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Nieto-Valle, A.

Publications and source records attributed to Nieto-Valle, A..

2 recordsLinked to original sources

Chemokine profiling of melanoma-macrophage crosstalk identifies CCL8 and CCL15 as prognostic factors in cutaneous melanoma

During cancer evolution, tumor cells attract and dynamically interact with monocytes/macrophages. To find biomarkers of disease progression in human melanoma, we used unbiased RNA sequencing and secretome analyses of tumor-macrophage co-cultures. Pathway analysis of genes differentially modulated in human macrophages exposed to melanoma cells revealed a general upregulation of inflammatory hallmark gene sets, particularly chemokines. A selective group of chemokines, including CCL20, CCL15 and CCL8, was actively secreted upon melanoma-macrophage co-culture. Because we previously described the role of CCL20 in melanoma, we focused our study in CCL8 and CCL15, and confirmed that in vitro both chemokines contributed to melanoma survival, proliferation and 3D invasion, through CCR1 signaling. In vivo, both chemokines enhanced primary tumor growth, spontaneous lung metastasis and circulating tumor cell (CTC) survival and lung colonization in mouse xenograft models. Finally, we explored the clinical significance of CCL8 and CCL15 expression in human skin melanoma, screening a collection of 67 primary melanoma samples, by multicolor staining and quantitative image analysis of chemokine-chemokine receptor content at the single cell level. Primary skin melanomas displayed high CCR1 expression, but there was no difference in its level of expression between metastatic and non-metastatic cases. By contrast, the comparative analysis between these two clinically divergent groups showed a highly significant difference in the cancer cell content of CCL8 (P= 0.025) and CCL15 (P< 0.0001). Kaplan-Meier curves showed that high content of CCL8 or CCL15 in cancer cells correlated with shorter disease-free and overall survival (log-rank test, p< 0.001). Our results highlight the role of CCL8 and CCL15, which are highly induced by melanoma-macrophage interactions in biologically aggressive primary melanomas, and could be clinically applicable biomarkers for patient profiling.

cancer biology↗

Accuracy of direct genomic values and methylation profile through genotype-by-LowPass sequencing using Nanopore technology

Genotype-by-sequencing has been proposed as an alternative to SNP genotyping arrays in genomic selection to obtain a high density of markers along the genome. It requires a low sequencing depth to be cost effective, which may increase the error at the genotype assigment. Third generation Nanopore sequencing technology offers low cost sequencing and the possibility to detect genome methylation, which provides added value to genotype-by-sequencing. The aim of this study was to evaluate the performance of genotype-by-LowPass Nanopore sequencing for estimating the direct genomic value in dairy cattle, and the possibility to obtain methylation marks simultaneously. Latest Nanopore chemistry (LSK14 and Q20) achieved a modal base calling accuracy of 99.55 %, whereas previous kit (LSK109) achieved slightly lower accuracy (99.1 %). The direct genomic value accuracy from genotype-by-Low Pass sequencing ranged between 0.79 and 0.99, depending on the trait, with a sequencing depth as low as 2x and using the latest chemistry (LSK114). Lower sequencing depth led to biased estimates, yet with high rank correlations. The LSK109 and Q20 achieved lower accuracies (0.57-0.93). More than one million high reliable methylated sites were obtained, even at low sequencing depth, located mainly in distal intergenic (87 %) and promoter (5 %) regions. This study showed that the latest Nanopore technology can be use in a LowPass sequencing framework to estimate direct genomic values with high reliability. It may provided advantages in populations with no available SNP chip, or when a large density of markers with a wide range of allele frequencies is needed. In addition, Low Pass sequencing provided with nucleotide methylation status of >1 million nucleotides at [&ge;] 10x, which is an added value for epigenetic studies.

genomics↗