Associations Between Loss of ARID1A Expression and Clinicopathologic and Genetic Variables in T1 Early Colorectal Cancer

Abstract Objectives To evaluate the relationships between adenine-thymine-rich interactive domain 1A (ARID1A) expression and the clinicopathologic features in T1 colorectal cancer (CRC) and to investigate whether the presence of ARID1A protein is related to genetic changes. Methods We retrospectively studied 219 surgically resected T1 CRCs. ARID1A expression was assessed by immunohistochemical methods, and the correlation between ARID1A expression and clinicopathologic features was evaluated. The relationship between ARID1A expression and 409 cancer-related gene mutations was also evaluated using next-generation sequencing (NGS). Results Immunohistochemical staining indicated negative ARID1A expression in 4.6%. Loss of ARID1A expression was significantly associated with younger age, lymphatic invasion, and lymph node metastasis (LNM). NGS showed that PKHD1, RNF213, and MSH6 mutations were more frequent in ARID1A-negative tumors, whereas KRAS mutations were more common in ARID1A-positive tumors. Conclusions In T1 CRC, negative ARID1A expression was correlated with early onset, lymphatic invasion, and LNM. Mutations in some cancer-related genes were possibly related with ARID1A expression.

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Clinicopathological and Molecular Profiles of Sporadic Microsatellite Unstable Colorectal Cancer with or without the CpG Island Methylator Phenotype (CIMP)

Cancers ◽

10.3390/cancers12113487 ◽

2020 ◽

Vol 12 (11) ◽

pp. 3487

Author(s):

Shih-Ching Chang ◽

Anna Fen-Yau Li ◽

Pei-Ching Lin ◽

Chun-Chi Lin ◽

Hung-Hsin Lin ◽

...

Keyword(s):

Colorectal Cancer ◽

Cpg Island ◽

Gene Mutations ◽

Proximal Colon ◽

Tnm Stage ◽

Cpg Island Methylator Phenotype ◽

Kras Mutations ◽

Methylator Phenotype ◽

Next Generation Sequencing Ngs ◽

Mutation Spectra

Background: The 5’-C-phosphate-G-3’ island methylator phenotype (CIMP) is a specific phenotype of colorectal cancer (CRC) associated with microsatellite instability-high (MSI-high) tumors. Methods: In this study, we determined the CIMP status using eight methylation markers in 92 MSI-high CRC patients after excluding five germline mismatch repair (MMR) gene mutations analyzed by next-generation sequencing (NGS) and confirmed by Sanger sequencing. The mutation spectra of 22 common CRC-associated genes were analyzed by NGS. Results: Of the 92 sporadic MSI-high tumors, 23 (25%) were considered CIMP-high (expressed more than 5 of 8 markers). CIMP-high tumors showed proximal colon preponderance and female predominance. The mutation profiles of CIMP-high tumors were significantly different from those of CIMP-low or CIMP-0 tumors (i.e., higher frequencies of BRAF, POLD1, MSH3, and SMAD4 mutations but lower frequencies of APC, TP53, and KRAS mutations). Multivariate analysis demonstrated that tumor, node, metastasis (TNM) stage was the independent prognostic factor affecting overall survival (OS). Among the MSI-high cases, the CIMP status did not impact the outcome of patients with MSI-high tumors. Conclusions: Only TNM stage was a statistically significant predictor of outcomes independent of CIMP profiles in MSI-high CRC patients. Sporadic MSI-high CRCs with different mechanisms of carcinogenesis have specific mutation profiles and clinicopathological features.

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KRAS and PIK3CA Mutation Frequencies in Patient-derived Xenograft Models of Pancreatic and Colorectal Cancer Are Reflective of Patient Tumors and Stable Across Passages

The American Surgeon ◽

10.1177/000313481408000920 ◽

2014 ◽

Vol 80 (9) ◽

pp. 873-877 ◽

Cited By ~ 16

Author(s):

Christopher J. Tignanelli ◽

Silvia G. Herrera Loeza ◽

Jen Jen Yeh

Keyword(s):

Colorectal Cancer ◽

Pik3ca Mutation ◽

Disease Patient ◽

Gene Mutations ◽

Ductal Adenocarcinoma ◽

Kras Mutations ◽

Genetic Changes ◽

Pik3ca Mutations ◽

Patient Derived Xenograft ◽

Pdx Models

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.

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Gene Therapy Targeting p53 and KRAS for Colorectal Cancer Treatment: A Myth or The Way Forward?

International Journal of Molecular Sciences ◽

10.3390/ijms222111941 ◽

2021 ◽

Vol 22 (21) ◽

pp. 11941

Author(s):

Hidayati Husainy Hasbullah ◽

Marahaini Musa

Keyword(s):

Colorectal Cancer ◽

Gene Therapy ◽

Cancer Treatment ◽

Ethical Issues ◽

Public Awareness ◽

Gene Mutations ◽

Suppressor Gene ◽

Genetic Alterations ◽

Early Screening ◽

Genetic Changes

Colorectal cancer (CRC) is the third most commonly diagnosed malignancy worldwide and is responsible as one of the main causes of mortality in both men and women. Despite massive efforts to raise public awareness on early screening and significant advancements in the treatment for CRC, the majority of cases are still being diagnosed at the advanced stage. This contributes to low survivability due to this cancer. CRC patients present various genetic changes and epigenetic modifications. The most common genetic alterations associated with CRC are p53 and KRAS gene mutations. Gene therapy targeting defect genes such as TP53 (tumor suppressor gene encodes for p53) and KRAS (oncogene) in CRC potentially serves as an alternative treatment avenue for the disease in addition to the standard therapy. For the last decade, significant developments have been seen in gene therapy for translational purposes in treating various cancers. This includes the development of vectors as delivery vehicles. Despite the optimism revolving around targeted gene therapy for cancer treatment, it also has various limitations, such as a lack of availability of related technology, high cost of the involved procedures, and ethical issues. This article will provide a review on the potentials and challenges of gene therapy targeting p53 and KRAS for the treatment of CRC.

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Fractionated small cell‐free DNA increases possibility to detect cancer‐related gene mutations in advanced colorectal cancer

JGH Open ◽

10.1002/jgh3.12379 ◽

2020 ◽

Vol 4 (5) ◽

pp. 978-986

Author(s):

Yasuaki Ishida ◽

Shinichi Takano ◽

Shinya Maekawa ◽

Tatsuya Yamaguchi ◽

Takashi Yoshida ◽

...

Keyword(s):

Colorectal Cancer ◽

Advanced Colorectal Cancer ◽

Gene Mutations ◽

Small Cell ◽

Related Gene ◽

Cell Free Dna ◽

Free Dna ◽

Cancer Related Gene

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Clinicopathologic features of KRAS-mutated colorectal tumors vary by site of mutation.

Journal of Clinical Oncology ◽

10.1200/jco.2013.31.15_suppl.3632 ◽

2013 ◽

Vol 31 (15_suppl) ◽

pp. 3632-3632 ◽

Cited By ~ 1

Author(s):

Van Karlyle Morris ◽

Michael J. Overman ◽

Cathy Eng ◽

Eduardo Vilar Sanchez ◽

Maria Morelli ◽

...

Keyword(s):

Colorectal Cancer ◽

Lung Metastases ◽

Pik3ca Mutation ◽

Cancer Center ◽

P Value ◽

Clinicopathologic Features ◽

Colorectal Tumors ◽

Wild Type ◽

Kras Mutations ◽

Survival Difference

3632 Background: KRAS mutations in codons 12 and 13 are present in approximately 40% of all colon cancers and predict a lack of response to monoclonal antibodies to the EGFR among patients with metastatic disease. Activating mutations in codons 61 and 146 occur less frequently, and the clinicopathologic features of this subpopulation of KRAS-mutant colorectal tumors have not been clearly defined. Methods: Records of patients treated at MD Anderson Cancer Center between December 2000 and August 2012 for metastatic colorectal cancer whose tumors underwent testing for a KRAS mutation were reviewed for clinical characteristics, concurrent mutations, and survival outcomes. Associations between mutation status and clinic features were measured by calculation of odds ratios, and survival was estimated according to the Kaplan-Meier method. Results: Among the 487 records reviewed, 225 KRAS 12/13 mutations (47.2%) and 14 KRAS 61/146 mutations (2.9%) were detected. Liver metastases were less common for patients with KRAS 61/146 mutations than for patients with KRAS 12/13 mutations (OR 0.26, p-value=0.02). No difference in lung metastases was identified for KRAS 61/146 mutated patients when compared to those with KRAS wild-type tumors (OR=2.1, p-value=0.26), even though lung metastases were more common for patients with KRAS 12/13 mutations (OR 2.86, p-value=0.001). There was no association between the presence of a KRAS 61/146 mutation and gender, stage at presentation, site of primary tumor, body mass index, tobacco history, or concurrent PIK3CA mutation. Whereas a worse survival difference from the time of metastasis detection was noted for KRAS 12/13 patients when compared to those with KRAS wild-type tumors (HR 1.74, p-value= 0.002), patients with KRAS 61/146 mutations demonstrated no change in survival outcome (HR 1.10, p-value=0.87). Conclusions: Patients with KRAS 61/146 mutations have different patterns of metastases compared to KRAS 12/13, but do not appear to share the poor prognosis associated with the more common KRAS 12/13. These results suggest that clinical phenotypes for patients afflicted with colorectal cancer may differ based on the specific codon mutated within the KRAS oncogene.

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Prevalence and coexistence of KRAS, BRAF, PIK3CA, NRAS, TP53, and APC mutations in Indian colorectal cancer patients: Next-generation sequencing–based cohort study

Tumor Biology ◽

10.1177/1010428317692265 ◽

2017 ◽

Vol 39 (2) ◽

pp. 101042831769226 ◽

Cited By ~ 12

Author(s):

Mayank Jauhri ◽

Akanksha Bhatnagar ◽

Satish Gupta ◽

Manasa BP ◽

Sachin Minhas ◽

...

Keyword(s):

Colorectal Cancer ◽

Next Generation Sequencing ◽

Cancer Patients ◽

Gene Mutations ◽

Next Generation ◽

Kras Mutations ◽

Pik3ca Mutations ◽

Potential Biomarker ◽

Colorectal Cancer Patients ◽

Generation Sequencing

Colorectal cancer incidences are on a rise in India. In this study, we have analyzed the mutation frequencies of six potential biomarkers, their coexistence, association with clinicopathological characteristics, and tumor location in Indian colorectal cancer patients. Next-generation sequencing was performed to identify mutations in the six potential biomarker genes using formalin-fixed paraffin-embedded tissue blocks of 112 colorectal cancer patients. The mutation frequency observed in KRAS, BRAF, PIK3CA, NRAS, TP53, and APC was 35.7%, 7.1%, 16.1%, 6.3%, 39.3%, and 29.5%, respectively. The significant associations of mutations were KRAS with age less than 60 years (p = 0.041), PIK3CA with males (p = 0.032), tumor stage I–II (p = 0.013), lack of metastasis in lymph nodes (p = 0.040), NRAS with rectum (p = 0.002), and APC with T2 stage of tumor growth (p = 0.013). No single patient harbored mutations in these six genes or any five genes simultaneously. Significance was noted in coexistence of KRAS with APC (p = 0.024) and mutual exclusion of KRAS with BRAF (p = 0.029). PIK3CA exon 9 was observed to be more frequently associated with KRAS mutations than PIK3CA exon 20 (p = 0.072). NRAS mutations were mutually exclusive with BRAF and PIK3CA mutations. As per our knowledge, this is the first next-generation sequencing–based biomarker study in Indian colorectal cancer patients. Frequent coexistence of gene mutations in pairs and triplets suggests that synergistic effect of overlapping mutations might further trigger the disease. In addition, infrequent coexistence of multiple gene mutations hints toward different signaling pathways for colorectal cancer tumorigenesis.

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Comparison of KRAS mutation analysis of colorectal cancer samples by standard testing and next-generation sequencing

Journal of Clinical Pathology ◽

10.1136/jclinpath-2014-202405 ◽

2014 ◽

Vol 67 (9) ◽

pp. 764-767 ◽

Cited By ~ 21

Author(s):

Nishi Kothari ◽

Michael J Schell ◽

Jamie K Teer ◽

Timothy Yeatman ◽

David Shibata ◽

...

Keyword(s):

Colorectal Cancer ◽

Next Generation Sequencing ◽

Clinical Laboratory ◽

Clinical Care ◽

Next Generation ◽

Illumina Platform ◽

Kras Mutations ◽

Standard Testing ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

AimsBased on KRAS testing, the subset of patients with metastatic colorectal cancer (CRC) that could benefit from anti-EGFR therapy can be better delineated. Though KRAS testing has become significantly more prevalent over the last few years, methods for testing remain heterogeneous and discordance has been reported between methods.MethodsIn this study, we examined a CRC patient population and compared KRAS testing done in Clinical Laboratory Improvement Amendments (CLIA) approved laboratories as part of standard clinical care and by next-generation sequencing (NGS) using the Illumina platform. Discordances were further evaluated with manual review of the NGS testing.ResultsOut of 468 CRC patient samples, 77 had KRAS testing done by both CLIA assay and NGS. There were concordant results between testing methodologies in 74 out of 77 patients, or 96% (95% CI 89% to 99%). There were three patient samples that showed discordant results between the two methods of testing. Upon further investigation of the NGS results for the three discordant cases, one sample showed a low level of the mutation seen in the standard testing, one sample showed low tumour fraction and a third did not show any evidence of the mutation that was found with the standard assay. Five patients had KRAS mutations not typically tested with standard testing.ConclusionsOverall there was a high concordance rate between NGS and standard testing for KRAS. However, NGS revealed mutations that are not tested for with standard KRAS assays that might have clinical impact with regards to the role for anti-EGFR therapy.

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Less frequently mutated genes in colorectal cancer: evidences from next-generation sequencing of 653 routine cases

Journal of Clinical Pathology ◽

10.1136/jclinpath-2015-203403 ◽

2016 ◽

Vol 69 (9) ◽

pp. 767-771 ◽

Cited By ~ 41

Author(s):

Umberto Malapelle ◽

Pasquale Pisapia ◽

Roberta Sgariglia ◽

Elena Vigliar ◽

Maria Biglietto ◽

...

Keyword(s):

Colorectal Cancer ◽

Next Generation Sequencing ◽

Somatic Mutations ◽

Gene Mutations ◽

Next Generation ◽

Genomic Landscape ◽

Next Generation Sequencing Ngs ◽

Pcr Targeting ◽

Diagnostic Setting ◽

Generation Sequencing

AimsThe incidence of RAS/RAF/PI3KA and TP53 gene mutations in colorectal cancer (CRC) is well established. Less information, however, is available on other components of the CRC genomic landscape, which are potential CRC prognostic/predictive markers.MethodsFollowing a previous validation study, ion-semiconductor next-generation sequencing (NGS) was employed to process 653 routine CRC samples by a multiplex PCR targeting 91 hotspot regions in 22 CRC significant genes.ResultsA total of 796 somatic mutations in 499 (76.4%) tumours were detected. Besides RAS/RAF/PI3KA and TP53, other 12 genes showed at least one mutation including FBXW7 (6%), PTEN (2.8%), SMAD4 (2.1%), EGFR (1.2%), CTNNB1 (1.1%), AKT1 (0.9%), STK11 (0.8%), ERBB2 (0.6%), ERBB4 (0.6%), ALK (0.2%), MAP2K1 (0.2%) and NOTCH1 (0.2%).ConclusionsIn a routine diagnostic setting, NGS had the potential to generate robust and comprehensive genetic information also including less frequently mutated genes potentially relevant for prognostic assessments or for actionable treatments.

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The value of haematological parameters and serum tumour markers for predicting KRAS mutations in 784 Chinese colorectal cancer patients: a retrospective analysis

BMC Cancer ◽

10.1186/s12885-020-07551-4 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Yinghao Cao ◽

Junnan Gu ◽

Lizhao Yan ◽

Shenghe Deng ◽

Fuwei Mao ◽

...

Keyword(s):

Colorectal Cancer ◽

Logistic Regression ◽

Predictive Value ◽

Gene Mutations ◽

Haematological Parameters ◽

Multivariate Logistic Regression ◽

Kras Gene ◽

Kras Mutations ◽

Mutation Status ◽

Serum Tumour

Abstract Background Identifying the mutation status of KRAS is important for optimizing treatment in patients with colorectal cancer (CRC). The aim of this study was to investigate the predictive value of haematological parameters and serum tumour markers (STMs) for KRAS gene mutations. Methods The clinical data of patients with colorectal cancer from January 2014 to December 2018 were retrospectively collected, and the associations between KRAS mutations and other indicators were analysed. Receiver operating characteristic (ROC) curve analysis was performed to quantify the predictive value of these factors. Univariate and multivariate logistic regression models were applied to identify predictors of KRAS mutations by calculating the odds ratios (ORs) and their corresponding 95% confidence intervals (CIs). Results KRAS mutations were identified in 276 patients (35.2%). ROC analysis revealed that age, CA12–5, AFP, SCC, CA72–4, CA15–3, FERR, CYFRA21-1, MCHC, and tumor location could not predict KRAS mutations (P = 0.154, 0.177, 0.277, 0.350, 0.864, 0.941, 0.066, 0.279, 0.293, and 0.053 respectively), although CEA, CA19–9, NSE and haematological parameter values showed significant predictive value (P = 0.001, < 0.001, 0.043 and P = 0.003, < 0.001, 0.001, 0.031, 0.030, 0.016, 0.015, 0.019, and 0.006, respectively) but without large areas under the curve. Multivariate logistic regression analysis showed that CA19–9 was significantly associated with KRAS mutations and was the only independent predictor of KRAS positivity (P = 0.016). Conclusions Haematological parameters and STMs were related to KRAS mutation status, and CA19–9 was an independent predictive factor for KRAS gene mutations. The combination of these clinical factors can improve the ability to identify KRAS mutations in CRC patients.

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Malignant transformation and genetic alterations are uncoupled in early colorectal cancer progression

BMC Biology ◽

10.1186/s12915-020-00844-x ◽

2020 ◽

Vol 18 (1) ◽

Author(s):

Soulafa Mamlouk ◽

Tincy Simon ◽

Laura Tomás ◽

David C. Wedge ◽

Alexander Arnold ◽

...

Keyword(s):

Colorectal Cancer ◽

Cancer Progression ◽

Genetic Alterations ◽

Driver Mutations ◽

Early Colorectal Cancer ◽

High Grade ◽

Neoplastic Progression ◽

Genetic Changes ◽

Chromosome 20 ◽

Genetic Profiles

Abstract Background Colorectal cancer (CRC) development is generally accepted as a sequential process, with genetic mutations determining phenotypic tumor progression. However, matching genetic profiles with histological transition requires the analyses of temporal samples from the same patient at key stages of progression. Results Here, we compared the genetic profiles of 34 early carcinomas with their respective adenomatous precursors to assess timing and heterogeneity of driver alterations accompanying the switch from benign adenoma to malignant carcinoma. In almost half of the cases, driver mutations specific to the carcinoma stage were not observed. In samples where carcinoma-specific alterations were present, TP53 mutations and chromosome 20 copy gains commonly accompanied the switch from adenomatous tissue to carcinoma. Remarkably, 40% and 50% of high-grade adenomas shared TP53 mutations and chromosome 20 gains, respectively, with their matched carcinomas. In addition, multi-regional analyses revealed greater heterogeneity of driver mutations in adenomas compared to their matched carcinomas. Conclusion Genetic alterations in TP53 and chromosome 20 occur at the earliest histological stage in colorectal carcinomas (pTis and pT1). However, high-grade adenomas can share these alterations despite their histological distinction. Based on the well-defined sequence of CRC development, we suggest that the timing of genetic changes during neoplastic progression is frequently uncoupled from histological progression.

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