Aldo Scarpa

BackgroundPancreatic ductal adenocarcinoma (PDAC) is an aggressive cancer with poor prognosis. It is marked by extraordinary resistance to conventional therapies including chemotherapy and radiation, as well as to essentially all targeted therapies evaluated so far. More than 90% of PDAC cases harbor an activating KRAS mutation. As the most common KRAS variants in PDAC remain undruggable so far, it seemed promising to inhibit a downstream target in the MAPK pathway such as MEK1/2, but up to now preclinical and clinical evaluation of MEK inhibitors (MEKi) failed due to inherent and acquired resistance mechanisms. To gain insights into molecular changes during the formation of resistance to oncogenic MAPK pathway inhibition, we utilized short-term passaged primary tumor cells from ten PDACs of genetically engineered mice. We followed gain and loss of resistance upon MEKi exposure and …

Plexins are a family of transmembrane receptors (Tamagnone and Comoglio, 2000), consisting of nine members, divided into four subfamilies, A thru D (PLXNA1, A2, A3, A4; B1, B2, B3; C1; D 1). In the human genome, the corresponding genes are located on chromosomes 1 (PLXNA2), 3 (PLXN s A1, B1, andD1), 7 (PLXNA4), 12 (PLXNC1), 22 (PLXNB2), and X (PLXN s A3 and B3)(see Supp. Table S1). Plexins are a part of the semaphorin gene superfamily, which includes the semaphorins and the receptor tyrosine kinases MET and RON. We have previously shown that plexins function as high-affinity receptors for semaphorins, either alone or in complex with the neuropilins (Tamagnone et al., 1999). Semaphorins are a large family of molecular signals controlling cell migration, axon guidance and the immune response (for a recent review, see (Zhou et al., 2008)).Several studies show the involvement of semaphorins and neuropilins in cancer, either as putative onco-suppressor genes or as mediators of tumor invasion and metastasis (Tomizawa et al., 2001; Bielenberg et al., 2004; Christensen et al., 2005; Basile et al., 2006; Catalano et al., 2006; for a review, see Neufeld and Kessler, 2008). An additional link between plexins and human tumors is provided by their ability to associate and functionally activate tyrosine kinase receptors, such as MET, RON, HER2, and KDR (Giordano et al., 2002; Conrotto et al., 2004; Toyofuku et al., 2004; Swiercz et al., 2008). These data suggest that plexins might play a role in the invasive and metastatic potential of cancer cells. Scattered reports have described the expression of individual plexins in human …

Temozolomide (TMZ)-based regimens represent a valid therapeutic option in well-differentiated neuroendocrine tumors (NETs G2 and G3). As an alkylating agent, it increases DNA alteration by altering guanine residues, which either triggers cell death or results in novel missense mutations especially in MGMT deficient cells. Here, we describe an exploratory case series of TMZ-treated NETs cases that underwent NGS analysis at the University Hospital of Verona. Methods. We included 32 patients (16 G2 and 16 G3). NGS was performed before TMZ treatment for 22 cases (54%), after for 19 (46%) and in both for 4 cases (13%). We performed NGS on tissue samples for 73% of assays and via liquid biopsy for the remaining 27%. For tissue NGS, in 77% of samples we used an in-house panel encompassing 174 genes and in 23% commercial test interrogating at least 500 genes. Only ACMG/AMP class IV-V …

Biliary tract cancers (BTCs) represent a spectrum of malignancies associated with a dismal prognosis. Recent genomic profiling studies have provided a deeper understanding of the complex and heterogenous molecular landscape of BTCs, identifying several actionable genetic alterations, and expanding treatment options. Due to the high number and complexity of genetic alterations which require testing, next-generation sequencing (NGS) is currently the preferred approach over conventional methods (i.e., immunohistochemistry, fluorescence in-situ hybridization and PCR) for molecular profiling of BTCs and should be performed upfront in all BTC patients. However, BTC sampling often yields low tumor cellularity tissue, hampering NGS analysis. Future perspectives to overcome this obstacle include liquid biopsy and optimization of biopsy protocols. In this position paper, the authors discuss the current …

Objectives The high incidence of prostate cancer causes prostatic samples to significantly affect pathology laboratories workflow and turnaround times (TATs). Whole-slide imaging (WSI) and artificial intelligence (AI) have both gained approval for primary diagnosis in prostate pathology, providing physicians with novel tools for their daily routine. Methods A systematic review according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines was carried out in electronic databases to gather the available evidence on the application of AI-based algorithms to prostate cancer. Results Of 6290 articles, 80 were included, mostly (59%) dealing with biopsy specimens. Glass slides were digitized to WSI in most studies (89%), roughly two-thirds of which (66%) exploited convolutional neural networks for computational analysis. The …

In the molecular era, proper archival conditions within pathology laboratories are crucial, especially for formalin-fixed paraffin-embedded (FFPE) tissue specimens retrieved years after the original diagnosis. Indeed, improper preservation can impact the integrity of nucleic acids and protein antigens. This study evaluates the quality status of stored FFPE blocks using multilevel omics approaches. FFPE blocks from 45 Non-Small Cell Lung Carcinoma (NSCLC) cases were analyzed. The blocks were collected from six different pathology archives across Italy with distinct environmental characteristics. Nucleic acids’ quantity and quality, as well as protein antigens, were assessed using various techniques, including MALDI-MSI. RNA was quantitatively higher, but more fragmented, compared to DNA. DNA quantity and quality were suitable for molecular analyses in 94.4% and 62.3% of samples, respectively. RNA quantity was adequate across all samples, but it was optimal only in 22.3% of cases. DNA quality started to deteriorate after 6–8 years, whereas RNA quality diminished only after 10 years of storage. These data might suggest a particular DNA susceptibility to FFPE blocks conservation. Immunohistochemical intensity decreased significantly after 6–8 years of storage, and MALDI-MSI analysis revealed that younger tissue blocks contained more unique proteomic signals than the older ones. This study emphasizes the importance of proper FFPE archiving conditions for molecular analyses. Governance should prioritize attention to pathology archives to ensure quality preservation and optimize predictive testing. By elucidating the nuances of …

Gene fusions and rearrangements play a crucial role in tumor biology. They are rare events typically detected in KRAS wild-type (WT) pancreatic tumors. Their identification can inform clinical management by enabling precision oncology, as fusions involving BRAF, FGFR2, RET, NTRK, NRG1, and ALK represent actionable targets in KRAS-WT cancers, and serve diagnostic purposes since fusions involving PRKACA/B represent the diagnostic hallmark of intraductal oncocytic papillary neoplasms (IOPNs). Although they are rare, the therapeutic and diagnostic importance of these genomic events should not be underestimated, highlighting the need for quality-ensured molecular diagnostics in the management of cancer. Herein we review the existing literature on the role of fusion genes in pancreatic tumors and their clinical potential as effective biomarkers and therapeutic targets.

Pulmonary large cell carcinoma (LCC) is an undifferentiated neoplasm lacking morphological, histochemical, and immunohistochemical features of small cell lung cancer, adenocarcinoma (ADC), or squamous cell carcinoma (SCC). The available molecular information on this rare disease is limited. This study aimed to provide an integrated molecular overview of 16 cases evaluating the mutational asset of 409 genes and the transcriptomic profiles of 20,815 genes. Our data showed that TP53 was the most frequently inactivated gene (15/16; 93.7%) followed by RB1 (5/16; 31.3%) and KEAP1 (4/16; 25%), while CRKL and MYB genes were each amplified in 4/16 (25%) cases and MYC in 3/16 (18.8%) cases; transcriptomic analysis identified two molecular subtypes including a Pure-LCC and an adenocarcinoma like-LCC (ADLike-LCC) characterized by different activated pathways and cell of origin. In the Pure-LCC …

Pancreatic ductal adenocarcinoma (PDAC) is characterized by a dense and stiff extracellular matrix (ECM) associated with tumor progression and therapy resistance. To further the understanding of how stiffening of the tumor microenvironment (TME) contributes to aggressiveness, a three‐dimensional (3D) self‐assembling hydrogel disease model is developed based on peptide amphiphiles (PAs, PA‐E3Y) designed to tailor stiffness. The model displays nanofibrous architectures reminiscent of native TME and enables the study of the invasive behavior of PDAC cells. Enhanced tuneability of stiffness is demonstrated by interacting thermally annealed aqueous solutions of PA‐E3Y (PA‐E3Yh) with divalent cations to create hydrogels with mechanical properties and ultrastructure similar to native tumor ECM. It is shown that stiffening of PA‐E3Yh hydrogels to levels found in PDAC induces ECM deposition, promotes …

Objective The dysregulation of the axon guidance pathway is common in pancreatic ductal adenocarcinoma (PDAC), yet our understanding of its biological relevance is limited. Here, we investigated the functional role of the axon guidance cue SEMA3A in supporting PDAC progression.Design We integrated bulk and single-cell transcriptomic datasets of human PDAC with in situ hybridisation analyses of patients’ tissues to evaluate SEMA3A expression in molecular subtypes of PDAC. Gain and loss of function experiments in PDAC cell lines and organoids were performed to dissect how SEMA3A contributes to define a biologically aggressive phenotype.Results In PDAC tissues, SEMA3A is expressed by stromal elements and selectively enriched in basal-like/squamous epithelial cells. Accordingly, expression of SEMA3A in PDAC cells is induced by both cell-intrinsic and cell-extrinsic determinants of the basal-like …

Trait‐based ecology has already revealed main independent axes of trait variation defining trait spaces that summarize plant adaptive strategies, but often ignoring intraspecific trait variability (ITV). By using empirical ITV‐level data for two independent dimensions of leaf form and function and 167 species across five habitat types (coastal dunes, forests, grasslands, heathlands, wetlands) in the Italian peninsula, we found that ITV: (i) rotated the axes of trait variation that define the trait space; (ii) increased the variance explained by these axes and (iii) affected the functional structure of the target trait space. However, the magnitude of these effects was rather small and depended on the trait and habitat type. Our results reinforce the idea that ITV is context‐dependent, calling for careful extrapolations of ITV patterns across traits and spatial scales. Importantly, our study provides a framework that can be used to start …

IntroductionAbout 90% of cholangiocarcinomas are adenocarcinomas with glandular or tubular structures lined by epithelial cells, with no bile production and with a variable degree of differentiation, arising in the background of desmoplastic stroma. The remaining 10% is represented by rarer histological variants of which there is little knowledge regarding the biological behavior, molecular characterization, and sensitivity to the various possible therapies, including molecular-based treatments. Such rare tumors are described only in case reports or small retrospective series because of their exclusion from clinical trials. This national initiative, here presented, aims to address the following knowledge gap: a) how much does histological diversity translate into clinical manifestation variety? b) are those chemotherapy regimens, recommended for conventional biliary tract cancers, potentially active in rare variants …

Pancreatic ductal adenocarcinoma (PDAC) is a tumor with a dismal prognosis that arises from precursor lesions called pancreatic intraepithelial neoplasias (PanINs). Progression from low- to high-grade PanINs is considered as tumor initiation, and a deeper understanding of this switch is needed. Here, we show that synaptic molecule neuroligin-2 (NLGN2) is expressed by pancreatic exocrine cells and plays a crucial role in the regulation of contact inhibition and epithelial polarity, which characterize the switch from low- to high-grade PanIN. NLGN2 localizes to tight junctions in acinar cells, is diffusely distributed in the cytosol in low-grade PanINs and is lost in high-grade PanINs and in a high percentage of advanced PDACs. Mechanistically, NLGN2 is necessary for the formation of the PALS1/PATJ complex, which in turn induces contact inhibition by reducing YAP function. Our results provide novel insights into …

Background Prognosis of perihilar cholangiocarcinoma (PHCC) is poor, and curative-intent resection is the most effective treatment associated with long-term survival. Surgery is technically demanding since it involves a major hepatectomy with en bloc resection of the caudate lobe and extrahepatic bile duct. Furthermore, to achieve negative margins, it may be necessary to perform concomitant vascular resection or pancreatoduodenectomy. Despite this aggressive approach, recurrence is often observed, considering 5-year recurrence-free survival below 15% and 5-year overall survival that barely exceeds 40%. Summary The literature reports that survival rates are better in patients with negative margins, and surprisingly, R0 resections range between 19% and 95%. This variability is probably due to different surgical strategies and the pathologist’s expertise with specimens. In fact, a proper pathological …

Somatostatin receptor (SST) PET/CT is the gold standard for well‐differentiated neuroendocrine tumours (NET) imaging. Higher grades of neuroendocrine neoplasms (NEN) show preferential [18F]FDG (FDG) uptake, and even low‐grade NET may de‐differentiate over time. FDG PET/CT's prognostic role is widely accepted; however, its impact on clinical decision‐making remains controversial and its use varies widely. A questionnaire‐based survey on FDG PET/CT use and perceived decision‐making utility in NEN was submitted to the ENETS Advisory Board Meeting attendees (November 2022, response rate = 70%). In 3/15 statements, agreement was higher than 75%: (i) FDG was considered useful in NET, irrespective of grade, in case of mis‐matched lesions (detectable on diagnostic CT but negative/faintly positive on SST PET/CT), especially if PRRT is contemplated (80%); (ii) in NET G3 if curative surgery …

Background: Treatment of locally advanced middle-low rectal cancer (LARC) involves neoadjuvant (chemo) radiotherapy followed by total mesorectal excision and adjuvant chemotherapy. However, only 10-15% of patients reach pathological complete response (pCR) and can be considered for organ preservation. Recent studies investigated the role of total neoadjuvant (TNT) protocols. Theoretically, the advantages of these protocols include better compliance, early treatment of distant micro-metastases as well as higher pCR rates. Despite promising results in term of pCR, few data are available on the tolerability of TNT as well as long-term survival. Therefore, our study aimed to assess the efficacy and tolerability of different neo-adjuvant protocols in patients with LARC by applying the statistical approach of network meta-analysis.Materials and Methods: NMA allows the incorporation of evidence from both direct …

The progress of genomic and biomedical research and the availability of innovative technologies allow to differentiate multifactorial diseases into precise diagnostic entities, an essential condition for the development of precision medicine, and to pursue the goal of effective treatments, reducing side effects, optimizing the design of clinical protocols, and improving prevention. To elucidate the etiology of complex diseases, it is necessary to have extensive homogeneous collections of biological samples and epidemiological, clinical, and biomolecular data on large numbers of patients and healthy subjects. The collection and analysis of biological samples is a necessary procedure for diagnosis. The close involvement of Laboratory Medicine and Pathological Anatomy services in material collection centers is essential for storing samples properly. In the not-too-distant future, the evaluation of various molecular …

Background: Lynch syndrome is an autosomal-dominant inherited condition that significantly increases the risk of developing cancer; within the Lynch syndrome spectrum, Muir-Torre syndrome is an autosomal-dominant genodermatosis, associated with keratoacanthomas and sebaceous neoplasms (adenoma, carcinoma or epithelioma). Both are characterized by the presence of defects in mismatch repair genes resulting in the high mutational rate that accounts for elective sensitivity to immunotherapy with checkpoint inhibitors. However, up to 30% of patients experience refractoriness to treatment.Case presentation: This report describes a potentially informative case of a Lynch/Muir-Torre syndrome patient, who developed gastric cancer while in complete metabolic response to immunotherapy for metastatic duodenal carcinoma and cutaneous epithelioma. Both tumors exhibited high mutational rates and microsatellite instability. Deregulation of the TGF-β2 axis and absence of CD11c-positive dendritic cells in tumor microenvironment together with the loss of IL-8 expression on tumor-associated macrophages represent intriguing findings in this Lynch Syndrome-related immuno-refractory neoplasia.Conclusions: A comprehensive evaluation of the genetic features of tumor cells together with the assessment of intratumoral immune infiltrate may provide insights into the heterogeneous mechanisms of resistance to checkpoint inhibitors.

BackgroundUpfront surgery followed by postoperative treatment is a commonly adopted treatment for resectable pancreatic ductal adenocarcinoma (rPDAC). However, the risk of positive surgical margins, the poor recovery that often impairs postoperative treatments, and the risk of recurrence might limit the outcome of this strategy. This study evaluated the safety and the activity of liposomal irinotecan 50 mg/m2 + 5-fluorouracil 2400 mg/m2 + leucovorin 400 mg/m2 + oxaliplatin 60 mg/m2 (NALIRIFOX) in the perioperative treatment of patients with rPDAC.MethodsEligible patients had a rPDAC with < 180° interface with major veins’ wall. Patients received 3 cycles before and 3 cycles after resection with NALIRIFOX, days 1 and 15 of a 28-day cycle. The primary endpoint was the proportion of patients undergoing an R0 resection.Results107 patients began preoperative treatment. Nine patients discontinued the …

Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers worldwide and further research on its biology is needed to fully understand the disease. Dysregulation of alternative RNA splicing is a common hallmark in cancer, including PDAC, which provides an emerging source of knowledge and of novel biomarkers and therapeutic tools. Here, we examined the role of EIF4A3, a core component of the Exon Junction Complex intimately linked to RNA splicing, in pancreatic cancer biology. EIF4A3 is overexpressed in PDAC tissue and associated to clinical parameters of malignancy and poorer patient survival. Mechanistically, exploration of PDAC RNA-seq data unveiled the link of EIF4A3 to diverse malignancy processes, in line with its association to key molecular pathways. Accordingly, EIF4A3 targeting in vitro decreased essential functional tumor features such as proliferation, migration, colony formation and sphere formation, while its in vivo targeting reduced tumor growth. EIF4A3 silencing in PDAC cell lines severely altered its transcriptional and spliceosomic landscapes, as shown by RNA-seq analyses, suggesting a role for EIF4A3 in maintaining RNA homeostasis. Our results indicate that EIF4A3 dysregulation in PDAC has a pleiotropic regulatory role on RNA biology, influencing key cellular functions. This paves the way to explore its potential as a novel biomarker and actionable target candidate for this lethal cancer.