Oncogenesis in cholangiocarcinoma.

Early detection and treatment of ovarian cancer: shifting from early stage to minimal volume of disease based on a new model of carcinogenesis

4E-BP1 Is a Key Effector of the Oncogenic Activation of the AKT and ERK Signaling Pathways that Integrates Their Function in Tumors

Molecular Biomarkers in the Personalized Treatment of Colorectal Cancer.

e14085 Background: The paraffin-embedded tumor samples of 183 Chinese patients (pts) with metastatic colorectal cancer (mCRC) who had chemotherapy (chemo) over a period of 3.3 years were analyzed for the presence of KRAS, PIK3CA and BRAF mutations. Methods: PCR-direct sequencing was performed in micro-dissected tumor cells. The relationship between mutation and survival was evaluated using the Proportional Hazard Model, and relationship with drug response was evaluated with logistic regression. Multivariate analysis was used to adjust for the influence of age, sex, prior lines of chemo, use of bevacizumab (Bev) and the number of sites of metastases. Results: The median age was 58 yrs, over 50% of pts had > 2 lines of chemo and 50% had cetuximab. The prevalence of KRAS, BRAF and PI3KCA mutations were: 55%, 5%, 20% respectively. The prevalence of each KRAS mutation subtype was: G12D (36%), G12V (22%) and G13D (16%). KRAS mutation and prior use of Bev were independent prognostic factors with respective hazard ratios (HR) of 1.5 (95% CI = 1.05-2.16, p = 0.03) and 0.51 (95% CI = 0.3-0.87, p = 0.01). In the subgroup of patients who received cetuximab and chemotherapy in the first-line setting, KRAS mutation was associated with a lack of response to chemo with odd ratio (OR) of 0.1 (95% CI = 0.01-0.79, p=0.03). There was no correlation between the presence of BRAF and/ or PIK3CA mutations and OS or drug response. Five pts had co-expression of KRAS and PIK3CA mutations and none of them responded to cetuximab. Of the 14 pts who had complete response or prolonged disease stabilization to cetuximab-chemo, 4 had KRAS mutation, 1 had PIK3CA mutation and none had BRAF mutations. Conclusions: The prevalence of KRAS, BRAF and PIK3CA mutations reported in this Chinese cohort is consistent with reports from other non-Asian populations. KRAS mutation is an independent negative prognostic factor in chemo-treated pts with mCRC. KRAS mutation was associated with poorer response to 1st line cetuximab-based chemo.

The prognostic significance of KRAS, NRAS, PIK3CA and BRAF mutations was evaluated in Chinese patients with metastatic colorectal cancer (CRC). Tumor samples from 183 patients were retrospectively tested for KRAS, NRAS, PIK3CA and BRAF mutations. Multivariate analysis was performed to determine the relationship between mutational status, drug response and survival. Over 70% of patients received two or more lines of chemotherapy, 50% had cetuximab and 18% had bevacizumab. The prevalence of KRAS, NRAS, BRAF and PIK3CA mutations was 45, 3.2, 5 and 20%, respectively. For the entire cohort, the median overall survival was 24 months (95% confidence interval [CI] = 20.4-26.4 months). Of the genes tested, only KRAS mutation was an independent prognostic factor with a multivariate hazard ratio of 1.5 (95% CI = 1.05-2.16, P = 0.03). In the subgroup of patients who received cetuximab-based therapy in the first-line setting, KRAS mutation was associated with a lack of response to chemotherapy (28% vs 66%, chi-square, P = 0.01). Patients with KRAS mutant tumors (or KRAS wild-type tumors that harbored BRAF and/or PIK3CA mutations) tended to have lower response rates to chemotherapy and/or cetuximab (P = not significant). The number of NRAS mutant cases was too small to allow any statistical analysis. The prevalence of KRAS, NRAS, BRAF and PIK3CA mutations in this cohort is consistent with reports from non-Asian populations, and KRAS mutation has both prognostic and predictive significance in Chinese patients with metastatic CRC.

Colorectal cancer (CRC) emerged due to genetic mutations that fuel tumor development and influence patient outcomes. This research investigates KRAS, BRAF, and PIK3CA mutations in Iraqi Kurdish patients to assess their biological relevance and impact on clinical outcomes. Clinical and pathological data were collected from 150 patients’ medical profiles. DNA was extracted from FFPE samples for KRAS, BRAF, and PIK3CA mutation analysis. Variations in KRAS and BRAF 600/601 were identified by polymerase chain reaction (PCR) amplification followed by hybridization assays. Real-time PCR was utilized to detect PIK3CA mutations. Tumors were predominantly located in the colon (80%) and classified as adenocarcinomas (88%), with stage III being the most frequent (36%). Metastases were observed in 72.67% of cases, primarily in the liver (46.67%). KRAS mutations were identified in 37.33% of cases (mainly in codons 12 and 13), while BRAF V600E mutations occurred in 10.67%, and PIK3CA mutations were detected in 18.67%, with exon 9 alterations more common than those in exon 20. KRAS mutations were strongly associated with liver metastases (p=0.006), and BRAF mutations correlated with peritoneal metastases (p=0.0001). Co-mutations of KRAS and PIK3CA appeared in 7.33% of cases, while BRAF and PIK3CA co-mutations were rarer (1.3%). Our study underscores the complexity of CRC and the pivotal role of KRAS, BRAF, and PIK3CA variations in tumor progression and outcomes in Iraq's Kurdistan Region, highlighting the importance of molecular profiling in clinical care.

BackgroundWe identified somatic PIK3CA mutations in 32.5% of 590 primary invasive breast cancers (BC) (manuscript in press: Clinical Cancer Research). Detected by massARRAY genotyping, PIK3CA mutations significantly associate with favorable clinicopathologic features and improved clinical outcome, including overall and breast cancer-specific survival. Given the strong association between PIK3CA mutations and hormone receptor (HR) positivity, one hypothesis is that PIK3CA mutations 'drive' HR positive BC and will be detected in pre-invasive breast tumors. As PIK3CA mutations offer a protective effect in BC, it has not been determined whether PIK3CA mutations are selected for in disease progression or whether additional collaborating mutations are required.MethodsTo determine the concordance of PIK3CA mutations and assess the acquisition of additional oncogene mutations, available matched tissue samples, from the previous database, were procured and underwent massARRAY genotyping (n = 83). Two mm cores were macro-dissected from matched formalin-fixed, paraffin embedded tissue, including normal breast tissue, benign lymph nodes (LN), ductal carcinoma-in-situ (DCIS), regional LN metastases (mets), and distant mets. MassARRAY (Sequenom) genotyping was performed on native DNA to identify rare and hotspot PIK3CA mutations, as well as AKT1 (E17K), RAS, and RET mutations.ResultsConcordance of PIK3CA mutations is noted between primary BC and DCIS, except for one rare PIK3CA mutation (Q546R) not detected in DCIS (4/5). No PIK3CA mutations are detected in normal breast tissue (0/8) or benign LN (0/6). Rare and hotspot PIK3CA mutations in primary BC are detected in 87.5% (7/8) matched regional LN met and 80 % (4/5) distant mets. For the patient with the disconcordant regional LN met, the rare PIK3CA mutation (H1047L) identified in primary BC is also present in the distant met site. Notably, for the single disconcordant PIK3CA met site, a rare PIK3CA mutation (E545A) is detected in a primary tumor, regional LN met, and bone met and is absent in a second bone met, in which a KRAS (G12C) mutation has been identified. One concomitant hotspot PIK3CA (E542K)/KRAS (G12C) mutation is present in both primary BC and paired DCIS. Complete concordance of AKT1 (E17K) mutations has been identified between in DCIS, primary BC, regional LN met, and distant mets (n=4).ConclusionsWe recently defined the positive prognostic significance of PIK3CA mutations in breast cancer. PIK3CA and AKT1 (E17K) mutations are early events in breast cancer, occurring in pre-invasive tumors. Despite the protective effect of PIK3CA mutations on clinical outcome, they persist and are selected for in disease progression, as they are detected in regional LN and distant mets. Complete concordance is identified between hotspot PIK3CA mutated primary BC and matched tumors samples, suggesting that PIK3CA mutations with higher oncogenic potency are maintained in tumor progression. These findings support that targeting the PI3K pathway may assist in tailoring therapy to appropriate patient populations. We are expanding matched tissue collection from a separate patient cohort to further assess genomic and functional genomic change with disease progression. Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 5164.

In endometrial carcinomas (ECs), previous report suggested that PIK3CA mutations do not coexist with KRAS mutations, but the significant mutual exclusiveness has not been demonstrated. In this study, we examined the mutation frequency of PIK3CA in EC and its mutual exclusiveness with KRAS mutation. We performed mutational analysis of PIK3CA through a polymerase chain reaction single-strand conformation polymorphism assay in 44 cases of endometrial cancer and analyzed the correlation with loss of PTEN, KRAS mutation, and RASSF1A hypermethylation. Somatic mutations of PIK3CA were detected in 14 of 44 (31.8%) of endometrial cancers. In exon 9, seven PIK3CA mutations were located, while seven mutations were located in exon 20. The most common mutation was E545A (35.7%), followed by H1047R (28.6%). Concomitant loss of PTEN expression and PIK3CA mutation was found in four cases of endometrial cancer. KRAS mutations were mutually exclusive with PIK3CA mutations, and those mutations were inversely correlated with statistical significance (P = 0.039). Also, we found that mutations in ERBB2 were mutually exclusive with PIK3CA mutations. RASSF1A and hMLH1 methylation were not correlated with the presence of PIK3CA mutations. PIK3CA was frequently mutated in endometrial cancers. KRAS and PIK3CA mutations are inversely correlated, suggesting that genetic alterations of KRAS and PIK3CA may play equivalent roles in endometrial carcinogenesis.

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.

The oncogenic hallmarks of pancreatic cancer (PC), such as the KRAS, BRAF, and PIK3CA mutations, have been widely investigated. However, almost all of the previous studies were limited by small sample sizes. In addition, previous data on the KRAS mutation and clinical outcomes in PC remain inconclusive. To clarify these data, we examined the mutation status of 126 PC patients and its relationship to clinical outcome. The frequencies of KRAS, BRAF, and PIK3CA mutations were determined from a non-biased database of 126 resected PCs and a high-throughput pyrosequencing assay. KRAS mutations were detected in 109 (86.5%) of the 126 cases; the most common mutation was c.34G>T (p.G12C), which was present in 80 tumors, followed by c.35G>T (p.G12V) in 52 tumors. The KRAS mutation was not associated with any clinical or pathological features (p>0.05 in all cases). In addition, the KRAS mutation was unrelated to overall survival (log rank p=0.21) and cancer-specific survival (log rank p=0.27). Importantly, the influence of KRAS mutation on patient outcome was not modified by any of the clinical or pathological variables (p for all interactions >0.05). Only one PIK3CA mutation (0.8%) was detected on exon 9 RS3 (c.1633G>A, p.E545K). The BRAF mutation was not detected in PC. KRAS mutations appear to be unrelated to clinical outcome in PC. BRAF and PIK3CA mutations were extremely rare in PC, suggesting that they play a limited role in PC development.

Characteristics and prevalence of KRAS, BRAF, and PIK3CA mutations in colorectal cancer by high-resolution melting analysis in Taiwanese population

Preclinical data suggest that PIK3CA mutations predict response to PI3K/AKT/mTOR inhibitors. Concomitant KRAS or BRAF mutations may mediate resistance. Therefore, tumors from patients referred to the phase I program for targeted therapy starting in October 2008 were analyzed for PIK3CA mutations using PCR-based DNA sequencing of exons 9 and 20. Consecutive patients with diverse tumor types and PIK3CA mutation were treated whenever possible with agents targeting the PI3K/AKT/mTOR pathway. Overall, PIK3CA mutations were detected in 25 of 217 patients (11.5%; exon 9, n = 11; exon 20, n = 14). In tumor types with more than 10 patients tested, PIK3CA mutations were most frequent in endometrial (3 of 14, 21%), ovarian (5 of 30, 17%), colorectal (9 of 54, 17%), breast (2 of 14, 14%), cervical (2 of 15, 13%), and squamous cell cancer of the head and neck (1 of 11, 9%). Of the 25 patients with PIK3CA mutations, 17 (68%) were treated on a protocol that included a PI3K/AKT/mTOR pathway inhibitor, and 6 (35%) achieved a partial response. In contrast, only 15 of 241 patients (6%) without documented PIK3CA mutations treated on the same protocols responded (P = 0.001). Of the 17 patients with PIK3CA mutations, 6 (35%) had simultaneous KRAS or BRAF mutations (colorectal, n = 4; ovarian, n = 2). Colorectal cancer patients with PIK3CA and KRAS mutations did not respond to therapy, whereas both ovarian cancer patients with PIK3CA and KRAS or BRAF mutations did. In conclusion, PIK3CA mutations were detected in 11.5% of patients with diverse solid tumors. The response rate was significantly higher for patients with PIK3CA mutations treated with PI3K/AKT/mTOR pathway inhibitors than for those without documented mutations.

One obstacle in the translation of advances in cancer research into the clinic is a deficiency of adequate preclinical models that recapitulate human disease. Patient-derived xenograft (PDX) models are established by engrafting patient tumor tissue into mice and are advantageous because they capture tumor heterogeneity. One concern with these models is that selective pressure could lead to mutational drift and thus be an inaccurate reflection of patient tumors. Therefore, we evaluated if mutational frequency in PDX models is reflective of patient populations and if crucial mutations are stable across passages. We examined KRAS and PIK3CA gene mutations from pancreatic ductal adenocarcinoma (PDAC) (n = 30) and colorectal cancer (CRC) (n = 37) PDXs for as many as eight passages. DNA was isolated from tumors and target sequences were amplified by polymerase chain reaction. KRAS codons 12/13 and PIK3CA codons 542/545/1047 were examined using pyrosequencing. Twenty-three of 30 (77%) PDAC PDXs had KRAS mutations and one of 30 (3%) had PIK3CA mutations. Fifteen of 37 (41%) CRC PDXs had KRAS mutations and three of 37 (8%) had PIK3CA mutations. Mutations were 100 per cent preserved across passages. We found that the frequency of KRAS (77%) and PIK3CA (3%) mutations in PDAC PDX was similar to frequencies in patient tumors (71 to 100% KRAS, 0 to 11% PIK3CA). Similarly, KRAS (41%) and PIK3CA (8%) mutations in CRC PDX closely paralleled patient tumors (35 to 51% KRAS, 12 to 21% PIK3CA). The accurate mirroring and stability of genetic changes in PDX models compared with patient tumors suggest that these models are good preclinical surrogates for patient tumors.

Vitamin D is associated with decreased risks of various cancers, including colon cancer. The vitamin D receptor (VDR) is a transcription factor, which plays an important role in cellular differentiation and inhibition of proliferation. A link between VDR and the RAS-mitogen-activated protein kinase (MAPK) or phosphatidylinositol 3-kinase (PI3K)-AKT pathway has been suggested. However, the prognostic role of VDR expression or its relationship with PIK3CA or KRAS mutation remains uncertain. Among 619 colorectal cancers in two prospective cohort studies, 233 (38%) tumors showed VDR overexpression by immunohistochemistry. We analyzed for PIK3CA and KRAS mutations and LINE-1 methylation by Pyrosequencing, microsatellite instability (MSI), and DNA methylation (epigenetic changes) in eight CpG island methylator phenotype (CIMP)-specific promoters [CACNA1G, CDKN2A (p16), CRABP1, IGF2, MLH1, NEUROG1, RUNX3, and SOCS1] by MethyLight (real-time PCR). VDR overexpression was significantly associated with KRAS mutation (odds ratio, 1.55; 95% confidence interval, 1.11-2.16) and PIK3CA mutation (odds ratio, 2.17; 95% confidence interval, 1.36-3.47), both of which persisted in multivariate logistic regression analysis. VDR was not independently associated with body mass index, family history of colorectal cancer, tumor location (colon versus rectum), stage, tumor grade, signet ring cells, CIMP, MSI, LINE-1 hypomethylation, BRAF, p53, p21, beta-catenin, or cyclooxygenase-2. VDR expression was not significantly related with patient survival, prognosis, or clinical outcome. In conclusion, VDR overexpression in colorectal cancer is independently associated with PIK3CA and KRAS mutations. Our data support potential interactions between the VDR, RAS-MAPK and PI3K-AKT pathways, and possible influence by KRAS or PIK3CA mutation on therapy or chemoprevention targeting VDR.

To understand the role of and differences in molecular alterations between endometrial and ovarian endometrioid adenocarcinomas. We investigated the microsatellite status of 26 ovarian endometrioid adenocarcinomas (OVEMs), 42 endometrial endometrioid adenocarcinomas (EMCAs), and 19 concurrent (endometrial and ovarian) endometrioid adenocarcinomas. We evaluated the expression of the mismatch repair proteins, PTEN and ARID1A, and mutations of PTEN, KRAS, CTNNB1, and PIK3CA. High levels of microsatellite instability (MSI-H) were present in one of 26 OVEMs, 12 of 42 EMCAs, and four of 19 concurrent endometrioid adenocarcinomas. Only four of 19 concurrent endometrioid adenocarcinomas showed identical molecular alterations in their endometrial and ovarian components. Loss of ARID1A or loss of PTEN expression, and MSI-H, were more common in EMCAs than OVEMs (P = 0.044, P = 0.004, and P = 0.012, respectively). MSI-H in endometrial endometrioid adenocarcinomas was also related to loss of ARID1A expression (P < 0.001). In the cohort of MSI-H endometrioid adenocarcinomas involving the endometrium (n = 16), MSH6-deficient cases showed higher frequencies of CTNNB1 and PIK3CA mutations (P = 0.008 and P = 0.036, respectively), but lower frequencies of KRAS mutation (P = 0.011), than PMS2-deficient cases. The different frequencies of molecular genetic alterations between endometrial endometrioid adenocarcinomas and ovarian endometrioid adenocarcinomas imply that distinct processes may be involved in their tumorigenesis or tumour progression.