BUSCADOR RECOLECTA

This repository contains experimental data, scripts used for the data analysis, scripts used for the numerical calculation and the microscopy analysis for the following paper: "Majorana-like Coulomb spectroscopy in the absence of zero bias peaks"., Peer reviewed

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/cancers14030670/s1, Figure S1. Sanger sequencing results of the CYBA (upper panel) and TRPM4 (lower panel) wild type and mutant sequences; Figure S2. Splicing functional assays of TRPM4 variant c.25-1G>T. (A) Fluorescent fragment analysis by capillary electrophoresis of RT-PCR products generated by the wild type and mutant minigenes. The canonical and the aberrant ∆(E2p2) transcripts are shown as blue and red peaks, respectively, while the LIZ500 size standard is displayed as orange peaks. (B) Schematic representation of the canonical (above) and anomalous (below) transcripts. Variant c.25-1G>T is shown in red; acceptor sites are underlined; splicing events are shown as broken arrows; Figure S3. SiRNA knockdown of CYBA or TRPM4 lead to reduced mRNA and protein of the respective genes: mRNA (A) and protein (B) levels of CYBA and TRPM4 decreased after siRNA knockdown of CYBA or TRPM4 in LS174T cells; mRNA (C) and protein (D) levels of CYBA and TRPM4, decreased after siRNA knockdown of CYBA or TRPM4 in HT-29 cells. For real-time PCR assays, three independent experiments in triplicate were performed and means and standard errors of the means are presented on the graphs. For western blot two independent experiments were performed;Table S1. Summary of the sequencing coverage and quality statistics for each sample; Table S2. Loss-of-function variants segregated with the disease in 15 colorectal cancer families., Peer reviewed

CiberAMP is an R package that uses differential expression analyses to stablish accurate correlations between specific SCNVs and changes in expression in the genes affected by them. The algorithm has been designed to be an easy-to-access tool for the TCGA, the largest database in the world with genomic and transcriptomic data ofr more than 10,000 samples of 33 different human cancers. Unlike other methods, CiberAMP can yield information on: (i) SCNV-DEGs (somatic copy number variations associated differentially expressed genes) in a cohort of TCGA tumor samples (ii) The type of copy number variation associated with each SCNV-DEG in terms of expression pattern and genomic context (iii) Insights on the potential functional relevance of each identified SCNV-DEG, Peer reviewed

The Integrated and Open Butterfly Database provide a massive dataset of curated COI sequences for West Palearctic butterflies and an updated checklist. Functions to manage the dataset are also provided., The IOdatabase is intended as a project integrating several datasets of butterflies from Western Palaearctic harmonised with a shared taxonomy. IOdatabase now includes a revised version of the species checklist from West Palerarctic (Wiemers et al. 2016 and Middleton Welling et al. 2020) and more than 30000 COI sequences for 532 species. COI sequences belong to three main sources: 1) De novo sequencing mostly for Maghreb and Macaronesia 2) Published DNA-barcode libraries and public BOLD projects compiled at regional level 3) Studies providing COI of single species or genera. In the latter case, we checked whether haplotypes, instead of specimens, were included in repositories (Paz‐Vinas et al. 2021). If the number of specimens sharing a given haplotype in a particular location was reported, we replicated the haplotype sequences to obtain data at the specimen level, otherwise the sequences were excluded. We verified species identifications by building neighbor-joining trees for each genus. When morphology could not be verified, we removed sequences not clustering within the species to which they were attributed if the mismatch did not involve one of the 74 species showing DNA-barcode sharing. Metadata are also available: coordinates in WGS84 (degrees) and Lambert projections (meters), BOLD and Genbank codes, Continental areas and country obtained by an autmatic attribution using the rworldextra R package. Using these data we also calculated some basic indexes of genetic diversity (number of haplotypes observed and predicted based on rarefaction curves, GST, DST, haplotype diversity and nucleotide diversity)., Peer reviewed

Supplementary Figure 1. Isolated EVs present typical size and topology. Supplementary Figure 2. Protein profiling from total cell lysates and their derived EVs from WT and KO-HDAC6 BMDCs. Supplementary Figure 3. Enrichment in acetylated and ubiquitinated DC proteins upon Lm infection. Supplementary Figure 4. Ubiquitination in K-48 and K-63 state in T lymphoblast total cell lysates and their derived EVs. Supplementary Figure 5. Pore filtration methods restrain Lm and do not induce strong antipathogenic responses. Supplementary Figure 6. IFN-β is detected following Lm infection. Table S1. List of antibodies used for Western-blot and Flow Cytometry and the used dilution. Table S2. List of primers, with their corresponding sequence, used for qPCR. Table S3: Protein quantification in total cell lysates Table S4: IPA analysis of total cell lysates: canonical pathways and diseases and functions category Table S5: Protein quantification in EVs Table S6: IPA analysis of EVs: diseases and functions category Table S7: Ubiquitinated and acetylated peptides in total cell lysates and EVs Table S8: Enrichment analysis of ubiquitinated and acetylated proteins, Peer reviewed

Supplementary Table 9. Gene ontology (GO) functional enrichment analysis of the differentially expressed genes (DEGs) for cellular component., Mouse models of cancer provide a powerful tool for investigating all aspects of cancer biology. In this study, we used our recently developed machine learning approach to identify the cellular morphometric biomarkers (CMB) from digital images of hematoxylin and eosin (H&E) micrographs of orthotopic Trp53-null mammary tumors (n = 154) and to discover the corresponding cellular morphometric subtypes (CMS). Of the two CMS identified, CMS-2 was significantly associated with shorter survival (p = 0.0084). We then evaluated the learned CMB and corresponding CMS model in MMTV-Erbb2 transgenic mouse mammary tumors (n = 53) in which CMS-2 was significantly correlated with the presence of metastasis (p = 0.004). We next evaluated the mouse CMB and CMS model on The Cancer Genome Atlas breast cancer (TCGA-BRCA) cohort (n = 1017). Kaplan–Meier analysis showed significantly shorter overall survival (OS) of CMS-2 patients compared to CMS-1 patients (p = 0.024) and added significant prognostic value in multi-variable analysis of clinical and molecular factors, namely, age, pathological stage, and PAM50 molecular subtype. Thus, application of CMS to digital images of routine workflow H&E preparations can provide unbiased biological stratification to inform patient care., Peer reviewed

Identification of genomic alterations that influence the immune response within the tumor microenvironment is mandatory in order to identify druggable vulnerabilities. In this article, by interrogating public genomic datasets we describe copy number variations (CNV) present in breast cancer (BC) tumors and corresponding subtypes, associated with different immune populations. We identified regulatory T-cells associated with the Basal-like subtype, and type 2 T-helper cells with HER2 positive and the luminal subtype. Using gene set enrichment analysis (GSEA) for the Type 2 T-helper cells, the most relevant processes included the ERBB2 signaling pathway and the Fibroblast Growth Factor Receptor (FGFR) signaling pathway, and for CD8+ T-cells, cellular response to growth hormone stimulus or the JAK-STAT signaling pathway. Amplification of ERBB2, GRB2, GRB7, and FGF receptor genes strongly correlated with the presence of type 2 T helper cells. Finally, only 8 genes were highly upregulated and present in the cellular membrane: MILR1, ACE, DCSTAMP, SLAMF8, CD160, IL2RA, ICAM2, and SLAMF6. In summary, we described immune populations associated with genomic alterations with different BC subtypes. We observed a clear presence of inhibitory cells, like Tregs or Th2 when specific chromosomic regions were amplified in basal-like or HER2 and luminal groups. Our data support further evaluation of specific therapeutic strategies in specific BC subtypes, like those targeting Tregs in the basal-like subtype., Peer reviewed

Identification of genomic alterations that influence the immune response within the tumor microenvironment is mandatory in order to identify druggable vulnerabilities. In this article, by interrogating public genomic datasets we describe copy number variations (CNV) present in breast cancer (BC) tumors and corresponding subtypes, associated with different immune populations. We identified regulatory T-cells associated with the Basal-like subtype, and type 2 T-helper cells with HER2 positive and the luminal subtype. Using gene set enrichment analysis (GSEA) for the Type 2 T-helper cells, the most relevant processes included the ERBB2 signaling pathway and the Fibroblast Growth Factor Receptor (FGFR) signaling pathway, and for CD8+ T-cells, cellular response to growth hormone stimulus or the JAK-STAT signaling pathway. Amplification of ERBB2, GRB2, GRB7, and FGF receptor genes strongly correlated with the presence of type 2 T helper cells. Finally, only 8 genes were highly upregulated and present in the cellular membrane: MILR1, ACE, DCSTAMP, SLAMF8, CD160, IL2RA, ICAM2, and SLAMF6. In summary, we described immune populations associated with genomic alterations with different BC subtypes. We observed a clear presence of inhibitory cells, like Tregs or Th2 when specific chromosomic regions were amplified in basal-like or HER2 and luminal groups. Our data support further evaluation of specific therapeutic strategies in specific BC subtypes, like those targeting Tregs in the basal-like subtype., Peer reviewed

S1. Sample preparation protocol for evaluation of OneFlow kits (BD). Figure S1. Impact of different BSA concentrations and different pH of the washing buffer on the relative percentage distribution of different cell populations identifiable in normal PB samples with LST. Figure S2. Impact of different BSA concentrations and different pH of the washing buffer on the expression levels of individual LST markers as assessed on different cell populations in normal PB samples. Table S1. Detailed information on the antibody reagents used in the current study, including the antibody titer used per test. Table S2. Absolute and relative percentage changes of particular cell populations, debris and doublets detectable in BM samples stained with ALOT tube at day 0 and after 24-h storage. Table S3. Ratios of percentage of debris, doublets, and pathological/clonal B-cells in particular BM and PB samples stained with LST tube at different time points. Table S4. Ratios of percentage of debris, doublets, and pathological/clonal B-cells in particular BM and PB samples stained with the first tube of B-CLPD panel at different time points. Table S5. Ratios of percentage of debris, doublets, and pathological/clonal plasma cells in particular BM and PB samples stained with PCD panel at different time points. Table S6. MFI values of LST markers evaluated on relevant cell populations obtained at different pH and BSA concentrations. Table S7. Expression of markers on relevant PB cell populations stained with LST tube at different pH on averaging the results for different BSA concentrations. Table S8. Selected additional markers that were not directly studied in the current study that may be influenced by the preparation-associated variables., Peer reviewed

Additional file 1: Figure S1. a, Relative mRNA expression of RRAS2 in different types of leukemia. Data comes from (Haferlach et al., 2010) and has been retrieved from www.oncomine.org . b, Schematic representation of the overexpression cassette inserted into the Rosa26 locus. c, Relative expression of RRAS2 measured by RT-qPCR in different organs of Rosa26-RRAS2fl/flxSox2-Cre (Sox2-Cre+) mice compared to that of WT C57BL/6 J Control mice using 18S as the reference gene. All expression numbers were normalized to those of liver from WT Control mice (mean = 1). Data show relative expression of RRAS2 in the indicated organs in n = 3–4 8 month-old independent mice. d, Quantification of spleen weight from control and 6 month-old Sox2-Cre + mice. Data shown correspond to four control mice and eleven Sox2-Cre mice. Two-tailed unpaired t-test with Welch’s correction. e, Two-parameter flow cytometry of the expression of CD5 and IgM in B cells in the spleen of 6 month-old control and Sox2-Cre + mice. f, Quantification of the number of CD5 + IgM+ B cells in the spleens and bone marrow of 6 month-old control and Sox2-Cre + mice. Data correspond to triplicate measurements of one control and three Sox2-Cre mice. Unpaired t-test with Welch’s correction. g, Quantification of the serum IgM concentration in the blood of 35–40 wk-old control (n = 3) and mb1-Cre (n = 8) mice by ELISA. Unpaired t-test with Welch’s correction. h, Representative images from Giemsa stainings of blood smears of 36 wk-old control and mb1-Cre mice. i, Two-parameter flow cytometry of the forward scatter and CD5 expression in CD19+ cells in the blood of 16 wk-old mb1-Cre mice. The gated population represents large cells. j, Two-parameter flow cytometry of CD5 expression and BrdU incorporation in CD19+ cells in the blood of 16 wk-old mb1-Cre mice. k, Quantification of the percentage of CD19+ cells that are CD5+ blasts and of the CD19+ CD5+ cells that have incorporated BrdU., Fundación Científica Asociación Española Contra el Cáncer Ministerio de Ciencia, Innovación y Universidades H2020 European Research Council Instituto de Salud Carlos III Consejería de Educación, Junta de Castilla y León, Peer reviewed