PIK3CA Exon Research Articles

Non-small cell lung carcinoma with co-expression of TTF1 and p40: a clinicopathological analysis of six cases

Objective: To investigate the clinicopathological features, molecular pathology characteristics, and prognosis of non-small cell lung carcinoma (NSCLC) exhibiting co-expression of p40 and thyroid transcription factor1 (TTF1). Methods: Clinical and pathological data of six NSCLC cases with co-expression of p40 and TTF1 diagnosed at the First People's Hospital of Xiaoshan District, Hangzhou, China from January 2016 to December 2023 were collected. Relevant literature was also reviewed. Results: NSCLC with co-expression of p40 and TTF1 commonly occurred in male smokers and had been in stage Ⅲ-Ⅳ when diagnosis. Microscopic examination revealed that the tumor cells were arranged in solid nests and sheets with marked atypia and visible mitotic figures. There was no prominent evidence of keratinization or glandular formation. The tumor cells diffusely co-expressed p40 and TTF1, exhibiting a dual immunophenotype characteristic of both squamous cell carcinoma and adenocarcinoma. Molecular testing of four NSCLC co-expressing p40 and TTF1 revealed the presence of common EGFR mutations, as well as mutations of NRAS (mutation rate of 2.09%), EML4-ALK (mutation rate of 24.77%), and PIK3CA (exon 10 c.1658 G>C p.S553T, mutation rate of 4.32%). All six tumors were poorly differentiated, highly invasive, and associated with poor prognosis. Four of the six patients experienced widespread metastasis and died within 7 to 30 months after the diagnosis or initial treatment. Conclusions: NSCLC with co-expression of p40 and TTF1 exhibits distinct clinicopathological features, immunophenotypes, molecular alterations, and clinical outcomes, characterized by rapid progression and poor prognosis. Pathologists should be vigilant in recognizing this entity to avoid misdiagnosis and missed diagnosis.

High Probability of Lynch Syndrome Among Colorectal Cancer Patients Is Associated With Higher Occurrence of KRAS and PIK3CA Mutations.

In Indonesia, early-onset colorectal cancer (EOCRC) rates are higher in patients < 50 years old compared to Western populations, possibly due to a higher frequency of Lynch syndrome (LS) in CRC patients. We aimed to examine the association of KRAS and PIK3CA mutations with LS. In this retrospective cross-sectional single-center study, the PCR-HRM-based test was used for screening of microsatellite instability (MSI) mononucleotide markers (BAT25, BAT26, BCAT25, MYB, EWSR1), MLH1 promoter methylation, and oncogene mutations of BRAF (V600E), KRAS (exon 2 and 3), and PIK3CA (exon 9 and 20) in FFPE DNA samples. All the samples (n = 244) were from Dr. Sardjito General Hospital Yogyakarta, Indonesia. KRAS and PIK3CA mutations were found in 151/244 (61.88%) and 107/244 (43.85%) of samples, respectively. KRAS and PIK3CA mutations were significantly associated with MSI status in 32/42 (76.19%) and 25/42 (59.52%) of samples, respectively. KRAS mutation was significantly associated with LS status in 26/32 (81.25%) of samples. The PIK3CA mutation was present in a higher proportion in LS samples of 19/32 (59.38%), but not statistically significant. Clinicopathology showed that KRAS mutation was significantly associated with right-sided CRC and higher histology grade in 39/151 (25.83%) and 24/151 (16.44%) samples, respectively. PIK3CA mutation was significantly associated with female sex and lower levels of tumor-infiltrating lymphocytes in 62/107 (57.94%) and 26/107 (30.23%) samples, respectively. KRAS and PIK3CA mutations did not significantly affect overall survival (120 months) in LS and non-LS patients. The high probability of LS in Indonesian CRC patients is associated with KRAS and PIK3CA mutations.

An analysis of PIK3CA hotspot mutations and response to neoadjuvant therapy in breast cancer patients from four prospective clinical trials.

The PI3K signaling pathway is frequently dysregulated in breast cancer (BC), and mutations in PIK3CA, are relevant for therapy resistance in HER2pos BC. Mutations in exons 9 or exon 20 may have different impact on response to neoadjuvant chemotherapy-based treatment regimens. We investigated PIK3CA mutations in 1691 early BC patients, randomized in four neoadjuvant multicenter trials: GeparQuattro (NCT00288002), GeparQuinto (NCT00567554), GeparSixto (NCT01426880) and GeparSepto (NCT01583426). The role of different PIK3CA exons and hotspots for pathological complete response (pCR) after neoadjuvant chemotherapy (NACT) and patient survival was evaluated for distinct molecular subgroups and anti-HER2 treatment procedures. A total of 302 patients (17.9%) of the full cohort of 1691 patients had a tumor with a PIK3CA mutation, with a different prevalence in molecular subgroups: luminal/HER2neg 95 of 404 patients (23.5%), HER2pos 170 of 819 patients (20.8%) and TNBC 37 of 431 patients (7.9%). We identified mutations in PIK3CA exon 20 to be linked with worse response to anti-HER2 treatment (OR=0.507, 95%CI 0.320-0.802, p=0.004), especially in HR positive HER2 positive BC (OR=0.445, 95%CI 0.237-0.837, p=0.012). In contrast, exon 9 hotspot mutations p.E452K and p.E545K revealed no noteworthy differences in response therapy response. Luminal/HER2neg patients show a trend to have worse treatment response when PIK3CA was mutated. Interestingly, patients with residual disease after neoadjuvant treatment, have better survival when PIK3CA was mutated. PIK3CA hotspot mutation p.H1047R are associated with worse pCR rates after NACT in HER2pos BC, while hotspot mutations in exon 9 seems to have less impact.

Study of single live circulating tumor cells capture and their genomic profile and enriched mutations of PIK3CA and HRR pathway in patients with breast cancer.

e13161 Background: Capturing live single circulating tumor cells (sCTC) for intra-cellular compressive genomic profiling and concordance with ctDNA is highly challenging. Utilization of single sCTC genomics holds promise for detecting clinically relevant, actionable insights to tailor personalized therapy, especially when No Mutations Detected (NMDs) using CfDNA. Despite numerous studies providing valuable insights on mutational landscapes from breast tumors, predicting cancer progression, metastasis, and relapse continue to pose major challenges. ctDNA is suboptimal for 30-40% population with disease relapse/progression after a primary therapy. We show comprehensive genetic profile (CGP) of live sCTCs and paired ctDNA from a diverse breast cancer population. Methods: 26 live sCTCs (2 CTC clusters) were isolated from 12 patients. Live sCTCs were isolated from 12 Breast Cancer patients using OncoRadar live sCTC capture method. Whole genomes were amplified using multiple displacement amplification, target enriched with hybridization capture using OncoIndx (CGP 1080 gene panel) to obtain sequencing libraries, and sequenced on Illumina platform in paired end mode (depth 500x). The raw sequence alignment and variant calling was performed using iCare software. Paired ctDNA samples were processed the same way, except for sequencing depth (5500x). Results: Compared to paired ctNDA, genomic profiling of sCTCs revealed complex mutational patterns. Whereas sCTCs showed least two pathogenic (P) or likely pathogenic (LP) variants, paired ctDNA was negative for 25% cases (3/12). 92% sCTCs showed mutations in the PIK3CA-MTOR pathway with PIK3CA being the most prevalent (73 %). A significant association was observed between co-occurrence of HER2 amplification and PIK3CA mutations (P =0.04, OR=10). Similarly, sCTCs showed a strong correlation between HRR pathway and PIK3CA pathway mutations (r=0.76, P =0.003, OR=3.43). Genomic profile of sCTCs and paired ctDNA showed concordance with at least one gene mutation when compared at individual patient level. Additionally, at individual mutation level, PIK3CA exon 10 mutations were most frequent (61.5%) along with BRCA2 pathway variants, followed by IDH1/2(54%), ARID1A (50%), NRAS (46%), FGFR2 (42%) and TP53 (42%). Interestingly, 70% sCTCs showed the presence of therapy resistance conferring variants (NF1, ARID1A, ESR1, RB1 and PTEN), compared to only 25 % observed in paired ctDNA. Conclusions: The genomic profile of sCTCs represents true tumor heterogeneity and can be combined with ctDNA for better clinical outcome. sCTCs exhibited high mutational heterogeneity compared to paired ctDNA. Therapy resistance signatures were more prevalent in sCTCs and may offer valuable clinical insights for patients unable to provide tissue biopsy or show negative ctDNA.

The genomic landscape of patients with advanced colorectal adenocarcinoma with PIK3CA mutations using comprehensive cell free tumor DNA next generation sequencing.

181 Background: PIK3CA mutations ( PIK3CAm) are highly prevalent in advanced CRC but the prognostic value is unclear. PIK3CAm are associated with advanced stage disease, tumor aggressiveness, resistance to therapy, and a poorer prognosis. In some cases, PIK3CAm co-occur with other genetic alterations leading to complex signaling networks. Understanding these genetics are crucial to devise effective treatments. In this study, evaluated the genomic landscape of PIK3CAm in advanced CRC using cell free tumor DNA (ctDNA) next generation sequencing. Methods: This analysis assessed advanced CRC samples between 2020-2022 from the Guardant360 database using plasma-based ctDNA (~15000 patients, ~17000 samples). PIK3CAm were assessed by patient demographics, MSI-H status, TMB score, and frequency of co-occurring alterations via cbioportal. A sub analysis was collected between 2021-2022 (~8000 samples) to examine the frequency of PIK3CA exon 9 vs. 20 mutations between BRAF V600E and non- V600E BRAF mutations, and separately between KRAS G12C and G13D. Comparisons were analyzed by two-sided Fisher’s exact test. Results: PIK3CAm were detected in ~21% (~3500) of mCRC samples. Of these samples, the median age was 63 years old and the sex distribution was 56% males. MSI-H was reported in 3.3% of samples. PIK3CAm included 25% E545 (Exon 9), 13% E542 (Exon 9), 5% Q546 (Exon 9), and 10% H1047 (Exon 20). PIK3CAm had increased median alterations per sample to PIK3CA not detected (8 vs. 5) and a significant increase in co-occurrence with most genes in the panel. Relevant clinical co-occurrences were APC (73.7% vs. 57.4%), BRAF (19.9% vs. 13.0%), EGFR (34.7% vs. 24.9%), ERBB2 (9.2% vs. 6.0%), and KRAS (62.9% vs. 41.2%). Additionally, PIK3CAm samples had higher median TMB scores (13.4 vs. 9.8 mut/Mb), with &gt;25% of PIK3CAm reporting a TMB score above the 80th percentile (20.19 mut/Mb). In a sub analysis, there were significantly greater frequencies of PIK3CAm in exon 20 in BRAF V600E samples vs. non-V600E BRAFm samples (p=0.0003) with no significant differences in exon 9 or 20 mutations in KRAS G12C vs. G13D. Conclusions: Our study shows the frequency of PIK3CAm and distribution of exons 9 and 20 are similar to those found previously in the literature by Tan (Xie) et al., 2022. Our results demonstrate PIK3CA having a low frequency of MSI-H co-occurrence, higher TMB scores, and increased co-occurring alterations with notable increased in APC, BRAF, EGFR, ERBB2 and KRAS, which may suggest higher genomic instability. Our findings underscore the clinical significance of PIK3CAm in the context of CRC, emphasizing their role as key drivers of oncogenesis, and supports the development of tailored therapeutic strategies such as combining PIK3CAi with immunotherapy or other targeted therapies.

Prevalence of PIK3CA Mutation Based on Tumour Locations Among Colorectal Cancer Patients in Bali

Colorectal tumour location is important in determining therapeutic strategies because the location of the tumour will affect the histological and molecular characteristics of the cancer. Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) is a gene known to be associated with colorectal cancer location. The prevalence of PIK3CA mutations in colorectal cancer (CRC) ranges from 10-20%. Although the prevalence is small, this gene has a potential as a predictive and prognostic biomarker in the management of CRC. 80% of PIK3CA mutations occur in exon 9 (codon 542 and 545) and exon 20 (codon 1047). This study aimed to determine the prevalence of PIK3CA gene mutations based on tumour location among colorectal cancer patients in Bali, especially in Prof. dr. I G.N.G. Ngoerah Hospital, Denpasar, Bali. DNA was isolated from formalin-fixed-paraffin embedded (FFPE) blocks of colorectal cancer samples which were stored in the Department of Pathology of Prof. dr. I G.N.G. Ngoerah Hospital. Mutation was detected using polymerase chain reaction (PCR) and direct sequencing. Data on age, gender, and tumour location were recorded from patient medical records. Our findings on 31 colorectal cancer samples showed 26 samples (96.3%) were found with heterozygous mutation in exon 9 with AC genotype, but no mutation was found on exon 20. Based on tumor location, among 26 samples with mutation, 16 samples (61.5%) were left colorectal cancer and 10 samples (38.5%) were right colorectal cancer. Further studies are needed to identify the association of this mutation with colorectal cancer location and the other clinicopathological aspects of CRC. Keywords: Colorectal cancer, PIK3CA gene mutation, PIK3CA exon 9, PIK3CA exon 20, colorectal cancer location, left-sided colorectal cancer, right-sided colorectal cancer

Pathogenic alterations in PIK3CA and KMT2C are frequent and independent prognostic factors in anal squamous cell carcinoma treated with salvage abdominoperineal resection.

The management of anal squamous cell carcinoma (ASCC) has yet to experience the transformative impact of precision medicine. Conducting genomic analyses may uncover novel prognostic biomarkers and offer potential directions for the development of targeted therapies. To that end, we assessed the prognostic and theragnostic implications of pathogenic variants identified in 571 cancer-related genes from surgical samples collected from a homogeneous, multicentric French cohort of 158 ASCC patients who underwent abdominoperineal resection treatment. Alterations in PI3K/AKT/mTOR, chromatin remodeling, and Notch pathways were frequent in HPV-positive tumors, while HPV-negative tumors often harbored variants in cell cycle regulation and genome integrity maintenance genes (e.g., frequent TP53 and TERT promoter mutations). In patients with HPV-positive tumors, KMT2C and PIK3CA exon 9/20 pathogenic variants were associated with worse overall survival in multivariate analysis (Hazard ratio (HR)KMT2C = 2.54, 95%CI = [1.25,5.17], P value = .010; HRPIK3CA = 2.43, 95%CI = [1.3,4.56], P value = .006). Alterations with theragnostic value in another cancer type was detected in 43% of patients. These results suggest that PIK3CA and KMT2C pathogenic variants are independent prognostic factors in patients with ASCC with HPV-positive tumors treated by abdominoperineal resection. And, importantly, the high prevalence of alterations bearing potential theragnostic value strongly supports the use of genomic profiling to allow patient enrollment in precision medicine clinical trials.

Negative hyperselection of elderly patients with RAS and BRAF wild-type metastatic colorectal cancer receiving initial panitumumab plus FOLFOX or 5-FU/LV

BackgroundUpfront anti-EGFR therapy represents the standard of care for patients with left-sided, MSS/pMMR, RAS and BRAF wild-type mCRC. Molecular ‘hyperselection’ may optimize EGFR inhibition by detecting additional resistance alterations. Materials and methodsWe used comprehensive genomic profiling on archival samples of elderly patients enrolled in the PANDA trial to detect: HER2 amplification/mutations; MET amplification; NTRK/ROS1/ALK/RET rearrangements; PIK3CA exon 20 mutations; PTEN alterations; AKT1 mutations; MAP2K1 mutations. We defined ‘Gene Altered’ (GA) patients whose tumour harboured at least one alteration, and ‘Hyperselected’ (HS) those without. Survival and tumour response outcomes were correlated to hyperselection status alone or combined with primary tumour sidedness or treatment arm. ResultsGenomic alterations were detected in 41/147 patients (27.9%). PFS, OS and ORR were inferior in GA versus HS (median PFS: 7.6 versus 12.8 months, HR = 2.08, 95% CI: 1.43–3.03, p < 0.001; median OS: 20.0 versus 29.5 months, HR = 1.82, 95% CI:1.23–2.69, p = 0.002; ORR: 51% versus 71%; OR = 0.43, 95% CI: 0.21–0.91, p = 0.02). In the multivariable models, the impact of hyperselection on PFS and OS was confirmed. Lower ORR was observed with 5-FU/LV/panitumumab in GA (40% versus 62%), but not in HS (70% versus 72%). GA was associated with worse survival and response regardless of primary tumour sidedness, whereas in the HS subgroup, right-and left sided tumours had similar outcomes. ConclusionsMolecular hyperselection and comprehensive genomic profiling have a potential usefulness in elderly patients with RAS/BRAF wild-type, pMMR/MSS mCRC, eligible for upfront EGFR inhibition.

PIK3CA mutations in breast cancer: A Tunisian series.

The aim of this study was to analyze PIK3CA mutations in exons 9 and 20 in breast cancers (BCs) and their association with clinicopathological characteristics. Mutational analysis of PIK3CA exon 9 and 20 was performed by Sanger sequencing in 54 primary BCs of Tunisian women. The associations of PIK3CA mutations with clinicopathological characteristics were analyzed. Fifteen exon 9 and exon 20 PIK3CA variants were identified in 33/54 cases (61%). PIK3CA mutations including pathogenic (class 5/Tier I) or likely pathogenic (class 4/Tier II) occurred in 24/54 cases (44%): 17/24 cases (71%) in exon 9, 5/24 cases (21%) in exon 20 and 2/24 cases (8%) in both exons. Of these 24 cases, 18 (75%) carried at least one of the three hot spot mutations: E545K (in 8 cases), H1047R (in 4 cases), E542K (in 3 cases), E545K/E542K (in one case), E545K/H1047R (in one case) and P539R/H1047R (in one case). Pathogenic PIK3CA mutations were associated with negative lymph node status (p = 0.027). Age distribution, histological SBR tumor grading, estrogen and progesterone receptors, human epidermal growth factor receptor 2, and molecular classification were not correlated with PIK3CA mutations (p > 0.05). The frequency of somatic PIK3CA mutations in BCs of Tunisian women is slightly higher than that of BCs of Caucasian women and more observed in exon 9 than in exon 20. PIK3CA mutated status is associated with negative lymph node status. These data need to be confirmed in larger series.

Giant juvenile fibroadenomas with and without prominentpseudoangiomatous stromal hyperplasia (PASH)-like change: clinicopathological and molecular characteristics.

Juvenile fibroadenomas (JFA) are biphasic fibroepithelial lesions (FEL) usually occurring in adolescent female patients. Giant (G) JFA, like other FEL, may exhibit prominent pseudoangiomatous stromal hyperplasia (PASH)-like change. We sought to determine clinicopathological and molecular characteristics of GJFA with and without PASH. Archives were searched for cases of GJFA (1985-2020). All were stained for androgen receptor (AR), beta-catenin, CD34 and progesterone receptor (PR). Cases were sequenced using a custom 16-gene panel - MED12 (exons 1 and 2), TERT promoter (-124C>T and -146Ctable>T), SETD2, KMT2D, RARA (exons 5-9), FLNA, NF1, PIK3CA (exons 10, 11 and 21), EGFR, RB1, BCOR, TP53, PTEN, ERBB4, IGF1R and MAP3K1. Twenty-seven GJFA from 21 female patients aged 10.1-25.2 years were identified. Size ranged from 5.2 to 21 cm. Two patients had multiple, bilateral and later recurrent GJFA. Thirteen (48%) cases showed prominent PASH-like stroma. All were positive for stromal CD34, negative for AR and beta-catenin and one case showed focal PR expression. Sequencing showed MAP3K1 and SETD2 mutations in 17 samples, with KMT2D, TP53 and BCOR aberrations in 10 (45%), 10 (45%) and seven (32%) cases, respectively. Tumours with a PASH-like pattern had higher prevalence of SETD2 (P = 0.004) and TP53 (P = 0.029) mutations, while those without PASH had more RB1 mutations (P = 0.043). MED12 mutation was identified in one case. TERT promoter mutation was observed in four (18%), including two recurrences. Gene mutations along more advanced phases of the proposed FEL pathogenetic pathway in GJFA are unusual, and suggest a mechanism for more aggressive growth in these tumours.

The impact of PIK3CA mutations and PTEN expression on the effect of neoadjuvant therapy for postmenopausal luminal breast cancer patients

BackgroundThere is pressing needs to find the biomarker in the selection of neoadjuvant therapy in postmenopausal luminal breast cancer patients. We examined the hypothesis that PIK3CA mutations and low phosphatase and tensin homolog (PTEN) expression affect the response to neoadjuvant therapy and prognosis in postmenopausal luminal breast cancer patients.MethodsPostmenopausal patients with estrogen receptor-positive, human epidermal growth factor receptor 2-negative breast cancer, up to stage II, who underwent neoadjuvant chemotherapy (NAC; n = 60) or neoadjuvant endocrine therapy (NAE; n = 55) were selected. PIK3CA exon 9 and exon 20 mutations were screened by high resolution melting analysis and confirmed by Sanger sequence. PTEN expression was evaluated by immunohistochemistry. The relationships among PIK3CA mutations, PTEN expression, clinicopathological features, the pathological effect of neoadjuvant therapy, recurrence-free survival (RFS) and overall survival were analyzed.ResultsAmong 115 patients, PIK3CA mutations and low PTEN expression before treatment were detected in 35 patients (30.4%) and in 28 patients (24.3%), respectively. In the NAC group, tumor with PIK3CA mutations showed significantly poorer response than tumor with PIK3CA wild-type (p = 0.03). On the other hand, in the NAE group, there was no significant difference in pathological therapeutic effect between tumor with PIK3CA mutations and tumor with PIK3CA wild-type (p = 0.54). In the NAC group, the log-rank test showed no difference in RFS between patients with PIK3CA mutations and PIK3CA wild-type (p = 0.43), but patients with low PTEN expression showed significantly worse RFS compared to patients with high PTEN expression (5 year RFS 0.64 vs. 0.87, p = 0.01). In the Cox proportional hazards model for RFS, PTEN expression, progesterone receptor, and pathological therapeutic effect were predictive factors for time to recurrence (All p < 0.05).ConclusionsPIK3CA mutations are associated with resistance to NAC but do not affect the response to NAE. Low PTEN expression does not affect response to either NAC or NAE but correlates with shorter RFS in patients who received NAC. These biomarkers will be further evaluated for clinical use to treat postmenopausal luminal breast cancer patients.

PIK3CA mutations and their impact on survival outcomes of patients with endometrial cancer: A systematic review and meta-analysis.

Several studies have highlighted the frequent alterations of the PI3K pathway in endometrial cancer leading to increased signaling activation with potential for targeted treatment. The objective of this meta-study was to evaluate how PIK3CA exon 9/20 mutations affect survival in endometrial cancer patients, based on available literature. Topic-based search strategies were applied to databases including CENTRAL, MEDLINE, Embase, Web of Science and COSMIC. All studies assessing the impact of mutations in exon 9 and exon 20 of PIK3CA on survival rates of endometrial cancer patients were selected for inclusion. Statistical meta-analysis was performed with the 'meta' package in RStudio. Overall, 7 of 612 screened articles were included in the present study, comprising 1098 women with endometrial cancer. Meta-analysis revealed a tendency of impaired survival for patients with PIK3CA exon 9 and/or exon 20 mutations (RR 1.28; 95% CI 0.84, 1.94; p = 0.25). This tendency was consistent in subgroup analyses stratified by histologic type or -grade, with the most prominent effect in low-grade endometrial cancers (RR 2.04; 95% CI 0.90, 4.62; p = 0.09). In summary, these results suggest that PIK3CA mutations negatively influence survival outcomes of patients with endometrial cancer, including those with low-grade tumors.

Paired Comparison of Routine Molecular Screening of Patient Samples with Advanced Non-Small Cell Lung Cancer in Circulating Cell-Free DNA Using Three Targeted Assays.

Progressive advanced non-small cell lung cancer (NSCLC) accounts for about 80-85% of all lung cancers. Approximately 10-50% of patients with NSCLC harbor targetable activating mutations, such as in-frame deletions in Exon 19 (Ex19del) of EGFR. Currently, for patients with advanced NSCLC, testing for sensitizing mutations in EGFR is mandatory prior to the administration of tyrosine kinase inhibitors. Plasma was collected from patients with NSCLC. We carried out targeted NGS using the Plasma-SeqSensei™ SOLID CANCER IVD kit on cfDNA (circulating free DNA). Clinical concordance for plasma detection of known oncogenic drivers was reported. In a subset of cases, validation was carried out using an orthogonal OncoBEAMTM EGFR V2 assay, as well as with our custom validated NGS assay. Somatic alterations were filtered, removing somatic mutations attributable to clonal hematopoiesis for our custom validated NGS assay. In the plasma samples, driver targetable mutations were studied, with a mutant allele frequency (MAF) ranging from 0.00% (negative detection) to 82.25%, using the targeted next-generation sequencing Plasma-SeqSensei™ SOLID CANCER IVD Kit. In comparison with the OncoBEAMTM EGFR V2 kit, the EGFR concordance is 89.16% (based on the common genomic regions). The sensitivity and specificity rates based on the genomic regions (EGFR exons 18, 19, 20, and 21) were 84.62% and 94.67%. Furthermore, the observed clinical genomic discordances were present in 25% of the samples: 5% in those linked to the lower of coverage of the OncoBEAMTM EGFR V2 kit, 7% in those induced by the sensitivity limit on the EGFR with the Plasma-SeqSensei™ SOLID CANCER IVD Kit, and 13% in the samples linked to the larger KRAS, PIK3CA, BRAF coverage of the Plasma-SeqSensei™ SOLID CANCER IVD kit. Most of these somatic alterations were cross validated in our orthogonal custom validated NGS assay, used in the routine management of patients. The concordance is 82.19% in the common genomic regions (EGFR exons 18, 19, 20, 21; KRAS exons 2, 3, 4; BRAF exons 11, 15; and PIK3CA exons 10, 21). The sensitivity and specificity rates were 89.38% and 76.12%, respectively. The 32% of genomic discordances were composed of 5% caused by the limit of coverage of the Plasma-SeqSensei™ SOLID CANCER IVD kit, 11% induced by the sensitivity limit of our custom validated NGS assay, and 16% linked to the additional oncodriver analysis, which is only covered by our custom validated NGS assay. The Plasma-SeqSensei™ SOLID CANCER IVD kit resulted in de novo detection of targetable oncogenic drivers and resistance alterations, with a high sensitivity and accuracy for low and high cfDNA inputs. Thus, this assay is a sensitive, robust, and accurate test.

KRAS, NRAS, BRAF, and PIK3CA mutation rates, clinicopathological association, and their prognostic value in Iranian colorectal cancer patients

Mutations in KRAS, NRAS, BRAF, and PIK3CA genes are critical factors in clinical evaluation of colorectal cancer (CRC) development and progression. In Iran, however, the data regarding genetic profile of CRC patients is limited except for KRAS exon2 and BRAF V600F mutations. This study aimed to investigate the mutational spectrum and prognostic effects of these genes and explore the relationship between these mutations and clinicopathological features of CRC. To achieve these objectives, mutations in KRAS (exons 2, 3, and 4), NRAS (exons 2, 3, and 4), PIK3CA (exons 9 and 20), and BRAF (exon 15) was determined using PCR and pyrosequencing in a total of 151 patients with colorectal cancer. KRAS, BRAF, NRAS, and PIK3CA mutations were identified in 41%, 5.96%, 3.97%, and 13.24% of the cases, respectively. There were some significant correlations between clinicopathological features and KRAS, PIK3CA, BRAF, and NRAS mutations. Mutations in KRAS and PIK3CA were shown to be independent risk factors for poor survival of the patients at stage I-IV (p <0.0001 and p =0.001, respectively). No significant impact on prognosis was observed in patients with BRAF mutations. Our study revealed the prevalence of CRC biomarkers mutations in Iranian patients and emphasized the role of KRAS and PIK3CA on shorter overall survival rates in this population.

KRAS, NRAS, BRAF, PIK3CA, and AKT1 signatures in colorectal cancer patients in south-eastern Romania.

Somatic mutations in the oncogenes of the epidermal growth factor receptor signaling pathway play vital roles in colorectal carcinogenesis and have been closely linked with clinical resistance to monoclonal therapy. In this study, we have analyzed the mutation frequencies of 5 genes and compared the genetic findings with clinicopathological variables in order to determine diagnostically relevant alterations and compare these findings with those of other studies In our Sanger sequencings, KRAS (exons 2, 3, and 4), NRAS (exons 2, 3, and 4), PIK3CA (exons 9 and 20), BRAF (exon 15), AKT1 (exon 2) genes, and microsatellite instability (MSI) status were analyzed using an ABI 3500 analyzer in a cohort of 58 Romanian colorectal cancer (CRC) patients who underwent surgical resection at Emergency County Clinical Hospital in Constanța, Romania. In our series, mutation rates of KRAS, BRAF, PIK3CA, and AKT1 genes were 39.63%, 8.62%, 6.88%, and 3.44%, respectively. By contrast, we did not find any tumor harboring mutation in the NRAS gene. Notably, the KRAS and PIK3CA mutations were not mutually exclusive, 1 patient harbored 2 mutations in exon2, codon 12 (Gly12Val) of KRAS and exon 20, codon 1047 (His1047Arg) of PIK3CA. The finding of our study are generally consistent with data found in the literature. Regarding to clinicopathological variables, mutation of KRAS was associated with distant metastasis at the time of diagnosis, while mutation of BRAF was significantly associated with MSI-H in contrast with MSI-L/MSS tumors. Moreover, PIK3CA mutation tends to be located in the proximal segment of the colon and to be well/moderately differentiated compared to wild-type tumors. In conclusion, the assessment of these mutations suggests that CRC patients from southeast Romania exhibit a mutation profile similar to other populations. These results could contribute to creating a better method of qualifying patients for molecularly targeted therapies and obtaining better screening strategies.

Abstract 1239: Prognostic and predictive value of PIK3CA mutations in metastatic CRC (mCRC)

Abstract Background: Molecular aberrations including MSI, RAS, RAF, and HER2 have been used to guide the management of mCRC. However, the role of PIK3CA mutations is unclear in mCRC. In this study, we aimed to determine the prognostic value of PIK3CA mutations and their predictive value of response to anti-EGFR therapy in mCRC patients (pts). Methods: Pts with mCRC and clinical next generation sequencing were identified from the Clinical Genomics Action Committee database at Moffitt Cancer Center. Clinical and molecular aberration data were retrospectively collected. Progression-free survival (PFS) was the time from treatment initiation to clinical or radiographic disease progression. Overall survival (OS) was the time from diagnosis of metastatic disease to death. Kaplan Meier method and log-rank test were used for survival analysis. A parametric exponential model was implemented for PIK3CA exon analysis to account for small sample size. Pearson correlation coefficient was determined for correlation between PIK3CA and co-mutations. An additional meta-analysis was performed including prior studies of pts with KRAS wild-type (wt) PIK3CA mutant (mut) mCRC receiving anti-EGFR therapy using random effects model. Results: Among 639 pts with mCRC, PIK3CA mutation was positively correlated with KRAS mutation (r=0.11, p=0.006) and negatively correlated with TP53 mutation (r=-0.18, p=&amp;lt;0.001). It was not correlated with BRAF or APC mutations. Among 335 pts with KRAS wt mCRC, 174 were PIK3CA wt without anti-EGFR therapy; 111 were PIK3CA wt with anti-EGFR therapy; 33 were PIK3CA mut without anti-EGFR therapy; and 16 were PIK3CA mut with anti-EGFR therapy. Median OS of PIK3CA mut pts was 35.5 months, significantly shorter (HR 2.0, 95%CI 1.2-3.1) that median OS of 55.3 months in PIK3CA wt mCRC pts. The same was observed in pts (n=10) with PIK3CA exon 20 mutation (mOS: 18.5 months, HR 2.6, 95%CI 1.1-6.0) and pts (n=18) with PIK3CA exon 9 mutation (mOS: 38 months, HR 2.15, 95%CI 1.1-4.3). Among 166 pts evaluable for response rate, 44% PIK3CA wt pts responded to anti-EGFR therapy compared to 56% PIK3CA mut pts (p=0.51). Median PFS between PIK3CA mut and PIK3CA wt pts receiving anti-EGFR therapy was 10.3 versus 7.2 months (p=0.6), respectively. Our study and previously published 12 studies from 2005 to 2015 were examined in a meta-analysis where the included studies lacked significant heterogeneity (I2=0%, p=0.6). Among 1047 pts with KRAS wt mCRC who received anti-EGFR therapy, 104 of them were PIK3CA mut. The estimated risk ratio for response to anti-EGFR therapy was 0.77 (95%CI 0.5-1.1) with prediction interval between 0.4 and 1.6. Conclusion: PIK3CA mutation has positive correlation with KRAS mutation and negative correlation with TP53 mutation in mCRC. PIK3CA mutation confers a worse prognosis but is not predictive for response to anti-EGFR therapy in pts with KRAS wt mCRC. The latter finding was confirmed in an updated meta-analysis of 13 studies including ours. Citation Format: Elaine Tan, Wenyi Fan, Michael Schell, Ibrahim Sahin, Jason Fleming, Todd Knepper, Hao Xie. Prognostic and predictive value of PIK3CA mutations in metastatic CRC (mCRC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1239.

Abstract 1269: Negative ultra-selection of patients with RAS/BRAF wild-type (wt), microsatellite stable (MSS) metastatic colorectal cancer (mCRC) receiving anti-EGFR-based therapy: The PRESSING2 study

Abstract Background: Several genomic alterations beyond RAS and BRAFV600E mutations have been preclinically validated as primary resistance drivers to EGFR inhibition in mCRC. We showed that our PRESSING panel (including PIK3CA exon 20/AKT1/PTEN mutations, ERBB2/MET amplification and ALK/ROS1/RET/NTRKs fusions) is useful to promote a new paradigm of negative hyper-selection, since patients with RAS/BRAF wt MSS mCRC and PRESSING alterations achieve significantly worse survival upon anti-EGFRs. With the aim of further refining molecular selection (negative ultra-selection), we investigated the clinical impact of candidate resistance alterations with even lower frequency (PRESSING2 panel) in a cohort of hyper-selected patients. Methods: A prospective dataset was developed at 3 Italian Academic Hospitals and included 650 mCRC patients with comprehensive genomic profiling of FFPE tumor tissue by means of FoundationOne CDx. We selected those with RAS/BRAF wt, MSS and PRESSING negative treated with anti-EGFRs. Alterations of the PRESSING2 panel were selected based on their actionability and biological value, as follows: ALK, ROS1, NTRKs, ERBB2/3/4, NF1, ARAF, MAP2K1 pathogenic mutations, PTEN loss, KRAS and AKT1-2 amplification, FGFR2 amplification/fusions, EGFR fusions. PRESSING2 status was correlated with progression-free survival (PFS) and overall survival (OS). Results: 163 molecularly hyper-selected patients with PRESSING negative status were identified; 30 (18%) had PRESSING2 alterations, which were mutually exclusive in 26 (87%) samples. No significant differences in baseline clinical and pathological characteristics - including sidedness - were found in PRESSING2 positive vs negative patients. The median follow-up was 34.6 months (IQR 23.5-49.3). Patients with PRESSING2 positive status had significantly worse PFS and OS vs those with PRESSING2 negative disease (median PFS 7.0 and 13.0 months; HR 3.54, 95%CI 2.26-5.52, P&amp;lt;0.001; median OS 24.5 and 51.2 months; HR 2.91, 95%CI 1.64-5.18, P&amp;lt;0.001). In the multivariable model, the adjusted HRs were 3.40 for PFS and 2.71 for OS, respectively. 121 (74%) patients received an anti-EGFR agent upfront. In this first-line cohort, median PFS were 8.1 vs 13.2 months for PRESSING2 positive and negative subgroups (HR 3.24, 95%CI 1.89-5.57; P&amp;lt;0.001; adjusted HR 2.96), whereas median OS were 26.2 vs 49.9 months, respectively (HR 2.28, 95%CI 1.15-4.54, P=0.018; adjusted HR 2.34). Conclusions: In the era of comprehensive genomic profiling, several resistance alterations with extremely low prevalence may be detected, especially in CRCs that do not bear other genomic drivers. Negative ultra-selection may represent a relevant step forward in precision medicine in patients with RAS/BRAF wt MSS mCRC potentially eligible for EGFR blockade. Citation Format: Giovanni Randon, Giulia Maddalena, Marco Maria Germani, Filippo Pagani, Francesca Bergamo, Mirella Giordano, Chiara Pircher, Caterina Sposetti, Luca Zambelli, Francesca Corti, Marta Bini, Alessandro Rametta, Andrea Spagnoletti, Aldo Montagna, Matteo Fassan, Alessandra Boccaccino, Guglielmo Vetere, Silvia Damian, Massimo Milione, Filippo de Braud, Chiara Cremolini, Sara Lonardi, Filippo Pietrantonio. Negative ultra-selection of patients with RAS/BRAF wild-type (wt), microsatellite stable (MSS) metastatic colorectal cancer (mCRC) receiving anti-EGFR-based therapy: The PRESSING2 study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1269.

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.

Single center experience with alpelisib-fulvestrant in heavily pretreated women with HR(+), HER-2 (−) metastatic breast cancer.

e13034 Background: HR-positive, Her2-negative metastatic breast cancer patients harboring PIK3CA mutations are associated with resistance to endocrine therapy and worse prognosis. Results from the phase III SOLAR-1 trial demonstrate improved PFS for patients treated with Alpelisib-Fulvestrant after failure on first or second line treatment with aromatase inhibitor. Methods: Within an early access program for Alpelisib in a single oncology center, patients diagnosed with metastatic HR-positive, Her2 -negative breast cancer were screened for PIK3CA mutations. New generation sequencing (NGS) was the preferred technique to identify carriers with PIK3CA mutations on soft tissue or liquid biopsy. Patients who progressed and carried PIK3CA mutations received Alpelisib and fulvestrant as subsequent line of therapy. Results: Among 32 patients (pts) screened, 13 (40,6%) had a PIK3CA mutation. In total, 11 pts received alpelisib. Median age at diagnosis was 57.5 years (range, 39-69). Eight pts (72.7%) had been operated for early-stage breast cancer, 6 (54.5%) had received adjuvant chemotherapy and 5 (45.5%) had received adjuvant radiotherapy. Of 11 pts with evaluable histology, 3 pts (27.3%) had high grade tumors at diagnosis. Ten pts (90.9%) had PR positive tumors. Median Ki67 was 20% (range, 2-80). Eight pts (72.7%) had PIK3CA exon 20 and 3 (27.3%) had exon 9 mutations. Six pts (54.5%) had received prior chemotherapy in the metastatic setting and 10 (90.9%) prior CDK4/6 inhibitor. Three pts (27.3%) received Alpelisib as 2nd line and all remaining patients received alpelisib beyond 3rd line treatment. All pts (100%) had metastasis to the bones, 8 pts (72.7%) to the liver, 6 pts (54.5%) to the lungs and 2 pts (18.2%) to the brain. Until the date of last assessment, Alpelisib was administered for a median of 5.1 months (range, 0.4-21.3). Ten pts were evaluable for response to treatment with Alpelisib. One (10%) had CR, 5 (50%) SD and 4 (40%) PD as best response. Median duration of disease control was not reached. Baseline characteristics were not associated with disease control. Adverse events noticed were thrombocytopenia grade II (1/11), diarrhea grade II (2/11), skin rash grade I &amp;II (4/11), weakness grade III (1/11) and hyperglycemia (3/11). Conclusions: Prevalence of PIK3CA mutations is consistent with published data. Furthermore, combination of Alpelisib-Fulvestrant is a highly active line of therapy even in heavily pretreated patients.

P-291 PIK3CA mutations in Tunisian patients with metastatic colorectal cancer: Patient stratification for targeted therapies

The PI3K signaling pathway plays a key role in the pathogenesis of many cancer types, including colorectal cancer. The PI3K signaling pathway is deregulated due to the amplification, genetic mutation of PIK3CA gene or one component of the PI3K pathway themselves. Mutations in PIK3CA exons 10 and/or 21 are present in 10-20% of colorectal cancers and are associated with other molecular alterations, including RAS mutations. Tumors harboring mutations in PI3K pathway may be less susceptible to treatment using anti-EGFR antibodies and to other targeted therapies.