Small non-coding RNAs and cancer: a bioinformatics approach

The development of Next-Generation Sequencing (NGS) technologies has added a new method to investigate the role of genes in several diseases, including breast cancer (BC). For example, RNA-Seq is mainly used to analyze the continuously changing cellular transcriptome and finding the pathways enriched/inhibited by the differently expressed genes. Small RNA-Seq is a very similar method allowing the detection of other classes of RNA such as small non-coding RNA (miRNA, piRNA, tRNA). In particular, microRNAs (miRNA) are a small non-coding RNA that regulate gene expression at the post-transcriptional level by binding to the 3'UTR (untranslated region) of target mRNAs, causing their degradation or translation inhibition. Several studies correlated an altered expression of these sncRNAs with the onset and /or progression of different diseases, including cancer. They can be used as biomarkers, playing a key role in the diagnosis, prognosis and prediction of response to specific therapies. Moreover, many studies have focused on the possibility of developing new therapeutic strategies based on microRNAs modulation and their potential use in the personalized management of cancer. Furthermore, also Piwi-interacting RNA (piRNA) is a class of small non-coding RNA molecules expressed in animal cells that are associated with both epigenetic and post-transcriptional gene silencing of retrotransposons and other genetic elements. They are distinct from miRNA in size (26–31 nt rather than 21–24 nt), lack of sequence conservation, and increased complexity. The aim of my research project was to understand the carcinogenic mechanisms and pathways modulated by these mRNAs and smallRNAs, since the clarification of the roles played by these molecules in cancer might provide new opportunities to develop novel strategies for diagnosing and treating this disease using bioinformatics tools and created it. Furthermore, a tool has been created that allows the analysis of smallRNAs by integrating various software to facilitate the use of this technology and to better explore the expected results

CD10, BCL6, and MUM1 expression in diffuse large B-cell lymphoma on FNA samples

BACKGROUND: Gene expression profiling has divided diffuse large B-cell lymphoma (DLBCL) into 2 main subgroups: germinal center B (GCB) and non-GCB type. This classification is reproducible by immunohistochemistry using specific antibodies such as CD10, B-cell lymphoma 6 (BCL6), and multiple myeloma oncogene 1 (MUM1). Fine-needle aspiration (FNA) plays an important role in the diagnosis of non-Hodgkin lymphoma, and in some cases FNA may be the only available pathological specimen. The objectives of the current study were to evaluate CD10, BCL6, and MUM1 immunostaining on FNA samples by testing the CD10, BCL6, and MUM1 algorithm on both FNA cell blocks (CB) and conventional smears (CS), evaluating differences in CB and CS immunocytochemical (ICC) performance, and comparing results with histological data. METHODS: Thirty-eight consecutive DLBCL cases diagnosed by FNA were studied. Additional passes were used to prepare CB in 22 cases and CS in 16 cases; the corresponding sections and smears were immunostained using CD10, BCL6, and MUM1 in all cases. The data obtained were compared with histological immunostaining in 24 cases. RESULTS: ICC was successful in 33 cases (18 CB and 15 CS) and not evaluable in 5 cases (4 CB and 1 CS). The CD10-BCL6-MUM1 algorithm subclassified DLBCL as GCB (9 cases) and non-GCB (24 cases). ICC data were confirmed on histologic staining in 24 cases. CONCLUSIONS: CD10, BCL6, and MUM1 ICC staining can be performed on FNA samples. The results herein prove it is reliable both on CB and CS, and is equally effective and comparable to immunohistochemistry data

Epithelioid variant of pleomorphic liposarcoma as potential mimic of metastatic carcinoma

We report a case of epithelioid variant of pleomorphic liposarcoma (EPL) found in the the infrapatellar fat pad of Hoffa of a 31-year old male. Histologically, the predominant population was formed by epithelioid cells with eosinophilic or clear cytoplasm admixed with rare pleomorphic lipoblasts. The immunohistochemical panel was not helpful in the diagnosis. FISH analysis using the locus-specific indicator CHOP (12q13) dual color break apart was applied to representative formalin-fixed, paraffin-embedded tissue sections. The result of FISH indicated a rearranged CHOP (DDIT3) gene and confirmed the diagnosis of EPL. The EPL should be differentiated from a metastatic carcinoma or other type of sarcoma. In these cases a clinicopathological correlation and an exhaustive sampling of the specimen for demonstration of lipogenic areas or pleomorphic lipoblasts is always necessary. FISH with demonstration of CHOP gene rearrangement is useful in providing specific ancillary information for the difficult differential diagnosis of this case

Small non-coding RNA landscape is modified by GPAT2 silencing in MDA-MB-231 cells

Glycerol-3-phosphate acyltransferase-2 is a member of “cancer-testis gene” family. Initially linked to lipid metabolism, this gene has been recently found involved also in PIWI-interacting RNAs biogenesis in germline stem cells. To investigate its role in piRNA metabolism in cancer, the gene was silenced in MDA-MB-231 breast cancer cells and small RNA sequencing was applied. PIWI-interacting RNAs and tRNA-derived fragments expression profiles showed changes following GPAT2 silencing. Interestingly, a marked shift in length distribution for both small RNAs was detected in GPAT2-silenced cells. Most downregulated PIWI-interacting RNAs are single copy in the genome, intragenic, hosted in snoRNAs and previously found to be upregulated in cancer cells. Putative targets of these PIWI-interacting RNAs are linked to lipid metabolism. Downregulated tRNA derived fragments derived from, socalled ‘differentiation tRNAs’, whereas upregulated ones derived from proliferationlinked tRNAs. miRNA amounts decrease after Glycerol-3-phosphate acyltransferase-2 silencing and functional enrichment analysis of deregulated miRNA putative targets point to mitochondrial biogenesis, IGF1R signaling and oxidative metabolism of lipids and lipoproteins. In addition, miRNAs known to be overexpressed in breast cancer tumors with poor prognosis where found downregulated in GPAT2-silenced cells. In conclusion, GPAT2 silencing quantitatively and qualitatively affects the population of PIWI-interacting RNAs, tRNA derived fragments and miRNAs which, in combination, result in a more differentiated cancer cell phenotype.Centro de Investigaciones Inmunológicas Básicas y AplicadasInstituto de Investigaciones Bioquímicas de La Plat

High Risk of Secondary Infections Following Thrombotic Complications in Patients With COVID-19

Background. This study’s primary aim was to evaluate the impact of thrombotic complications on the development of secondary infections. The secondary aim was to compare the etiology of secondary infections in patients with and without thrombotic complications. Methods. This was a cohort study (NCT04318366) of coronavirus disease 2019 (COVID-19) patients hospitalized at IRCCS San Raffaele Hospital between February 25 and June 30, 2020. Incidence rates (IRs) were calculated by univariable Poisson regression as the number of cases per 1000 person-days of follow-up (PDFU) with 95% confidence intervals. The cumulative incidence functions of secondary infections according to thrombotic complications were compared with Gray’s method accounting for competing risk of death. A multivariable Fine-Gray model was applied to assess factors associated with risk of secondary infections. Results. Overall, 109/904 patients had 176 secondary infections (IR, 10.0; 95% CI, 8.8–11.5; per 1000-PDFU). The IRs of secondary infections among patients with or without thrombotic complications were 15.0 (95% CI, 10.7–21.0) and 9.3 (95% CI, 7.9–11.0) per 1000-PDFU, respectively (P = .017). At multivariable analysis, thrombotic complications were associated with the development of secondary infections (subdistribution hazard ratio, 1.788; 95% CI, 1.018–3.140; P = .043). The etiology of secondary infections was similar in patients with and without thrombotic complications. Conclusions. In patients with COVID-19, thrombotic complications were associated with a high risk of secondary infections

A case of multicentric low-grade neuroendocrine breast tumor with an unusual histological pattern

Neuroendocrine features are detectable in carcinomas of the breast either as scattered cells, that are recognized by their expression of neuroendocrine cell markers. Instead, pure breast carcinomas with neuroendocrine features (NEBC) are very rare and represent <1% of all breast cancer. Usually NEBC may be well or poorly differentiated and more frequent in older woman. These tumors showed variable histological pattern but a common feature is represented by expression of neuroendocrine markers. Here we report a case of a primary multicentric low-grade neuroendocrine carcinoma of the breast presented because of its rarity and for the unusual tubular and cribriform pattern resembling a well-differentiated conventional breast carcinoma. The tumor was treated with left quadrantectomy with concomitant wide excisional biopsy of other two nodules and lymph node sentinel biopsy. No recurrence was observed during 1-year follow-up. Because of its rarity and variability of morphologic features, there exist diagnostic challenges for pathologists to differentiate primary NEBC to some conventional breast carcinomas and to the breast metastasis from neuroendocrine tumor of the lung or gastrointestinal tract. It is important to be able recognize this tumor in order to avoid potential misdiagnosis and improper management of afflicted patients