Cell-free DNA analysis in current cancer clinical trials: a review

Cell-free DNA (cfDNA) analysis represents a promising method for the diagnosis, treatment selection and clinical follow-up of cancer patients. Although its general methodological feasibility and usefulness has been demonstrated, several issues related to standardisation and technical validation must be addressed for its routine clinical application in cancer. In this regard, most cfDNA clinical applications are still limited to clinical trials, proving its value in several settings. In this paper, we review the current clinical trials involving cfDNA/ctDNA analysis and highlight those where it has been useful for patient stratification, treatment follow-up or development of novel approaches for early diagnosis. Our query included clinical trials, including the terms 'cfDNA', 'ctDNA', 'liquid biopsy' AND 'cancer OR neoplasm' in the FDA and EMA public databases. We identified 1370 clinical trials (FDA = 1129, EMA = 241) involving liquid-biopsy analysis in cancer. These clinical trials show promising results for the early detection of cancer and confirm cfDNA as a tool for real-time monitoring of acquired therapy resistance, accurate disease-progression surveillance and improvement of treatment, situations that result in a better quality of life and extended overall survival for cancer patients.

Population and breast cancer patients' analysis reveals the diversity of genomic variation of the BRCA genes in the Mexican population

Interpretation of variants of unknown significance (VUS) in genetic tests is complicated in ethnically diverse populations, given the lack of information regarding the common spectrum of genetic variation in clinically relevant genes. Public availability of data obtained from high-throughput genotyping and/or exome massive parallel sequencing (MPS)-based projects from several thousands of outbred samples might become useful tools to evaluate the pathogenicity of a VUS, based on its frequency in different populations. In the case of the Mexican and other Latino populations, several thousands of samples have been genotyped or sequenced during the last few years as part of different efforts to identify common variants associated to common diseases. In this report, we analyzed Mexican population data from a sample of 3985 outbred individuals, and additional 66 hereditary breast cancer patients were analyzed in order to better define the spectrum of common genomic variation of the BRCA1 and BRCA2 genes. Our analyses identified the most common genetic variants in these clinically relevant genes as well as the presence and frequency of specific pathogenic mutations present in the Mexican population. Analysis of the 3985 population samples by MPS identified three pathogenic mutations in BRCA1, only one population sample showed a BRCA1 exon 16-17 deletion by MLPA. This resulted in a basal prevalence of deleterious mutations of 0.10% (1:996) for BRCA1 and 11 pathogenic mutations in BRCA2, resulting in a basal prevalence of deleterious mutations of 0.276% (1:362) for BRCA2, combined of 0.376% (1:265). Separate analysis of the breast cancer patients identified the presence of pathogenic mutations in 18% (12 pathogenic mutations in 66 patients) of the samples by MPS and 13 additional alterations by MLPA. These results will support a better interpretation of clinical studies focused on the detection of BRCA mutations in Mexican and Latino populations and will help to define the general prevalence of deleterious mutations within these populations.

Abstract P6-09-18: Predictive factors of pathologic complete response to neoadjuvant chemotherapy in patients with Luminal HER2(-) local advanced breast cancer using the DMET microarray

Introduction

Patients with similar local advanced breast cancer (LABC) could respond different to neoadjuvant chemotherapy (NC). Luminal HER2(-) tumors have pathologic complete response (pCR) by 5-7%. Ki67, tumor grade and hormonal receptors, could be helpful but not enough to choice between NC vs. initial surgery. Response to drugs depends on enzymes involved in absorption, distribution, metabolism and elimination (ADME); the drug-metabolizing enzyme and transporter platform (DMET), could identify 1936 single nucleotide polymorphism (SNP) from 225 genes involved in ADME proccess.

Objective

To identify predictive factors to pCR in patients with Luminal HER2(-) LABC underwent NC, to distinguish wish patients could have a real benefit from NC.

Material and Methods

This is a prospective nested case control study (1:4) with LABC patients, pure invasive ductal carcinoma Luminal HER2(-) subtypes, and sequential NC (anthracyclines and taxanes). Cases were defined as patients with pCR (Residual Cancer Burden=0), and controls those without pCR. SNPs were evaluated from DNA of leucocytes using DMET microarrays by Affymetrix.

Bivariate analyses were used as appropriate. Microarrays were processed by the DMET analyzer console. OR and 95%CI were used to test association between pCR and variables with a non-conditional logistic regression analysis; p value ≤0.05 was considered statistically significant (two-sided).

Results

From 2005 to 2014, of 3762 treated patients, 287 women met inclusion criteria. We included 117 patients, 21 cases and 96 controls. Patients with pCR were 5 years younger than controls (45.4 vs 49.4), have more grade-3 tumors, (66.7 vs 22.3%), more Luminal B subtypes (90.5 vs 64.6%), lower expression of estrogen receptor (60 vs 80%) and higher Ki67 expression (65 vs 12%), all with p≤0.05. No differences in toxicity existed between groups.

In an initial screening procedure, 13 SNPs were identified, but only 4 SNPs (4 genes) are known to participate in ADME of antineoplastic agents. All pCR cases did not have the C/C allelic variant in the rs2072671 SNP (CDA gene); while in rs1883322 SNP (PPARD gene) all had T/T variant

SNPs identified in DMET microarray known to participate with antineoplastic agentsGENESNPAllelic variantpCR, n=21No pCR, n=96pDPYDrs17376848T/T13 (61.9%)83 (86.4%)0.007  C/T8 (38.1%)11 (11.4%) CDArs2072671A/A6 (28.5%)51 (53.1%)0.013  A/C15 (71.4%)36 (37.5%)   C/C09 (9.3%) PPARDrs1883322T/T21 (100%)69 (71.8%)0.022  C/T022 (22.9%)   C/C05 (5.2%) GSTM3rs7483A/A7 (33.3%)20 (20.8%)0.024  A/G13 (61.9%)43 (44.7%)   G/G1 (4.7%)33 (34.3%) pCR= pathologic complete response

After logistic regression analysis, pCR predictive factors were the presence of grade-3 tumors OR=6.66 (95%CI=1.67-26.56), Ki67 ≥14% OR=15.45 (95%CI=1.71–138.86), premenopausal status OR=6.540 (95%CI=1.50–28.38) and A/A or A/G allele in rs7483 SNP (GSTM3 gene) OR=19.16 (95%CI=1.97–185.93).

Conclusions

Genetic variability encoded in the DMET-chip, could be helpful as a predictive factor of pCR in patients with Luminal HER2(-) LABC, but only in combination with other factors such as grade-3 tumors, elevated Ki67, and premenopausal status.

Citation Format: Ruvalcaba-Limon E, Rodriguez-Cuevas S, Hidalgo-Miranda A, Villa-Romero A, Bautista-Piña V, Rebollar-Vega R, Fernandez-Lopez JC, Morales-Vasquez F. Predictive factors of pathologic complete response to neoadjuvant chemotherapy in patients with Luminal HER2(-) local advanced breast cancer using the DMET microarray [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-09-18.

Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016

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Polfus, CHARGE and NHLBI Exome Sequence Project Working Groups P48 Association of adipoq gene with type 2 diabetes and related phenotypes in african american men and women: The jackson heart study S. Davis, R. Xu, S. Gebeab, P Riestra, A Gaye, R. Khan, J. Wilson, A. Bidulescu P49 Common variants in casr gene are associated with serum calcium levels in koreans S. H. Jung, N. Vinayagamoorthy, S. H. Yim, Y. J. Chung P50 Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with multiple exponential functions Y. Zhou, S. Xu P51 A Bayesian framework for generalized linear mixed models in genome-wide association studies X. Wang, V. Philip, G. Carter P52 Targeted sequencing approach for the identification of the genetic causes of hereditary hearing impairment A. A. Abuzenadah, M. Gari, R. Turki, A. Dallol P53 Identification of enhancer sequences by ATAC-seq open chromatin profiling A. Uyar, A. Kaygun, S. Zaman, E. Marquez, J. George, D. Ucar P54 Direct enrichment for the rapid preparation of targeted NGS libraries C. L. Hendrickson, A. Emerman, D. Kraushaar, S. Bowman, N. Henig, T. Davis, S. Russello, K. Patel P56 Performance of the Agilent D5000 and High Sensitivity D5000 ScreenTape assays for the Agilent 4200 Tapestation System R. Nitsche, L. Prieto-Lafuente P57 ClinVar: a multi-source archive for variant interpretation M. Landrum, J. Lee, W. Rubinstein, D. Maglott P59 Association of functional variants and protein physical interactions of human MUTY homolog linked with familial adenomatous polyposis and colorectal cancer syndrome Z. Abduljaleel, W. Khan, F. A. Al-Allaf, M. Athar , M. M. Taher, N. Shahzad P60 Modification of the microbiom constitution in the gut using chicken IgY antibodies resulted in a reduction of acute graft-versus-host disease after experimental bone marrow transplantation A. Bouazzaoui, E. Huber, A. Dan, F. A. Al-Allaf, W. Herr, G. Sprotte, J. Köstler, A. Hiergeist, A. Gessner, R. Andreesen, E. Holler P61 Compound heterozygous mutation in the LDLR gene in Saudi patients suffering severe hypercholesterolemia F. Al-Allaf, A. Alashwal, Z. Abduljaleel, M. Taher, A. Bouazzaoui, H. Abalkhail, A. Al-Allaf, R. Bamardadh, M. Athar

On the effects of CP 55-940 and other cannabinoid receptor agonists in C6 and U373 cell lines

Cannabinoid receptor (CBs) agonists affect the growth of tumor cells via activation of deadly cascades. The spectrum of action of these agents and the precise role of the endocannabinoid system (ECS) on oncogenic processes remain elusive. Herein we compared the effects of synthetic (CP 55-940 and WIN 55,212-2) and endogenous (anandamide or AEA) CBs agonists (10-20 μM) on morphological changes, cell viability, and induction of apoptosis in primary astrocytes and in two glioblastoma cell lines (C6 and U373 cells) in order to characterize their possible differential actions on brain tumor cells. None of the CBs agonist tested induced changes in cell viability or morphology in primary astrocytes. In contrast, CP 55-940 significantly decreased cell viability in C6 and U373 cells at 5 days of treatment, whereas AEA and WIN 55,212-2 moderately decreased cell viability in both cell lines. Treatment of U373 and C6 for 3 and 5 days with AEA or WIN 55,212-2 produced discrete morphological changes in cell bodies, whereas the exposure to CP 55-940 induced soma degradation. CP 55-940 also induced apoptosis in both C6 and U373 cell lines. Our results support a more effective action of CP 55-940 to produce cell death of both cell lines through apoptotic mechanisms. Comparative aspects between cannabinoids with different profiles are necessary for the design of potential treatments against glial tumors.

MRNA and miRNA expression patterns associated to pathways linked to metal mixture health effects

Metals are a threat to human health by increasing disease risk. Experimental data have linked altered miRNA expression with exposure to some metals. MiRNAs comprise a large family of non-coding single-stranded molecules that primarily function to negatively regulate gene expression post-transcriptionally. Although several human populations are exposed to low concentrations of As, Cd and Pb as a mixture, most toxicology research focuses on the individual effects that these metals exert. Thus, this study aims to evaluate global miRNA and mRNA expression changes induced by a metal mixture containing NaAsO2, CdCl2, Pb(C2H3O2)2·3H2O and to predict possible metal-associated disease development under these conditions. Our results show that this metal mixture results in a miRNA expression profile that may be responsible for the mRNA expression changes observed under experimental conditions in which coding proteins are involved in cellular processes, including cell death, growth and proliferation related to the metal-associated inflammatory response and cancer.

Differential gene expression between skin and cervix induced by the E7 oncoprotein in a transgenic mouse model

HPV16 E7 oncoprotein expression in K14E7 transgenic mice induces cervical cancer after 6 months of treatment with the co-carcinogen 17β-estradiol. In untreated mice, E7 also induces skin tumors late in life albeit at low penetrance. These findings indicate that E7 alters cellular functions in cervix and skin so as to predispose these organs to tumorigenesis. Using microarrays, we determined the global genes expression profile in cervical and skin tissue of young adult K14E7 transgenic mice without estrogen treatment. In these tissues, the E7 oncoprotein altered the transcriptional pattern of genes involved in several biological processes including signal transduction, transport, metabolic process, cell adhesion, apoptosis, cell differentiation, immune response and inflammatory response. Among the E7-dysregulated genes were ones not previously known to be involved in cervical neoplasia including DMBT1, GLI1 and 17βHSD2 in cervix, as well as MMP2, 12, 14, 19 and 27 in skin.

Gene expression profile of cervical and skin tissues from human papillomavirus type 16 E6 transgenic mice

Background

Although K14E6 transgenic mice develop spontaneous tumors of the skin epithelium, no spontaneous reproductive tract malignancies arise, unless the transgenic mice were treated chronically with 17β-estradiol. These findings suggest that E6 performs critical functions in normal adult cervix and skin, highlighting the need to define E6-controlled transcriptional programs in these tissues.

Methods

We evaluated the expression profile of 14,000 genes in skin or cervix from young K14E6 transgenic mice compared with nontransgenic. To identify differentially expressed genes a linear model was implemented using R and the LIMMA package. Two criteria were used to select the set of relevant genes. First a set of genes with a Log-odds ≥ 3 were selected. Then, a hierarchical search of genes was based on Log Fold Changes.

Results

Microarray analysis identified a total of 676 and 1154 genes that were significantly up and down-regulated, respectively, in skin from K14E6 transgenic mice. On the other hand, in the cervix from K14E6 transgenic mice we found that only 97 and 252 genes were significantly up and down-regulated, respectively. One of the most affected processes in the skin from K14E6 transgenic mice was the cell cycle. We also found that skin from transgenic mice showed down-regulation of pro-apoptotic genes and genes related to the immune response. In the cervix of K14E6 transgenic mice, we could not find affected any gene related to the cell cycle and apoptosis pathways but did observe alterations in the expression of immune response genes. Pathways such as angiogenesis, cell junction and epidermis development, also were altered in their gene expression profiles in both tissues.

Conclusion

Expression of the HPV16 E6 oncoprotein in our model alters expression of genes that fell into several functional groups providing insights into pathways by which E6 deregulate cell cycle progression, apoptosis, the host resistance to infection and immune function, providing new opportunities for early diagnostic markers and therapeutic drug targets.