Patient-Derived Explants of Colorectal Cancer: Histopathological and Molecular Analysis of Long-Term Cultures

Colorectal cancer (CRC) is one of the most common cancers worldwide. Although short-term cultures of tumour sections and xenotransplants have been used to determine drug efficacy, the results frequently fail to confer clinically useful information. Biomarker discovery has changed the paradigm for advanced CRC, though the presence of a biomarker does not necessarily translate into therapeutic success. To improve clinical outcomes, translational models predictive of drug response are needed. We describe a simple method for the fast establishment of CRC patient-derived explant (CRC-PDE) cultures from different carcinogenesis pathways, employing agitation-based platforms. A total of 26 CRC-PDE were established and a subset was evaluated for viability (n = 23), morphology and genetic key alterations (n = 21). CRC-PDE retained partial tumor glandular architecture and microenvironment features were partially lost over 4 weeks of culture. Key proteins (p53 and Mismatch repair) and oncogenic driver mutations of the original tumours were sustained throughout the culture. Drug challenge (n = 5) revealed differential drug response from distinct CRC-PDE cases. These findings suggest an adequate representation of the original tumour and highlight the importance of detailed model characterisation. The preservation of key aspects of the CRC microenvironment and genetics supports CRC-PDE potential applicability in pre- and co-clinical settings, as long as temporal dynamics are considered.

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Mutational analysis of rare insertions and deletions in exon 18 and 19 of HER2 in Chinese patients with different cancer types.

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.15_suppl.3069 ◽

2021 ◽

Vol 39 (15_suppl) ◽

pp. 3069-3069

Author(s):

Jianwen Qin ◽

Dongsheng Shi ◽

Lijie Song ◽

Yan Yin ◽

Bin Liu ◽

...

Keyword(s):

Breast Cancer ◽

Colorectal Cancer ◽

Lung Cancer ◽

Drug Response ◽

Chinese Patients ◽

Driver Mutations ◽

Wild Type ◽

Cancer Types ◽

Exon 20

3069 Background: HER2 belongs to the same family with EGFR and is known as an important cancer driver gene. Kinase domain insertions and deletions (KD indels) are frequent driver mutations in both EGFR and HER2. The most common HER2 KD indels are the exon 20 insertions while others are rarely reported. Our study aimed to investigate the role of less common HER2 KD indels in solid tumors. Methods: This study was performed in 63,267 Chinese patients including 53,591 patients with lung cancer, 5,888 patients with colorectal cancer, 3,774 patients with breast cancer and 14 patients with renal pelvis cancer. Tissue or plasma samples from the patients were subjected to capture-based targeted sequencing covering HER2 and other cancer related genes. The sequencing data of each patient were retrospectively collected and analyzed. The HER2 exon 18/19 indels identified in our study were compared with data from COSMIC and MSKCC. In vitro analysis in Ba/F3 cell lines was performed to assess drug response of different HER2 exon 18/19 indels. Results: We identified recurrent HER2 KD indels in exon 18 and 19, with a frequency of 0.04% (25/63,267). The data from COSMIC and MSKCC reported the prevalence of HER2 exon 18/19 indels ranging from 0.04% to 0.23% among breast, cervical, and pancreatic cancers. In our study, HER2 exon 18/19 indels were identified in 20 patients with lung cancer (0.037%), two with colorectal cancer (0.034%), two with breast cancer (0.053%) and one with renal pelvis cancer (7.143%). Only two patients (8%) harbored concurrent actionable driver mutations including EGFR mutation and MET amplification. Meanwhile, high level of normalized allelic frequency of HER2 exon 18/19 indels was presented in most patients (22/25, 88%). In lung cancer, the presence of EGFR driver mutation was less common in patients with HER2 exon 18/19 indels than wild type HER2 (5% vs. 47.4%, p < 0.01). The rates of concurrent driver mutations in lung cancer were comparable between HER2 exon 18/19 indels and the two established HER2 drivers, exon 20 insertions and S310 mutations. The in vitro proliferation assay demonstrated that E698_P699insLL mutation in HER2 exon 18 and L755_E757delinsPQ mutation in HER2 exon 19 both conferred a survival advantage to Ba/F3 cells. Dose-response curves showed inhibitory effects on cell viability of several HER2 tyrosine kinase inhibitors including neratinib, lapatinib, poziotinib and afatinib. In particular, lapatinib, poziotinib and afatinib demonstrated comparable or stronger inhibitory ability toward the two HER2 mutants than wild type HER2 in terms of IC50. Conclusions: Our study revealed a novel class of HER2 KD indels in exon 18/19 that may act as driver mutations in several cancer types. The drug response observed in vitro indicated the potential to use anti- HER2 targeted therapies for HER2 exon 18/19 indels. Further studies on this rare type of HER2 mutation are warranted.

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Identification of Novel Mutations in Colorectal Cancer Patients Using AmpliSeq Comprehensive Cancer Panel

Journal of Personalized Medicine ◽

10.3390/jpm11060535 ◽

2021 ◽

Vol 11 (6) ◽

pp. 535

Author(s):

Bader Almuzzaini ◽

Jahad Alghamdi ◽

Alhanouf Alomani ◽

Saleh AlGhamdi ◽

Abdullah A. Alsharm ◽

...

Keyword(s):

Colorectal Cancer ◽

Personalized Medicine ◽

Cancer Patients ◽

Biomarker Discovery ◽

Local Population ◽

Network Analyses ◽

Functional Perspective ◽

Novel Variants ◽

Colorectal Cancer Patients ◽

Cancer Panel

Biomarker discovery would be an important tool in advancing and utilizing the concept of precision and personalized medicine in the clinic. Discovery of novel variants in local population provides confident targets for developing biomarkers for personalized medicine. We identified the need to generate high-quality sequencing data from local colorectal cancer patients and understand the pattern of occurrence of variants. In this report, we used archived samples from Saudi Arabia and used the AmpliSeq comprehensive cancer panel to identify novel somatic variants. We report a comprehensive analysis of next-generation sequencing results with a coverage of >300X. We identified 466 novel variants which were previously unreported in COSMIC and ICGC databases. We analyzed the genes associated with these variants in terms of their frequency of occurrence, probable pathogenicity, and clinicopathological features. Among pathogenic somatic variants, 174 were identified for the first time in the large intestine. APC, RET, and EGFR genes were most frequently mutated. A higher number of variants were identified in the left colon. Occurrence of variants in ERBB2 was significantly correlated with those of EGFR and ATR genes. Network analyses of the identified genes provide functional perspective of the identified genes and suggest affected pathways and probable biomarker candidates. This report lays the ground work for biomarker discovery and identification of driver gene mutations in local population.

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Metabonomics of Human Colorectal Cancer: New Approaches for Early Diagnosis and Biomarker Discovery

Journal of Proteome Research ◽

10.1021/pr500443c ◽

2014 ◽

Vol 13 (9) ◽

pp. 3857-3870 ◽

Cited By ~ 51

Author(s):

Yan Ni ◽

Guoxiang Xie ◽

Wei Jia

Keyword(s):

Colorectal Cancer ◽

Early Diagnosis ◽

Biomarker Discovery ◽

Human Colorectal Cancer ◽

New Approaches

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Reconstructing single-cell karyotype alterations in colorectal cancer identifies punctuated and gradual diversification patterns

Nature Genetics ◽

10.1038/s41588-021-00891-2 ◽

2021 ◽

Author(s):

Yannik Bollen ◽

Ellen Stelloo ◽

Petra van Leenen ◽

Myrna van den Bos ◽

Bas Ponsioen ◽

...

Keyword(s):

Colorectal Cancer ◽

Single Cell ◽

Temporal Dynamics ◽

De Novo ◽

Tumor Evolution ◽

Genome Wide ◽

Aneuploid Tumor ◽

Evolutionary Paths ◽

Tumor Biopsies ◽

Punctuated Evolution

AbstractCentral to tumor evolution is the generation of genetic diversity. However, the extent and patterns by which de novo karyotype alterations emerge and propagate within human tumors are not well understood, especially at single-cell resolution. Here, we present 3D Live-Seq—a protocol that integrates live-cell imaging of tumor organoid outgrowth and whole-genome sequencing of each imaged cell to reconstruct evolving tumor cell karyotypes across consecutive cell generations. Using patient-derived colorectal cancer organoids and fresh tumor biopsies, we demonstrate that karyotype alterations of varying complexity are prevalent and can arise within a few cell generations. Sub-chromosomal acentric fragments were prone to replication and collective missegregation across consecutive cell divisions. In contrast, gross genome-wide karyotype alterations were generated in a single erroneous cell division, providing support that aneuploid tumor genomes can evolve via punctuated evolution. Mapping the temporal dynamics and patterns of karyotype diversification in cancer enables reconstructions of evolutionary paths to malignant fitness.

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Peptidomic Analysis via One-Step Direct Transfer Technology for Colorectal Cancer Biomarker Discovery

Journal of Proteomics & Bioinformatics ◽

10.4172/jpb.s5-005 ◽

2015 ◽

Vol s5 ◽

Cited By ~ 1

Author(s):

Kazuhiko Uchiyama

Keyword(s):

Colorectal Cancer ◽

Biomarker Discovery ◽

Cancer Biomarker ◽

Direct Transfer ◽

One Step ◽

Peptidomic Analysis

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Targeting vitamin E TPGS–cantharidin conjugate nanoparticles for colorectal cancer therapy

RSC Advances ◽

10.1039/c5ra08154h ◽

2015 ◽

Vol 5 (66) ◽

pp. 53846-53856 ◽

Cited By ~ 3

Author(s):

Shihou Sheng ◽

Tao Zhang ◽

Shijie Li ◽

Jun Wei ◽

Guangjun Xu ◽

...

Keyword(s):

Colorectal Cancer ◽

Drug Delivery ◽

Vitamin E ◽

Chinese Medicine ◽

Side Effects ◽

Cancer Therapy ◽

Traditional Chinese Medicine ◽

Drug Efficacy ◽

Vitamin E Tpgs ◽

Colorectal Cancer Cells

A traditional Chinese medicine cantharidin which was previously found to be effective on colorectal cancer cells was translated into nanoparticles for drug delivery to reduce its side effects and enhance its drug efficacy.

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Uncovering Potential Therapeutic Targets in Colorectal Cancer by Deciphering Mutational Status and Expression of Druggable Oncogenes

Cancers ◽

10.3390/cancers11070983 ◽

2019 ◽

Vol 11 (7) ◽

pp. 983 ◽

Cited By ~ 3

Author(s):

Otília Menyhart ◽

Tatsuhiko Kakisaka ◽

Lőrinc Sándor Pongor ◽

Hiroyuki Uetake ◽

Ajay Goel ◽

...

Keyword(s):

Gene Expression ◽

Colorectal Cancer ◽

Gene Expression Data ◽

Drug Targets ◽

Therapeutic Targets ◽

Independent Set ◽

Driver Mutations ◽

Expression Data ◽

Expression Levels ◽

Mutational Status

Background: Numerous driver mutations have been identified in colorectal cancer (CRC), but their relevance to the development of targeted therapies remains elusive. The secondary effects of pathogenic driver mutations on downstream signaling pathways offer a potential approach for the identification of therapeutic targets. We aimed to identify differentially expressed genes as potential drug targets linked to driver mutations. Methods: Somatic mutations and the gene expression data of 582 CRC patients were utilized, incorporating the mutational status of 39,916 and the expression levels of 20,500 genes. To uncover candidate targets, the expression levels of various genes in wild-type and mutant cases for the most frequent disruptive mutations were compared with a Mann–Whitney test. A survival analysis was performed in 2100 patients with transcriptomic gene expression data. Up-regulated genes associated with worse survival were filtered for potentially actionable targets. The most significant hits were validated in an independent set of 171 CRC patients. Results: Altogether, 426 disruptive mutation-associated upregulated genes were identified. Among these, 95 were linked to worse recurrence-free survival (RFS). Based on the druggability filter, 37 potentially actionable targets were revealed. We selected seven genes and validated their expression in 171 patient specimens. The best independently validated combinations were DUSP4 (p = 2.6 × 10−12) in ACVR2A mutated (7.7%) patients; BMP4 (p = 1.6 × 10−04) in SOX9 mutated (8.1%) patients; TRIB2 (p = 1.35 × 10−14) in ACVR2A mutated patients; VSIG4 (p = 2.6 × 10−05) in ANK3 mutated (7.6%) patients, and DUSP4 (p = 7.1 × 10−04) in AMER1 mutated (8.2%) patients. Conclusions: The results uncovered potentially druggable genes in colorectal cancer. The identified mutations could enable future patient stratification for targeted therapy.

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FORESEE: a tool for the systematic comparison of translational drug response modeling pipelines

10.7287/peerj.preprints.27256v1 ◽

2018 ◽

Author(s):

Lisa-Katrin Turnhoff ◽

Ali Hadizadeh Esfahani ◽

Maryam Montazeri ◽

Nina Kusch ◽

Andreas Schuppert

Keyword(s):

Drug Response ◽

Drug Efficacy ◽

Response Prediction ◽

R Package ◽

Supplementary Information ◽

Supplementary File ◽

Data Sets ◽

Training Algorithms ◽

Model Training

Translational models that utilize omics data generated in in vitro studies to predict the drug efficacy of anti-cancer compounds in patients are highly distinct, which complicates the benchmarking process for new computational approaches. In reaction to this, we introduce the uniFied translatiOnal dRug rESponsE prEdiction platform FORESEE, an open-source R-package. FORESEE not only provides a uniform data format for public cell line and patient data sets, but also establishes a standardized environment for drug response prediction pipelines, incorporating various state-of-the-art preprocessing methods, model training algorithms and validation techniques. The modular implementation of individual elements of the pipeline facilitates a straightforward development of combinatorial models, which can be used to re-evaluate and improve already existing pipelines as well as to develop new ones. Availability and Implementation: FORESEE is licensed under GNU General Public License v3.0 and available at https://github.com/JRC-COMBINE/FORESEE . Supplementary Information: Supplementary Files 1 and 2 provide detailed descriptions of the pipeline and the data preparation process, while Supplementary File 3 presents basic use cases of the package. Contact: [email protected]

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MDR1 polymorphisms are not related to Xeliri and Xelox chemoresistance in colorectal cancer

10.21203/rs.2.14185/v1 ◽

2019 ◽

Author(s):

Ayat B. Al-Ghafari ◽

Areej M. Alqahtani ◽

Suzan N. Alturki ◽

Huda Abdulaziz Al Doghaither ◽

Hanaa M. Tashkandi ◽

...

Keyword(s):

Colorectal Cancer ◽

Drug Response ◽

Fragment Length Polymorphism ◽

Protective Role ◽

Genotype Distribution ◽

Chain Reaction ◽

P Glycoprotein ◽

Significant Difference ◽

Pcr Rflp ◽

Polymerase Chain

Abstract Background Multidrug resistance member 1 (MDR1) is located on chromosome 7 and encodes P-glycoprotein (Pgp), which is universally accepted as a drug resistance biomarker. MDR1 polymorphisms may change either the protein expression or function, suggesting its possible association with cancers, including colorectal cancer (CRC). Thus, this study aimed to determine the effects of MDR1 polymorphisms on the drug response of Saudi CRC patients.Methods DNA samples were obtained from 62 CRC patients and 100 healthy controls. The genotypes and allele frequencies of the MDR1 polymorphisms G2677T and T1236C were determined by polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP).Results No significant difference was observed in the genotype distribution and allele frequency of T1236C between the CRC the patients and the controls. However, G2677T was found to play a highly significant protective role against the progression of CRC. Moreover, the results showed that none of the genotypes in SNPs T1236C and G2677T affected chemoresistance to Xeliri and Xelox.Conclusions T1236C in the MDR1 gene is not related to CRC risk, and G2677T protects against the development of CRC. Both MDR1 polymorphisms are not associated with the risk of chemoresistance.

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