PIK3CA Pathway Research Articles

RAIDS atlas of significant genetic and protein biomarkers in cervical cancer.

Loss of function in epigenetic acting genes together with driver alterations in the PIK3CA pathway have been shown significantly associated with poor outcome in cervical squamous cell cancer. More recently, a CoxBoost analysis identified 16 gene alterations and 30 high level activated proteins to be of high interest, due to their association with either good or bad outcome, in the context of treatment received by chemoradiation. The objectives here were to review and confirm the significance of these molecular alterations as suggested by literature reports and to pinpoint alternate treatments options for poor-responders to chemoradiation.

Salivary Gland Intraductal Carcinoma: How Do 183 Reported Cases Fit Into a Developing Classification.

Salivary gland intraductal carcinoma (IDC) is a very uncommon group of neoplasms. Many names, variations in diagnostic criteria, and newly observed molecular findings (including NCOA4 :: RET , TRIM27 :: RET , HRAS point mutations, and PIK3CA pathway alterations) have generated further confusion in being able to recognize and categorize this group of tumors. Different histologic appearances and patterns of growth suggest there is more than one tumor category, with intercalated duct, apocrine, oncocytic, and hybrid features seen. Frankly destructive invasion further complicates the category, as the name "intraductal" would suggest an "in situ" neoplasm. Recent evidence on fusion-positive IDC demonstrates the same molecular underpinnings in both the ductal and the myoepithelial cells, which aids in further separating these tumors. This article summarizes the historical group of 183 neoplasms classified under the umbrella of IDC and highlights the unique histologic, immunohistochemistry, and molecular features that may further guide nomenclature standardization and harmonization.

Overcoming Resistance to HER2-Directed Therapies in Breast Cancer.

Simple SummaryBreast cancer is the most common cancer in women in the United States. Around 15% of all breast cancers overexpress the HER2 protein. These HER2-positive tumors have been associated with aggressive behavior if left untreated. Drugs targeting HER2 have greatly improved the outcomes of patients with HER2-positive tumors in the last decades. Despite these improvements, many patients with early breast cancer have recurrences, and many with advanced disease experience progression of disease on HER2-targeted drugs, suggesting that patients can develop resistance to these medications. In this review, we summarize several mechanisms of resistance to HER2-targeted treatments. Understanding how the tumors grow despite these therapies could allow us to develop better treatment strategies to continue to improve patient outcomes.Human epidermal growth factor receptor 2 (HER2)-positive breast cancer accounts for around 15% of all breast cancers and was historically associated with a worse prognosis compared with other breast cancer subtypes. With the development of HER2-directed therapies, the outcomes of patients with HER2-positive disease have improved dramatically; however, many patients present with de novo or acquired resistance to these therapies, which leads to early recurrences or progression of advanced disease. In this narrative review, we discuss the mechanisms of resistance to different HER2-targeted therapies, including monoclonal antibodies, small tyrosine kinase inhibitors, and antibody-drug conjugates. We review mechanisms such as impaired binding to HER2, incomplete receptor inhibition, increased signaling from other receptors, cross-talk with estrogen receptors, and PIK3CA pathway activation. We also discuss the role of the tumor immune microenvironment and HER2-heterogeneity, and the unique mechanisms of resistance to novel antibody-drug conjugates. A better understanding of these mechanisms and the potential strategies to overcome them will allow us to continue improving outcomes for patients with breast cancer.

Unraveling the Mechanisms of Clinical Drugs-Induced Neural Tube Defects Based on Network Pharmacology and Molecular Docking Analysis.

Chemotherapeutic agents such as methotrexate (MTX), raltitrexed (RTX), 5-fluorouracil (5-FU), hydroxyurea (HU), and retinoic acid (RA), and valproic acid (VPA), an antiepileptic drug, all can cause malformations in the developing central nervous system (CNS), such as neural tube defects (NTDs). However, the common pathogenic mechanisms remain unclear. This study aimed to explore the mechanisms of NTDs caused by MTX, RTX, 5-FU, HU, RA, and VPA (MRFHRV), based on network pharmacology and molecular biology experiments. The MRFHRV targets were integrated with disease targets, to find the potential molecules related to MRFHRV-induced NTDs. Protein-protein interaction analysis and molecular docking were performed to analyze these common targets. Utilizing the kyoto encyclopedia of genes and genomes (KEGG) signaling pathways, we analyzed and searched the possible causative pathogenic mechanisms by crucial targets and the signaling pathway. Results showed that MRFHRV induced NTDs through several key targets (including TP53, MAPK1, HSP90AA1, ESR1, GRB2, HDAC1, EGFR, PIK3CA, RXRA, and FYN) and multiple signaling pathways such as PI3K/Akt pathway, suggesting that abnormal proliferation and differentiation could be critical pathogenic contributors in NTDs induced by MRFHRV. These results were further validated by CCK8 assay in mouse embryonic stem cells and GFAP staining in embryonic brain tissue. This study indicated that chemotherapeutic and antiepileptic agents induced NTDs might through predicted targets TP53, MAPK1, GRB2, HDAC1, EGFR, PIK3CA, RXRA, and FYN and multiple signaling pathways. More caution was required for the clinical administration for women with childbearing potential and pregnant.

Genomic profiling and PD-L1 expression of advanced cervical cancer to predict response to programmed death-1 inhibitor combination therapy: a secondary analysis of the CIBI308ALTER-C201 trial (035)

Genomic profiling and PD-L1 expression of advanced cervical cancer to predict response to programmed death-1 inhibitor combination therapy: a secondary analysis of the CIBI308ALTER-C201 trial (035)

The landscape of genetic alterations of UVB-induced skin tumors in DNA repair-deficient mice.

Non-melanoma skin cancer (NMSC) is mainly caused by ultraviolet (UV)-induced somatic mutations and is characterized by UV signature modifications. Xeroderma pigmentosum group A (Xpa) knockout mice exhibit extreme UV-induced photo-skin carcinogenesis, along with a photosensitive phenotype. We performed whole-exome sequencing (WES) of squamous cell carcinoma (SCC) samples after repetitive ultraviolet B (UVB) exposure to investigate the differences in the landscape of somatic mutations between Xpa knockout and wild-type mice. Although the tumors that developed in mice harboured UV signature mutations in a similar set of cancer-related genes, the pattern of transcriptional strand asymmetry was largely different; UV signature mutations in Xpa knockout and wild-type mice preferentially occurred in transcribed and non-transcribed strands, respectively, reflecting a deficiency in transcription-coupled nucleotide excision repair in Xpa knockout mice. Serial time point analyses of WES for a tumor induced by only a single UVB exposure showed pathogenic mutations in Kras, Fat1, and Kmt2c, which may be driver genes for the initiation and promotion of SCC in Xpa knockout mice. Furthermore, the inhibitory effects on tumor production in Xpa knockout mice by the anti-inflammatory CXCL1 monoclonal antibody affected the pattern of somatic mutations, wherein the transcriptional strand asymmetry was attenuated and the activated signal transduction was shifted from the RAS/RAF/MAPK to the PIK3CA pathway.

Artificial intelligence to identify genetic alterations in conventional histopathology.

Precision oncology relies on the identification of targetable molecular alterations in tumor tissues. In many tumor types, a limited set of molecular tests is currently part of standard diagnostic workflows. However, universal testing for all targetable alterations, especially rare ones, is limited by the cost and availability of molecular assays. From 2017 to 2021, multiple studies have shown that artificial intelligence (AI) methods can predict the probability of specific genetic alterations directly from conventional hematoxylin and eosin (H&E) tissue slides. Although these methods are currently less accurate than gold standard testing (e.g. immunohistochemistry, polymerase chain reaction or next-generation sequencing), they could be used as pre-screening tools to reduce the workload of genetic analyses. In this systematic literature review, we summarize the state of the art in predicting molecular alterations from H&E using AI. We found that AI methods perform reasonably well across multiple tumor types, although few algorithms have been broadly validated. In addition, we found that genetic alterations in FGFR, IDH, PIK3CA, BRAF, TP53, and DNA repair pathways are predictable from H&E in multiple tumor types, while many other genetic alterations have rarely been investigated or were only poorly predictable. Finally, we discuss the next steps for the implementation of AI-based surrogate tests in diagnostic workflows. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

A rare case of macrodystrophia lipomatosa progressiva

A non-heritable congenital expansion of a digit is known as macrodactyly. It happens as a result of a mutation in the PIK3CA pathway, which regulates healthy cell proliferation. It is usually associated with gigantism, neurofibromatosis, lipofibromatosis, digital hyperostosis and hemihypertrophy. It is not always evident at birth, but at about age 2, the affected fingers begin to grow significantly faster than the normal fingers. Ninety percent (90%) of it is unilateral, and 70% of it involves more than one digit-most often the index. The expansion might only affect the digit or it might spread to the palm, forearm, or arm. The digit may exhibit angulation deformity. The distal interphalangeal joint occasionally exhibits motion restriction. The patient presented to us with a loss of two-point discrimination and sensory deficit. In this condition, the motor deficit is rarely seen. Our patient reported a tingling sensation and the possibility of carpal tunnel syndrome was ruled out as an enlarged median nerve might result in carpal tunnel syndrome. Inspection & palpation revealed thick, fibrofatty tissue with restricted movements. The patient’s symptoms were relieved by NSAIDs and Pregabalin 75mg, symptomatic relief was present, and the patient was advised debulking surgery as the treatment modality.

Abstract P123: Antitumor activity of tipifarnib and PI3K pathway inhibitors in HRAS-associated HNSCC

Abstract HRAS-MAPK and PI3K-AKT-mTOR are important oncogenic pathways in head and neck squamous cell carcinoma (HNSCC) and other squamous cell carcinomas (SCCs). HRAS is mutated in ~5% and overexpressed in approximately 30% of HNSCC patients, raising the possibility that some HRAS wild-type (WT) HNSCCs may also display a degree of dependence on HRAS. RAS proteins undergo several post-translational modifications, including the addition of a farnesyl isoprenoid moiety by the enzyme farnesyltransferase (FT), which facilitate their attachment to membranes. This dependence prompted the development of selective inhibitors (FTIs) for the treatment of RAS-driven cancers. Tipifarnib is a potent and selective FTI that has demonstrated antitumor activity in recurrent/metastatic HNSCC carrying HRAS mutations. Based on these data, a pivotal study (NCT03719690) evaluating the efficacy of tipifarnib in HRAS mutant HNSCC (AIM-HN) is currently ongoing. PIK3CA (the catalytic subunit of PI3K), another prominent driver in HNSCC, is commonly activated either by gain of function mutations or gene amplification with some overlap between the two subsets. Multiple reports indicate that HRAS and PIK3CA pathways cooperate and crosstalk in driving tumor progression in SCCs and resistance to inhibitors of respective pathways. In this study, we explored whether combined inhibition of HRAS farnesylation (by tipifarnib) and inhibition of PI3K pathway signaling (with inhibitors of PI3K-a, AKT or mTORC1/2) would be more effective in CDX and PDX models of HRAS-associated SCCs relative to the monotherapy approaches. In a panel of HNSCC cell lines harboring HRAS and/or PIK3CA alterations (mutation, overexpression or amplification), tipifarnib reduced cell growth and, in combination with PI3K-a inhibitor alpelisib, induced cytotoxicity. Consistent with in vitro findings, robust inhibition of tumor growth was observed in majority of animals treated with the combination of tipifarnib and alpelisib. Similar activity was noted with the AKT inhibitor uprosertib and the mTORC1/2 inhibitor sapanisertib. Regressions with the FTI-PI3K-a inhibitor doublet were observed both in tumors that were HRAS mutant or HRAS overexpressed with or without mutation or amplification of the PIK3CA gene or carried the latter without alterations in HRAS, suggesting that concomitant blockade of both targets may have surprisingly broad and potent anti-tumor activity in HNSCC. In dose-scheduling experiments in PDX models, simultaneous blockade of both targets was superior to split intermittent dosing of the two drugs, underlining the cooperativity of the two pathways in these models. Mechanistically, tipifarnib repressed the compensatory MAPK pathway activation induced by alpelisib at the level of phosphorylated ribosomal S6 protein. Impact of tipifarnib and alpelisib combination on additional MAPK and AKT signaling mediators will be reported. Citation Format: Francis Burrows, Shivani Malik, Stacia Chan, Asako Mccloskey, Zhiyong Wang, Mara Gilard, Silvio Gutkind. Antitumor activity of tipifarnib and PI3K pathway inhibitors in HRAS-associated HNSCC [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P123.

Radiosensitivity and Immune Cell Infiltration Signature Predict Clinical Outcome of Patients in the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) Study Cohort

There is growing evidence that tumor radiosensitivity is associated with immune activation in solid tumors. However, previous studies have not examined the relationship between patterns of immune infiltration and radiation response according to diverse molecular subtypes of breast cancer. This study evaluated radiosensitivity and immune infiltration signature to define a group of patients would benefit most from radiation therapy.We performed integrative analyses of the clinical, genomic, transcriptomic, and immunogenomic data to characterize the molecular features associated with radiosensitivity. We analyzed 1,903 data sets of METABRIC Study cohort using the radiosensitivity index (RSI), CIBERSORT and xCell, gene expression deconvolution algorithm which estimates the immune composition of tumor samples. According to RSI cut-point (0.3745), the patients were grouped into radiosensitive (RS, RSI-low tumors, n = 1,082) versus radioresistant (RR, RSI-high tumors, n = 821). Next, patients were divided into two groups according to immune and stromal scores, immune infiltrated (IF, n = 650) and immune excluded (IE, n = 1253) subgroups.RR group showed poorer relapse free survival compared to RS group in multivariate (HR 1.52, 95% CI 1.23-1.89, P < 0.001) analyses and this tendency was only significant in ER negative group. In multivariate logistic regression analysis, CD8+ T cells (OR = 1.21 95% CI 1.1-1.33 P < 0.001), gamma/delta T cells (OR = 1.3 95% CI 1.19-1.43 P < 0.001), dendritic cell resting (OR = 1.54 95% CI 1.22-1.95 P < 0.001), memory B cells (OR = 1.17 95% CI 1.03-1.33 P = 0.013), Pam50 luminal B1 subtype (OR = 1.59 95% CI 1.25-2.02 P < 0.001), and triple negative InClust 10 (OR = 1.67 95% CI 1.17-2.4 P = 0.005) were significantly enriched in RS group. In contrast, M0 macrophages (OR = 0.86 95% CI 0.78-0.94 P = 0.001), HER2 enriched integrative cluster subtype (InClust) 5 (OR = 0.43 95% CI 0.31-0.61 P < 0.001), ER positive InClust 4+ (OR = 0.5 95% CI 0.37-0.68 P < 0.001), and PIK3CA pathway alteration (OR = 0.75 95% CI 0.62-0.92 P = 0.005) were significantly associated with RR group.Taken together, these results suggested that tumor radiosensitivity was associated with activation of antitumor immunity and led to better relapse free survival particularly in ER negative group.

Bio-P-02 - Genetic expression profile in the prognosis of mycosis fungoides

We present a historic cohort study with 57 patients diagnosed with mycosis fungoides in early stages during the years 1999 to 2002. Our group performed a cDNA microarray on the diagnosis skin biopsies samples with the CNIO (oncologic investigation national center of Spain) Onco-Chip. This chip includes 6386 cancer-related clones. Since the samples were processed in two deferent years the initial set of 57 patients was divided in two groups of 29 and 28 patients due to the heterogeneity of the sample array results. The patients had a medium of 14 years of follow-up and were divided in two groups: progression (development of tumor, nodes, erythroderma, blood involvement or metastasis) and no progression. And we performed volcano pot analysis and GSEA to determine whether there are different genes expressions at diagnosis that determine prognosis. Several pathways were up and down regulated differently in patients progressing. We performed a GSEA analysis with the following results. Pathways related with progression: CXCR4 pathway (p=0.000) Normalized Enrichment Score (NES) 1.91 and FDR 0.027; genes: BCAR1, PXN, PIK3CA, PTK2, PIK3R1, PRKCA, HRAS, RAF1, CXCL12, PIK3C2G, GNB1. Other pathways with p<5% were: ERK5 pathway p=0.035, NES 1.15, FDR 0.92; genes: PIK3CA, PIK3R1, HRAS, RPS6KA1, SHC1. AKT pathway p=0.049, NES 1.52, FDR 0.70; genes: PIK3CA, PIK3R1, GHR, CASP9, YWHAH. Cytokine pathway p=0.034, NES 1.49, FDR 0.66; genes: SOCS6, SOD2, CCL2. PIK 3-CL1 pathway p=0.035, NES 1.39, FDR 0.63; genes: PIK3CA and PIK3CD INFAR1 pathway p=0.012, NES –1.51, FDR 1; genes: IFNAR1, JAK1, IFNAR2. P53 pathway p=0.032, NES –1.48, FDR 1; genes: MDM2, ABCB1, TP53. Pathways related with no progression: lymphocyte pathway p=0.000, FDR 0.31 NES –1.67; genes: ITGA, ITGB1, SELL, SELP. UV response pathway p=0.007, NES 1.62, FDR 0.40; genes: NTRK3, CCNE1, RAB27A, LYN, CEBPG, IL6ST, GAL, PSMC3, RRAD, ATF3, SOD2, BAK1, STIP1, GCH1, BMP2, PRKCD, RFC4, E2F2, IRF1, RASGRP1, BTG3, CDKN1C, ATP6V1F, CHKA, EIF5, POLE3, CDC5, UROD, CDC34, NR4A1, ENO2, JUNB, SLC6A8, DNAJB1, IGFB2, CDK2, PPIF, ABCB1, RXRB, PPT1, SPOP, KIT, MET, EIF5, FURIN. Other pathway with p<5% was: ERK pathway p=0.048, NES –1.48, FDR 0.93; genes: SRC, NGFB, HRAS; IGF1R, RPS6KA1, MYC, EGFR, RAF, SHC1, PDGFRA, GNB1, STAT3, NGFR, ITGB1, GNAS. We also performed a volcano pot study that showed overexpression of PPP1R3C a gene related with the mTOR pathway in the progression cases. Although our sample size was limited, we believe that pathways related with JAK/STAT, PIK/AKT/mTOR, MAPK, and cellular cycle can be differentially expressed in patients that have progression of the disease from the early stages of mycosis fungoides. Further studies are necessary to validate our results.

Abstract PO-086: Selective radiosensitization in preclinical models of HPV-negative squamous cell carcinoma

Abstract Background: Radiotherapy is a mainstay of curative treatment for squamous cell carcinomas (SCC) and is frequently combined with radiosensitizing drugs to improve efficacy. Outcomes for HPV-negative SCCs remain heterogeneous, in part due to variable resistance to ionizing radiation (IR) and modest benefit of existing radiosensitizing drugs. Hypothesis driven testing of novel radiosensitizing drugs has previously been limited due to a lack of robust, efficient, and reproducible methods to assess drug radiation combinations. Aims: To improve the throughput of preclinical studies on radiosensitizers, we have developed an in vitro system for assessing drug/radiation combinations, validated using the known radiosensitizing chemotherapeutic drug cisplatin. We extended the assay to assess the effect of ML-385, a NRF2 inhibitor that increases cellular reactive oxygen species (ROS), and abemaciclib and palbociclib, two CDK4/6 inhibitors predicted to radiosensitize cancer cells by inhibiting entry into more resistant phases of the cell cycle. Experimental Methods: We adapted the 9-day viability assay of Abazeed et al. (Cancer Res., 2013) to enable drug/radiation efficacy assessments. We first validated the assay’s ability to recapitulate clonogenic survival among 19 HPV-negative SCC cell lines. Drug/radiation experiments were performed in the 6 most radioresistant SCC cell lines. ROS levels after 4Gy IR was used to confirm NRF2 suppression. Flow cytometry was used to evaluate cell cycle phase. AKT inhibitor GSK690693 was used in combination with a NRF2 shRNA knockdown cell line to investigate the mechanism of sensitivity. Western blot was used to detect p16. Cellular response to multiple IR doses was summarized using an area-under-the-curve (AUC) metric. The delta AUC across drug doses was used to evaluate radiosensitization. Results: Among the 19 cell lines, AUCs with the clonogenic and 9-day viability assays were strongly correlated (Pearson r=0.74, p=3.00 × 10–4). Six (32%) of the cell lines were reproducibly radioresistant (AUC &amp;gt;3.5) using both assays. All of these cell lines saw sensitization with cisplatin. None of these 6 cell lines harboured mutations in the canonical NRF2 pathway, whereas all 6 harboured either CCND1 amplification, CDKN2A mutation, or both. Only one cell line showed radiosensitization with the NRF2 inhibitor ML-385, an effect that was abrogated by PIK3CA or AKT pathway inhibition. In contrast, 5 of the 6 cell lines showed reproducible radiosensitization following CDK4/6 inhibition; with robust p16 expression detected in the lone unaffected cell line. Conclusion: The 9-day viability assay allows efficient evaluation of putative radiosensitizers. Our tests of putative radiosensitizing drugs in a cohort of radioresistant cell lines have identified CDK4/6 inhibitors to be of interest for further investigation in biomarker-selected populations. Citation Format: Meghan Lambie, Rita Gill, Laurie Ailles, Scott V. Bratman. Selective radiosensitization in preclinical models of HPV-negative squamous cell carcinoma [abstract]. In: Proceedings of the AACR Virtual Special Conference on Radiation Science and Medicine; 2021 Mar 2-3. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(8_Suppl):Abstract nr PO-086.

A systematic review and meta-analysis of the prevalence of therapeutic targets in cervical cancer.

Cervical Cancer (CC) is a significantly prevalent disease in developing countries. Currently, targeted therapies are not a primary standard of care in CC. This information could be crucial for developing directed therapies and patient screening for biomarkers that would allow personalised treatment of CC. This systematic review aimed to estimate the prevalence of potential therapeutic targets such as the epidermal growth factor receptor (EGFR) and the PI3K/Akt/mTOR and Ras/Raf/MAPK pathways in patients with CC, identified through genomic and non-genomic testing. Studies were identified through an ad-hoc search strategy from the available on MEDLINE (Ovid), CENTRAL, LILACS, SCOPUS, through the Clinical Trial registry on Clinicaltrials.gov, International Clinical Trials Registry Platform, RENIS (Argentine National Registry of Health Research) and grey literature sources. We included 74 studies which represented a total pool of 7,862 participants. Forty-five studies informed mutations of EGFR, with a combined positivity rate of 53% (95%CI: 45%–60%; I2 = 95%). Twenty studies informed the presence of mutations in PIK3CA with a combined positivity rate of 30% (95%CI: 21%–39%; I2 = 96%). Twenty-three studies reported a mutation in Ras, with a combined positivity rate of 14% (95%CI: 8%–21%; I2 = 95%). Raf mutations were informed in six studies. Six studies informed the presence of Akt mutations, two studies informed mTOR mutations and only one study reported mutations of MAPK. The most frequently described therapeutic targets were EGFR, and the PIK3CA and Ras pathways, though inconsistency in positivity rates was significant. Our study did not allow the identification of any specific clinical characteristics that might explain the observed heterogeneity. Despite the overall good quality of the included studies, the applicability of these results to patients’ general population with CC is still unclear.

HPV-16 positive clinically advanced squamous cell carcinoma of the urinary bladder (mBSCC): A comprehensive genomic profiling (CGP) study.

481 Background: mBSCC is an uncommon form of urinary bladder malignancy when compared with the much higher urothelial carcinoma incidence. We studied the genomic alteration (GA) landscape in a series of mBSCC based on the association with HPV-16 to determine if differences would be observed between the positive and negative groups. Methods: Using a hybrid capture-based FDA-approved CGP assay, a series of 171 mBSCC were sequenced to evaluate all classes of GA. Tumor mutational burden (TMB) was determined on up to 1.1 Mbp of sequenced DNA and microsatellite instability (MSI) was determined on 114 loci. PD-L1 expression was determined by IHC (Dako 22C3) with low tumor cell positive staining set at 1-49% and high staining at ≥50% expression. Results: Overall, 11 (6.4%) of the mBSCC were found to harbor HPV-16 sequences (Table). HPV-16+ status was identified slightly more often in women (NS) and in younger patients (P = .04); 2 female patients with mBSCC had prior history of SCC including 1 anal SCC and 1 vaginal SCC. HPV-16+ mBSCC had fewer GA/tumor (P &lt; .0001), and fewer inactivating GA in CDKN2A (P &lt; .0001), CDKN2B (P = .05), TERT promoter (P = .0004) and TP53 (P &lt; .0001). GA in genes associated with urothelial carcinoma including FGFR2 and FGFR3 were similar in both HPV-16+ and HPV-16- mBSCC groups. MTOR and PIK3CA pathway GA were not significantly different in the 2 groups. MSI and TMB were also similar in the 2 groups. The 3 HPV-16+ mBSCC cases showed high positive PD-L1 IHC staining. Conclusions: HPV-16+ mBSCC tends to occur more often in women and younger patients. As reported in other HPV-associated squamous cell carcinomas, HPV-16+ mBSCC demonstrates significantly reduced frequencies of inactivating mutations in cell cycle regulatory genes with similar GA in MTOR and PIK3CA pathways. The implication of HPV in the pathogenesis of bladder cancer remains unknown but warrants further exploration and clinical validation. [Table: see text]

Cerebellar dysplasia related to PIK3CA mutation: a three-case series.

The term PROS (PIK3CA-Related Overgrowth Spectrum) indicates a wide spectrum of overgrowth disorders related to somatic mutations in PIK3CA (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha) pathway. We present three cases with PIK3CA mutation and clinical characteristics encompassing MCAP (megalencephaly-capillary malformation) condition but lacking all criteria to a certain diagnosis, most of all showing prevalent and peculiar involvement of cerebellar structures at MRI (magnetic resonance imaging) mainly consisting in cortical rim thickening and abnormal orientation of folia axis. These cases expand the spectrum of intracranial MRI features in PIK3CA disorders.

Mutational Landscape of Esophageal Squamous Cell Carcinoma in an Indian Cohort.

Esophageal squamous cell carcinoma (ESCC) is the most common histological subtype of esophageal cancer in India. Cigarette smoking and chewing tobacco are known risk factors associated with ESCC. However, genomic alterations associated with ESCC in India are not well-characterized. In this study, we carried out exome sequencing to characterize the mutational landscape of ESCC tumors from subjects with a varied history of tobacco usage. Whole exome sequence analysis of ESCC from an Indian cohort revealed several genes that were mutated or had copy number changes. ESCC from tobacco chewers had a higher frequency of C:G > A:T transversions and 2-fold enrichment for mutation signature 4 compared to smokers and non-users of tobacco. Genes, such as TP53, CSMD3, SYNE1, PIK3CA, and NOTCH1 were found to be frequently mutated in Indian cohort. Mutually exclusive mutation patterns were observed in PIK3CA–NOTCH1, DNAH5–ZFHX4, MUC16–FAT1, and ZFHX4–NOTCH1 gene pairs. Recurrent amplifications were observed in 3q22-3q29, 11q13.3-q13.4, 7q22.1-q31.1, and 8q24 regions. Approximately 53% of tumors had genomic alterations in PIK3CA making this pathway a promising candidate for targeted therapy. In conclusion, we observe enrichment of mutation signature 4 in ESCC tumors from patients with a history of tobacco chewing. This is likely due to direct exposure of esophagus to tobacco carcinogens when it is chewed and swallowed. Genomic alterations were frequently observed in PIK3CA-AKT pathway members independent of the history of tobacco usage. PIK3CA pathway can be potentially targeted in ESCC which currently has no effective targeted therapeutic options.

Abstract LB-171: Assessing the impact of PIK3CA mutation on the three-dimensional organization of chromatin

Abstract Background: Three-dimensional organization of chromatin within the nucleus is an important and dynamic regulator of cellular transcription. Changes in chromatin topology are implicated in processes like cell differentiation and cell fate decisions, but have been largely unstudied with regards to mutations and cancer cell transformation. Our goal is to assess the changes in chromatin topology that occur in response to a single oncogenic mutation and how these changes may influence cancer cell transformation. Methods: Using AAV-mediated homologous recombination, a E545K “hotspot” PIK3CA mutation was incorporated into MCF10A breast epithelial cells and conversely, corrected back to wild-type in MCF7 breast cancer cells that natively harbor a E545K PIK3CA mutation. To interrogate the chromatin topology of these cell lines and the unmodified versions we will use a technique called tethered chromosome conformation capture (TCC). TCC maps chromatin topology by combining the proximity ligation of interacting DNA segments with next generation sequencing to create a matrix of interacting DNA elements. We can analyze and overlay these matrices to look for significant differences in topologically associating domains (TADs). Results: Preliminary results comparing MCF7 parental cells and MCF7 cells with the PIK3CA exon 9 mutation corrected suggest rearrangement of TADs at many key cancer-associated genes. One of these rearrangements is the formation of a de novo TAD on chromosome 10 near PTEN, a tumor suppressor gene that acts antagonistically to PIK3CA. Rearrangement of chromatin topology at this locus could lead to downregulation of a negative actor on this pathway further stimulating downstream elements of the PIK3CA pathway. Conclusions: Oncogenic mutations can cause changes that can have a drastic impact on transcription. Rearrangement of chromatin topology is a key mechanism by which the transcriptional program of a cell can be modified. Our experiments reveal key sites of chromatin rearrangement caused by a single oncogenic mutation that may promote a cancer phenotype in our cells. We plan to investigate the degree to which the expression of PTEN is altered by chromosomal rearrangements as well as perform CRISPR-KO of the interacting loci to determine the transcriptional effect of removing the loop. These assays will also be conducted for other sites of chromatin rearrangement. Results from these experiments will reveal the influence oncogenic mutations may have on chromatin topology and expression. Citation Format: Adam X. Miranda, Ben H. Park, Emily Hodges. Assessing the impact of PIK3CA mutation on the three-dimensional organization of chromatin [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-171.

Progress in the management of endometrial cancer (subtypes, immunotherapy, alterations in PIK3CA pathway): data and perspectives.

Changes in molecular classification together with a deeper knowledge of both immune disregulation and phosphatidylinositol-3 kinase (PI3K) pathway alterations are leading to a new endometrial cancer treatment paradigm. This review will address the cutting-edge data in this field. This article will cover the updated data in endometrial cancer molecular classification and its correlation with the outcomes in randomized clinical trials (e.g., PORTEC-3). Moreover, we will review the latest data regarding checkpoint blockade molecules (CPB) in the recurrent setting and how they are changing the treatment landscape. In addition, the role of the PI3K inhibitors, their activity, and toxicity profile will be described. As result of the incorporation of molecular classification in our daily practice, the adjuvant treatment in endometrial cancer is rapidly evolving and leading to a new paradigm. The promising data observed with CPB in the recurrent setting have led to the food and drug administration approval of pembrolizumab as monotherapy and in combination with lenvatinib. Additionally, the current outcomes achieved with PI3K inhibitor agents encourage us to continue our clinical research to identify those patients who may benefit the most.

Biomarker analysis from a phase I study using gedatolisib+palbociclib+hormone therapy in ER+/HER2- metastatic breast cancer (mBC).

1052 Background: Endocrine therapy with a CDK4/6 inhibitor (CDKi) is standard of care (SOC) for patients (pts) with estrogen-receptor-positive (ER+) metastatic breast cancer (mBC). Resistance to therapy may arise from mutations in ESR1, PIK3CA, and activation of receptor tyrosine kinase signaling pathways. In this study, gedatolisib (G), a PI3KCA/mTOR inhibitor, was added to a CDKi (palbociclib, P) + letrozole (L) or fulvestrant (F) for treatment of pts with ER+/HER2- mBC. Methods: This phase 1b study (NCT02684032) comprises a dose escalation phase evaluating the dose-limiting toxicity and maximum tolerated dose of G+P+L/F and a dose expansion phase assessing the objective response rate of G+P+L/F, compared with historical data for P+L or P+F. Response was assessed using RECIST v1.1. Genomic and transcriptomic analyses were performed on archival pt tumor biopsies. Longitudinal plasma ctDNA analysis was performed on samples taken at baseline, on-treatment, and end-of-treatment. Unsupervised data analysis was conducted. Results: Genomic information was available for 25 of 35 pts with measurable disease (G+P+L: 11; G+P+F: 14). No relationship was observed between responses (1 complete response [CR] and 11 partial responses [PR]) and baseline PIK3CA pathway alterations. Pt tumor tissue analysis (n = 25) confirmed pts with FGF3/4/19 amplification (n = 4) had larger changes in tumor size in response to G+P+L/F (p = 0.029). Of the 6 pts with an ESR1 mutation, 1 pt with an ESR1 Y537S mutation exhibited a partial response (PR) to G+P+L. Longitudinal plasma ctDNA analysis (73-gene panel) revealed that decreases in PIK3CA and PTEN were most associated with clinical response. Plasma sample analysis (n = 21) showed that pts with somatic alterations in EGFR (n = 4) had a greater response to therapy (p = 0.066), compared with pts without somatic EGFR alterations. Transcriptomic profiling also revealed responsive patients had higher levels of EGFR expression. Pts exhibiting CR/PR had a lower somatic tumor mutation burden at Cycle 5 Day 1 compared with baseline (p = 0.0013). Conclusions: The addition of G to SOC endocrine + CDKi therapy may help overcome resistance due to activation of FGFR or EGFR signaling pathways and the ESR1 Y537S mutation. Somatic frequency changes of PI3K pathway alterations were most correlated with clinical response. Genomic data analysis from dose expansion samples is currently ongoing. Clinical trial information: NCT02684032 .

Abstract OT2-01-04: Phase IB-II combination neoadjuvant chemotherapy with docetaxel plus atezolizumab plus herceptin SC and pertuzumab (TAHP) for patients with HER2-positive early breast cancer and subsequent atezolizumab plus herceptin SC and pertuzumab (AHP) adjuvant therapy after surgery (Neo-PATH)

Abstract Background Dual HER2-targeting with trastuzumab and pertuzumab combined with cytotoxic chemotherapy as neoadjuvant treatment increased rate of pathologic complete response to 50-65%. Subset of HER2-positive breast cancer has shown adaptive immune infiltrates which was correlated with better prognosis, including whom treated with dual anti-HER2 treatment. Immune checkpoint inhibitor including anti-PD-L1 modulate tumor microenvironment to restore tumor-induced or antibody-treatment induced immunosuppression. Here we investigate an efficacy of combining immunotherapy with anti-HER2 treatment as a neoadjuvant treatment in clinical stage II-III, HER2-positive breast cancer. Trial design This is a Phase Ib-II single arm study of six cycles of neoadjuvant docetaxel, atezolizumab, trastuzumab SC, and pertuzumab combination in patients with HER2-positive breast cancer. After 6 cycles of TAHP, surgery followed by 12 cycles of adjuvant atezolizumab, trastuzumab SC, and pertuzumab(AHP) will be performed. Patients without pCR will receive additional four cycles of doxorubicin and cyclophosphamide between surgery and adjuvant AHP. Eligibility criteria - Locally advanced, inflammatory, or early stage histologically confirmed invasive carcinoma of breast - HER2-positive breast cancer (immunohistochemistry score 3+, or HER2 SISH (or FISH, CISH) positive) - Primary tumor size&amp;gt;2cm or histologically or cytologically confirmed ipsilateral axillary lymph node metastases by fine needle aspiration (clinical stage IIA-IIIC by TNM 7th staging system) - ECOG Performance status 0-1 Specific aims Primary endpoint is a rate of pathologic complete response (pCR) after neoadjuvant docetaxel, atezolizumab, trastuzumab SC, and pertuzumab. Secondary endpoints are comparison of 3-year event free survival rate, disease free survival, and overall survival according to pCR achievement, toxicities, quality of life parameters, biomarker analyses (PD-L1 expression, immune signature, PIK3CA pathway, tumor mutation burden) for pCR and survival, multiomic profiling of tumor tissue using F1CDx. Statistical methods For sample size calculation, we used a Simon’s two-stage optimal design, with a 80 % power and 10% significance. The expected sample size is 60 to test the null hypothesis of pCR rate of ≤ 50% versus the alternative hypothesis of pCR rate of ≥ 65%. Stage 1: If pCR were observed in ≤ 12 patients among the first 23 patients, the alternative hypothesis will be rejected and the study will be discontinued Stage 2: If pCR were observed in ≥ 13 patients among the first 23 patients, additional 37 patients will be accrued (a total of 60 patients). If pCR were observed in &amp;gt; 34 patients, the null hypothesis will be rejected. Considering drop-out rate of 10%, we will accrue 67 patients. Our planned study duration is 42 months (patients accrual 6 months, follow up duration 36 months). Citation Format: Hee Kyung Ahn, Ji- Yeon Kim, Koung Jin Suh, Gun Min Kim, Sung Hoon Sim, Ki Hyeong Lee, Kyung Hae Jung, Seok- Ah Im, Yeon Hee Park. Phase IB-II combination neoadjuvant chemotherapy with docetaxel plus atezolizumab plus herceptin SC and pertuzumab (TAHP) for patients with HER2-positive early breast cancer and subsequent atezolizumab plus herceptin SC and pertuzumab (AHP) adjuvant therapy after surgery (Neo-PATH) [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr OT2-01-04.