Dissecting the transcriptome of CD44 in triple negative breast cancer

The CD44 receptor is a transmembrane glycoprotein involved in the recognition of specific extracellular matrix (ECM) ligands. It has a complex transcriptional regulation characterized by different splicing variants, many of which play a role in promoting tumorigenesis. Therefore, CD44 variants may serve as prognostic biomarkers and therapeutic targets. Triple-negative breast cancer (TNBC) is a poor prognosis subtype of breast adenocarcinomas characterized by the lack of druggable molecular hallmarks. TNBC represents a prototypical model for studying CD44's pro-tumoral activity. However, the regulation of the CD44 transcriptome and its influence on TNBC aggressiveness remains elusive.In this study, we dissected the CD44 transcriptome in the TNBC cell lines MDA-MB-231 and MDA-MB-468, which exhibit different malignant properties. MDA-MB-231 cells display higher extracellular matrix invasive potential, more prominent metastatic potential, and poorer response to chemotherapy compared to MDA-MB-468 cells. Finally, we induced the overexpression of a differentially expressed CD44 isoform between the two cell lines using transfection assays. We then performed whole transcriptome RNA-sequencing analysis of the transfected cells and their control. We identified distinct patterns in the CD44 transcriptome between the two TNBC cell lines. Specifically, among the top 5 differentially expressed (DE) CD44 isoforms compared to the control cell line, we detected the predicted transcript variant XM_017018585.2. This variant will be further confirmed through PCR and Sanger sequencing assays. To functionally characterize XM_017018585.2, we performed overexpression of the exogenous transcript in the MDA-MB-468 cell line using viral transfection. The overexpression of XM_017018585.2 induced upregulation of transcripts involved in the MAPK8 signaling pathway and downregulation of interferon response programs. Interestingly, the same downregulated genes were also observed in the estrogen-responsive breast cancer cell line MCF-7 upon silencing of specific pathways.The CD44 transcriptome analysis of TNBC cell models revealed novel transcriptional variants with potential significance in the modulation of the malignant phenotype. This study could shed light on the role of previously unidentified CD44 isoforms in promoting tumorigenesis. Furthermore, it could uncover new candidate diagnostic and prognostic biomarkers based on CD44 variant expression

The Mixed Virtual Element Method on curved edges in two dimensions

In this work, we propose an extension of the mixed Virtual Element Method (VEM) for bi-dimensional computational grids with curvilinear edge elements. The approximation by means of rectilinear edges of a domain with curvilinear geometrical feature, such as a portion of domain boundary or an internal interface, may introduce a geometrical error that degrades the expected order of convergence of the scheme. In the present work a suitable VEM approximation space is proposed to consistently handle curvilinear geometrical objects, thus recovering optimal convergence rates. The resulting numerical scheme is presented along with its theoretical analysis and several numerical test cases to validate the proposed approach

Salivary Microbiota Composition in Patients with Oral Squamous Cell Carcinoma: A Systematic Review

This review aimed to analyse the current knowledge regarding the composition of salivary microbiota of patients with oral squamous cell carcinoma (OSCC). The protocol for this study was designed following the PRISMA guidelines. Observational studies, in human subjects with histological diagnosis of OSCC, concerning the analysis of salivary microbiota, were selected. Eleven papers were included. The salivary microbiomes of 1335 patients were analysed. Periodontal pathogens were the most frequent bacteria detected in patients with OSCC. We have found that although there are evident alterations in the composition of the salivary microbiota in OSCC patients, due to the great heterogeneity of the studies, it is still a challenge to identify a specific microbiota pattern. If the associations between alterations in the salivary microbiome and OSCC are confirmed, microbiome analysis could represent a useful tool for the screening and follow‐up of patients affected by OSCC

A new tool for investigation platelet activation in endometriosis patients

Objectives: Endometriosis (EM) is a gynecological disease characterized by chronic inflammation, due to the interaction of inflammatory cells with ectopic endometrium (1). Platelets (PLTs), recruited by procoagulant factors released from endometriotic stromal cells, secrete angiogenetic factors and induce overexpression of genes involved in pro-survival/ anti-apoptotic propensity, inflammationand extracellular matrix remodeling (2). We aimed to develop a tool to measure PLT activation (by small extracellular vesicles, s-EVs) in EM peritoneal fluids, as a potential predictive marker of EM severity. Materials & methods: S-EVs were isolated from EM peritoneal fluids and characterized with imaging (Atomic Force Microscopy; AFM) and protein expression analyses (Western blot, WB) (3). We explored gene expression in peritoneum and EM lesions using EndometDB (4). Results: We demonstrated the presence of s-EVs isolated from EM peritoneal fluids by liquid AFM, as showed by contact angle vs diameter scatterplot (Fig.1A-B), and by WB detecting the s-EV markers CD63, CD9, and TSG101 (Fig.1C). Using Endomet-DB, we highlighted the differentially expressed genes between control and EM peritoneum samples (Fig.1D). The protein expression of a panel of biomarkers of PTL in s-EVs was further confirmed by WB (Fig.1E). Conclusions: We propose applying s-EV research to EM investigation, generating a novel biochemical tool for PLT activation assessment and for the development of new diagnostics and therapies

RNA Sequencing of Primary Cutaneous and Breast-Implant Associated Anaplastic Large Cell Lymphomas Reveals Infrequent Fusion Transcripts and Upregulation of PI3K/AKT Signaling via Neurotrophin Pathway Genes

Cutaneous and breast implant-associated anaplastic large-cell lymphomas (cALCLs and BI-ALCLs) are two localized forms of peripheral T-cell lymphomas (PTCLs) that are recognized as distinct entities within the family of ALCL. JAK-STAT signaling is a common feature of all ALCL subtypes, whereas DUSP22/IRF4, TP63 and TYK gene rearrangements have been reported in a proportion of ALK-negative sALCLs and cALCLs. Both cALCLs and BI-ALCLs differ in their gene expression profiles compared to PTCLs; however, a direct comparison of the genomic alterations and transcriptomes of these two entities is lacking. By performing RNA sequencing of 1385 genes (TruSight RNA Pan-Cancer, Illumina) in 12 cALCLs, 10 BI-ALCLs and two anaplastic lymphoma kinase (ALK)-positive sALCLs, we identified the previously reported TYK2-NPM1 fusion in 1 cALCL (1/12, 8%), and four new intrachromosomal gene fusions in 2 BI-ALCLs (2/10, 20%) involving genes on chromosome 1 (EPS15-GNG12 and ARNT-GOLPH3L) and on chromosome 17 (MYO18A-GIT1 and NF1-GOSR1). One of the two BI-ALCL samples showed a complex karyotype, raising the possibility that genomic instability may be responsible for intra-chromosomal fusions in BI-ALCL. Moreover, transcriptional analysis revealed similar upregulation of the PI3K/Akt pathway, associated with enrichment in the expression of neurotrophin signaling genes, which was more conspicuous in BI-ALCL, as well as differences, i.e., over-expression of genes involved in the RNA polymerase II transcription program in BI-ALCL and of the RNA splicing/processing program in cALCL

Lipid Remodeling in Hepatocyte Proliferation and Hepatocellular Carcinoma.

BACKGROUND AND AIMS: Hepatocytes undergo profound metabolic rewiring when primed to proliferate during compensatory regeneration and in hepatocellular carcinoma (HCC). However, the metabolic control of these processes is not fully understood. In order to capture the metabolic signature of proliferating hepatocytes, we applied state-of-the-art systems biology approaches to models of liver regeneration, pharmacologically and genetically activated cell proliferation, and HCC. APPROACH AND RESULTS: Integrating metabolomics, lipidomics, and transcriptomics, we link changes in the lipidome of proliferating hepatocytes to altered metabolic pathways including lipogenesis, fatty acid desaturation, and generation of phosphatidylcholine (PC). We confirm this altered lipid signature in human HCC and show a positive correlation of monounsaturated PC with hallmarks of cell proliferation and hepatic carcinogenesis. CONCLUSIONS: Overall, we demonstrate that specific lipid metabolic pathways are coherently altered when hepatocytes switch to proliferation. These represent a source of targets for the development of therapeutic strategies and prognostic biomarkers of HCC.J.L.G., Z.H. and M.V. are funded by the Medical Research Council (MRC grant MC UP A90 1006 & MC PC 13030). J.L.G. and Z.H. are supported by the Imperial Biomedical Research Centre, NIHR. M.A., A.V-P., F.O., Q.M.A. and M.V. are members of the EPoS consortium, which is funded by the Horizon 2020 Framework Program of the European Union under Grant Agreement 634413. F.O. is supported by MRC program grants (MR/K0019494/1 and MR/R023026/1). J.L is supported by MRC PhD studentship and a CRUK program grant (C18342/A23390). M.V. and A.V-P. are supported by MRC MDU and MRC DMC (MC UU 12012/2). Q.M.A. received additional research support from The Liver Research Trust and is a Newcastle NIHR Biomedical Research Centre investigator. M.A., M.V., A.V-P. and J.L.G. received research support from the Evelyn Trust and the NIHR Cambridge Biomedical Research Centre (Gastroenterology Theme)

A longitudinal study of C1q and anti-C1q autoantibodies in homologous and heterologous pregnancies for predicting pre-eclampsia

C1q, the recognition molecule of the classical pathway of the complement system, plays a central role in pregnancy. Lack of C1q is characterized by poor trophoblast invasion and pregnancy failure. C1q can be the target of an antibody response: anti-C1q autoantibodies (anti-C1q) are present in several infectious and autoimmune diseases. The presence of these autoantibodies has been detected also in 2-8% of the general population. Recent evidence indicates that women who undergo assisted reproductive technology (ART) have an increased risk of developing pre-eclampsia (PE), particularly oocyte donation (OD) pregnancies. The aim of this study was to characterize the levels of C1q and anti-C1q in PE gestations, in healthy spontaneous, homologous and heterologous ART pregnancies. Serum of the following four groups of women, who were followed throughout two or three trimesters, were collected: PE, patients diagnosed with PE; OD, oocyte donation recipients; HOM, homologous ART women; Sp, spontaneous physiological pregnancy. Our results indicate that PE patients have lower levels of anti-C1q. In ART pregnant women, the trend of C1q and anti-C1q levels were similar to PE patients, even though these women did not develop PE-like symptoms during pregnancy. This finding suggests an immunological dysfunction at the foetal-maternal interface in ART pregnancies, a hypothesis confirmed by the observation of C1q deposition in placentae derived from OD, comparable to PE. Since significantly lower levels of anti-C1q were detected in PE compared to healthy control sera, we hypothesize the possible binding on placental syncytiotrophoblast microvesicles (STBM), which are increased in the circulation of PE mothers. Furthermore, the characterization of the binding-epitope of anti-C1q revealed that "physiological" autoantibodies were mainly directed against C1q globular domain. We concluded that anti-C1q could have a physiological role in pregnancy: during the healthy spontaneous pregnancy the raised levels of these autoantibodies can be important for the clearance of STBM. In PE and in pathological pregnancies (but also in OD pregnancies), the increase in syncytiotrophoblast apoptosis and consequent increase of the circulating STMB levels lead to a consumption of C1q and anti-C1q

Author Correction: Mutant p53 sustains serine-glycine synthesis and essential amino acids intake promoting breast cancer growth

Reprogramming of amino acid metabolism, sustained by oncogenic signaling, is crucial for cancer cell survival under nutrient limitation. Here we discovered that missense mutant p53 oncoproteins stimulate de novo serine/glycine synthesis and essential amino acids intake, promoting breast cancer growth. Mechanistically, mutant p53, unlike the wild-type counterpart, induces the expression of serine-synthesis-pathway enzymes and L-type amino acid transporter 1 (LAT1)/CD98 heavy chain heterodimer. This effect is exacerbated by amino acid shortage, representing a mutant p53-dependent metabolic adaptive response. When cells suffer amino acids scarcity, mutant p53 protein is stabilized and induces metabolic alterations and an amino acid transcriptional program that sustain cancer cell proliferation. In patient-derived tumor organoids, pharmacological targeting of either serine-synthesis-pathway and LAT1-mediated transport synergizes with amino acid shortage in blunting mutant p53-dependent growth. These findings reveal vulnerabilities potentially exploitable for tackling breast tumors bearing missense TP53 mutation

Mutant p53 sustains serine-glycine synthesis and essential amino acids intake promoting breast cancer growth

Reprogramming of amino acid metabolism, sustained by oncogenic signaling, is crucial for cancer cell survival under nutrient limitation. Here we discovered that missense mutant p53 oncoproteins stimulate de novo serine/glycine synthesis and essential amino acids intake, promoting breast cancer growth. Mechanistically, mutant p53, unlike the wild-type counterpart, induces the expression of serine-synthesis-pathway enzymes and L-type amino acid transporter 1 (LAT1)/CD98 heavy chain heterodimer. This effect is exacerbated by amino acid shortage, representing a mutant p53-dependent metabolic adaptive response. When cells suffer amino acids scarcity, mutant p53 protein is stabilized and induces metabolic alterations and an amino acid transcriptional program that sustain cancer cell proliferation. In patient-derived tumor organoids, pharmacological targeting of either serine-synthesis-pathway and LAT1-mediated transport synergizes with amino acid shortage in blunting mutant p53-dependent growth. These findings reveal vulnerabilities potentially exploitable for tackling breast tumors bearing missense TP53 mutations.Mutant p53 induces serine/glycine synthesis and essential amino acids intake. Under amino acid restriction, mutant p53 is stabilized and activates a transcriptional program that sustains a metabolic adaptive response promoting breast cancer cells growt