Jeff Palatini

University of Warsaw | UW · Centre of New Technologies

To sustain tumor growth, cancer cells must be able to adapt to fluctuations in energy availability. We have identified a single microRNA that controls glioma cell proliferation, migration, and responsiveness to glucose deprivation. Abundant glucose allows relatively high miR-451 expression, promoting cell growth. In low glucose, miR-451 levels decr...

Chromosomal abnormalities, immunoglobulin heavy chain variable-region (IGHV) gene mutation status, and zeta-associated protein 70 (ZAP-70) expression levels have independent prognostic relevance in chronic lymphocytic leukemia (CLL); however, their concordance is variable. Because deregulation of microRNAs has been linked to disease initiation and...

Background: Despite the positive effects of endurance training on the cardiovascular (CV) system, excessive exercise induces not only physiological adaptations but also adverse changes in CV system, including the heart. We aimed to evaluate the selected miRNAs expression based on bioinformatic analysis and their changes before and after an ultramar...

The transition from ductal carcinoma in situ to invasive ductal carcinoma is a key event in breast cancer progression that is still not well understood. To discover the microRNAs regulating this critical transition, we used 80 biopsies from invasive ductal carcinoma, 8 from ductal carcinoma in situ, and 6 from normal breast. We selected them from a...

p53 suppresses tumor progression and metastasis. Epithelial-mesenchymal transition (EMT) is a key process in tumor progression and metastasis. The transcription factors ZEB1 and ZEB2 promote EMT. Here, we show that p53 suppresses EMT by repressing expression of ZEB1 and ZEB2. By profiling 92 primary hepatocellular carcinomas (HCCs) and 9 HCC cell l...

Altered expression of circular RNAs (circRNAs) has previously been investigated in breast cancer. However, little is known about the effects of drugs on their regulation and relationship with the cognate linear transcript (linRNA). We analyzed the dysregulation of both 12 cancer-related circRNAs and their linRNAs in two breast cancer cell lines und...

Altered expression of circular RNAs (circRNAs) has previously been investigated in breast cancer. However, little is known about the effects of drugs on their regulation and relationship with the cognate linear transcript (linRNA). We analyzed the dysregulation of both 12 cancer-related circRNAs and their linRNAs in two breast cancer cell lines und...

Citation: Crudele, F.; Bianchi, N.; Terrazzan, A.; Ancona, P.; Frassoldati, A.; Gasparini, P.; D'Adamo, A.P.; Papaioannou, D.; Garzon, R.; Wójcicka, A.; et al. Circular RNAs Could Encode Unique Proteins and Affect Cancer Pathways. Biology 2023, 12, 493. https://doi. Simple Summary: In this study, we investigated human genes encoding circular RNAs (...

Multiple sclerosis (MS) is a central nervous system chronic neuroinflammatory disease followed by neurodegeneration. The diagnosis is based on clinical presentation, cerebrospinal fluid testing and magnetic resonance imagining. There is still a lack of a diagnostic blood-based biomarker for MS. Due to the cost and difficulty of diagnosis, new and m...

There are 481 ultra-conserved regions (UCRs) longer than 200 bases in the genomes of human, mouse and rat. These DNA sequences are absolutely conserved and show 100% identity with no insertions or deletions. About half of these UCRs are reported as transcribed and many correspond to long non-coding RNAs (lncRNAs). We used custom microarrays with 96...

Background: The purpose of this study is to determine whether microRNA for pluripotent stem cells are also expressed in breast cancer and are associated with metastasis and outcome. Methods: We studied global microRNA profiles during differentiation of human embryonic stem cells (n =26) and in breast cancer patients (n = 33) and human cell lines...

MicroRNAs regulate several aspects of tumorigenesis and cancer progression. Most cancer tissues are archived formalin-fixed and paraffin-embedded (FFPE). While microRNAs are a more stable form of RNA thought to withstand FFPE-processing and degradation there is only limited evidence for the latter assumption. We examined whether microRNA profiling...

For many years breast cancer classification has been based on histology and immune-histochemistry. New techniques, more strictly related to cancer biology, partially succeeded in fractionating patients, correlated to survival and better predicted the patient response to therapy. Nowadays, great expectations arise from massive parallel or high throu...

The histological definition of Barrett's esophagus (BE) is debated, particularly regarding the phenotype of its metaplastic columnar epithelium. Histologically proven intestinal metaplasia (IM) was the sine qua non condition for a diagnosis of BE but, more recently, non-intestinalized (i.e., cardiac gastric-type; GM) columnar metaplasia has been re...

MicroRNAs (miRNAs) have important roles in the initiation and progression of human cancer, but their role in head and neck cancer development and progression is not well defined. We aimed to determine whether specific miRNAs and their target mRNAs contribute to head and neck cancer pathogenesis and progression. To identify miRNAs associated with he...

Osteosarcoma remains a leading cause of cancer death in adolescents. Treatment paradigms and survival rates have not improved in two decades. Driving the lack of therapeutic inroads, the molecular etiology of osteosarcoma remains elusive. MicroRNAs (miRNAs) have demonstrated far-reaching effects on the cellular biology of development and cancer. Th...

Barrett's esophagus (BE) is characterized by the native stratified squamous epithelium (N) lining the esophagus being replaced by a columnar epithelium with intestinal differentiation (Barrett's mucosa; BM). BM is considered as the main risk factor for esophageal adenocarcinoma (Barrett's adenocarcinoma; BAc). MicroRNAs (miRNAs) are a class of smal...

For nearly the last two decades, the diagnosis of Barrett's mucosa (BM) strictly required histologically documented intestinal metaplasia (IM). More recently, a precancerous potential has been also associated to non-goblet columnar metaplasia (i.e. gastric metaplasia, [GM]). Molecular profiling can be applied to characterize the precancerous meanin...

Renal cell carcinoma (RCC) accounts for 3% of all adult malignancies in the United States, and represents the most common cancer in the adult kidney. The most frequent histotype of RCC is the clear-cell variant (ccRCC) which occurs in 80–90% of RCC cases. Despite the advent of new target-oriented therapies, a radical surgery still represents the be...

Introduction: MicroRNAs (miRNAs) are small non-coding RNAs 18-24 nucleotides in length that regulate gene expression by targeting the 3’ untranslated region of mRNAs. MiRNAs are often dysregulated in cancer, suggesting they play a role in tumorigenesis. Canine diffuse large B-cell lymphoma (DLBCL) represents one of the most common spontaneously occ...

Sporadic Burkitt lymphoma (sBL) can be delineated from diffuse large B-cell lymphoma (DLBCL) by a very homogeneous mRNA expression signature. However, it remained unclear whether all three BL variants-sBL, endemic BL (eBL) and human immunodeficiency virus-associated BL (HIV-BL)-represent a uniform biological entity despite their differences in geog...

Supplemental Figure 1: Cell lines subjected to Onconase treatment at 20 µg/mL (A) Control proliferation has been normalized to a value of 1 for each time point. Significantly decreased proliferation compared to control is seen at 48 and 72 hours. (B) Significantly decreased invasion of MPM cell lines at both time points.

Supplemental Figure 2: Dose effects of Onconase on the proliferation of three mesothelioma cell lines. Although effects were seen with as little as 5 ug/ml, maximum effects were seen with 20ug/ml.

Supplemental Figure 5: Quantification of effects of Onconase-associated microRNAs on genes downstream of NFKB. The gene expression was uniformly decreased by hsa-mir-17* and has-mir-30c inhibitor and the degree of decrease was cell line dependent.

Supplemental Figure 3: Cell lines subjected to Onconase treatment at 20 µg/mL for 72 hours resulted in decreased expression of multidrug resistance gene ABCB. NFKB(p50) expression was also reduced at both time points.

Supplemental Figure 4: Western Blot demonstrates that cell lines subjected to Onconase treatment at 20 µg/mL for 72 hours have decreased protein for multidrug resistance genes ABCB1 and NFKB. ERK2, unaffected by Onconase, was used as a loading control.

Purpose Treatment of malignant pleural mesothelioma (MPM) with Ranpirnase (Onconase) results in disruption of protein translation and cell apoptosis. We hypothesize that Onconase acts via down regulation of nuclear factor kappa B (NFKβ) by specific microRNAs (miRNA) and that interference of this pathway could have implications for MPM resistance to...

Next-generation sequencing (NGS) methods have the potential for changing the landscape of biomedical science, but at the same time pose several problems in analysis and interpretation. Currently, there are many commercial and public software packages that analyze NGS data. However, the limitations of these applications include output which is insuf...

Barrett's Mucosa (BM) is a metaplastic replacement of the native esophageal (squamous) epithelium (ESq) by columnar-intestinalized mucosa. BM is the main risk factor for Barrett's adenocarcinoma (BAc). MicroRNAs (miRNAs) are a class of small non-coding RNAs that control gene expression by targeting mRNAs; miRNAs deregulation has been associated wit...

We studied miRNA profiles in 4419 human samples (3312 neoplastic, 1107 nonmalignant), corresponding to 50 normal tissues and 51 cancer types. The complexity of our database enabled us to perform a detailed analysis of microRNA (miRNA) activities. We inferred genetic networks from miRNA expression in normal tissues and cancer. We also built, for the...

We devised a novel procedure to identify human cancer genes acting in a recessive manner. Our strategy was to combine the contributions of the different types of genetic alterations to loss of function: amino-acid substitutions, frame-shifts, gene deletions. We studied over 20,000 genes in 3 Gigabases of coding sequences and 700 array comparative g...

Genomic structures are correctly identified by the aCGH protocol. Track analysis in UCSC Genome Browser of Xp22 Pseudo-Autosomal Region 1 (PAR1). The Pseudo-Autosomal Region 1 is correctly identified as normal (diploid) by the array CGH analysis, while the rest of X chromosome is reported, also as expected, “pseudo-amplified”. The chromosome X gene...

Functional (Gene ontology, biological process) chart of the candidate cancer recessive genes, FDR<0.5 (0.22 MB DOC)

Distribution of gene size in the candidate recessive cancer gene-set. The recessive cancer gene sizes do not differ significantly from the gene sizes in the human genome (most common genes range between 32 and 128 kb). (0.28 MB TIF)

Array CGH datasets. (0.04 MB DOC)

BACKGROUND The majority of patients with lymphoma undergo a single biopsy for diagnosis, and there are few opportunities to acquire posttreatment material. Fine-needle aspiration (FNA) biopsy is a minimally invasive procedure, and acquiring routine posttreatment material would require minimal effort and provide needed material for gene expression p...

Adenosine A3 receptors (ADOA3Rs) are emerging as novel purinergic targets for treatment of inflammatory diseases. Our goal was to assess the protective effect of the ADOA3R agonist N(6)-(3-iodobenzyl)-adenosine-5-N-methyluronamide (IB-MECA) on gene dysregulation and injury in a rat chronic model of 2,4,6-trinitrobenzene sulfonic acid (TNBS)--induce...

Motivation: Oligonucleotide expression arrays exhibit systematic and reproducible variation produced by the multiple distinct probes used to represent a gene. Recently, a gene expression index has been proposed that explicitly models probe effects, and provides improved fits of hybridization intensity for arrays containing perfect match (PM) and m...

Myotonic dystrophy (DM) is an autosomal dominant neuromuscular disease with highly variable multisystemic manifestations. The mutation underlying DM is an unstable (CTG)n expansion in the 3' UTR of the myotonic dystrophy protein kinase gene (DMPK). The pathophysiological mechanism(s) of the expanded (CTG)n repeat remains unclear. Various effects ha...