AKT1 Mutations Research Articles

Comparative oncology analysis using genomic profiling of canine cancers by tissue and liquid biopsy testing reveals actionable somatic alterations with orthologs in human cancers.

e15012 Background: Targeted therapies offer great potential for cancer treatment in humans; however, enrollment in clinical trials may be slow, particularly for rare cancer types. The high homology between human and canine cancer genomes provides an opportunity for comparative oncology analyses that can inform the development of therapeutics for the benefit of both species. Currently, there is no well-established canine cancer genomic database. This study presents preliminary findings from an ongoing initiative aimed at building a foundational database of canine cancer genomic variants and their human orthologs via tissue and liquid biopsy profiling of multiple cancer types. Methods: Matched blood and tissue samples were collected from an all-comers cohort of over 150 cancer-diagnosed, client-owned dogs undergoing surgical resection or tissue sampling by biopsy. Cancer types included those found in both humans and dogs, such as lymphoma, osteosarcoma, mammary gland tumors and melanoma. Blood samples were processed to obtain plasma and white blood cells, and all samples were subjected to DNA extraction, library preparation, and next-generation sequencing. Somatic variants detected by liquid biopsy and tissue testing were mapped to human orthologs targeted by therapeutic agents approved by the FDA or listed in NCCN guidelines, and to orthologs with therapeutic or prognostic levels of evidence annotated in human oncology databases. Results: Somatic alterations were identified in over half of the tissue and/or liquid biopsy samples tested. Results from tissue and liquid biopsy showed high concordance, and liquid biopsy revealed additional alterations that may have been missed in single-site tissue biopsies due to tumor heterogeneity. Of the mutations identified in plasma and/or tissue but absent in matched white blood cells, 10% mapped to a human ortholog listed as a biomarker targeted by either an approved therapeutic agent or a therapeutic currently undergoing clinical trials; examples include NRAS, HRAS and AKT1 mutations. Over 10% of canine cancer patients also harbored orthologs of somatic TP53 mutations reported to be prognostic in multiple human cancers. In particular, TP53 mutations were found in > 20% of canine osteosarcoma patients, which aligns with prior findings in human osteosarcoma and highlights the potential of comparative oncology for cancer types that are rare in humans but common in dogs. Conclusions: The results confirm the homology between canine and human cancers and emphasize the potential to translate genomic knowledge for biomarker discovery and therapeutic development between species. The high concordance between tumor and liquid biopsy findings support the prospect of using a noninvasive blood test to expand the genomic characterization effort to much larger cohorts of cancer-diagnosed dogs.

Combination of AKT1 and CDH1 mutations predicts primary resistance to immunotherapy in dMMR/MSI-H gastrointestinal cancer

BackgroundGastrointestinal (GI) cancer is the second most common cancer type with mismatch repair-deficient (dMMR)/microsatellite instability-high (MSI-H) phenotype that is expected to respond to immune-checkpoint inhibitors (ICIs). However, approximately half of...

Fulvestrant plus capivasertib versus fulvestrant plus placebo after relapse or progression on an aromatase inhibitor in metastatic, estrogen receptor–positive breast cancer (FAKTION): Overall survival and updated progression-free survival data with enhanced biomarker analysis.

1005 Background: Previous results from the Phase 2 FAKTION trial (NCT01992952) showed progression free survival (PFS) in patients with aromatase inhibitor (AI) resistant ER+/HER2− advanced breast cancer was significantly longer with fulvestrant plus capivasertib vs fulvestrant plus placebo. At the time of analysis, PFS benefit associated with capivasertib was not restricted to patients with activating mutations in PIK3CA (E542K, E545K, H1047R or H1047L) or PTEN protein null. We report now mature overall survival (OS) data with enhanced biomarker analysis. Methods: For the enhanced analysis, available tissue and plasma samples were sent for targeted next generation sequencing (NGS) with Foundation One CDx and GuardantOMNI assays. ‘Pathway altered’ (PA) was defined as any activating mutation in PIK3CA (exons 1,4,7,9,20) or AKT1 (E17K only) or inactivating alterations in PTEN. For samples not tested by targeted NGS, previously reported digital droplet PCR (ddPCR) results for PIK3CA were used, in addition to tissue AKT1 ddPCR analysis performed after the initial publication. Concordance between mutations identified by ddPCR and subsequent NGS was 97%. Results: In January 2022, 108 OS events were reported (77% maturity) in the intention to treat (ITT) population. The median OS was 29.3 vs 23.4 months (mo) in the capivasertib (n = 69) vs placebo (n = 71) arms respectively (HR 0.66, 95% CI 0.45–0.97; p = 0.035). In the enhanced biomarker analysis, 76 participants were classified as PA compared to 59 in the original analysis. In the PA group, OS was 39.0 vs 20.0 mo in the capivasertib vs placebo arms respectively (HR 0.46, 95% CI: 0.27–0.79; p = 0.005). Within the pathway non-altered (PNA) group, median OS was 26.0 vs 25.2 mo in the capivasertib vs placebo arms respectively (HR 0.86, 95% CI: 0.49–1.52; p = 0.60). In the updated PFS analysis, the advantage in the ITT population persisted with capivasertib vs placebo (median 10.3 vs 4.8 mo, HR 0.56, 95% CI: 0.38–0.81; p = 0.002). PFS analysis against the updated biomarker subgroups shows a significant improvement in PFS in the PA group: 12.8 vs 4.6 mo in the capivasertib vs placebo arms respectively (HR 0.44, 95% CI: 0.26–0.72; p = 0.001). In the PNA group, median PFS was 7.7 vs 4.9 mo in the capivasertib vs placebo arms respectively (HR 0.70, 95% CI: 0.40–1.25; p = 0.23). Conclusions: Updated analysis of the FAKTION trial data show a significant improvement in OS in the ITT population. Enhanced subgroup analysis suggests that the benefit of capivasertib in both PFS and OS may be predominantly in patients with PIK3CA/AKT1/PTEN pathway altered tumours, but further elucidation will be forthcoming from the ongoing Phase 3 CAPItello-291 study in which participants with PA and PNA tumours have been recruited. Clinical trial information: NCT01992952.

Proposal of a molecular testing algorithm for differentiated thyroid cancer (DTC).

e18090 Background: In the growing era of precision medicine and tumor-agnostic therapies, the molecular testing of DTC is becoming mandatory to optimize diagnostic and therapeutical strategies. Even if the most frequent oncogenic events, occurring in a mutually exclusive manner, are BRAF V600E, followed by RAS, gene fusions mainly occurring in RET, NTRK1-3, and ALK genes have been also found. In this scenario, the definition of a molecular testing algorithm to be implemented for clinical practice is needed, in order to optimize resources and time for better clinical patient management. Methods: Gene mutations and gene fusions were evaluated on DNA and RNA extracted from cytologic or histologic samples. Mutations were tested using a lab-developed multi-gene panel able to analyze the hot-spot regions of 28 genes (total of 343 amplicons, 21.77 kb); gene fusions were tested using the Oncomine Focus assay panel. Results: Molecular characterization was performed on a total of 63 DTC (50 papillary thyroid carcinoma - PTC, 8 – follicular thyroid carcinoma - FTC, 5 – hurthle cell carcinoma - HCC) by the treating clinician for diagnostic, prognostic or clinical reasons. In 27 cases (42.8%) at least one DNA mutation was detected, 17 cases (26.9%) were positive for gene fusion rearrangement, in only 2 cases (3.1%) both DNA mutations and gene rearrangements were found and in the remaining 17 (26.9%) cases no DNA mutations or rearrangements were detected. Among mutated-subgroup, BRAF V600E mutation was the most common (14 of 63 cases – 22.2%), followed by RAS mut (9 cases – 14.2%: 4 NRAS, 3 HRAS, and 3 KRAS), both as single event in 7 and 4 cases respectively. Substitutions in TERT promoter region was found in 16 cases (25.3%), of which 14 as secondary event. Other mutations in TP53 (4 cases –6.3 %, of which 2 as single event), PIK3CA (1 case – 1.5%), AKT1(1 case – 1.5%), and RNF43 (1 case – 1.5%) were detected. Among riarranged subgroup, RET fusions and NTRK1-3 was found in 8 cases respectively (12.6%), while ALK fusion was found 1 case (1.5%). The concomitant mutational and fusion events found in 2 cases were the following: 1) HRAS and PAX8/PPARG; 2) PIK3CA/TP53/TERT and RET/CCDC6. Conclusions: As expected, BRAF and RAS mutations represent the most common genetic events in DTC and occur in a mutual exclusive manner. However, in about 30% of patients, mostly of young age, with papillary histology and lymph nodal involvement, a clinically actionable gene rearrangement has been found. Thus, we propose a two-step molecular testing algorithm with a first-level test to identify the most common mutations and a second-level test, including less common mutations and gene rearrangements, if the genes analyzed with the first level test are wild-type. The second-level test may be performed up-front in cases where there are clinicopathologic features suggestive of fusion gene TC gene or in clinically aggressive unconventional cases for which molecular therapy is being considered.

High incidence of PI3K pathway gene mutations in South Indian cervical cancers

IntroductionCervical cancer is the second most common cancer in India. The phosphatidylinositol-3 kinase (PI3K) signaling is one of the most commonly activated pathways in cancer and comprises key molecules commonly targeted in cancer therapy. This study analyzed six PI3K pathway gene mutations. MethodsWe carried out targeted next-generation sequencing of six PI3K pathway genes (PIK3CA, PIK3R1, PTEN, AKT1, TSC2, and mTOR) in a total of 93 South Indian cervical cancer samples and confirmed them by sanger sequencing. ResultsThe PI3K pathway gene mutations were observed in 54.8% (51/93) of the tumors and PIK3CA was the most mutated (34.4%, 32/93), followed by TSC2 (18.3%, 17/93), and PIK3R1 (14%, 13/93). The PIK3CA hotspot mutations E542K and E545K observed in this study were likely to disrupt the p110α-p85α interaction that could result in the PI3K pathway activation. We also found a few novel mutations in PIK3R1, PTEN, AKT1, TSC2, and mTOR genes while some of the tumors harbored multiple mutations in the genes of the PI3K pathway. The majority of the tumors were positive for high-risk HPV16/18 (60.7%). ConclusionsThe high incidence of the PI3K pathway gene mutations observed in this study could be exploited for the therapeutic management of cervical cancers.

ITK signaling regulates IL-10 production by CD8+ T cells and lung immunopathology during influenza infection

Abstract Influenza (flu) infections cause 250,000 deaths and 3–5 million cases of severe illness during the average flu season. Severe influenza infections are associated with a combination of strong pro-inflammatory and weak anti-inflammatory immune responses. Production of the immunomodulatory cytokine IL-10 by T cells restricts immunopathology during flu infections, however knowledge of the signaling pathways regulating IL-10 induction during flu is limited. Using IL-10GFP reporter mouse models, we found Interleukin-2 inducible T cell kinase (ITK), a critical component in T cell receptor (TCR) signaling, regulates the development of IL-10-producing CD8+ T cells during influenza A infection. Compared to wild type (WT) mice, Itk−/− mice displayed increased morbidity and mortality after influenza infection, accompanied by a significant reduction of IL-10-producing CD8+ T cells in the airways. The absence of ITK and chemical inhibition of the PI3K/AKT/mTOR signaling pathway impaired both BLIMP1 expression and IL-10 production in CD8+ T cells in vitro. Introduction of Blimp-1 or a constitutively active AKT mutant via retroviral transduction rescued IL-10 production and Blimp-1 expression in Itk−/− CD8+ T cells. Utilizing a transgenic allele sensitive Itk (ITKas) mouse model to specifically inhibit ITK kinase activity in coculture, we found ITK kinase activity is not required for the suppressive function of IL-10 producing CD8+ T cells. Together, our data suggests that ITK is a critical regulator of the development and suppressive function of IL-10 producing CD8+ T cells and flu-induced pulmonary immunopathology. Modulating ITK signaling may be a strategy for regulating immunopathology due to respiratory viral infections. This work was supported in part by grants from the National Institutes of Health (R01 AI151139, R56 AI146226 and P20 GM130555). W. Huang also received research support from MegaRobo Technologies Corporation.

Clinical Significance of Molecular Alterations and Systemic Therapy for Meningiomas: Where Do We Stand?

Simple SummaryMeningiomas are the most frequent intracranial tumors and comprise a heterogeneous spectrum of diseases, ranging from small, asymptomatic tumors that do not need treatment to large, symptomatic ones causing seizures or neurological deficits that require surgery and/or radiotherapy. Systemic therapy is reserved for progressive or recurrent meningiomas when surgery and/or radiotherapy options have been exhausted, with only modest activity in terms of disease control and survival. Novel molecular alterations are correlated with grading, location, and prognosis of meningiomas. Moreover, some of these driver alterations regulate meningioma growth and progression and may be targeted by specific drugs that are under investigation in clinical trials. Lastly, the microenvironment surrounding meningiomas may also contribute to regulating tumor growth: in particular, PD-L1 and/or M2 macrophage expression may represent a target for immunotherapy.Meningiomas are common intracranial tumors that can be treated successfully in most cases with surgical resection and/or adjuvant radiotherapy. However, approximately 20% of patients show an aggressive clinical course with tumor recurrence or progressive disease, resulting in significant morbidity and increased mortality. Despite several studies that have investigated different cytotoxic agents in aggressive meningiomas in the past several years, limited evidence of efficacy and clinical benefit has been reported thus far. Novel molecular alterations have been linked to a particular clinicopathological phenotype and have been correlated with grading, location, and prognosis of meningiomas. In this regard, SMO, AKT, and PIK3CA mutations are typical of anterior skull base meningiomas, whereas KLF4 mutations are specific for secretory histology, and BAP1 alterations are common in progressive rhabdoid meningiomas. Alterations in TERT, DMD, and BAP1 correlate with poor outcomes. Moreover, some actionable mutations, including SMO, AKT1, and PIK3CA, regulate meningioma growth and are under investigation in clinical trials. PD-L1 and/or M2 macrophage expression in the microenvironment provides evidence for the investigation of immunotherapy in progressive meningiomas.

AKT mutant allele-specific activation dictates pharmacologic sensitivities

AKT- a key molecular regulator of PI-3K signaling pathway, is somatically mutated in diverse solid cancer types, and aberrant AKT activation promotes altered cancer cell growth, survival, and metabolism1–8. The most common of AKT mutations (AKT1 E17K) sensitizes affected solid tumors to AKT inhibitor therapy7,8. However, the pathway dependence and inhibitor sensitivity of the long tail of potentially activating mutations in AKT is poorly understood, limiting our ability to act clinically in prospectively characterized cancer patients. Here we show, through population-scale driver mutation discovery combined with functional, biological, and therapeutic studies that some but not all missense mutations activate downstream AKT effector pathways in a growth factor-independent manner and sensitize tumor cells to diverse AKT inhibitors. A distinct class of small in-frame duplications paralogous across AKT isoforms induce structural changes different than those of activating missense mutations, leading to a greater degree of membrane affinity, AKT activation, and cell proliferation as well as pathway dependence and hyper-sensitivity to ATP-competitive, but not allosteric AKT inhibitors. Assessing these mutations clinically, we conducted a phase II clinical trial testing the AKT inhibitor capivasertib (AZD5363) in patients with solid tumors harboring AKT alterations (NCT03310541). Twelve patients were enrolled, out of which six harbored AKT1-3 non-E17K mutations. The median progression free survival (PFS) of capivasertib therapy was 84 days (95% CI 50-not reached) with an objective response rate of 25% (n = 3 of 12) and clinical benefit rate of 42% (n = 5 of 12). Collectively, our data indicate that the degree and mechanism of activation of oncogenic AKT mutants vary, thereby dictating allele-specific pharmacological sensitivities to AKT inhibition.

Epigenetic and genomic profiling of chordoid meningioma: implications for clinical management

Chordoid meningioma is a morphological variant of meningioma designated as WHO grade 2. However, the recurrence rates varied widely in different case series, and to date, a unifying molecular genetic signature has not been identified. Among 1897 meningiomas resected at our institution, we identified 12 primary chordoid meningiomas from 12 patients. Histologically, all 12 cases had predominant (> 50%) chordoid morphology. Ten were otherwise grade 1, and two were also atypical. We performed DNA global methylation profile, copy number variation analysis, and targeted next-generation sequencing on 11 chordoid meningiomas, and compared to those of 51 non-chordoid, mostly high grade meningiomas. The chordoid meningiomas demonstrated a unique methylation profile in tSNE, UMAP, and hierarchical heatmap clustering analyses of the most differentially methylated CpGs. The most common copy number variation in chordoid meningioma was loss of 1p (7/11, 64%). Three chordoid meningiomas had 2p loss, which was significantly higher than the non-chordoid control cohort (27% vs 7.2%, p = 0.035). 22q loss was only seen in the two cases with additional atypical histological features. Chordoid meningiomas were enriched in mutations in chromatin remodeling genes EP400 (8/11,73%) KMT2C (4/11, 36%) and KMT2D (4/11, 36%), and showed low or absent NF2, TERT, SMO, and AKT1 mutations. Prognosis wise, only one case recurred. This case had atypical histology and high-grade molecular features including truncating NF2 mutation, 1p, 8p, 10, 14, 22q loss, and homozygous deletion of CDKN2A/B. Progression free survival of chordoid, otherwise grade 1 meningioma was comparable to non-chordoid WHO grade 1 meningioma (p = 0.75), and significantly better than chordoid WHO grade 2 meningioma (p = 0.019). Conclusion: the chordoid histology alone may not justify a universal WHO grade 2 designation. Screening for additional atypical histological or molecular genetic features is recommended.

In vitro effect of PIK3CA/mTOR inhibition in triple-negative breast cancer subtype cell lines.

Agents targeting the PI3K pathway in triple negative breast cancer did not show any significant efficacy so far mostly because of the complex nature of these targeted inhibitors. Targeting the cancer cells with the combination of inhibitors may help in decelerating the regulatory pathways further achieving optimum clinical benefit. In this study, we investigated the effect of PIK3CA and mTOR inhibition in-vitro in triple-negative breast cancer (TNBC) cell lines. Three TNBC cell lines; MDA MB231, MDA MB468, and MDA MB453 were subtyped using immunohistochemistry and were screened for hotspot mutations in PIK3CA and AKT1. All cell lines were treated with different concentrations of inhibitors; PI3K inhibitor (BKM 120), mTOR inhibitor (AZD 8055), and dual PI3K/mTOR inhibitor (BEZ 235), and cell viability was assessed by MTT (3-(4, 5-Dimethylthiazol-2-yl)-2, 5-Diphenyltetrazolium Bromide), Trypan blue and Annexin-V/PI Assays. Using immunohistochemistry, TNBC cell lines were subtyped as; mesenchymal subtype-specific cell line (MDA MB231), basal subtype-specific cell line (MDA MD468), and Luminal androgen receptor (LAR) subtype-specific cell line (MDA MB453). PIK3CA hot spot mutation (p.H1047R) in exon 20 was identified in the Luminal androgen receptor subtype (MDA MB453 cells) cell line. Cell viability assays showed that the Mesenchymal subtype-specific cell line (MDA MB231) was the most resistant to all inhibitors and the Luminal Androgen subtype (MDA MB453 cells) cell line was more sensitive to BKM120 (PI3K inhibitor) inhibition compared to other subtypes. This study identified that the Luminal androgen receptor subtype of triple-negative breast cancer with PIK3CA mutation may be targeted with PIK3CA inhibitors with a favorable outcome.

Urocortin 2 promotes hypertrophy and enhances skeletal muscle function through cAMP and insulin/IGF-1 signaling pathways

ObjectiveAlthough it is well established that urocortin 2 (Ucn2), a peptide member of the corticotrophin releasing factor (CRF) family, and its specific corticotrophin-releasing factor 2 receptor (CRF2R) are highly expressed in skeletal muscle, the role of this peptide in the regulation of skeletal muscle mass and protein metabolism remains elusive. MethodsTo elucidate the mechanisms how Ucn2 directly controls protein metabolism in skeletal muscles of normal mice, we carried out genetic tools, physiological and molecular analyses of muscles in vivo and in vitro. ResultsHere, we demonstrated that Ucn2 overexpression activated cAMP signaling and promoted an expressive muscle hypertrophy associated with higher rates of protein synthesis and activation of Akt/mTOR and ERK1/2 signaling pathways. Furthermore, Ucn2 induced a decrease in mRNA levels of atrogin-1 and in autophagic flux inferred by an increase in the protein content of LC3-I, LC3-II and p62. Accordingly, Ucn2 reduced both the transcriptional activity of FoxO in vivo and the overall protein degradation in vitro through an inhibition of lysosomal proteolytic activity. In addition, we demonstrated that Ucn2 induced a fast-to-slow fiber type shift and improved fatigue muscle resistance, an effect that was completely blocked in muscles co-transfected with mitogen-activated protein kinase phosphatase 1 (MKP-1), but not with dominant-negative Akt mutant (Aktmt). ConclusionsThese data suggest that Ucn2 triggers an anabolic and anti-catabolic response in skeletal muscle of normal mice probably through the activation of cAMP cascade and participation of Akt and ERK1/2 signaling. These findings open new perspectives in the development of therapeutic strategies to cope with the loss of muscle mass.

GNE-493 inhibits prostate cancer cell growth via Akt-mTOR-dependent and -independent mechanisms

GNE-493 is a novel PI3K/mTOR dual inhibitor with improved metabolic stability, oral bioavailability, and excellent pharmacokinetic parameters. Here GNE-493 potently inhibited viability, proliferation, and migration in different primary and established (LNCaP and PC-3 lines) prostate cancer cells, and provoking apoptosis. GNE-493 blocked Akt-mTOR activation in primary human prostate cancer cells. A constitutively-active mutant Akt1 restored Akt-mTOR activation but only partially ameliorated GNE-493-induced prostate cancer cell death. Moreover, GNE-493 was still cytotoxic in Akt1/2-silenced primary prostate cancer cells. Significant oxidative stress and programmed necrosis cascade activation were detected in GNE-493-treated prostate cancer cells. Moreover, GNE-493 downregulated Sphingosine Kinase 1 (SphK1), causing ceramide accumulation in primary prostate cancer cells. Daily single dose GNE-493 oral administration robustly inhibited the growth of the prostate cancer xenograft in the nude mice. Akt-mTOR inactivation, SphK1 downregulation, ceramide level increase, and oxidative injury were detected in GNE-493-treated prostate cancer xenograft tissues. Together, GNE-493 inhibited prostate cancer cell growth possibly through the Akt-mTOR-dependent and -independent mechanisms.

Prognostic impact of genetic alterations and methylation classes in meningioma.

Meningiomas are classified based on histological features, but genetic and epigenetic features are emerging as relevant biomarkers for outcome prediction and may supplement histomorphological evaluation. We investigated meningioma‐relevant mutations and their correlation with DNA methylation clusters and patient survival times. Formalin‐fixed and paraffin‐embedded samples of 126 meningioma patients (WHO grade I 52/126; 41.3%; WHO grade II: 48/126; 38.1%; WHO grade III: 26/126; 20.6%) were investigated. We analyzed NF2, TRAF7, KLF4, ARID, SMO, AKT, TERT promotor, PIK3CA, and SUFU mutations using panel sequencing and correlated them to DNA methylation classes (MC) determined using 850k EPIC arrays. The TRAKL mutation genotype was characterized by the presence of any of the following mutations: TRAF7, AKT1, and KLF4. Survival data including progression‐free survival (PFS) and overall survival (OS) was retrieved from chart review. Mutations were evident in 90/126 (71.4%) specimens with mutations in NF2 (39/126; 31.0%), TRAF7 (39/126; 31.0%) and KLF4 (25/126; 19.8%) being the most frequent ones. Two or more mutations were observed in 35/126 (27.8%) specimens. While TRAKL was predominantly found in benign MC, NF2 was associated with malign MC (p < 0.05). TRAF7, KLF4, and TRAKL mutation genotype were associated with improved PFS and OS (p < 0.05). TERT promotor methylation, intermediate, and malign MC were associated with impaired PFS and OS (p < 0.05). Methylation cluster showed better prognostic discrimination for PFS and OS (c‐index 0.77/0.75) than each of the individual mutations (c‐index 0.63/0.68). In multivariate analysis correcting for age, gender, MC, and WHO grade, none of the individual mutations except TERT remained an independent significant prognostic factor for PFS. Molecular profiling including mutational analysis and DNA methylation classification may facilitate more precise prognostic assessment and identification of potential targets for personalized therapy in meningioma patients.

Abstract PD6-04: Mutational landscape and immune infiltration of breast cancer metastases to gynecologic and other organs

Abstract Introduction: Breast cancer metastases (BCM), which cause most breast cancer (BC)-associated mortality, have increased genetic complexity compared to early-stage disease. However, the contribution of genetic alterations to site of BCM is not well-understood. Different breast cancer subtypes have varying patterns of BCM, e.g., lobular carcinoma more frequently spreads to gynecologic (Gyn) organs and the GI tract, perhaps hinting at selection pressures wherein some organs are hospitable to tumors with certain genetic alterations. Methods: Relationships between BCM site and mutations detected by DNA next-generation sequencing (NGS; NextSeq 592 gene panels or NovaSeq whole exome sequencing) were investigated using 12,464 BC samples sequenced at Caris Life Sciences (sample sizes, Table 1). PD-L1 expression was tested through IHC (Clone SP-142 (cut-off ≥1, 1%)). Tumor mutational burden (TMB) was measured by totaling somatic mutations per tumor (high ≥ 10 mutations per MB). Immune cell fractions were calculated by deconvolution of whole-transcriptome data (NovaSeq) using Quantiseq (reference). Statistical significance was determined using chi-square and Wilcoxon rank sum tests adjusted for multiple comparisons. Results: Compared to primary breast tumors, BCM had increased frequency of TMB-H (10.08% vs. 4.94%), decreased PD-L1 positivity (21.09% vs. 35.82%), and were enriched for PIK3CA (34.62% vs 30.53%) and ESR1 mutations (13.34% vs 2.17%) (all P&amp;lt;0.001). PD-L1 positivity was highest in BCM to lymph nodes (43.06%) and axilla (39.77%). BCM to Gyn organs had more lobular histology, the highest rate of hormone receptor (HR)+ tumors (77.17%), and rarely had high TMB (6.73%) or were PD-L1 positive (11.39%). Double dendrogram hierarchical clustering of BCM site by mutation frequency and pathway alterations revealed BCM to Gyn organs as a simplicifolious clade with a unique mutational pattern. Compared to BC in breast, BCM to Gyn organs had higher rates of mutations of PIK3CA, AKT1, and BRAF; more mutations in DNA repair (0.79% vs 0.06%), transcription factor (4.72% vs 0.93%), and Wnt signaling pathways (2.36% vs 1.47%); but no increase in BRCA mutations. BCM to brain had the most p53 pathway and homologous recombination (HR) pathway mutations (64.71% and 14.01%), while Gyn had the least (19.69% and 7.09%). Quantiseq RNA deconvolution revealed differences in tumor immune cell infiltrate by BCM site. Gyn metastases vs breast tumors had increased B cells (6.20% vs 5.40%), M2 macrophages (5.71% vs 4.07%), and NK cells (3.82% vs 3.18%) (all P&amp;lt;0.01) and a M2/M1 macrophage ratio of 22.8:1 vs 1.3:1. Conclusions: BCM to Gyn organs have a unique mutational and immune suppression profile. Integrating the profiling with clinical outcomes may extend this prognostic signature and set the stage for improved treatment strategies for these patients. Confirmation from matched or sequential specimens could clarify tumor evolution. Our data support repeat biopsy of Gyn site metastases since more targetable mutations might be revealed. Targeting mechanisms of immunosuppression in Gyn BCM could expand therapeutic options. Table 1.Breast Cancer TumorsTumor SiteTotalPredominant Breast Cancer SubtypeAll12464HR+/HER2- (51.6%)Breast5014HR+/HER2- (46.5%)Liver2003HR+/HER2- (63.3%)Bone1132HR+/HER2- (69.4%)Axilla1051HR+/HER2- (47.7%)Lung823HR+/HER2- (46.1%)Lymph Node647HR+/HER2- (43.4%)Chest/Chest Wall375HR+/HER2- (44.8%)Brain359TNBC (38.2%)Other315HR+/HER2- (57.1%)Skin282HR+/HER2- (50.7%)Connective Tissue193HR+/HER2- (51.8%)GI Organs143HR+/HER2- (69.9%)Gynecologic Organs127HR+/HER2- (76.4%) Citation Format: Anna D Louie, Rani Chudasama, Sharon Wu, Marzia Capelletti, Daniel Magee, W. Michael Korn, Virginia Kaklamani, Antoinette R Tan, Pavani Chalasani, Wafik S El-Deiry, Don Dizon, Stephanie L. Graff. Mutational landscape and immune infiltration of breast cancer metastases to gynecologic and other organs [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr PD6-04.

Abstract P2-01-01: Genetic alterations detected by circulating tumor DNA (ctDNA) in HER2-low metastatic breast cancer (MBC)

Abstract Introduction: Approximately 40-50% of breast cancers are characterized by low HER2 expression (HER2-low), defined as immunohistochemistry (IHC) 1+ or 2+ and HER2 fluorescence in situ hybridization (FISH) unamplified, encompassing a large and heterogeneous subgroup that may confer benefit from novel HER2 directed therapies. Circulating tumor DNA (ctDNA) has emerged as a minimally invasive technique to detect cancer-specific gene aberrations. Genetic alterations in ctDNA of HER2-low MBC have not been well described, and we hypothesized that HER2-low MBC may have a distinct genomic profile, beyond standard histopathologic features. Methods: This retrospective cohort study included patients with MBC treated at Washington University in St. Louis, Northwestern University (Chicago, IL) and Massachusetts General Hospital (Boston, MA) who had undergone ctDNA analysis during the course of treatment using the commercially available Guardant360® assay. HER2 expression was evaluated by IHC/FISH according to ASCO/CAP guidelines on metastatic tissue biopsies (or primary breast tumor tissue if a metastatic site biopsy was not available). Tumors were classified as HER2-low (IHC 1+ or 2+/FISH negative), HER2-0 (IHC 0) or HER2-positive (IHC 3+ or IHC 2+/FISH amplified). Clinicopathologic characteristics and ctDNA genetic alterations for HER2-low MBC were described and compared with the HER2-0 and HER2-positive subgroups. Chi-square and Fisher’s exact tests were used for categorical variables. Logistical regression was performed for multivariable analyses. Results: A total of 991 patients with MBC were analyzed, including 160 (16.1%) HER2-positive, 351 (35.4%) HER2-0, and 480 (48.4%) HER2-low MBC. The majority (89.2%) of HER2-low MBC were estrogen-receptor positive (ER+). Compared with HER2-0 MBC, HER2-low MBC had a significantly higher incidence of PIK3CA mutations (OR 1.54, p=0.027). PDGFRA and MYC amplifications were also more common among HER2-low MBC (2.3% vs 0.28% and 8.1% vs 4.6%, respectively), although not significantly associated with this subtype in multivariable analysis. Within the ER+ MBC cohort, those with HER2-low also had higher rates of PIK3CA mutations (OR 1.66, p=0.012) and MYC amplification (OR 2.29, p=0.034), as compared to HER2-0. Compared with HER2-positive, HER2-low MBC had significantly lower rates of ERBB2 alterations (OR 0.26, p=0.0076 for ERBB2 mutations and OR 0.022, p&amp;lt;0.001 for ERBB2 amplification). ESR1, AKT1, and RB1 mutations were more common in HER2-low compared with HER2-positive MBC (14.0% vs 6.9%; 3.1% vs none; 3.1% vs none, respectively), but were not significant in multivariable analysis. Conclusions: Among patients with ER+ MBC, HER-low had a higher incidence of PIK3CA mutations and MYC amplification compared to HER2-0 MBC, and both of these alterations have been implicated as mechanisms of endocrine resistance. We did not demonstrate a high incidence of ERBB2 alterations in patients with HER2-low MBC. To our knowledge, this is the first study to describe genetic alterations detected by ctDNA in patients with HER2-low MBC. Given the emergence of novel HER2-targeted antibody drug conjugates with clinical activity in HER2-low MBC, these findings may guide combination treatment strategies and patient selection for future studies. Further studies are needed to confirm whether HER2-low MBC represents a truly unique biologic subtype. Citation Format: Whitney L Hensing, Lorenzo Gerratana, Katherine Clifton, Marko Velimirovic, Ami Shah, Paolo D'Amico, Carolina Reduzzi, Qiang Zhang, Charles S Dai, Nusayba A Bagegni, Mateusz Opyrchal, Foluso O Ademuyiwa, Bose Ron, Amir Behdad, Cynthia X Ma, Aditya Bardia, Massimo Cristofanilli, Andrew A Davis. Genetic alterations detected by circulating tumor DNA (ctDNA) in HER2-low metastatic breast cancer (MBC) [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-01-01.

Plasma-informed minimal residual disease (MRD) assay: A multicenter prospective study in Japanese patients with stage II colorectal cancer.

161 Background: ̃80% of stage II colorectal cancer (CRC) can be cured by surgery alone. However, adjuvant chemotherapy is recommended for patients with high risk features such as bowel obstruction, &lt; 12 lymph nodes examined and T4 tumors. Traditional pathological grading and biomarkers such as carcinoembryonic antigen has limited sensitivity. Several reports indicated circulating tumor DNA (ctDNA) may represent a promising prognostic factor to assess MRD as a factor for prediction of recurrence after surgery. Here, we present a proof-of-concept study for the development of a novel plasma-based highly sensitive Next Generation Sequencing (NGS) panel using SafeSEQ technology in operable CRC Japanese patients. Methods: This multicenter prospective study recruited patients diagnosed as operable clinical stage II CRC (n = 46) with pre- and post- (4̃6 weeks) operative plasma samples collected between Nov, 2019 and Jan, 2021. ctDNA were extracted and a 14-gene NGS panel was used to analyze single nucleotide variants (SNVs) and Indels covered by gene-specific amplicons. MRD variant was defined as same variant detected in both pre- and post- operative plasma samples. Tissue NGS by a 500-gene panel was also performed in a small number of tissue samples (n = 5) to compare the concordance of plasma and tissue variants. Results: Pre- and post-operative ctDNA status of 46 patients were analyzed. ctDNA positive was observed in 69.6% (32/46, 95%CI 55.2, 81.0) pre- and 34.8% (16/46, 95%CI 22.7, 49.3) post- samples. AKT1, CTNNB1, NRAS, POLE and PPP2R1A mutation were not detected in this study. TP53 mutation was most frequently detected in both pre- (22/46) and post- (11/46) samples, whereas APC mutation was ranked 2nd in pre- (15/46) but none in post- samples. A combined 96 variants were detected in all samples, in which 76 of them were &lt; 0.5% mutant allele frequency (MAF). MRD variants were detected in 17.4% (8/46, 95%CI 8.82, 30.99) post- samples. Evaluation of positive percentage agreement between tissue and pre- plasma samples in three patients show that a total 7 variants detected in plasma, and 3 of them were detected in tissue samples. Conclusions: This study assesses the feasibility of a plasma-informed NGS panel by evaluating pre- and post- operative plasma samples. The presence of variants with &lt; 0.5% MAF detected in this study indicate a highly sensitive method is required for accurate MRD detection. Further observation is required to explore the relationship between MRD variant and clinical outcome such as 2-year progression-free survival.

AKT1 and PIK3CA activating mutations in Moroccan bladder cancer patients´ biopsies and matched urine.

Introductionin cancer cells, activating mutations in PIK3CA and AKT1 genes, major players of PI3K-AKT-mTOR signalling pathway, are widely reported in many cancers and present attractive targets for the identification of new therapeutics and better cancer management. The present study was planned to evaluate the mutational status of PIK3CA and AKT1 genes in bladder cancer patients and to assess the association between these mutations and patients´ clinico-pathological features.Methodsin this prospective study, bladder cancer biopsies and matched urine sediments samples were collected form 70 patients. Mutations were assessed by deoxyribonucleic acid (DNA) sequencing and correlation with clinico-pathological data was performed using SPSS software.ResultsAKT1 alterations were poorly detected. Only one patient with pT1 stage and high-grade tumour carried the E17K mutation. In PIK3CA exon 9, 2 point mutations, E545K and Q546E, and a SNP (E547E) were reported, whereas in exon 20, 2 point mutations (L989V and H1047R) and 2 SNPs (I1022I and T1025T) were detected. PIK3CA mutations were mainly observed in early stages and high-grade tumours. Statistical analysis showed no significant association between the studied AKT1 and PIK3CA mutations and patients´ clinico-pathological parameters (p > 0.05). Detection of these mutations in voided urine samples showed a high specificity (100%) for both genes and a moderate sensitivity: 100% for AKT1 and 66.7% for PIK3CA genes.Conclusionthis study shows clearly that mutations in AKT1 and PIK3CA are rare events and could not be considered as valuable biomarkers for bladder cancer management.

Integrated Analysis of Ovarian Juvenile Granulosa Cell Tumors Reveals Distinct Epigenetic Signatures and Recurrent TERT Rearrangements.

Adult granulosa cell tumor (AGCT) is characterized by the somatic FOXL2 p.C134W mutation, and recurrences have been associated with TERT promoter and KMT2D-truncating mutations. Conversely, the molecular underpinnings of the rare juvenile granulosa cell tumor (JGCT) have not been well elucidated. To this end, we applied a tumor-only integrated approach to investigate the genomic, transcriptomic, and epigenomic landscape of 31 JGCTs to identify putative oncogenic drivers. Multipronged analyses of 31 JGCTs were performed utilizing a clinically validated next-generation sequencing (NGS) panel targeting 580 cancer-related genes for genomic interrogation, in addition to targeted RNA NGS for transcriptomic exploration. Genome-wide DNA methylation profiling was conducted using an Infinium Methylation EPIC array targeting 866,562 CpG methylation sites. We identified frequent KMT2C-truncating mutations along with other mutated genes implicated in the switch/sucrose nonfermentable (SWI/SNF) chromatin remodeling complex, in addition to previously reported hotspot AKT1 and DICER1 mutations. Targeted transcriptome sequencing revealed recurrent TERT rearrangements (13%) involving partners CLPTM1L or DROSHA, and differential gene expression analysis showed FGFR1 upregulation in the TERT non-rearranged JGCTs under direct promoter control. Genome-wide DNA methylation rendered a clear delineation between AGCTs and JGCTs at the epigenomic level, further supporting its diagnostic utility in distinguishing among these tumors. This is the largest comprehensive molecular study of JGCTs, where we further expand our current understanding of JGCT pathogenesis and demonstrate putative oncogenic drivers and TERT rearrangements in a subset of tumors. Our findings further offer insights into possible targeted therapies in a rare entity.

Rationale and design of the CRAFT (Continuous ReAssessment with Flexible ExTension in Rare Malignancies) multicenter phase II trial

BackgroundApprovals of cancer therapeutics are primarily disease entity specific. Current molecular diagnostic approaches frequently identify actionable alterations in rare cancers or rare subtypes of common cancers for which the corresponding treatments are not approved and unavailable within clinical trials due to entity-related eligibility criteria. Access may be negotiated with health insurances. However, approval rates vary, and critical information required for a scientific evaluation of treatment-associated risks and benefits is not systematically collected. Thus clinical trials with optimized patient selection and comprehensive molecular characterization are essential for translating experimental treatments into standard care.Patients and methodsContinuous ReAssessment with Flexible ExTension in Rare Malignancies (CRAFT) is an open-label phase II trial for adults with pretreated, locally advanced, or metastatic solid tumors. Based on the evaluation by a molecular tumor board, patients are assigned to combinations of six molecularly targeted agents and a programmed death-ligand 1 (PD-L1) antagonist within seven study arms focusing on (i) BRAF V600 mutations; (ii) ERBB2 amplification and/or overexpression, activating ERBB2 mutations; (iii) ALK rearrangements, activating ALK mutations; (iv and v) activating PIK3CA and AKT mutations, other aberrations predicting increased PI3K–AKT pathway activity; (vi) aberrations predicting increased RAF–MEK–ERK pathway activity; (vii) high tumor mutational burden and other alterations predicting sensitivity to PD-L1 inhibition. The primary endpoint is the disease control rate (DCR) at week 16; secondary and exploratory endpoints include the progression-free survival ratio, overall survival, and patient-reported outcomes. Using Simon’s optimal two-stage design, 14 patients are accrued for each study arm. If three or fewer patients achieve disease control, the study arm is stopped. Otherwise, 11 additional patients are accrued. If the DCR exceeds 7 of 25 patients, the null hypothesis is rejected for the respective study arm.ConclusionsCRAFT was activated in October 2021 and will recruit at 10 centers in Germany.Trial registration numbersEudraCT: 2019-003192-18; ClinicalTrials.gov: NCT04551521.

Nano-scale physical properties characteristic to metastatic intestinal cancer cells identified by high-speed scanning ion conductance microscope

Recent genetic studies have indicated relationships between gene mutations and colon cancer phenotypes. However, how physical properties of tumor cells are changed by genetic alterations has not been elucidated. We examined genotype-defined mouse intestinal tumor-derived cells using a high-speed scanning ion conductance microscope (HS-SICM) that can obtain high-resolution live images of nano-scale topography and stiffness. The tumor cells used in this study carried mutations in Apc (A), Kras (K), Tgfbr2 (T), Trp53 (P), and Fbxw7 (F) in various combinations. Notably, high-metastatic cancer-derived cells carrying AKT mutations (AKT, AKTP, and AKTPF) showed specific ridge-like morphology with active membrane volume change, which was not found in low-metastatic and adenoma-derived cells. Furthermore, the membrane was significantly softer in the metastatic AKT-type cancer cells than other genotype cells. Importantly, a principal component analysis using RNAseq data showed similar distributions of expression profiles and physical properties, indicating a link between genetic alterations and physical properties. Finally, the malignant cell-specific physical properties were confirmed by an HS-SICM using human colon cancer-derived cells. These results indicate that the HS-SICM analysis is useful as a novel diagnostic strategy for predicting the metastatic ability of cancer cells.