This work addresses the detection of Helicobacter pylori a bacterium classified since 1994 as class 1 carcinogen to humans. By its highest specificity and sensitivity, the preferred diagnosis technique is the analysis of histological images with immunohistochemical staining, a process in which certain stained antibodies bind to antigens of the biological element of interest. This analysis is a time demanding task, which is currently done by an expert pathologist that visually inspects the digitized samples. We propose to use autoencoders to learn latent patterns of healthy tissue and detect H. pylori as an anomaly in image staining. Unlike existing classification approaches, an autoencoder is able to learn patterns in an unsupervised manner (without the need of image annotations) with high performance. In particular, our model has an overall 91% of accuracy with 86\% sensitivity, 96% specificity and 0.97 AUC in the detection of H. pylori.
<p>Analysis of TAGLN expression and dasatinib target interaction in cancer cell lines</p>
Lymph node (LN) metastasis is an important prognostic factor in colorectal cancer (CRC). We aimed to demonstrate the presence of lymphatic vessels (LV) in the mucosa of in-situ (pTis) CRC, and of detectable tumour burden in regional LNs. This is an observational retrospective study of 39 surgically resected in situ CRCs. The number of LVs was evaluated in both pTis and normal mucosa using D2-40 immunostains. All LNs were assessed with both H&E and the One Step Nucleic Acid Amplification (OSNA) assay, and the results were correlated with clinicopathological features. D2-40 immunohistochemisty revealed LVs in the lamina propria of all pTis CRC (100%), being absent in normal mucosa. A median of 16 LNs were freshly dissected per patient, and all cases were pN0 with H&E. Molecular LN analysis with OSNA revealed the presence of low amounts of tumour burden in 11/39 (28%) cases (range 400 to 4270 CK19 mRNA copies/µL), which had no clinical consequences. This study demonstrates the presence of LVs in the lamina propria in 100% of pTis CRC, as well as the presence of low amounts of tumour burden in regional LNs, only detected by molecular methods. Given the prognostic value of LN tumour burden, its molecular quantification may help a patient's clinical management.
AIMS: Pathological evaluation of colorectal carcinoma (CRC) diagnosed at stage pT1 is challenging. Nevertheless, it is crucial for treatment guiding and to determine the patient's prognosis. This study aimed to assess the interobserver variability in the histopathological evaluation of pT1 CRC. METHODS AND RESULTS: A retrospective multicentre pT1 CRC cohort study was designed (EpiT1 consortium). A task force comprising 20 experienced pathologists conducted the histopathological evaluation using digitalized haematoxylin-eosin (H&E) slides. A pilot study was performed with 10 cases, and afterwards, a consensus meeting was held to assess interobserver variability. Then, a concordance study was performed by assessing 70 new pT1 CRC cases. We used percentage agreement and Gwet's Agreement Coefficient 1 for categorical variables, and intraclass correlation coefficient (ICC) for continuous variables. In the pilot study, histological grade and perineural invasion (PNI) demonstrated 100% agreement, with good concordance for lymphovascular invasion (LVI), tumour budding (TB), poorly differentiated clusters (PDC) and margin assessment. The concordance study showed high agreement (≥90%) on histological grade, PDC, PNI and LVI. Submucosal invasion depth showed excellent reliability in the concordance study (ICC = 0.97). Notably, in both studies, the agreement of PDC was higher than for TB. Lower concordance was observed on stromal lymphocytes and the status of muscularis mucosae. CONCLUSIONS: Our results emphasize the need for standardization in evaluating pT1 CRC to improve the concordance among pathologists, and the precision of digital measurements. Moreover, the addition of PDC assessment in pT1 CRC diagnostic guidelines could help to improve the accuracy of risk stratification and reliably predict prognosis.
Read more<p>Expression of LC-associated genes in murine mammary epithelial subpopulations</p>
Read moreMetastatic colorectal cancer (mCRC) currently lacks reliable biomarkers for precision medicine, particularly for chemotherapy-based treatments. This study examines the behavior of 11 CXC chemokines in the blood of 104 mCRC patients undergoing first-line oxaliplatin-based treatment to pinpoint predictive and prognostic markers. Serum samples were collected before treatment, at response evaluation (EVAR), and at disease progression or last follow-up. Chemokines were assessed in all samples using a Luminex® custom panel. CXCL13 levels increased at EVAR in responders, while in non-responders it decreased. Increasing levels of CXCL13 at EVAR, independently correlated with improved progression-free survival (PFS) and overall survival (OS). Nanostring® analysis in primary tumor samples showed CXCL13 gene expression's positive correlation not only with gene profiles related to an immunogenic tumor microenvironment, increased B cells and T cells (mainly CD8+) but also with extended OS. In silico analysis using RNAseq data from liver metastases treated or not with neoadjuvant oxaliplatin-based combinations, and deconvolution analysis using the MCP-counter algorithm, confirmed CXCL13 gene expression's association with increased immune infiltration, improved OS, and Tertiary Lymphoid Structures (TLSs) gene signatures, especially in neoadjuvant-treated patients. CXCL13 analysis in serum from 36 oxaliplatin-treated patients from the METIMMOX study control arm, reported similar findings. In conclusion, the increase of CXCL13 levels in peripheral blood and its association with the formation of TLSs within the metastatic lesions, emerges as a potential biomarker indicative of the therapeutic efficacy in mCRC patients undergoing oxaliplatin-based treatment • In CRC, Oxalipatin-based combinations often fail due to resistance and/or toxicity. • Lack of biomarkers complicates treatment decision-making. . • We examined serum levels of 11 CXC chemokines in patients on oxaliplatin. • Increased CXCL13 levels correlate with response, prognosis, tumor immunity and TLSs. • CXCL13 may serve as a predictive and prognostic biomarker for treatment efficacy.
Read more<p>Expression and prognostic impact of tB-markers in TNBC. <b>A,</b> Unsupervised hierarchical clustering of the percentage of positive cells/sample in the discovery and validation cohorts of TNBC (<i>n</i> = 243). Color code denotes percentage of expression (blue, 0%; red, 100%). <b>B,</b> Scatter plots representing the percentage of tumor cells positive for SMA, TAGL, and TPM2 in two independent TNBC cohorts: the commercial TMA BR1301a (left) and the Cartagena cohort (right). Each dot represents one patient sample; horizontal lines indicate mean ± SEM. Statistical significance was determined using two-way ANOVA. ****, <i>P</i> < 0.0001. <b>C,</b> Heatmap showing the expression levels of the tB-markers across breast cancer samples. Expression values are row-normalized, ranging from low (blue) to high (red). The top annotations indicate relevant clinical and molecular characteristics of each sample, including histologic type, disease stage, intrinsic PAM50 subtype, and Lehmann classification (TNBC type_4). NA, not available; NOS, not otherwise specified. <b>D,</b> KM plot depicting RFS of patients with TNBC stratified by tB-marker expression. <b>E,</b> KM plot showing RFS in patients with TNBC treated exclusively with chemotherapy, based on tB-marker expression. <b>F,</b> KM plot illustrates OS of patients with TNBC based on tB-marker expression. In panels <b>D–F</b>, patient subgroups were defined through trichotomization, in which the lower quartile represents the “low expression” group (black), and the upper quartile represents the “high expression” group (red). Patients with intermediate expression levels were excluded to ensure a robust comparison between high and low expressers.</p>
Read moreAbstract Colorectal cancer (CRC) remains a major global health concern, partly due to resistance to therapy and the lack of new effective treatments for advanced disease. The combination of 5-Fluorouracil (5FU, a thymidylate synthase inhibitor) and irinotecan (a topoisomerase 1 inhibitor) is widely used in first-line and subsequent treatments. This study aimed to identify novel therapeutic targets to enhance combinatorial therapy, improving treatment efficacy and durability of response. We performed a loss-of-function screen using HT29 CRC cell line and a retroviral library containing 7296 shRNAs targeting 912 chromatin genes. Cells were then treated with 5FU and SN38 (the active metabolite of irinotecan) or left untreated for 4 weeks. Genes enriched in resistant clones were identified through next-generation sequencing. Among candidate genes, PARG was selected for functional validation. CRISPR/Cas9-mediated knockout (HT29 PARG-KO) resulted in increased global poly(ADP-ribosyl)ation after 5FU and SN38 treatment. PARG depletion led to reduced cell viability and increased apoptosis, particularly after 5FU exposure. Pharmacological PARG inhibition (PDD00017273) synergized with 5FU and SN38 across three CRC models (HT29, DLD1, HT115). In vivo , HT29 PARG-KO xenografts were more sensitive to 5FU. Immunohistochemical analysis of 170 CRC patient tumors revealed that positive PARG expression correlated with poor response to 5FU + Irinotecan, increased liver metastases, and worse long-term survival. Our findings highlight PARG as a promising therapeutic target for CRC, where its inhibition enhances the efficacy of standard chemotherapy.
Read more<p>Contains supplemental methods and materials, 2 figures, a table and supplemental references. Figure 1. Preliminary evidence suggesting that PADI2 re-expression in colon cancer cells conveys sensitivity to calcium treatment. Figure S2. The association of PADI2 levels in adjacent mucosa is independent of inflammation and immune cell infiltration. Table S1. Inflammatory hallmark gene set (extracted from MSigDB).</p>
Read more<p>Contains supplemental methods and materials, 2 figures, a table and supplemental references. Figure 1. Preliminary evidence suggesting that PADI2 re-expression in colon cancer cells conveys sensitivity to calcium treatment. Figure S2. The association of PADI2 levels in adjacent mucosa is independent of inflammation and immune cell infiltration. Table S1. Inflammatory hallmark gene set (extracted from MSigDB).</p>
Read more<div>Abstract<p>Peptidyl arginine deiminases (PADI) are a family of enzymes that catalyze the poorly understood posttranslational modification converting arginine residues into citrullines. In this study, the role of PADIs in the pathogenesis of colorectal cancer was investigated. Specifically, RNA expression was analyzed and its association with survival in a cohort of 98 colorectal cancer patient specimens with matched adjacent mucosa and 50 controls from donors without cancer. Key results were validated in an independent collection of tumors with matched adjacent mucosa and by mining of a publicly available expression data set. Protein expression was analyzed by immunoblotting for cell lines or IHC for patient specimens that further included 24 cases of adenocarcinoma with adjacent dysplasia and 11 cases of active ulcerative colitis. The data indicate that PADI2 is the dominantly expressed PADI enzyme in colon mucosa and is upregulated during differentiation. PADI2 expression is low or absent in colorectal cancer. Frequently, this occurs already at the stage of low-grade dysplasia. Mucosal PADI2 expression is also low in ulcerative colitis. The expression level of PADI2 in tumor and adjacent mucosa correlates with differential survival: low levels associate with poor prognosis.</p><p><b>Implications:</b> Downregulation of PADI2 is an early event in the pathogenesis of colorectal cancer associated with poor prognosis and points toward a possible role of citrullination in modulating tumor cells and their microenvironment. <i>Mol Cancer Res; 14(9); 841–8. ©2016 AACR</i>.</p></div>
Read moreTumour budding (TB) correlates with increased local invasion in various neoplasms. Certain basal cell carcinomas (BCCs) exhibit local aggressiveness. Detecting adverse prognostic factors in partial biopsies could aid in identifying cases with heightened local risk. The absolute number of TB (≤ 3 tumour cells) in excision specimens of 271 infiltrative BCCs (0: absent; 1: 1-2 foci; 2: ≥ 3 foci; 3: ≥ 10 foci), the histopathological subtype and depth of infiltration, perineural invasion, and other histological features were evaluated. A significant correlation was found between TB and both depth of infiltration (rho 0.445, p < 0.001) and perineural invasion (p = 0.009). In the multivariate analysis of depth and perineural invasion (multiple regression, stepwise), TB was identified as a significant covariate together with diameter, inflammation, and perineural invasion for the former, and depth for the latter. Conversely, no correlation existed between the WHO histological subtypes (infiltrating, sclerosing, and micronodular), and depth of infiltration or perineural invasion. This study demonstrates the value of TB as a biomarker for local invasiveness in BCC. In routine practice, a count of ≥ 3 TB foci in lesions incompletely excised or with narrow tumour-free surgical margins would be a straightforward and reproducible method to guide BCC treatment.
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