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Transvaginal ultrasound-guided oocyte retrieval (commonly called OPU) and in vitro embryo production (IVP) in cattle has shown significant progress in recent years, in part, as a result of a better understanding of the full potential of these tools by end users. The combination of OPU and IVP (OPU-IVP) has been successfully and widely commercially used worldwide. The main advantages are a greater number of embryos and pregnancies per unit of time, faster genetic progress due to donor quick turn around and more elite sires mating combinations, larger spectrum of female age (calves, prepuberal, heifer, cow) and condition (open, pregnant) from which to retrieve oocytes, a reduced number of sperm (even sexed) required to fertilize the oocytes, among other benefits. OPU-IVP requires significant less donor preparation in comparison to conventional embryo transfer (50% of usual FSH injections needed) to the extent of no stimulating hormones (FSH) are necessary. Donor synchronization, stimulation, OPU technique, oocyte competence, embryo performance, and its impact on cryopreservation and pregnancy are discussed.

Objective: To analyze the frequency of KRAS, NRAS and BRAF hotspot mutations in circulating tumor DNA (ctDNA) from patients with metastatic colorectal cancer (mCRC). Methods: Observational, descriptive and retrospective study in mCRC patients with available ctDNA-based genotype of KRAS, NRAS and BRAF. Results: The frequencies of plasma mutations for KRAS, NRAS and BRAF were 34% (± 7), 4% (± 3) and 4% (± 3), respectively. Median overall survival of plasma-tested RAS/BRAF-mutated patients was 26.6 months (95% CI: 14.4–not estimable [NE]), while RAS/BRAF wild-type patients did not reach the median survival during follow-up. Median progression-free survival for RAS/BRAF wild-type and RAS/BRAF-mutated patients was 12 (95% CI: 7–NE) and 4 months (95% CI: 4–NE), respectively. Conclusion: Our work supports the utility of KRAS, NRAS and BRAF analysis in liquid biopsy from mCRC patients.

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-driven gene expression signatures obtained from these murine models predicted the clinical outcome of patients with HER2-enriched breast cancer subtypes. In total, the results reveal that SPARC and its downstream effectors are attractive targets for antimetastatic therapies in breast cancer.Implications: These findings shed light on the prometastatic role of SPARC, a key protein expressed by breast cancer cells and surrounding stroma, with important consequences for disease outcome. Mol Cancer Res; 15(3); 304–16. ©2016 AACR.

This file contains legends of Supplementary Figures S1-S8

Figure S1. Association between SPARC expression and distant metastasis free survival (RFS) in breast cancer patients with different PAM50 subtypes. Figure S2. Downregulation of SPARC expression in 4T1 and LM3 murine breast cancer cell lines. Figure S3. SPARC targeting inhibits primary tumor growth and lung metastasis establishment. Figure S4. SPARC-deficient cells exhibit a delay in cell cycle progression. Figure S5. Transcriptomic analysis of SPARC-deficient tumors revealed changes in cell-ECM interaction and immune response. Figure S6. Enforced expression of COX-2 in SPARC-deficient 4T1 cells partially restores cells capacity to grow as primary tumor. Figure S7. SPARC targeting impairs invasive capacity of breast cancer cells. Figure S8. Association between hS-PT and hS-ESM expression and distant metastasis free survival (RFS) in breast cancer patients with different PAM50 subtypes.

This file contains Supplementary Tables S1-S12

This file contains Supplementary Materials and Methods

Circulating Tumor Cells (CTCs) are considered a prognostic marker in pancreatic cancer. In this study we present a new approach for counting CTCs and CTC clusters in patients with pancreatic cancer using the IsofluxTM System with the Hough transform algorithm (Hough-IsofluxTM). The Hough-IsofluxTM approach is based on the counting of an array of pixels with a nucleus and cytokeratin expression excluding the CD45 signal. Total CTCs including free and CTC clusters were evaluated in healthy donor samples mixed with pancreatic cancer cells (PCCs) and in samples from patients with pancreatic ductal adenocarcinoma (PDAC). The IsofluxTM System with manual counting was used in a blinded manner by three technicians who used Manual-IsofluxTM as a reference. The accuracy of the Hough-IsofluxTM approach for detecting PCC based on counted events was 91.00% [84.50, 93.50] with a PCC recovery rate of 80.75 ± 16.41%. A high correlation between the Hough-IsofluxTM and Manual-IsofluxTM was observed for both free CTCs and for clusters in experimental PCC (R2 = 0.993 and R2 = 0.902 respectively). However, the correlation rate was better for free CTCs than for clusters in PDAC patient samples (R2 = 0.974 and R2 = 0.790 respectively). In conclusion, the Hough-IsofluxTM approach showed high accuracy for the detection of circulating pancreatic cancer cells. A better correlation rate was observed between Hough-IsofluxTM approach and with the Manual-IsofluxTM for isolated CTCs than for clusters in PDAC patient samples.

Triple negative breast cancer (TNBC) has poor prognosis and neither established biomarkers nor therapeutic targets. On the one hand, the androgen receptor (AR), a steroid hormone receptor (SR) which is expressed in 10-53% of TNBC and proved to be critical for BC proliferation, has been proposed as a new target in TNBC. On the other, we and others have shown that membrane ErbB-2 migrates to the nucleus (nuclear ErbB-2, NErbB-2) where it binds DNA at HER-2 associated sequences (HAS) to regulate BC proliferation and migration. Since we have previously shown a functional interplay between growth factors and SR signaling pathways in BC, we propose the existence of an interaction between AR and ErbB-2 which is involved in NErbB-2+/AR+ BC growth. The experimental model used was the human TNBC cell line MDA-MB-453 which displays high expression levels of AR and NErbB-2. We have previously shown that dihydrotestosterone (DHT)-activated AR induces Src-mediated ErbB-2 rapid activation and its migration to the nucleus where it binds to HAS sites in the DNA. By coimmunoprecipitation and WB studies, we have now shown that this crosstalk involves ErbB-2 and AR physical association which is inhibited by the AR antagonist enzalutamide. By microarray and bioinformatics analysis we have also previously identified a set of differentially expressed genes (DEGs) in the presence of DHT and NErbB-2 eviction to define an independent predictor of better clinical outcome in TNBC. By using the Tumor Immune Estimation Resource (TIMER) we found a significant association of the expression of the gene signature and the abundance of tumor immune infiltrates, in accordance with the involvement of the gene signature in the immune response and interferon pathways. We have validated the regulation of the gene signature in MDA-MB-453 cells and found that in the presence of DHT, eviction of NErbB-2 significantly induces the mRNA expression of the genes CXCL10, HLA-A, NMI, STAT1 and TAP1, members of said gene signature. We have also identified AREs and HAS sites in STAT1, NMI and TAP1 and studied AR and ErbB-2 recruitment to the chromatin by ChIP assays. We found that DHT induces ErbB-2 binding to its HAS sites in STAT1 in regulatory regions. Our findings evidence that DHT-activated AR induces ErbB-2 rapid activation and its migration to the nucleus where it binds to HAS sites in regulatory regions of a set of genes involved in the immune response in TNBC. Presentation: No date and time listed

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, most of them related to immune mechanisms. No missense variants in ACE2, the receptor responsible for the entry of the SARS CoV-2 virus, were found in any individual. Population genomics and phylogenetic analyses demonstrated stratification in a Northern-Central-Southern axis, with major substructure in the Central region. The Seri, a northern group with the most genetic divergence in our study, showed a distinctive genomic context with the most novel variants, and the most population specific genotypes. Genome-wide analysis showed that the average haplotype blocks are longer in Native Mexicans than in other world populations. With this dataset we describe previously undetected population level variation in Native Mexicans, helping to reduce the gap in genomic data representation of such groups.

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 follow-up who tested HC2-positive, 39·77% cleared the viral infection, 37·43% showed viral persistence, and 22·81% were treated after the detection via colposcopy/biopsy of histological HSIL. Interpretation: The prevalence of hrHPV in this population was 0·08, with HSIL histology detection rates of 17·32 per 1000 screened women. Cytology could be considered a prognostic factor in women with an HC2-positive test, an association which has not yet been described. This evidence suggests that the introduction of co-testing could diminish the burden of cervical cancer in low- and middle-income countries, acting as a tool against inequity in healthcare. Funding: The implementation of this program was possible thanks to the inclusion of cotesting into CEMIC’s private health insurance coverage. Declaration of Interest: VD has received personal fees (as a consultant and/or speaker bureau) from Thermo Fisher, BMS, Novartis, Amgen, and Roche; and their researches are sponsored by BMS, Novartis, Amgen, AstraZeneca, and Roche, unrelated to the current work. FvP has been sponsored by Roche and Megablabs (academic grant/attending meetings), unrelated to the current work. VF has been sponsored by Roche (academic grant), unrelated to the current work. AA has been sponsored by AMGEN (academic grant), unrelated to the current work. FM has been sponsored by Tecnolab and Roche (academic grant/attending meetings), unrelated to the current work. The other authors declare no conflict of interest. Ethical Approval: This protocol was reviewed and approved by the local Institutional Review Board (IRB).

Next-Generation Sequencing (NGS) is widely used to investigate genomic variation. In several studies, the genetic variation ofMycobacterium tuberculosishas been analyzed in sputum samples without previous culture, using target enrichment methodologies for NGS. Alignments obtained by different programs generally map the sequences under default parameters, and from these results, it is assumed that onlyMycobacteriumreads will be obtained. However, variants of interest microorganism in clinical samples can be confused with a vast collection of reads from other bacteria, viruses, and human DNA. Currently, there are no standardized pipelines, and the cleaning success is never verified since there is a lack of rigorous controls to identify and remove reads from other sputum-microorganisms genetically similar toM.tuberculosis. Therefore, we designed a bioinformatic pipeline to process NGS data from sputum samples, including several filters and quality control points to identify and eliminate non-M.tuberculosisreads to obtain a reliable genetic variant report. Our proposal uses the SURPI software as a taxonomic classifier to filter input sequences and perform a mapping that provides the highest percentage ofMycobacteriumreads, minimizing the reads from other microorganisms. We then use the filtered sequences to perform variant calling with the GATK software, ensuring the mapping quality, realignment, recalibration, hard-filtering, and post-filter to increase the reliability of the reported variants. Using default mapping parameters, we identified reads of contaminant bacteria, such asStreptococcus,Rhotia,Actinomyces, andVeillonella. Our final mapping strategy allowed a sequence identity of 97.8% between the input reads and the wholeM.tuberculosisreference genomeH37Rvusing a genomic edit distance of three, thus removing 98.8% of the off-target sequences with aMycobacteriumreads loss of 1.7%. Finally, more than 200 unreliable genetic variants were removed during the variant calling, increasing the report’s reliability.

Patients with substance use disorders (SUD) are at high risk to die by suicide. So far, the neurobiology of the suicide-SUD association has not been elucidated. This study aimed to identify potential pharmacological targets among hub genes from brain gene co-expression networks of individuals with SUD in a suicidal and non-suicidal context. Post-mortem samples from the prefrontal cortex of 79 individuals were analyzed. Individuals were classified into the following groups: suicides with SUD (n = 28), suicides without SUD (n = 23), nonsuicides with SUD (n = 9), nonsuicides without SUD (n = 19). Gene expression profiles were evaluated with the Illumina HumanHT-12 v4 array. Co-expression networks were constructed in WGCNA using the differentially expressed genes found in the comparisons: (a) suicides with and without SUD and (b) nonsuicides with and without SUD. Hub genes were selected for drug-gene interaction testing in the DGIdb database. Among drugs interacting with hub genes in suicides we found MAOA inhibitors and dextromethorphan. In the nonsuicide individuals, we found interactions with eglumegad and antipsychotics (olanzapine, clozapine, loxapine). Modafinil was found to interact with genes in both suicides and nonsuicides. These drugs represent possible candidate treatments for patients with SUD with and without suicidal behavior and their study in each context is encouraged.

There is evidence supporting the presence of brain gene expression differences between suicides and non-suicides. Such differences have been implicated in suicide pathophysiology. However, regulatory factors underlying these gene expression differences have not been fully understood. Therefore, the identification of differences in regulatory mechanisms, i.e., transcriptional factors between suicides and non-suicides is crucial for the understanding of suicide neurobiology. In this study, we conducted a transcription factor network meta-study with freely available data from the prefrontal cortex of suicides and non-suicides with different mental disorders, including major depression disorder, bipolar disorder and schizophrenia, as well as healthy controls. Disorder-specific characteristics of suicides and non-suicides transcription factor networks were detected, i.e., the presence of immune response genes in both suicides and non-suicides with major depression disorder networks. Also, we found the presence of ESR1, which has been implicated to give resilience to social stress, in the non-suicides network but not in the suicides with major depression network. Suicides and non-suicides with bipolar disorder shared only three genes in common: FOS, CRY1 and PER2. In addition, we found a higher number of genes involved in immune response in the non-suicides with bipolar disorder compared to the suicides with bipolar disorder network. The suicides and non-suicides with schizophrenia networks exhibited clear differences, including the presence of circadian cycle genes in the suicides with schizophrenia network and their absence in the non-suicides with schizophrenia network. The results of this study provide insight on the regulatory mechanisms underpinning transcriptional changes in the suicidal brain.

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 regime between power law and Weibull distributions, with distinctive contributions corresponding to different chromosomes. This behaviour may have biological implications in terms of the organization of the gene regulatory program, and the changes found in this program between health and disease.

BackgroundAround 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.MethodsCohort 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.ResultsThis 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.ConclusionsSince the majority of the healthcare workforce is female, Mexican women are still underrepresented in executive and directive management positions at national healthcare organizations.

Los espermatozoides bovinos presentan una bajo relación de colesterol/fosfolípidos en la membrana plasmática. Esta característica es importante ya que el colesterol juega un papel fundamental en el mantenimiento de la estructura y funcionalidad de la membrana espermática tras la congelación, y, por lo tanto, en la supervivencia del espermatozoide tras el proceso de criopreservación. El proceso de sexado podría agravar todavía aún más esta situación. El objetivo de este trabajo es estabilizar las membranas plasmáticas de espermatozoides sexados mediante el agregado de ciclodextrinas cargadas con colesterol (CLC) post-descongelado y consecuentemente, prolongar su funcionalidad, aumentar su capacidad de fecundar ovocitos in vitro y producción de embriones. Para ello se trataron espermatozoides sexados con CLC a diferentes concentraciones e incubados por 15 minutos antes de evaluar el patrón de motilidad mediante un sistema computarizado CASA y fertilizar ovocitos in vitro. Los espermatozoides tratados con 3 mg de metil-β-ciclodextrina saturada de colesterol cada 120x106 espermatozoides presentaron mejor motilidad y vigor y se mantuvieron elevados durante el tiempo analizado. La concentración de 3 mg de CLC también produjo mayor clivaje, MOR/eBL, BL y embriones totales. Bovine sperm have a low cholesterol/phospholipids ratio in the sperm plasma membrane. This characteristic is important due to cholesterol plays a key role in maintaining the structure and function of sperm membrane after freezing, and therefore, increasing sperm survival. This situation could be amplified in case of sexed semen. The aim of this study is to stabilize the plasma membranes of sperm sexed by adding cholesterol-loaded cyclodextrins (CLC) post-thaw and consequently extend their functionality, increase their ability to fertilize oocytes and produce embryos in vitro. Sexed sperm were treated with CLC at different concentrations and incubated for 15 minutes before evaluating different motility parameters by a computerized system (CASA) and fertilize oocytes in vitro. Sperm treated with 3 mg of methyl-β-cyclodextrin saturated cholesterol for each 120x106 of sperm, showed higher motility parameters and remained high during the analyzed period. The concentration of 3 mg of CLC also increased cleavage rate, early (MOR/eBL), late (BL) and total embryo development. EEA Rafaela Fil: Ferre, Luis Bernardo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela; Argentina. Fil: Grötter, L. Universidad Nacional del Litoral. Facultad de Ciencias Veterinarias; Argentina Fil: Fresno, C. National Institute of Genomic Medicine (INMEGEN). Computational Genomics Division; México Fil: Cattáneo, Luciano. Universidad Nacional del Litoral. Facultad de Ciencias Veterinarias; Argentina

Objective ST-segment elevation myocardial infarction (STEMI) has an important economic burden that poised the urgent need to evaluate its catastrophic medical expense. This study evaluates the first 5 years of the national health initiative called Popular Insurance (PI) at the National Institute of Cardiology in Mexico. Study design Retrospective data analysis. Methods STEMI patients with ( n = 317 ) and without ( n = 260 ) PI were selected. Analysed variables included socio-economical context, management care, cost evaluation and three outcomes (mortality, hospital readmission and therapeutic adherence). Descriptive statistical analyses, Kaplan–Meier survival and Support Vector Machine models were used accordingly. Results Treatment costs were higher for PI-covered individuals ( P = 0.022 ) and only 1.89 % of them remained in debt, in contrast to 16.15 % of those without PI. Statistically significant differences were found in relation to days in hospital wards ( P 0.001 ) , imaging studies ( P 0.001 ) and surgical materials ( P = 0.04 ) . Survival analysis ( P = 0.44 ) and therapeutic adherence ( P = 0.38 ) showed no differences. Hospital readmission was predicted with an 81.97% accuracy. The most important predictive variables included were stent type, number of days at the coronary care unit and hospital wards. Conclusions The PI has proven to be a successful program where no differences were found in terms of health care and survival, whereas it provides timely financial support for families facing catastrophic health challenging events.

Straws of sex-sorted sperm are usually packaged at a low concentration (e.g., ~2.1 × 106 sperm/ml) and cost significantly more than unsorted conventional semen from the same sire. In order to maximize the efficiency of using sex-sorted sperm under in vitro fertilization conditions, the selection of an appropriate sperm separation technique is essential. In this study, the effect of using different silane-coated silica colloid dilutions and layering configurations during centrifugation of sex-sorted sperm was examined over an extended period of incubation time. Sperm recovery and viability after centrifugation using the colloid separation technique were measured along with several sperm motility parameters using CASA. For this purpose, frozen and thawed sex-sorted sperm samples were centrifuged using mini-volume single-layer (40%, 60% and 80%) and mini-volume two-layer (45%/90%, 40%/80% and 30%/60%) separation configurations using PureSperm®. A single layer of 40% PureSperm® recovered significantly more sex-sorted sperm (78.07% ± 2.28%) followed by a single layer of 80% PureSperm® (68.43% ± 2.33%). The lowest sperm recovery was obtained using a two-layer PureSperm® dilution of 45%/90% (47.57% ± 2.33%). Single-layer centrifugation recovered more sorted sperm (68.67% ± 1.74%) than two layer (53.74% ± 1.74%) (p

Targeted sequencing (TS) 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, undercovered relevant clinical variants may not be reported, affecting 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 TS, quality control should assess experiment, gene, and genomic region performances based on achieved coverages. Here, we propose TarSeqQC R package for quality control in TS experiments. The tool is freely available at Bioconductor repository. TarSeqQC was used to analyze two datasets; low-performance primer pools and features were detected, enhancing the quality of experiment results. Read count profiles were also explored, showing TarSeqQC's effectiveness as an exploration tool. Our proposal may be a valuable bioinformatic tool for routinely TS experiments in both research and medical genetics.

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 contrary, Tlalpan borough is the one with the lowest mortality rates in all the study groups. Interestingly, post-productive mortality is the first age-specific cause of death, followed by infant, productive, pre-school and scholar groups. Conclusion The combinations of spatio-temporal Kriging estimation and time-evolution mixed effect models, allowed us to unveil relevant time and location trends that may be useful for public policy planning in Mexico City.

Objective: Dual diagnosis (DD) is the co-occurrence of at least one substance use disorder and one or more mental disorders in a given individual. Despite this comorbidity being highly prevalent an...

Estrogen (E2) and Progesterone (Pg), via their specific receptors (ER and PR respectively), are major determinants in the development and progression of endometrial malignancies. Here, we have studied how E2 and the synthetic progestin R5020 affect genomic functions in Ishikawa endometrial cancer cells. Using ChIPseq in cells exposed to the corresponding hormones, we identified cell specific binding sites for ER (ERbs) and PR (PRbs), which mostly correspond to independent sites but both adjacent to sites bound by PAX2. Analysis of long-range interactions by Hi-C showed enrichment of regions co-bound by PR and PAX2 inside TADs that contain differentially progestin-regulated genes. These regions, which we call “progestin control regions” (PgCRs), exhibit an open chromatin state prior to the exposure to the hormone. Our observations suggest that endometrial response to progestins in differentiated endometrial tumor cells results in part from binding of PR together with partner transcription factors to PgCRs, compartmentalizing hormone-independent open chromatin.

Background Suicide rates vary substantially by sex. Suicides committed by males significantly outnumber female suicides. Disparities in community and social factors provide a partial explanation for this phenomenon. Thus, the evaluation of sex differences at a biological level might contribute to the elucidation of the factors involved in this imbalance. The aim of the present study was to evaluate sex-specific gene expression patterns in the suicidal brain. Methods postmortem samples from the dorsolateral prefrontal cortex (DLPFC) of 75 Latino individuals were analyzed. We considered the following groups: i) male suicides (n = 38), ii) female suicides (n = 10), iii) male controls (n = 20), and iv) female controls (n = 7). Gene expression profiles were evaluated by microarrays. Differentially expressed genes among the groups were identified with a linear model. Similarities and differences in the gene sets between the sexes were identified. Results Differentially expressed genes were identified between suicides and controls of each sex: 1,729 genes in females and 1,997 genes in males. Female-exclusive suicide genes were related to cell proliferation and immune response. Meanwhile, male-exclusive suicide genes were associated to DNA binding and ribonucleic protein complex. Sex-independent suicide genes showed enrichment in mitochondrial and vesicular functions. Limitations Relatively small sample size. Our diagnosis approach was limited to information found on coroner's records. The analysis was limited to a single brain area (DLPFC) and we used microarrays. Conclusion Previously unexplored sex differences in the brain gene expression of suicide completers were identified, providing valuable foundation for the evaluation of sex-specific factors in suicide.

Triple negative breast cancer (TNBC) has poor prognosis and neither established biomarkers nor therapeutic targets. On the one hand the androgen receptor (AR), a steroid hormone receptor (SR) which is expressed in 10-53% of TNBC and proved to be critical for BC proliferation, has been proposed as a new target in TNBC. On the other hand, we and others have shown that membrane ErbB-2 migrates to the nucleus (nuclear ErbB-2, NErbB-2) where it binds DNA at HER-2 associated sequences (HAS) to regulate BC proliferation and migration. Since we have previously shown a functional interplay between growth factors and SR signaling pathways in BC, we propose the existence of an interaction between AR and ErbB-2 which is involved in NErbB-2+/AR+ BC growth. The experimental model used was the human TNBC cell line MDA-MB-453 which displays high expression levels of AR and NErbB-2. By Western Blot (WB) we found that dihydrotestosterone (DHT) treatment for short times (minutes) did not regulate ErbB-2 phosphorylation status at residues Tyr1221/1222 and 1248 which were constitutively activated. However, DHT led to an increase in ErbB-2 phosphorylation at residue Tyr877 which we have proved to be required for ErbB-2 nuclear migration. The latter effect was blocked by the AR antagonist enzalutamide (enza). Blockage of Src activity with dasatinib inhibited DHT-induced ErbB-2 phosphorylation at Tyr877. By Immunofluorescence and confocal microscopy analyses and subcellular fractionation studies we demonstrated that DHT induced ErbB-2 nuclear migration which was inhibited by enza. By chIP we found that DHT induced ErbB-2 recruitment to a HAS site in ERK5, a gene involved in BC proliferation, and to a HAS site in FKBP5, a classical AR responsive gene. By WB we demonstrated that transfection with an ErbB-2 mutant which is unable to translocate to the nucleus and functions as a dominant negative inhibitor of ErbB-2 nuclear migration (hErbB-2ΔNLS), inhibited FKBP51 up-regulation by DHT. Finally, by microarray and bioinformatics analysis we identified 315 differentially expressed genes (DEGs) in the presence of DHT and NErbB-2 eviction. Enrichment analyses showed that the DEGs belonged to the immune response and interferon pathways. Kaplan-Meier analysis revealed that the expression of 6 genes was significantly associated with overall survival in TNBC patients from the METABRIC cohort: CXCL10, TAP1, STAT1, NMI, HLA-A and NLRC5. Multivariate Cox regression analysis identified the combined expression of the 6 genes as an independent predictor of better clinical outcome in TNBC (HR: 0.56, 95% CI 0.38-0.82, P = 0.003). In conclusion, our findings evidence that DHT-activated AR induces Src-mediated ErbB-2 rapid activation and its migration to the nucleus where it binds to HAS sites in the DNA. Moreover, based on the DEGs of NErbB-2 eviction in presence of DHT we identified a gene signature associated with favorable outcome in TNBC.

Background Dual diagnosis is the co-occurrence of at least one substance use disorder (SUD) and one or more mental disorders in a given individual. Despite this comorbidity is highly prevalent and associated with adverse clinical outcomes, its neurobiology remains unclear. Furthermore, patients with dual diagnosis are at higher risk for suicidal behavior in comparison with single disorder patients. Our objective was to evaluate brain gene expression patterns in individuals with dual diagnosis who died by suicide. Methods We compared the gene expression profile in the dorsolateral prefrontal cortex of suicides with DD (n= 10) to the transcriptome of suicides with SUD alone (n=10), suicides with mood disorders alone (n=13), and suicides without mental comorbidities (n=5). Gene expression profiles were assessed by microarrays. Microarray data quality control was performed. Then, microarray data were background corrected and quantile normalized. Differentially expressed genes among the conditions were identified by a linear model implemented in the limma package. Results When comparing the transcriptome of suicides with dual diagnosis to suicides with SUD alone and suicides with mood disorders alone, we identified 255 and 172 differentially expressed genes, respectively. When comparing suicides with DD to suicides without mental comorbidities, we identified 330 differentially expressed genes, mainly enriched in neurogenesis. Discussion Our results suggest that suicides with dual diagnosis present a gene expression profile distinct from that of suicides with a single disorder and suicides without mental disorders. Also, suicides with dual diagnosis, SUD and mood disorders exhibited alterations in the expression of synaptic genes. However, suicides with each condition (dual diagnosis, SUD or mood disorders) exhibited unique gene expression changes at different levels within synaptic signaling. These gene expression differences might contribute to the phenotypical and clinical discrepancies observed in patients with dual diagnosis and patients with a single disorder

Breast carcinomas are characterized by anomalous gene regulatory programs. As is well known, gene expression programs are able to shape phenotypes. Hence, the understanding of gene co-expression may shed light on the underlying mechanisms behind the transcriptional regulatory programs affecting tumor development and evolution. For instance, in breast cancer, there is a clear loss of inter-chromosomal (trans-) co-expression, compared with healthy tissue. At the same time cis- (intra-chromosomal) interactions are favored in breast tumors. In order to have a deeper understanding of regulatory phenomena in cancer, here, we constructed Gene Co-expression Networks by using 848 RNA-seq whole-genome samples corresponding to the four breast cancer molecular subtypes, as well as healthy tissue. We quantify the cis-/trans- co-expression imbalance in all phenotypes. Additionally, we measured the association between co-expression and physical distance between genes, and characterized the proportion of intra/inter-cytoband interactions per phenotype. We confirmed loss of trans- co-expression in all molecular subtypes. We also observed that gene cisco-expression decays abruptly with distance in all tumors in contrast with healthy tissue. We observed co-expressed gene hotspots, that tend to be connected at cytoband regions, and coincide accurately with already known copy number altered regions, such as Chr17q12, or Chr8q24.3 for all subtypes. Our methodology recovered different alterations already reported for specific breast cancer subtypes, showing how co-expression network approaches might help to capture distinct events that modify the cell regulatory program.

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. Fil: Taravini, Irene Rita Eloisa. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Farmacológicas. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones Farmacológicas; Argentina Fil: Larramendy, Celia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Farmacológicas. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones Farmacológicas; Argentina Fil: Gomez, Gimena. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Farmacológicas. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones Farmacológicas; Argentina Fil: Saborido, Mariano Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Farmacológicas. Universidad de Buenos Aires. Facultad de Farmacia y Bioquímica. Instituto de Investigaciones Farmacológicas; Argentina Fil: Spaans, Floor. University of Groningen; Países Bajos Fil: Fresno Rodríguez, Cristóbal. Area de Cs. Agrarias, Ingeniería, Cs. Biológicas y de la Salud de la Universidad Catolica de Córdoba; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: González, Germán A.. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Area de Cs. Agrarias, Ingeniería, Cs. Biológicas y de la Salud de la Universidad Catolica de Córdoba; Argentina Fil: Fernandez, Elmer Andres. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Area de Cs. Agrarias, Ingeniería, Cs. Biológicas y de la Salud de la Universidad Catolica de Córdoba; Argentina Fil: Murer, Mario Gustavo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Fisiología y Biofísica Bernardo Houssay. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Fisiología y Biofísica Bernardo Houssay; Argentina Fil: Gershanik, Oscar Samuel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Fisiología y Biofísica Bernardo Houssay. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Fisiología y Biofísica Bernardo Houssay; Argentina

Adult male Llamas (Lama glama) (n = 6) were collected using a receptive female and a thermo-electric artificial vagina assembled with a polyethylene collection bag with the following objectives: (a) to develop a reliable and repeatable semen collection technique for Llama, (b) validate semen evaluation tests for Llama, and (c) to determine the effect of collection frequency and season on Llama semen characteristics. First, the semen and sperm variables were recorded and validated through their own repeatability. Semen collection intervals tested were: 1X/week for three weeks and 3X/week for another three weeks, the second collection period occurring after two weeks of sexual rest. The collection frequency of 3X/week significantly reduced (P

The control of pre-analytical-factors in human biospecimens collected for health research is currently required. Only two previous reports using post-mortem brain samples have tried to address the impact of cold-ischemia on tissue pH. Here we report pH variations according to time (third-order polynomial model) in mice for liver, kidney and lung samples. Tissue alkalosis in cold-ischemia time may be an underlying mechanism of gene expression changes. Therefore, tissue-pH regulation after organ removal may minimize biological stress in human tissue samples.

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 10mM caffeine (CA), 5mMtheophylline (TH), 10mM caffeine and 5mMtheophylline (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 lower for the shortest fertilisation time (8 h) in M199-FERT medium (42% and 12%, respectively). The SOF-FERT medium with an 8 h fertilisation time resulted in the highest cleavage rates and blastocyst formation (74% and 29%, respectively). The SOF-FERT medium produced the highest embryo quality (50% Grade 1) and hatching rate (66%). Motility enhancers did not affect polyspermy rates, whereas polyspermy was affected when fertilisation length was extended from 8 h (3%) to 18 h (9%) and in M199-FERT (14%) compared with SOF-FERT (6%). We conclude that adding the motility enhancers CA and TH to sex sorted spermatozoa and Tyrode´s albumin lactate pyruvate (TALP)-Sperm can improve cleavage and embryo development rates without increasing polyspermy. In addition, shortening the oocyte-sperm coincubation time (8 h) resulted in similar overall embryo performance rates compared with the prolonged (18 h) interval. Fil: Ferré, Luis Bernardo. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires; Argentina Fil: Bogliotti, Yanina. University of California; Estados Unidos Fil: Chitwood, James L.. University of California; Estados Unidos Fil: Fresno Rodríguez, Cristóbal. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Católica de Córdoba; Argentina Fil: Ortega, Hugo Hector. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Ciencias Veterinarias del Litoral. Universidad Nacional del Litoral. Facultad de Ciencias Veterinarias. Instituto de Ciencias Veterinarias del Litoral; Argentina Fil: Kjelland, Michael E.. Conservation, Genetics and Biotech; Estados Unidos Fil: Ross, Pablo J.. University of California; Estados Unidos