients, 75% of cases had more than one somatic alteration in DICER1, and the most frequent commutation was TP53. Seven patients were treated with surgery, Ifosfamide, Cisplatin, and Etoposide (ICE) chemotherapy and radiotherapy. The objective response was 75%, and the median time to progression (TTP) was 14.5 months. At progression, the most common mutations were in KRAS and NF1. Overall survival was 30.8 months. DCS is an aggressive tumor with limited therapeutic options that requires a comprehensive diagnostic approach, including molecular characterization. Most cases had mutations in TP53, NF1, and PTEN, and most alterations at progression were related to MAPK, RAS and PI3K signaling pathways.

Abstract P2-11-28: Copy number alteration is an independent prognostic biomarker in triple-negative breast cancer patients

Abstract Background: Triple-negative breast cancer (TNBC) is the most fatal breast cancer subtype, which often shows aggressive progression, a high potential to metastasize, and resistance to chemotherapy. Comprehensive genomic profiling using next-generation sequencing (NGS) has been expected to identify gene alterations that are targetable by drugs. However, the significance of these genomic alterations in the cancer biology of TNBC patients has not yet been fully understood due to the lack of accurate clinical outcome data to compare with the genomic data. The aim of this study was to clarify the clinical impact of genomic profiling data, including copy number alterations (CNAs), in TNBC by comparing comprehensive genomic data with clinical outcomes. Methods: A total of 47 patients diagnosed with stage I-III TNBC (from the cohort reported in JCO Precis Oncol. 2018;2:PO.17.00211) were enrolled in this study. The genomic profiling of 435 known cancer genes by NGS with clinical outcomes were analyzed. Overall survival (OS) was evaluated for its association to gene alterations and distinctively CNAs. The cut-off values of CNA for OS were determined from the receiver operating characteristic curve using the Youden index for area under the curve (AUC). Kaplan-Meier plots and log-rank tests of OS were applied for each group. Univariate and multivariate analyses for OS were performed using a Cox proportional-hazards model to obtain the hazard ratio (HR) and 95% confidence intervals. Results: Utilizing NGS-based genomic profiling, at least one alteration was found in 82 of the 435 cancer-associated genes, and a total of 162 alterations were found in the 47 patients. Among the 82 genes with alterations, the presence or absence of TP53 and PTEN alterations was significantly associated with OS of TNBC patients; patients with TP53 alterations (n = 31) showed significantly shorter OS than those without TP53 alterations (n = 16, p = 0.023), and patients with PTEN alterations (n = 9) showed significantly shorter OS than those without PTEN alterations (n = 38, p = 0.023). The cut-off value of CNA for OS was set at 25 (AUC, 0.788; sensitivity, 0.727; specificity, 0.900). Interestingly, CNA-high patients (n = 20) showed significantly shorter OS than CNA-low patients (n = 27, p = 0.014). Univariate analysis revealed that TP53 alterations and CNAs were significant prognostic factors for OS (HR, 8.81; p = 0.008; and HR, 8.00; p = 0.014, respectively). Finally, multivariate analysis using background clinical data revealed that CNA was an independent prognostic factor for OS in TNBC patients (HR, 7.15; p = 0.044). Conclusion: Our data suggest that CNA is an independent prognostic marker in TNBC, and that can be estimated from comprehensive genomic profiling data by NGS. Further investigation is needed to clarify the mechanisms of how CNAs are associated with this lethal disease. Citation Format: Masayuki Nagahashi, Chie Toshikawa, YiWei Ling, Tetsu Hayashida, Yuko Kitagawa, Manabu Futamura, Takashi Kuwayama, Seigo Nakamura, Hideko Yamauchi, Teruo Yamauchi, Koji Kaneko, Chizuko Kanbayashi, Nobuaki Sato, Junko Tsuchida, Kazuki Moro, Masato Nakajima, Yoshifumi Shimada, Hiroshi Ichikawa, Stephen Lyle, Yasuo Miyoshi, Kazuaki Takabe, Shujiro Okuda, Toshifumi Wakai. Copy number alteration is an independent prognostic biomarker in triple-negative 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 P2-11-28.

Abstract GS3-04: GS3-04 Capivasertib and fulvestrant for patients with aromatase inhibitor-resistant hormone receptor-positive/human epidermal growth factor receptor 2-negative advanced breast cancer: results from the Phase III CAPItello-291 trial

Abstract Background: AKT pathway activation has been implicated in the development of endocrine therapy resistance in hormone receptor-positive/human epidermal growth factor receptor 2-negative (HR+/HER2–) advanced breast cancer (ABC). In the Phase II, placebo (PBO)-controlled FAKTION trial, the addition of the pan-AKT inhibitor capivasertib to fulvestrant significantly improved progression-free survival (PFS) and overall survival in postmenopausal women with aromatase inhibitor (AI)-resistant HR+/HER2– ABC. The Phase III, randomized, double-blind, PBO-controlled CAPItello-291 trial (NCT04305496) investigated the efficacy and safety of capivasertib + fulvestrant in patients with AI-resistant HR+/HER2– ABC. Methods: Eligible pre/peri or postmenopausal women or men with HR+/HER2– ABC that had recurred or progressed on or after AI therapy with or without a cyclin-dependent kinase 4 and 6 (CDK4/6) inhibitor were randomized 1:1 to receive fulvestrant (per standard dosing schedule) with either PBO or capivasertib (400 mg twice daily; 4 days on, 3 days off). Randomization was stratified by the presence of liver metastases, prior use of CDK4/6 inhibitors, and geographic location. AKT pathway alteration status (at least one qualifying PIK3CA, AKT1, or PTEN alteration) was determined using next-generation sequencing in tumor tissue. The dual primary endpoint was investigator-assessed PFS in the overall population and in patients with AKT pathway-altered tumors. Results: A total of 708 patients were randomized: 355 to capivasertib + fulvestrant and 353 to PBO + fulvestrant. Overall, 41% of patients had AKT pathway-altered tumors (48% [n=289/602] of patients with tumor sequencing results), 22% were pre/perimenopausal and 77% postmenopausal, with 1% male. Prior therapy for advanced disease included: 87% of patients with ≥1 line of prior treatment, 69% with a prior CDK4/6 inhibitor, and 18% with prior chemotherapy. Demographic and baseline characteristics were broadly balanced between the overall and altered populations and by treatment groups. At primary analysis (data cut-off Aug 15, 2022), 551 and 236 PFS events had occurred in the overall and pathway-altered populations, respectively. Overall, the median PFS was 7.2 months with capivasertib + fulvestrant and 3.6 months with PBO + fulvestrant (hazard ratio [HR] 0.60; 95% confidence interval [CI] 0.51–0.71; p<0.001). In patients with AKT pathway-altered tumors, median PFS was 7.3 months with capivasertib + fulvestrant and 3.1 months with PBO + fulvestrant (HR 0.50; 95% CI 0.38–0.65; p<0.001). The objective response rate in patients with measurable disease was 22.9% for capivasertib + fulvestrant vs 12.2% for PBO + fulvestrant overall and 28.8% vs 9.7% in the AKT pathway-altered population. The most frequent all-grade adverse events (AEs) with capivasertib + fulvestrant were diarrhea (72.4% vs 20.0% PBO + fulvestrant arm), rash (group term of rash, rash macular, rash maculo-papular, rash papular, rash pruritic; 38.0% vs 7.1%) and nausea (34.6% vs 15.4%). The most frequently reported grade ≥3 AEs were rash (group term; 12.1% vs 0.3%), diarrhea (9.3% vs 0.3%), and hyperglycemia (2.3% vs 0.3%); grade ≥3 stomatitis was 2.0% vs 0%. AEs leading to discontinuation of capivasertib/placebo were reported in 13.0% and 2.3% of patients, respectively. Conclusions: Capivasertib + fulvestrant significantly improved PFS compared to fulvestrant alone in the overall population, and in patients with AKT pathway-altered tumors, and may become a future treatment option in this setting. The safety profile of capivasertib + fulvestrant was generally manageable and consistent with prior data. Funding: CAPItello-291 is sponsored by AstraZeneca. Editorial acknowledgment: AstraZeneca-funded medical writing support was provided by Suzanne Patel, Ph.D., from BOLDSCIENCE Inc. Capivasertib was discovered by AstraZeneca subsequent to a collaboration with Astex Therapeutics (and its collaboration with the Institute of Cancer Research and Cancer Research Technology Limited). Citation Format: Nicholas Turner, Mafalda Oliveira, Sacha J. Howell, Florence Dalenc, Javier Cortés, Henry Gomez, Xichun Hu, Komal Jhaveri, Sibylle Loibl, Serafin Morales Murillo, Zbigniew Nowecki, Meena Okera, Yeon H. Park, Masakazu Toi, Lyudmila Zhukova, Chris Yan, Gaia Schiavon, Andrew Foxley, Hope Rugo. GS3-04 Capivasertib and fulvestrant for patients with aromatase inhibitor-resistant hormone receptor-positive/human epidermal growth factor receptor 2-negative advanced breast cancer: results from the Phase III CAPItello-291 trial [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 GS3-04.

Abstract P1-13-07: Investigating NF1 Mutations in Circulating Tumor DNA of Patients with Hormone-receptor Positive (HR+) Breast Tumors Resistant to CDK4/6 Inhibition (CDK4/6i): A Retrospective Clinical Analysis

Abstract Background: CDK4/6 inhibitors (CDK4/6i) are standard of care for the management of HR+/HER2- metastatic breast cancer (MBC). Genomic alterations that drive resistance to CDK4/6i are diverse, and while the molecular landscape is heterogeneous, several mechanisms of CDK4/6i resistance converge on the RAS/MAPK and PI3K/AKT/mTOR signaling pathways. NF1 downregulates RAS and dampens cellular proliferation. Laboratory-based models demonstrate that loss of NF1 is associated with resistance to endocrine therapy (ET), and emergence of NF1 mutations (NF1m) are correlated with progressive disease (PD) in circulating tumor DNA (ctDNA). While NF1m may diminish CDK4/6i susceptibility, a clear relationship has not been elucidated. The primary objective of this study was to characterize patient (pt) response to CDK4/6i in NF1m HR+/HER2- MBC. Methods: We identified 47 pts with NF1m via a database with one or more ctDNA samples sequenced at variable time-points as part of routine care for MBC. NF1m were categorized as pathogenic (p)NF1m or variants of uncertain significance (VUS) based on their associated Guardant report. We identified 27 pts with HR+/HER2- MBC and NF1m that received at least 1 line of CDK4/6i in the metastatic setting. Intrinsic resistance was defined as PD < 6 months on a CDK4/6i regimen, and acquired resistance was defined as PD >6 months. Pts with intrinsic resistance or acquired resistance and NF1m detected post-PD were categorized as having a resistance phenotype potentially driven by NF1m. Pts with NF1m detected prior to therapy and >6 months clinical response on a CDK4/6i were categorized as having NF1m tumors sensitive to CDK4/6i. Results: The NF1m cohort (n = 27) had 9 pts with pNF1m, while 18 pts expressed VUS. The median age at MBC diagnosis was 54 years, and 67% had visceral metastasis at ctDNA collection. Pts received a median of 1 prior line (range: 0 - 6) of ET or chemotherapy in the metastatic setting before CDK4/6i. Amongst pts with pathogenic variants (n = 9), we found 3 pts with pNF1m were intrinsically resistant to CDK4/6i. Acquired resistance was seen in 1 pt with pNF1m detected post-PD, and 2 pts had evidence of both acquired and subsequent intrinsic resistance to a later line of CDK4/6i. Overall, 67% (6/9) of pNF1m pts demonstrated a CDK4/6i resistance phenotype; mutant allele fraction (AF) ranged from 0.2% - 29.9%, and the mean maximum allele fraction (MAF) was 6.0%. Pre- and post-treatment samples were available on 3 pts with pNF1m, and 1 of these pts had an AF rise from 2.7% to 12.3% when comparing ctDNA pre- and post-CDK4/6i. ctDNA from 4 of 6 resistant tumors harbored other putative drivers including alterations in FGFR, KRAS, PTEN, and RB. We identified 2 counter-examples of pNF1m tumors sensitive to CDK4/6i. These pts expressed relatively low NF1m AF, ranging 0.1% - 0.5% with a mean MAF 0.3%. Another pNF1m pt had intrinsic resistance to initial CDK4/6i but was sensitive to later-line CDK4/6i. In the subgroup of pts with VUS-NF1m (n = 18), a more mixed picture of resistance and sensitivity was seen. 8 pts had intrinsic or acquired resistance, 8 pts had NF1m tumors sensitive to CDK4/6i, and 1 pt had evidence of both; 61% (n = 11) of pts expressed alterations in other resistance mediating genes. 1 pt stopped therapy due to toxicity rather than PD. Conclusions: Our work demonstrates that tumor expression of pNF1m may be associated with CDK4/6i resistance in pts with HR+/HER2- MBC, and allele fraction could be predictive of drug susceptibility. Tumors harboring VUS had varied sensitivity, suggesting that some of these mutations may not be pathogenic, and counter-examples of pNF1m MBC benefiting from CDK4/6i plus ET highlight the complexities in predicting drug response based on single gene alteration. Future effort is warranted to explore the potential impact of NF1 on CDK4/6i resistance, as well as the potential role for therapies targeting the MAPK pathway in this patient population. Citation Format: Maxwell R. Lloyd, Lianne Ryan, Arielle J. Medford, Jennifer C. Keenan, Laura M. Spring, Neelima Vidula, Beverly Moy, Dejan Juric, Leif Ellisen, Aditya Bardia, Seth A. Wander. Investigating NF1 Mutations in Circulating Tumor DNA of Patients with Hormone-receptor Positive (HR+) Breast Tumors Resistant to CDK4/6 Inhibition (CDK4/6i): A Retrospective Clinical Analysis [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 P1-13-07.

Clinical implications of Wnt signaling alterations in patients (pts) with advanced prostate cancer (aPC).

229 Background: Aberrant Wnt signaling has been implicated in prostate cancer tumorigenesis, progression, and metastasis in preclinical models. While studies have identified recurrent molecular alterations in the Wnt signaling components in about 20% of aPC pts, the clinical significance of these alterations has been incompletely characterized. Methods: PROMISE is a multi-institutional, retrospective, clinical-genomic database - inclusive of aPC pts who had tissue and/or blood-based genomic testing by commercially available CLIA-certified platforms. We evaluated outcomes in pts with alterations leading to the activation of the canonical Wnt pathway, specifically activating mutations in CTNNB1 or RSPO2 or inactivating mutations in APC, RNF43, or ZNRF3 (Wnt altered), compared to those lacking such alterations (Wnt wild type). Multiple endpoints were evaluated, including the frequency of metastatic disease to different sites and co-occurring alterations. Results: 1596 pts with aPC were included with a median age of 63 years at diagnosis. Wnt pathway alterations were identified in 12.4% (198/1596). Wnt altered pts had a statistically significant increase in liver and lung metastases compared with Wnt wild type pts at diagnosis (4.5% vs 2.1%, p=0.0438; 6.1% vs 2.9%, p=0.0292), at first metastatic disease (11.6% vs 5.4%, p= 0.0015; 14.8% vs 6.6%, p<0.0001), and at diagnosis of CRPC (14.2% vs 7.9%, p=0.01436; 16.1% vs 6.8%, p=0.0003). Fewer Wnt altered pts had bone metastases at CRPC compared with wild type pts (67.7% vs 75.2%, p=0.04948) without significant difference of bone metastases at the time of diagnosis or at the time of first metastatic disease. The frequency of metastases to other sites was similar between the cohorts. More Wnt altered pts had ductal features on histology at diagnosis compared with Wnt wild type pts (4.0% v 1.6%, p=0.02415) without difference in PSA, Gleason score, TNM stage, or presence of neuroendocrine or intraductal features. Co-occurring genomic alterations that were more common in Wnt altered pts included PTEN loss/mutation (25.3% vs 18.3%, p=0.0270), RB1 loss/mutation (10.6% vs 5.8%, p=0.0079), AR mutations or gain (37.9% vs 24.0%, p< 0.0001), and SPOP mutations (14.1% vs 3.9%, p< 0.0001) as compared with Wnt wild type pts. Conclusions: Wnt pathway alterations were associated with ductal histology, an increase in visceral metastases at all time points evaluated, and an increase in co-occurring PTEN, RB1, AR, and SPOP alterations. The clinical heterogeneity of aPC and differences in co-occurring mutations between the cohorts make isolating the effect of alterations in a single pathway challenging. Analysis of overall survival outcomes is currently in process, and future multivariable analysis is planned to adjust for established clinical factors and co-occurring mutations to identify the independent contributions of Wnt alterations to clinical outcomes.

Genomic alterations associated with resistance to EGFR monoclonal antibodies (mAb) in real-world patients with metastatic colorectal cancer (mCRC).

52 Background: mCRC patients with RAS and BRAF mutant tumors do not benefit from treatment with EGFR mAb. However, some RAS/BRAF wild-type patients do not benefit from EGFR mAbs. We sought to investigate additional primary and acquired biomarkers of resistance to EGFR mAb in mCRC. We hypothesized (1) alterations in pre-specified genes of known biological but unconfirmed clinical significance are associated with less favorable outcomes in patients treated with EGFR mAb; (2) these alterations are acquired during treatment and are associated with the time of exposure to these drugs. Methods: We included mCRC patients with RAS/ BRAF wild-type tumors receiving EGFR mAb (cetuximab or panitumumab) in 1st line (1L, n = 248) or in 2L+ of therapy (n = 2,118). This study used the US-based de-identified Flatiron Health-Foundation Medicine real-world mCRC clinico-genomic database, originating from ~280 US cancer clinics between 01/2011 and 04/2022. Pre-specified genes included PIK3CA, PTEN, MAP2K1, and RTKs. Real-world progression-free survival (rwPFS) and overall survival (rwOS) were compared between patients +/- alterations by Cox models, adjusted for a risk score generated from known clinical prognostic features. Alterations were compared between patients with biopsies collected before and after starting treatment with EGFR mAb by chi-square, adjusted for multiple comparisons. The association between the amount of time on drug exposure and alterations was evaluated by linear regression. Results: Patients with RTK/ MAP2K1 alterations (n = 38, 15.3%) had less favorable outcomes (PFS HR 1.83, 95% CI 1.27-2.65, p = 0.001/ OS HR 1.59, 95% CI 1.00-2.51, p = 0.048). The same trend was observed for patients with PIK3CA/ PTEN alterations (n = 31, 12.5%, PFS HR 1.35, 95% CI 0.89-2.03, p = 0.155/ OS HR 1.75, 95% CI 1.08 -2.85, p = 0.024) and ERBB2amp (n = 21, 8.5%, PFS HR 1.52, 95% CI 0.93-2.5, p = 0.096/ OS HR 1.33, 95% CI 0.71-2.5, p = 0.373). Compared to biopsies obtained before (n = 1,834), those obtained after treatment initiation were enriched for RTK alterations (n = 284, +9%, p = 0.001), especially for METamp (+3%, p = 0.04). Compared to unexposed patients, patients exposed to EGFR inhibitors had higher odds (p < 0.001) of developing RTK alterations (OR: 1.84, 95% CI 1.54-2.19; OR 3.33, 95% CI 2.60-4.24; and OR 2.28, 95% CI 1.56-3.26 for 0-12, 12-24, and 24+ months of exposure, respectively). Additional analyses will be presented. Conclusions: RAS/RAF WT mCRC patients with baseline alterations in RTK genes have less favorable outcomes on EGFR inhibitors (intrinsic resistance), and post-EGFR mAb samples (acquired resistance) converge around RTK and MAPK alterations, particularly MET, in real-world data.

Clinical utility of circulating tumor DNA sequencing with a large panel: a National Center for Precision Medicine (PRISM) study

Circulating tumor DNA (ctDNA) sequencing is a promising approach for tailoring therapy in patients with cancer. We report hereby the results from a prospective study where we investigated the impact of comprehensive molecular profiling of ctDNA in patients with advanced solid tumors. Genomic analysis was performed using the FoundationOne Liquid CDx Assay [324 genes, tumor mutational burden (TMB), microsatellite instability status]. Each individual genomic report was reviewed and discussed weekly by a multidisciplinary tumor board (MTB). Actionable targets were classified by ESMO Scale for Clinical Actionability of Molecular Targets (ESCAT) tier leading to molecular-based treatment suggestions wherever it was possible. Between December 2020 and November 2021, 1772 patients with metastatic solid tumors underwent molecular profiling. Median time to assay results was 12 days. Results were contributive for 1658 patients (94%). At least one actionable target was detected in 1059 patients (64%) with a total of 1825 actionable alterations including alteration of the DNA damage repair response pathway (n= 336, 18%), high TMB (>16 mutations/Mb; n= 243, 13%), PIK3CA mutations (n= 150, 8%), ERBB family pathway alterations (n= 127, 7%), PTEN alterations (n= 95, 5%), FGFR alterations (n= 67, 4%) and MET activations (n= 13, 0.7%). The MTB recommended a matched therapy for 597 patients (56%) with a total of 819 therapeutic orientations: clinical trials (n= 639, 78%), off-label/compassionate use (n= 81, 10%), approved drug (n= 51, 6%), and early access program (n= 48, 6%). In total, 122 patients (21%) were treated. Among the assessable patients (n= 107), 4 (4%) had complete response, 35 (33%) had partial response, 27 (25%) had stable disease, and 41 (38%) a progressive disease as best response. The median progression-free survival and median overall survival were 4.7 months (95% confidence interval 2.7-6.7 months) and 8.3 months (95% confidence interval 4.7-11.9 months) respectively. ctDNA sequencing with a large panel is an efficient approach to match patients with advanced cancer with targeted therapies.