Cristobal Fresno

The Human Papillomavirus (HPV) test is a crucial technology for cervical cancer prevention because it enables programs to identify women with high-risk HPV infection who are at risk of developing cervical cancer. Current U.S. Preventive Services Task Force recommendations include cervical cancer screening every three years with cervical cytology alone or every five years with either high-risk HPV testing alone or high-risk HPV testing combined with cytology (co-testing). In Argentina, 7,548 new cervical cancer cases are diagnosed each year with 3,932 deaths attributed to this cause. Our study aims to show the clinical implementation of a cervical cancer screening program by concurrent HPV testing and cervical cytology (co-testing); and to evaluate the possible cervical cancer screening scenarios for Latin America, focusing on their performance and average cost. A cervical cancer screening five year program via co-testing algorithm (Hybrid-2-Capture/cytology) was performed on women a...

Breast cancer is the leading cause of death on women worldwide. Whereas surgical resection and adjuvant therapy can cure well-confined primary tumors, metastatic disease is largely incurable because of its systemic nature and the resistance of disseminated tumor cells to existing therapeutic agents. SPARC (Secreted Protein Acidic and Rich in Cystein) is a matricellular protein whose normal expression is associated with remodeling tissues. In this context SPARC was described as involved in cell cycle and proliferation, invasion, adhesion, migration, angiogenesis and apoptosis. Expression array technology among other approaches identified SPARC as marker of poor prognosis, very often associated with most aggressive tumors in the vast majority of human cancer types. However, there is confusing data regarding the role of this protein during the development and progression of breast tumors. In order to achieve a better understanding of the role of this protein during breast cancer progression, we used the murine metastatic breast cancer model, 4T1. We found that silencing SPARC in these epithelial cells, after transduction with a lentiviral vector carrying a siRNA against murine SPARC, results in the completely loss of their metastatic capability (p Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1417. doi:1538-7445.AM2012-1417

Background RNA_seq technology is emerging as a promising tool for transcriptomics analysis. In general it implies the identification of gene and evaluates some experimental condition in terms of expression, using millions of reads produced by a high-throughput sequencing machine. The huge output is processed in several steps and requires taking in consideration many aspects. Although the technique is revolutionary, it is not stable yet. Therefore many variation sources including technical and random effects should be properly accounted in order to reduce bias from the results [1]. In addition, when you plan to do functional analysis it is compulsory to use the most appropriate gene identifier which depends on the functional platform. In this context, gene symbols are unsteady. Hence, a combination of data bases is necessary to retrieve the appropriate gene annotations. Here we propose a standard operating procedure for RNA_seq analysis, to detect and remove some bias sources from th...

RESUMEN El control de calidad es una etapa fundamental para remover artefactos técnicos en datos de expresión de genes obtenidos a través de microarreglos de ADN. Los abordajes tradicionales sólo emplean estrategias univariadas, con el fin de comprobar el supuesto de normalidad global de los genes, al igual que para obtener valores de expresión comparables entre las diferentes muestras. No obstante, los anteriores presentan dos falencias: i) no incluyen la información del diseño experimental en el control de calidad; ii) la exploración de los genes se realiza de forma univariada. En este contexto, se presenta como alternativa para el control de calidad, descomponer los valores observados de expresión utilizando la información del diseño experimental a través de un análisis de la varianza (ANOVA). Luego, la contribución de los diferentes factores puede ser analizada de forma multivariada mediante dos técnicas de exploración como los son el Análisis de Componentes Principales (PCA por...

The lmdme package implements analysis of variance (ANOVA) decomposition through linear models on designed multivariate experiments in R (R Development Core Team, 2012), allowing ANOVA-principal component analysis (APCA) and ANOVA-simultaneous component analysis (ASCA). It also extends both methods with the application of partial least squares (PLS) through the specification of a desired output matrix. The package is freely available on the Bioconductor website (Gentleman et al., 2004), licenced under GNU general public license. ANOVA decomposition methods for multivariate designed experiments are becoming popular in “omics ” experiments (transcriptomics, metabolomics, etc.) where measurements are performed according to a predefined experimental design (Smilde et al., 2005), with several experimental factors or including subject specific clinical covariates, such as those present in current clinical genomic studies. ANOVA-PCA and ASCA are well-suited methods to study interaction patt...

Background: In 2020, cervical cancer was the fourth most common cancer globally, with an incidence of 13·3. In Argentina, 7548 new cases are diagnosed each year, with 3932 women dying from this cause. This study aims to show the clinical implementation of a cervical cancer screening program by concurrent HPV testing and cervical cytology (co-testing), in women aged 30-65 years, at a University Hospital setting; and to analyze the five-year cumulative incidence rate of cervical cancer. Methods: Between July 2013 and June 2018, cervical samples were collected from women between the ages of 30 to 65 for cervical cancer screening via co-testing (HC2/PAP). Descriptive statistical analysis, multinomial logistic regression and classification metrics were applied over the data. Findings: A total of 2273 women were included. 91·11% of the participants tested double negative, 2·55% double positive, 5·90% HC2-positive/PAP-negative, and 0·44% HC2-negative/PAP-positive. Of the 171 women with fol...

There has been limited study of Native American whole genome diversity to date, which impairs effective implementation of personalized medicine and a detailed description of its demographic history. Here we report high coverage whole genome sequencing of 76 unrelated individuals, from 27 indigenous groups across Mexico, with more than 97% average Native American ancestry. On average, each individual has 3.26 million Single Nucleotide Variants and short indels, that together comprise a catalog of 9,737,152 variants, 44,118 of which are novel. We report 497 common Single Nucleotide Variants (with allele frequency > 5%) mapped to drug responses and 316,577 in enhancer or promoter elements; interestingly we found some of these enhancer variants in PPARG, a nuclear receptor involved in highly prevalent health problems in Mexican population, such as obesity, diabetes, and insulin resistance. By detecting signals of positive selection we report 24 enriched key pathways under selection, ...

Background Around the world, there is a significant difference in the proportion of women with access to leadership in healthcare with respect to men. This article studies gender imbalance and wage gap in managerial, executive, and directive job positions at the Mexican National Institutes of Health. Methods Cohort data were described using a visual circular representation and modeled using a generalized linear model. Analysis of variance was used to assess model significance, and posterior Fisher’s least significant differences were analyzed when appropriate. Results This study demonstrated that there is a gender imbalance distribution among the hierarchical position at the Mexican National Health Institutes and also exposed that the wage gap exists mainly in the (highest or lowest) ranks in hierarchical order. Conclusions Since the majority of the healthcare workforce is female, Mexican women are still underrepresented in executive and directive management positions at national he...

Background Understanding the spatial and temporal patterns of mortality rates in a highly inhomogeneous metropolis, is a matter of public policy interest. In this context, there is no previous study that correlates both spatio-temporal and age-specific mortality rates in Mexico City. Methods Spatio-temporal kriging modelling was used over six age-specific mortality rates (from the years 2000 to 2016 in Mexico City), to gain both spatial (borough and neighbourhood) and temporal (year and trimester) data level description. Resulting data were modelled using time-evolution mixed effect models to unblurred mortality age-specific patterns. Posterior tests were carried out to compare mortality averages between geospatial locations. Results Mortality correlation extends in all study groups for as long as 12 years and as far as 13.27 km. The highest mortality rate takes place in the Cuauhtémoc borough, as it is the commercial, touristic and cultural core downtown Mexico City. On the contrar...

Breast cancer is a complex heterogeneous disease. A clear example is given by the four molecular subtypes: Luminal A, Luminal B, HER2-Enriched and Basal-like. These subtypes give way to different therapeutic approaches to deal with different prognosis. Despite these differences, common hallmark features of cancer can be found, which its origin is traced back to the intricate relationships governing regulatory programs. In our recent work, by constructing RNA-Seq normal tissue and breast cancer gene regulatory networks, we have observed the phenomenon of loss of inter-chromosomal regulation. Our results showed that cis- regulation in breast cancer tissue occurs mostly between neighbour genes. On the contrast, in non-cancerous tissue, gene-gene regulation appears along the whole genome. Here, we extend the aforementioned approach, in order to observe into what extent the loss of trans- regulation occurs in the different intrinsic breast cancer subtypes. A collection of 780 RNA-Seq The...

Biological systems exhibit unique phenotypes as the result of the expression of a genomic program. The regulation of this program is a complex phenomenon, wherein different regulatory mechanisms are involved. The deregulation of this program is at the centre of the emergence of diseases such as breast cancer. In particular, it has been observed that coregulation patterns between physically distant genes are lost in breast cancer. In this work, we present a systematic study of chromosome-wide gene coregulation patterns in breast cancer as inferred by information theoretical measures over large (whole-genome expression in several hundred transcriptomes) experimental data corpora. We analyzed the chromosomal distance decay of correlations and found it to be with fat-tail distribution in breast cancer while being fundamentally constant in nontumour samples. After model discrimination analyses, we concluded that the behaviour of the breast cancer distributions belongs to an intermediate ...

Understanding the mechanism of metastatic dissemination is crucial for the rational design of novel therapeutics. The secreted protein acidic and rich in cysteine (SPARC) is a matricellular glycoprotein which has been extensively associated with human breast cancer aggressiveness although the underlying mechanisms are still unclear. Here, shRNA-mediated SPARC knockdown greatly reduced primary tumor growth and completely abolished lung colonization of murine 4T1 and LM3 breast malignant cells implanted in syngeneic BALB/c mice. A comprehensive study including global transcriptomic analysis followed by biological validations confirmed that SPARC induces primary tumor growth by enhancing cell cycle and by promoting a COX-2-mediated expansion of myeloid-derived suppressor cells (MDSC). The role of SPARC in metastasis involved a COX-2-independent enhancement of cell disengagement from the primary tumor and adherence to the lungs that fostered metastasis implantation. Interestingly, SPARC...

Targeted sequencing is growing as a screening methodology used in research and medical genetics to identify genomic alterations causing human diseases. In general, a list of possible genomic variants is derived from mapped reads through a variant calling step. This processing step is usually based on variant coverage, although it may be affected by several factors. Therefore, under-covered relevant clinical variants may not be reported, impacting on pathology diagnosis or treatment. Thus, a prior quality control of the experiment is critical to determine variant detection accuracy and to avoid erroneous medical conclusions. There are several quality control tools, but they are focused on issues related to whole genome sequencing. However, in targeted sequencing, quality control should assess experiment, gene and genomic region performances based on achieved coverages. Here, we propose TarSeqQC R package for quality control in targeted sequencing experiments. The tool is freely avail...

Transcriptome analysis is essential to understand the mechanisms regulating key biological processes and functions. The first step usually consists of identifying candidate genes; to find out which pathways are affected by those genes, however, functional analysis (FA) is mandatory. The most frequently used strategies for this purpose are Gene Set and Singular Enrichment Analysis (GSEA and SEA) over Gene Ontology. Several statistical methods have been developed and compared in terms of computational efficiency and/or statistical appropriateness. However, whether their results are similar or complementary, the sensitivity to parameter settings, or possible bias in the analyzed terms has not been addressed so far. Here, two GSEA and four SEA methods and their parameter combinations were evaluated in six datasets by comparing two breast cancer subtypes with well-known differences in genetic background and patient outcomes. We show that GSEA and SEA lead to different results depending o...

High throughput mRNA sample sequencing, known as RNA-seq, is as a powerful approach to detect differentially expressed genes starting from millions of short sequence reads. Although several workflows have been proposed to analyze RNA-seq data, the experiment quality control as a whole is not usually considered, thus potentially biasing the results and/or causing information lost. Experiment quality control refers to the analysis of the experiment as a whole, prior to any analysis. It not only inspects the presence of technical effects, but also if general biological assumptions are fulfilled. In this sense, multivariate approaches are crucial for this task. Here, a multivariate approach for quality control in RNA-seq experiments is proposed. This approach uses simple and yet effective well-known statistical methodologies. In particular, Principal Component Analysis was successfully applied over real data to detect and remove outlier samples. In addition, traditional multivariate exploration tools were applied in order to asses several controls that can help to ensure the results quality. Based on differential expression and functional enrichment analysis, here is demonstrated that the information retrieval is significantly enhanced through experiment quality control. Results show that the proposed multivariate approach increases the information obtained from RNA-seq data after outlier samples removal.

The aim of the present study was to evaluate the effects of sperm motility enhancers and different IVF times on cleavage, polyspermy, blastocyst formation, embryo quality and hatching ability. In Experiment 1, sex-sorted X chromosome-bearing Bos taurus spermatozoa were incubated for 30 min before 18 h fertilisation with hyperactivating factors, namely 10 mM caffeine (CA), 5 mM theophylline (TH), 10 mM caffeine and 5 mM theophylline (CA + TH); and untreated spermatozoa (control). In Experiment 2, matured B. taurus oocytes were fertilised using a short (8 h) or standard (18 h) fertilisation length, comparing two different fertilisation media, namely synthetic oviducal fluid (SOF) fertilisation medium (SOF-FERT) and M199 fertilisation medium (M199-FERT). Cleavage and blastocyst formation rates were significantly higher in the CA + TH group (77% and 27%, respectively) compared with the control group (71% and 21%, respectively). Cleavage rates and blastocyst formation were significantly ...

RESUMEN Uno de los objetivos más frecuentes en los análisis de expresión génica es identificar genes cuyos niveles de expresión cambian entre dos o más condiciones experimentales. Para este fin es habitual utilizar modelos paramétricos [1] o no paramétricos [2] sobre cada gen de manera independiente. Este enfoque es adecuado en diseños simples pero se vuelve insuficiente cuando el diseño experimental adquiere mayor complejidad. En este marco, los modelos mixtos se presentan como una herramienta potente y flexible para el análisis de experimentos multifactoriales complejos, como aquellos que involucran diseños desbalanceados, medidas repetidas o dependencias entre los datos. Sin embargo, los mismos presentan algunas dificultades técnicas que han complicado su uso en forma extendida. En primer lugar, los algoritmos utilizados son computacionalmente intensivos, lo cual no es despreciable cuando se deben ajustar miles de modelos en simultáneo. Además, la selección del modelo más plausib...

Whether the treatment of Parkinson's disease has to be initiated with levodopa or a D2 agonist like pramipexole remains debatable. Levodopa is more potent against symptoms than D2 agonists, but D2 agonists are less prone to induce motor complications and may have neuroprotective effects. Although regulation of plastic changes in striatal circuits may be the key to their different therapeutic potential, the gene expression patterns induced by de novo treatments with levodopa or D2 agonists are currently unknown. By studying the whole striatal transcriptome in a rodent model of early stage Parkinson's disease, we have identified the gene expression patterns underlying therapeutically comparable chronic treatments with levodopa or pramipexole. Despite the overall relatively small size of mRNA expression changes at the level of individual transcripts, our data show a robust and complete segregation of the transcript expression patterns induced by both treatments. Moreover, transcripts related to oxidative metabolism and mitochondrial function were enriched in levodopa-treated compared to vehicle-treated and pramipexole-treated animals, whereas transcripts related to olfactory transduction pathways were enriched in both treatment groups compared to vehicle-treated animals. Thus, our data reveal the plasticity of genetic striatal networks possibly contributing to the therapeutic effects of the most common initial treatments for Parkinson's disease, suggesting a role for oxidative stress in the long term complications induced by levodopa and identifying previously overlooked signaling cascades as potentially new therapeutic targets.