Genomic characterization of hepatoid tumors: context matters

Hepatoid tumors (HT) are rare neoplasms morphologically resembling hepatocellular carcinoma, which arise in several organs other than the liver. A comprehensive molecular profile of this group of neoplasms is still lacking. Genomic characterization of 19 HTs from different organs (three colon HTs, four esophagogastric HTs, four biliary HTs, six genitourinary HTs, two lung HTs) was performed using a multigene next-generation sequencing panel. NGS unraveled a composite molecular profile of HT. Their genetic alterations were clearly clustered by tumor site: (i) colorectal HT displayed microsatellite instability, high tumor mutational burden, mutations in ARID1A/B genes and NCOA4-RET gene fusion (2/3 cases); (ii) gastric HT had TP53 mutations (2/4); (iii) biliary HT displayed loss of CDKN2A (3/4) and loss of chromosome 18 (2/4); (iv) genital HT showed gain of chromosome 12 (3/6); (v) lung HT had STK11 somatic mutations (2/2). The only commonly mutated gene occurring in HT of different sites was TP53 (8/19 cases: colon 2, esophagogastric 2, biliary 2, genital 1, lungs 1). This study shows that most genetic alterations of HT were clustered by site, indicating that context matters. The novel potential targets for HT precision oncology are also clustered based on the anatomic origin. This study shed light on the biology of these rare cancers and may have important consequences for treatment decisions and clinical trial selection for HT patients.

Solid Pseudopapillary Neoplasm of the Pancreas and Abdominal Desmoid Tumor in a Patient Carrying Two Different BRCA2 Germline Mutations: New Horizons from Tumor Molecular Profiling

This case report describes the history of a 41 year-old woman with a solid pseudopapillary neoplasm (SPN) of the pancreas and a metachronous abdominal desmoid tumor (DT) that occurred two years after the SPN surgical resection. At next-generation sequencing of 174 cancer-related genes, both neoplasms harbored a CTNNB1 somatic mutation which was different in each tumor. Moreover, two BRCA2 pathogenic mutations were found in both tumors, confirmed as germline by the sequencing of normal tissue. The BRCA2 mutations were c.631G>A, resulting in the amino-acid change p.V211I, and c.7008-2A>T, causing a splice acceptor site loss. However, as the two neoplasms showed neither loss of heterozygosity nor somatic mutation in the second BRCA2 allele, they cannot be considered as BRCA-dependent tumors. Nevertheless, this study highlights the important opportunities opened by extensive tumor molecular profiling. In this particular case, it permitted the detection of BRCA2-germline mutations, essential for addressing the necessary BRCA-related genetic counseling, surveillance, and screening for the patient and her family.

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.

Common genetic variants associated with pancreatic adenocarcinoma may also modify risk of pancreatic neuroendocrine neoplasms

Pancreatic neuroendocrine neoplasms (pNEN) account for less than 5% of all pancreatic neoplasms and genetic association studies on susceptibility to the disease are limited. We sought to identify possible overlap of genetic susceptibility loci between pancreatic ductal adenocarcinoma (PDAC) and pNEN; therefore, PDAC susceptibility variants (n = 23) from Caucasian genome-wide association studies (GWAS) were genotyped in 369 pNEN cases and 3277 controls from the PANcreatic Disease ReseArch (PANDoRA) consortium to evaluate the odds associated with pNEN risk, disease onset and tumor characteristics. Main effect analyses showed four PDAC susceptibility variants-rs9854771, rs1561927, rs9543325 and rs10919791 to be associated with pNEN risk. Subsequently, only associations with rs9543325, rs10919791 and rs1561927 were noteworthy with false positive report probability (FPRP) tests. Stratified analyses considering age at onset (50-year threshold), showed rs2736098, rs16986825 and rs9854771 to be associated with risk of developing pNEN at a younger age. Stratified analyses also showed some single nucleotide polymorphisms to be associated with different degrees of tumor grade, metastatic potential and functionality. Our results identify known GWAS PDAC susceptibility loci, which may also be involved in sporadic pNEN etiology and suggest that some genetic mechanisms governing pathogenesis of these two entities may be similar, with few of these loci being more influential in younger cases or tumor subtypes.

Vascular Access for Chronic Haemodialysis in Lombardy

To evaluate the organisation of vascular access surgery, the techniques used to monitor surgical access and the central catheters, a survey was conducted amongst dialysis Units of Lombardy. A questionnaire was sent out to the 43 dialysis centres in Lombardy, 96% of which replied.

In almost 90% of dialysis units nephrologists perform vascular access albeit in close cooperation with vascular surgeons for the more complex cases.

First choice access is by distal arteriovenous fistula (AVF): 36% end-to-end, 31.7% side-to-end, and 19.5% side-to-side with distal ligature of the vein.

As second choice proximal AVF is more widely used than AV grafts, which are implanted only when all native vessels and related surgical procedures are exhausted.

Central venous catheters offer valid solutions not only as temporary access, but also as an alternative permanent one. In both cases the jugular vein is the most frequent site of insertion. Despite the documented incidence of related episodes of stenosis/obstruction, the subclavian vein is used as a temporary access in quite a high percentage of cases.

Only in selected cases are diagnostic procedures (mainly Venography and Doppler studies) performed prior to permanent access choice. Similarly vascular access is monitored mainly using a recirculation test albeit not routinely. In case of vascular access thrombosis, surgical revision is the most common approach.

miRNA array screening reveals cooperative MGMT-regulation between miR-181d-5p and miR-409-3p in glioblastoma

The levels of expression of O⁶-methylguanine-DNA methyltransferase (MGMT) are relevant in predicting the response to the alkylating chemotherapy in patients affected by glioblastoma. MGMT promoter methylation and the published MGMT regulating microRNAs (miRNAs) do not completely explain the expression pattern of MGMT in clinical glioblastoma specimens. Here we used a genome-wide microarray-based approach to identify MGMT regulating miRNAs. Our screen unveiled three novel MGMT regulating miRNAs, miR-127-3p, miR-409-3p, and miR-124-3p, in addition to the previously identified miR-181d-5p. Transfection of these three novel miRNAs into the T98G glioblastoma cell line suppressed MGMT mRNA and protein expression. However, their MGMT- suppressive effects are 30–50% relative that seen with miR-181d-5p transfection. In silico analyses of The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) revealed that miR-181d-5p is the only miRNA that consistently exhibited inverse correlation with MGMT mRNA expression. However, statistical models incorporating both miR-181d-5p and miR-409-3p expression better predict MGMT expression relative to models involving either miRNA alone. Our results confirmed miR-181d-5p as the key MGMT-regulating miRNA. Other MGMT regulating miRNAs, including the miR-409-3p identified in this report, modify the effect of miR-181d-5p on MGMT expression. MGMT expression is, thus, regulated by cooperative interaction between key MGMT-regulating miRNAs.

Abstract 3617: Digital sorting rescues low-cellularity tumor FFPE samples for genome-wide copy-number profiling

Introduction: The analysis of formalin-fixed paraffin embedded (FFPE) cancer specimens is particularly challenging due to minute amount of tissue, low-tumor cellularity and heterogeneity, associated with low quality DNA. This results in an imprecise characterization of somatic variants and copy-number alterations (CNA). Here we show how digital sorting combined with low-pass whole genome sequencing (WGS) can resolve genome-wide copy-number profiling even for the more challenging FFPE samples.

Methods: An archival FFPE sample from one pancreatic cancer patient, rejected by the International Cancer Genome Consortium (ICGC) criteria due to low tumor content (<25%), was dissociated into a single cell suspension. Using the DEPArray™ digital sorter, tumor and normal stromal cell subpopulations (range = 70-77) were recovered using Keratin/Vimentin immunofluorescence and DNA ploidy, from which 0.4-0.5ng DNA was obtained. After lysis, Illumina®-compatible libraries were prepared from one pool of pseudo-diploid sorted tumor cells, one pool of stromal cells and one unsorted sample (1500 cells, i.e. about 10ng gDNA) using the Accel-NGS® 2S DNA Library Kit from Swift Biosciences. Libraries were used for low-pass whole genome sequencing on Illumina® MiSeq. Paired-end (2×100) reads were aligned to hg19 human reference using BWA software and copy-number profiles were generated with Control-FREEC.

Results: A total of 11M paired-end reads and a mean coverage of 0.12x were obtained from low-pass WGS, enabling the detection of CNAs at good resolution. The resulting copy-number profiles clearly show the difference between the stromal and tumor populations, with the first characterized by a flat profile (0 gains, 0 losses) and the second presenting several somatic copy-number alterations (6 gains, 22 losses). As expected due to dilution by normal cells, CNA profiles of unsorted samples missed most of the gains and losses (only 5/28 = 18% of aberrant genomic regions were detected). At a single base level, the difference between unsorted and sorted samples was more significant as the unsorted fraction missed >99% of CNA bases found in the sorted tumor population.

Conclusions: DEPArray™ sorting combined with Accel-NGS® 2S kits and Illumina® low-pass whole genome sequencing enables high quality genome-wide profiling of pure tumor and stromal populations. The capacity of this method to deal with low DNA input (0.5ng) from archival FFPE samples characterized by low cancer cell content (<25%) makes it a valuable and easily accessible tool for studying tumor CNA profiles.

Citation Format: Claudio Forcato, Julie Lalibertè, Chiara Bolognesi, Ivana Cataldo, Genny Buson, Chiara Mangano, Cinzia Cantù, Francesca Fontana, Paola Tononi, Gianni Medoro, Tim Harkins, Rita T. Lawlor, Aldo Scarpa, Nicolò Manaresi. Digital sorting rescues low-cellularity tumor FFPE samples for genome-wide copy-number profiling. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3617.

Regulation of IL-8 gene expression in gliomas by microRNA miR-93

Background

Different strategies have been proposed to target neoangiogenesis in gliomas, besides those targeting Vascular Endothelial Growth Factor (VEGF). The chemokine Interleukin-8 (IL-8) has been shown to possess both tumorigenic and proangiogenic properties. Although different pathways of induction of IL-8 gene expression have been already elucidated, few data are available on its post-transcriptional regulation in gliomas.

Methods

Here we investigated the role of the microRNA miR-93 on the expression levels of IL-8 and other pro-inflammatory genes by RT-qPCR and Bio-Plex analysis. We used different disease model systems, including clinical samples from glioma patients and two glioma cell lines, U251 and T98G.

Results

IL-8 and VEGF transcripts are highly expressed in low and high grade gliomas in respect to reference healthy brain; miR-93 expression is also increased and inversely correlated with transcription of IL-8 and VEGF genes. Computational analysis showed the presence of miR-93 consensus sequences in the 3′UTR region of both VEGF and IL-8 mRNAs, predicting possible interaction with miR-93 and suggesting a potential regulatory role of this microRNA. In vitro transfection with pre-miR-93 and antagomiR-93 inversely modulated VEGF and IL-8 gene expression and protein release when the glioma cell line U251 was considered. Similar data were obtained on IL-8 gene regulation in the other glioma cell line analyzed, T98G. The effect of pre-miR-93 and antagomiR-93 in U251 cells has been extended to the secretion of a panel of cytokines, chemokines and growth factors, which consolidated the concept of a role of miR-93 in IL-8 and VEGF gene expression and evidenced a potential regulatory role also for MCP-1 and PDGF (also involved in angiogenesis).

Conclusion

In conclusion, our results suggest an increasing role of miR-93 in regulating the level of expression of several genes involved in the angiogenesis of gliomas.

Electronic supplementary material

The online version of this article (doi:10.1186/s12885-015-1659-1) contains supplementary material, which is available to authorized users.

GBA2-encoded β-glucosidase activity is involved in the inflammatory response to Pseudomonas aeruginosa

Current anti-inflammatory strategies for the treatment of pulmonary disease in cystic fibrosis (CF) are limited; thus, there is continued interest in identifying additional molecular targets for therapeutic intervention. Given the emerging role of sphingolipids (SLs) in various respiratory disorders, including CF, drugs that selectively target the enzymes associated with SL metabolism are under development. Miglustat, a well-characterized iminosugar-based inhibitor of β-glucosidase 2 (GBA2), has shown promise in CF treatment because it reduces the inflammatory response to infection by P. aeruginosa and restores F508del-CFTR chloride channel activity. This study aimed to probe the molecular basis for the anti-inflammatory activity of miglustat by examining specifically the role of GBA2 following the infection of CF bronchial epithelial cells by P. aeruginosa. We also report the anti-inflammatory activity of another potent inhibitor of GBA2 activity, namely N-(5-adamantane-1-yl-methoxy)pentyl)-deoxynojirimycin (Genz-529648). In CF bronchial cells, inhibition of GBA2 by miglustat or Genz-529648 significantly reduced the induction of IL-8 mRNA levels and protein release following infection by P. aeruginosa. Hence, the present data demonstrate that the anti-inflammatory effects of miglustat and Genz-529648 are likely exerted through inhibition of GBA2.

Nicotine-induced phosphorylation of phosphorylated cyclic AMP response element-binding protein (pCREB) in hippocampal neurons is potentiated by agrin

The scope of this study was to test whether increased levels of the extracellular matrix molecule (ECM) agrin might enhance nicotine effects on those molecular mechanisms that initiate neuroadaptative processes in the hippocampus, a key brain area for learning and memory. We studied the effects of repetitive applications of neuronal agrin to primary hippocampal cell culture on nicotine-induced phosphorylated cyclic AMP response element-binding protein (pCREB) expression, a marker of neuroadaptation, by using immunofluorescence-based assessment of pCREB-positive neurons. We also tested agrin effects on nicotine-induced expression of a marker of metabolic activation, the immediate early gene c-fos. Agrin was shown to significantly enhance nicotine-induced pCREB, but not c-fos, expression. By using Western blotting analysis, cumulative agrin has been shown to increase nicotine-induced pCREB phosphorylation. These analyses, however, showed that inhibition of the CaMKII pathway blocked general pCREB phosphorylation, whereas inhibition of the MAPK pathway potentiated the synergistic effect of cumulative agrin and nicotine. These findings suggest that increasing the concentration of an ECM molecule, i.e. agrin, may enhance nicotine effects on pCREB and that both MAPK and CaMKII signalling may play a regulatory role.

Spatial perception in normal and strabismic subjects: role of stereopsis and monocular clues

PURPOSE

To evaluate the roles of binocular vision, monocular clues, and experience in spatial perception in a prospective, nonrandomized, case-control study.

METHODS

A test was created consisting of three wood blocks arranged along the frontal plane inside Panum area. To produce some degrees of horizontal disparity, blocks were moved along a sagittal plane. Thirteen normal subjects (control group) and 13 nonamblyopic strabismic subjects (study group) were asked to identify, both under binocular and monocular vision, the position of the blocks in a series of 12 randomized presentations (phase 1). In phase II of the trial, a letter E in three different sizes, acting as a monocular clue, marked the three blocks. In both phases, the number of correct answers to the test during binocular and monocular vision was recorded.

RESULTS

Binocular normal responses appeared greater than monocular normal responses and strabismic binocular responses in both phases (p < 0.001). Binocular strabismic responses and monocular answers of both groups appeared similar.

CONCLUSIONS

In our experimental model, spatial orientation of strabismic subjects in binocular vision is substantially identical to that of normal subjects in monocular vision. Monocular clues were used in the same manner in both groups of subjects, and experience seemed to play no role in spatial localization of visual objects.

Vitreous hemorrhage following phakic anterior chamber intraocular lens implantation in severe myopia

PURPOSE

To describe two cases of vitreous hemorrhage following phakic anterior chamber lens (AC-IOL) implantation in high myopia.

CASE REPORT

In case 1, hemorrhage developed one month after surgery, without retinal involvement, and visual acuity (VA) resulted 20/200 after pars-plana vitrectomy (PPV). In Case 2, vitreous hemorrhage was complicated by retinal detachment (RD). PPV and silicone oil injection were performed, with AC-IOL removal and cristalline lens extraction. After 2 years the retina was attached and VA was 20/80.

DISCUSSION

Only few cases of RD, posterior uveitis and endophthalmitis are reported following phakic AC-IOL implant. Vitreous hemorrhage could represent an additional posterior segment complication. Intraoperative manoeuvres, hypotony-induced posterior vitreous detachment and/or peripheral retina traction could play a role in engendering this complication in highly myopic eyes.

Older age as risk factor for deviation from emmetropia in pseudophakia

PURPOSE

To find risk factors for deviation from emmetropia after cataract surgery in clinical practice.

METHODS

We evaluated the refractive outcome in 106 patients who had underone phacoemulsification and in-the-bag IOL placement 115 +/- 10 days after surgery. Postoperative optical correction and refractive error (diopters of spherical equivalent--ED) were related to age and sex, pre-operative axial length and keratometric diopter power, and operative incision technique.

RESULTS

Emmetropia was achieved in 15% of cases; 65% of eyes needed a myopic correction, averaging = 0.46 +/- 0.91 ED. The refractive error was 0.74 +/- 0.61 ED (< or = 1 ED in 77% of cases, < or = 2 ED in 97%). Both optical correction and refractive error were correlated to older age at the time of surgery (p=0.002 and p=0.001, respectively). Astigmatism appeared greater in clear-cornea incision than in limbar incision cases (p=0.05).

CONCLUSIONS

The higher refractive error in patients aged over 73 years suggests that age may be a risk factor for deviation from emmetropia after cataract surgery.

Second Generation Binocular Polaroid Test

BACKGROUND

The aim of the study was to introduce a new test to detect small areas of suppression in the binocular visual field and to lower the minimum age at which a suppression test could be identified correctly. Two tests were compared: the Binocular Polaroid Test (poltest), introduced in clinical practice a few years ago and used in screening programs for vision impairment; and the Second Generation Binocular Polaroid Test (polstar), more recently designed to have simpler answers than the poltest.

METHODS

One hundred and eighty-two children were examined consecutively. To assess the validity of the two tests, sensitivity, specificity, predictive value, and phi coefficient were calculated. The applicability of the two tests and the speed of the responses was assessed by means of the test of probability of binomial distribution.

RESULTS

The polstar has appeared to be simpler and easier in younger patients (age range 20 to 36 months, P = 0.078), and has shown 100% of specificity with a sensitivity of 84% for the polstar 1 and of 100% for the polstar 2.

CONCLUSION

The results appear to demonstrate that the poltest has been improved, and that the polstar may be considered an interesting investigation device for early detection of monocular visual impairment.