Papers by Alessandro WEISZ
Scientific Reports
Clonal hematopoiesis of indeterminate potential (CHIP) is characterized by the presence of clones... more Clonal hematopoiesis of indeterminate potential (CHIP) is characterized by the presence of clones of mutated blood cells without overt blood diseases. In the last few years, it has emerged that CHIP is associated with atherosclerosis and coronary calcification and that it is an independent determinant of cardiovascular mortality. Recently, CHIP has been found to occur frequently in patients with calcific aortic valve disease (CAVD) and it is associated with a poor prognosis after valve replacement. We assessed the frequency of CHIP by DNA sequencing in the blood cells of 168 CAVD patients undergoing surgical aortic valve replacement or transcatheter aortic valve implantation and investigated the effect of CHIP on 12 months survival. To investigate the pathological process of CAVD in CHIP carriers, we compared by RNA-Seq the aortic valve transcriptome of patients with or without CHIP and non-calcific controls. Transcriptomics data were validated by immunohistochemistry on formalin-em...
Cancer Cell International
Background Ovarian cancer (OC) is characterized by a low response rate and high frequency of resi... more Background Ovarian cancer (OC) is characterized by a low response rate and high frequency of resistance development to currently available treatments. The therapeutic potential of histone methyltransferase DOT1L inhibitor in OC cells has been demonstrated, but optimal efficacy and safety of this targeted therapy approach still require improvement. We set forth to evaluate if this problem can be overcome by combinatorial targeting of this epigenetic modifier and menin, one of its functional partners in chromatin. Methods siRNA-mediated gene knock-down and pharmacological inhibition of menin, a key component of the MLL/SET1 complex and a fitness gene in OC cells, coupled to cell proliferation assays on a panel of high grade serous OC cell lines, including chemotherapy-sensitive and -resistant clones, were applied in order to evaluate how depletion or blockade of this enzyme influences growth and viability of OC cells. RNA sequencing was applied to identify menin target genes and pathw...
Breast Cancer Research
Background Targeting vulnerabilities of cancer cells by inhibiting key regulators of cell prolife... more Background Targeting vulnerabilities of cancer cells by inhibiting key regulators of cell proliferation or survival represents a promising way to overcome resistance to current therapies. In breast cancer (BC), resistance to endocrine therapy results from constitutively active or aberrant estrogen receptor alpha (ERα) signaling to the genome. Targeting components of the ERα pathway in these tumors represents, therefore, a rational way toward effective new treatments. Interaction proteomics identified several proteins associated with ERα in BC cells, including epigenetic complexes controlling gene transcription comprising the scaffold protein menin and the histone methyltransferase Dot1L. Methods We combined chromatin immunoprecipitation, transcriptome sequencing, siRNA-mediated gene knockdown (kd), pharmacological inhibition coupled to cellular and functional assays and interaction proteomics in antiestrogen (AE)-sensitive and AE-resistant human BC cell models to: map menin and Dot1...
Diagnostics
Dilated cardiomyopathy (DCM) is a complex disease affecting young adults. It is a pathological co... more Dilated cardiomyopathy (DCM) is a complex disease affecting young adults. It is a pathological condition impairing myocardium activity that leads to heart failure and, in the most severe cases, transplantation, which is currently the only possible therapy for the disease. DCM can be attributed to many genetic determinants interacting with environmental factors, resulting in a highly variable phenotype. Due to this complexity, the early identification of causative gene mutations is an important goal to provide a genetic diagnosis, implement pre-symptomatic interventions, and predict prognosis. The advent of next-generation sequencing (NGS) has opened a new path for mutation screening, and exome sequencing provides a promising approach for identifying causal variants in known genes and novel disease-associated candidates. We analyzed the whole-exome sequencing (WES) of 15 patients affected by DCM without overloading (hypertension, valvular, or congenital heart disease) or chronic isch...
Journal of Translational Medicine
Background Neuroendocrine neoplasms (NENs) represent a heterogeneous class of rare tumors with in... more Background Neuroendocrine neoplasms (NENs) represent a heterogeneous class of rare tumors with increasing incidence. They are characterized by the ability to secrete peptide hormones and biogenic amines but other reliable biomarkers are lacking, making diagnosis and identification of the primary site very challenging. While in some NENs, such as the pancreatic ones, next generation sequencing technologies allowed the identification of new molecular hallmarks, our knowledge of the molecular profile of NENs from other anatomical sites is still poor. Methods Starting from the concept that NENs from different organs may be clinically and genetically correlated, we applied a multi-omics approach by combining multigene panel testing, CGH-array, transcriptome and miRNome profiling and computational analyses, with the aim to highlight common molecular and functional signatures of gastroenteropancreatic (GEP)-NENs and medullary thyroid carcinomas (MTCs) that could aid diagnosis, prognosis an...
<p>Among the entire gene set considered in the MCF-7 cell experiment, 1270 also responded i... more <p>Among the entire gene set considered in the MCF-7 cell experiment, 1270 also responded in ZR-75.1 cells. These are referred to as common ‘estrogen-regulated genes’ (E2R genes) in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088485#pone.0088485-Cicatiello1" target="_blank">[4]</a>. ‘Primary genes’ are their subgroup having a ER transcription factor binding site within 10 kb around the TSS. The figures show how E2R and primary genes are responding across the single-cell states of a six-state model. (<b>A</b>) Fraction of up-regulated and down-regulated E2R genes. (<b>B</b>) Fraction of first-responding E2R genes, i.e., of genes that respond for the first time in a given state. (<b>C</b>) and (<b>D</b>) show the analogous pattern of primary genes.</p
Frontiers in Genetics
The histone lysine methyltransferase DOT1L (DOT1-like histone lysine methyltransferase) is respon... more The histone lysine methyltransferase DOT1L (DOT1-like histone lysine methyltransferase) is responsible for the epigenetic regulation of gene expression through specific methylation of lysine79 residue of histone H3 (H3K79) in actively transcribed genes. Its normal activity is crucial for embryonic development and adult tissues functions, whereas its aberrant functioning is known to contribute to leukemogenesis. DOT1L is the only lysine methyltransferase that does not contain a SET domain, which is a feature that allowed the development of selective DOT1L inhibitors that are currently investigated in Phase I clinical trials for cancer treatment. Recently, abnormal expression of this enzyme has been associated with poor survival and increased aggressiveness of several solid tumors. In this review evidences of aberrant DOT1L expression and activity in breast, ovarian, prostate, colon, and other solid tumors, and its relationships with biological and clinical behavior of the disease and...
Transcriptional activation of the cyclin D1 gene (CCND1) plays a pivotal role in G 1-phase progre... more Transcriptional activation of the cyclin D1 gene (CCND1) plays a pivotal role in G 1-phase progression, which is thereby controlled by multiple regulatory factors, including nuclear receptors (NRs). Appropriate CCND1 gene activity is essential for normal development and physiology of the mammary gland, where it is regulated by ovarian steroids through a mechanism(s) that is not fully elucidated. We report here that CCND1 promoter activation by estrogens in human breast cancer cells is mediated by recruitment of a c-Jun/c-Fos/estrogen receptor ␣ complex to the tetradecanoyl phorbol acetate-responsive element of the gene, together with Oct-1 to a site immediately adjacent. This process coincides with the release from the same DNA region of a transcriptional repressor complex including Yin-Yang 1 (YY1) and histone deacetylase 1 and is sufficient to induce the assembly of the basal transcription machinery on the promoter and to lead to initial cyclin D1 accumulation in the cell. Later on in estrogen stimulation, the cyclin D1/Cdk4 holoenzyme associates with the CCND1 promoter, where E2F and pRb can also be found, contributing to the long-lasting gene enhancement required to drive G 1-phase completion. Interestingly, progesterone triggers similar regulatory events through its own NRs, suggesting that the gene regulation cascade described here represents a crossroad for the transcriptional control of G 1-phase progression by different classes of NRs.
Identification of genes involved in growth inhibition of breast cancer cells transduced with estr... more Identification of genes involved in growth inhibition of breast cancer cells transduced with estrogen receptor
Cancers, 2021
Integrins are cell-extracellular matrix adhesion molecules whose expression level undergoes quant... more Integrins are cell-extracellular matrix adhesion molecules whose expression level undergoes quantitative changes upon neoplastic transformation and are considered functionally related to the development of cancer metastasis. We analyzed the largest mRNA-seq dataset available to determine the expression pattern of integrin family subunits in papillary thyroid carcinomas (PTC). ITGA2, 3, 6, V, and ITGB1 integrin subunits were overexpressed in PTC compared to normal thyroid tissue. The PTC histology variants “classical” and “tall cell” displayed a similar integrin expression profile with a higher level of ITGA3, ITGAV, and ITGB1, which differed from that of the “follicular” variant. Interestingly, compared to RAS mutations, BRAFV600E mutation was associated with a significantly higher expression of integrins. Some integrin subunits were associated with advanced disease stage, lymph node metastasis, extrathyroidal extension, and high-risk groups. Among them, ITGA3 expression displayed t...
BMC Bioinformatics, 2021
Background Next-Generation-Sequencing (NGS) enables detection of microorganisms present in biolog... more Background Next-Generation-Sequencing (NGS) enables detection of microorganisms present in biological and other matrices of various origin and nature, allowing not only the identification of known phyla and strains but also the discovery of novel ones. The large amount of metagenomic shotgun data produced by NGS require comprehensive and user-friendly pipelines for data analysis, that speed up the bioinformatics steps, relieving the users from the need to manually perform complex and time-consuming tasks. Results We describe here HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities), an exhaustive pipeline for metagenomics data analysis, comprising three independent analytical modules designed for an inclusive analysis of large NGS datasets. Conclusions HOME-BIO is a powerful and easy-to-use tool that can be run also by users with limited computational expertise. It allows in-depth analyses by removing low-complexity/ problematic reads, integrating the analytical steps that...
F1000Research, 2021
Current bioinformatics workflows for PIWI-interacting RNA (piRNA) analysis focus primarily on ger... more Current bioinformatics workflows for PIWI-interacting RNA (piRNA) analysis focus primarily on germline-derived piRNAs and piRNA-clusters. Frequently, they suffer from outdated piRNA databases, questionable quantification methods, and lack of reproducibility. Often, pipelines specific to miRNA analysis are used for the piRNA research in silico. Furthermore, the absence of a well-established database for piRNA annotation, as for miRNA, leads to uniformity issues between studies and generates confusion for data analysts and biologists. For these reasons, we have developed WIND (Workflow for pIRNAs aNd beyonD), a bioinformatics workflow that addresses the crucial issue of piRNA annotation, thereby allowing a reliable analysis of small RNA sequencing data for the identification of piRNAs and other small non-coding RNAs (sncRNAs) that in the past have been incorrectly classified as piRNAs. WIND allows the creation of a comprehensive annotation track of sncRNAs combining information availa...
Cancers, 2020
Ovarian cancer (OC) shows the highest mortality rate among gynecological malignancies and, becaus... more Ovarian cancer (OC) shows the highest mortality rate among gynecological malignancies and, because of the absence of specific symptoms, it is frequently diagnosed at an advanced stage, mainly due to the lack of specific and early biomarkers, such as those based on cancer molecular signature identification. Indeed, although significant progress has been made toward improving the clinical outcome of other cancers, rates of mortality for OC are essentially unchanged since 1980, suggesting the need of new approaches to identify and characterize the molecular mechanisms underlying pathogenesis and progression of these malignancies. In addition, due to the low response rate and the high frequency of resistance to current treatments, emerging therapeutic strategies against OC focus on targeting single factors and pathways specifically involved in tumor growth and metastasis. To date, loss-of-function screenings are extensively applied to identify key drug targets in cancer, seeking for mor...
Communications Biology, 2021
miRNAs modulate cardiomyocyte specification by targeting mRNAs of cell cycle regulators and actin... more miRNAs modulate cardiomyocyte specification by targeting mRNAs of cell cycle regulators and acting in cardiac muscle lineage gene regulatory loops. It is unknown if or to-what-extent these miRNA/mRNA networks are operative during cardiomyocyte differentiation of adult cardiac stem/progenitor cells (CSCs). Clonally-derived mouse CSCs differentiated into contracting cardiomyocytes in vitro (iCMs). Comparison of “CSCs vs. iCMs” mRNome and microRNome showed a balanced up-regulation of CM-related mRNAs together with a down-regulation of cell cycle and DNA replication mRNAs. The down-regulation of cell cycle genes and the up-regulation of the mature myofilament genes in iCMs reached intermediate levels between those of fetal and neonatal cardiomyocytes. Cardiomyo-miRs were up-regulated in iCMs. The specific networks of miRNA/mRNAs operative in iCMs closely resembled those of adult CMs (aCMs). miR-1 and miR-499 enhanced myogenic commitment toward terminal differentiation of iCMs. In conclu...
PROTEOMICS, 2020
Estrogen receptor alpha (ERα) is a ligand‐inducible transcription factor which mediates estrogen ... more Estrogen receptor alpha (ERα) is a ligand‐inducible transcription factor which mediates estrogen actions in hormone‐responsive tumors and is targeted by effective anticancer therapies based on the ERα antagonist ligands, selective estrogen receptor modulators (such as Tamoxifen/TAM) or disruptors (such as Fulvestrant/ICI). Despite its importance for cancer therapy, including acquired resistance to endocrine therapy, the molecular basis of ERα response to different ligands is not fully known to date. Interaction proteomics shows great potential to identify and characterize molecular mechanisms of disease based on physical and functional protein‐protein interaction networks. Tandem affinity purification coupled to mass spectrometry is applied here for mapping in hormone‐responsive breast cancer cells nuclei, the ERα interactomes, induced by each of the two classes of antiestrogens. The results provide new insights on the molecular bases for antiestrogen‐mediated control of ERα function and reveal new potential ways to overcome endocrine therapy resistance in cancer.
Virology Journal, 2021
A growing number of emerging SARS-CoV-2 variants is being identified worldwide, potentially impac... more A growing number of emerging SARS-CoV-2 variants is being identified worldwide, potentially impacting the effectiveness of current vaccines. We report the data obtained in several Italian regions involved in the SARS-CoV-2 variant monitoring from the beginning of the epidemic and spanning the period from October 2020 to March 2021.
Journal of Biological Chemistry, 1994
Production of nitric oxide (NO) by macrophages is enhanced upon activation by bacterial endotoxin... more Production of nitric oxide (NO) by macrophages is enhanced upon activation by bacterial endotoxins and cytokines mainly via an increase of the intracellular content of the inducible isoform of nitric oxide synthase (i-NOS). W e have studied in detail the effect of several modulators of macrophage activity on steady state levels of i-NOS mRNA in the mouse macrophage-like cell line RAW 264.7. Bacterial lipopolysaccharide (LPS) and interferon-y (IFN-y) were found to be effective inducers of i-NOS mRNA, in accordance with their known ability to stimulate both i-NOS activity and NO production in macrophages from different sources, while TNF-a, IL-1, or IL-6 was ineffective in this regard. Accumulation of i-NOS mRNA in response to either LPS or IFN-y stimulation was accompanied by increased i-NOS gene transcription, as detected both by using a nuclear "run-on" transcription assay and by transient transfection of the cloned gene promoter in RAW 264.7 cells. Co-stimulation of the cells with both inducers resulted in higher steady state levels of i-NOS mRNA in the absence, however, of a corresponding potentiation of the rate of gene transcription. This was due primarily to a considerable effect of LPS on i-NOS mRNA stability, with prolongation of its half-life from 1-1.5 h, in the presence of IFN-y alone, to 4-6 h in the presence of both LPS and IFN-y. Nitric oxide (NO), a simple gas with free radical chemical properties, is a bioregulator that plays an important role in diverse physiological processes, including smooth muscle relaxation and penile erection, plateIet inhibition, neurotransmission, immune responses, and inflammation (1-3). Production of nitric oxide (NO) from L-arginine and molecular oxygen is catalyzed by NO synthase (NOS)I enzymes, P-450-type cytoplasmic hemeproteins that in their active form are homodimers containing FAD and FMN and require tetrahydrobiopterin and
Cancers, 2020
Estrogen receptors (ERα and ERβ) are ligand-activated transcription factors that play different r... more Estrogen receptors (ERα and ERβ) are ligand-activated transcription factors that play different roles in gene regulation and show both overlapping and specific tissue distribution patterns. ERβ, contrary to the oncogenic ERα, has been shown to act as an oncosuppressor in several instances. However, while the tumor-promoting actions of ERα are well-known, the exact role of ERβ in carcinogenesis and tumor progression is not yet fully understood. Indeed, to date, highly variable and even opposite effects have been ascribed to ERβ in cancer, including for example both proliferative and growth-inhibitory actions. Recently ERβ has been proposed as a potential target for cancer therapy, since it is expressed in a variety of breast cancers (BCs), including triple-negative ones (TNBCs). Because of the dependence of TNBCs on active cellular signaling, numerous studies have attempted to unravel the mechanism(s) behind ERβ-regulated gene expression programs but the scenario has not been fully r...
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Papers by Alessandro WEISZ