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IHC for different proteins. a IHC for RET protein on a metastasis in the liver (Table 1, patient 19II). The protein (colored in red) is located in the cytoplasm and/or membrane in the tumor cells. b IHC for Cadherin 2 on a metastasis in the liver (Table 1, patient 4). The protein (colored in red) is located in the cytoplasm and/or membrane in the tumor cells. c IHC for ''dapper, antagonist of betacatenin , homolog 2'' (encoded by the DACT2 gene) on a metastases in the stomach (Table 1, patient 7). The protein (colored in red is located in the cytoplasm and/or membrane in the tumor cells. d The metastases of tumor sample 19 consist of negative tumor cells for IL-8 (Table 1, patient 19)
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A characteristic of human gastroenteropancreatic neuroendocrine tumors (GEP-NET) is a minute unobtrusive primary tumor which often cannot be detected by common physical examinations. It therefore remains unidentified until the tumor has spread and space-occupying metastases cause clinical symptoms leading to diagnosis. Cases in which the primary ca...
Citations
... S75 for human ABHD14B), that might be regulate catalysis by possible allosteric mechanisms, a fact previously unknown for these enzymes. The knowledge and resources generated from this study will also be of biomedical importance, as it is now evident from several recent population-wide genetic association studies that dysregulation in ABHD14B expression has strong associations with different types of cancers [37][38][39][40][41][42] , while anomaly in ABHD14A expression is found to be associated with neurodegenerative conditions [43][44][45][46][47] , and even some cancers [48][49][50][51] . ...
Over the course of evolution, enzymes have developed remarkable functional diversity in catalyzing important chemical reactions across various organisms, and understanding how new enzyme functions might have evolved remains an important question in modern enzymology. To systematically annotate functions, based on protein sequences and available biochemical studies, enzymes with similar catalytic mechanisms and/or aspects of catalysis have been clustered together into an enzyme superfamily. Typically, enzymes within a superfamily have similar overall three-dimensional structures, conserved key catalytic residues, but large variations in substrate recognition sites and residues to accommodate the diverse biochemical reactions that are catalyzed within the superfamily. The serine hydrolases are an excellent example of such an enzyme superfamily, that based on known enzymatic activities and protein sequences, is split almost equally into the serine proteases and metabolic serine hydrolases. Within the metabolic serine hydrolases, are two outlying members, ABHD14A and ABHD14B, that have high sequence similarity, but their functions remained cryptic till recently. While ABHD14A still lacks any functional annotation to date, we recently showed that ABHD14B functions as a lysine deacetylase in mammals. Given their high sequence similarity, automated databases wrongly assign ABHD14A and ABHD14B as the same enzyme, and therefore, annotating functions to them in various organisms maybe problematic. In this paper, we present a bioinformatics study coupled to biochemical experiments, that identifies key sequence determinants for both ABHD14A and ABHD14B, and enables better classification for them. Additionally, we map these enzymes on an evolutionary timescale, and provide a resource in studying these interesting enzymes in different organisms.
... As C-type lectin receptor, CD302 has roles in cell immune and migration (35,36), and acts as a prognostic biomarker in myeloma (37), is also a potential therapeutic target for acute myeloid leukemia (38). In addition, CD302 had been identified as a biomarker to categorize the metastases of neuroendocrine tumors (NET) (39), and it is reported to be overexpressed in high grade NET (40). Fatty acid-binding protein 5 (FABP5) is involved in fatty acid transport, and acts as a prognostic biomarker in cervical cancer, triple-negative breast cancer and clear cell renal cell carcinoma (41)(42)(43). ...
Glioma is the most frequent primary brain tumor that causes high mortality and morbidity with poor prognosis. There are four grades of gliomas, I to IV, among which grade II and III are low-grade glioma (LGG). Although less aggressive, LGG almost universally progresses to high-grade glioma and eventual causes death if lacking of intervention. Current LGG treatment mainly depends on surgical resection followed by radiotherapy and chemotherapy, but the survival rates of LGG patients are low. Therefore, it is necessary to use prognostic biomarkers to classify patients into subgroups with different risks and guide clinical managements. Using gene expression profiling and long-term follow-up data, we established an Online consensus Survival analysis tool for LGG named OSlgg. OSlgg is comprised of 720 LGG cases from two independent cohorts. To evaluate the prognostic potency of genes, OSlgg employs the Kaplan-Meier plot with hazard ratio and p value to assess the prognostic significance of genes of interest. The reliability of OSlgg was verified by analyzing 86 previously published prognostic biomarkers of LGG. Using OSlgg, we discovered two novel potential prognostic biomarkers (CD302 and FABP5) of LGG, and patients with the elevated expression of either CD302 or FABP5 present the unfavorable survival outcome. These two genes may be novel risk predictors for LGG patients after further validation. OSlgg is public and free to the users at http://bioinfo.henu.edu.cn/LGG/LGGList.jsp.
... In this study, we found miR-629-5p promotes the cell migration and invasion in LUADs via inhibiting the gene expression level of PPWD1 (Peptidyl Prolyl isomerase domain and WD repeat-containing protein 1), which has been reported related to tumor metastasis [17,18] in tumor cells. Besides, miR-629-5p secreted by tumor cells could downregulate CELSR1 (Cadherin EGF LAG sevenpass G-type receptors 1) in endothelial cells, leading to the increase of endothelial monolayers permeability. ...
... Results showed that miR-629-5p inhibited the expression of PPWD1 manifestly (Fig. 4a). PPWD1 has been reported downregulation in gastroenteropancreatic neuroendocrine tumors metastases from the pancreas as the primary site [17,18]. Therefore, first, we confirmed the downregulation effect of PPWD1 by miR-629-5p. ...
... As the direct target of miR-629-5p in tumor cells, PPWD1 is a multidomain cyclophilin, which participates in the process of chromatin modification, transcription, and pre-mRNA splicing [53,54]. Previous studies found that testing the expression of PPWD1 in metastases could predict the localization of the primary tumor in gastroenteropancreatic neuroendocrine neoplasm [18]. We examined the inhibition effects of PPWD1 on cell migration and invasion by overexpressing and knocking down PPWD1 in LUAD cells, showing the critical role of PPWD1 in LUAD cells migration and invasion. ...
Tumor invasion underlies further metastasis, the leading cause for cancer-related deaths. Deregulation of microRNAs has been identified associated with the malignant behavior of various cancers, including lung adenocarcinoma (LUAD), the major subtype of lung cancer. Here, we showed the significantly positive correlation between miR-629-5p level and tumor invasion in LUAD specimens (n = 49). In a human LUAD metastasis mouse model, H1650 cells (high level of miR-629-5p) were more aggressive than A549 cells (low level of miR-629-5p) in vivo, including higher incidence of vascular invasion and pulmonary colonization. Ectopic expression of miR-629-5p in A549 cells also increased their invasive capability. Then we identified that miR-629-5p promotes LUAD invasion in a mode of dual regulation via tumor cells invasion and endothelial cells permeability, respectively. In tumor cells, miR-629-5p enhanced motility and invasiveness of tumor cells by directly targeting PPWD1 (a cyclophilin), which clinically related to tumor invasion in LUAD specimens. Restoring PPWD1 protein significantly attenuated the invasion-promoting effects of miR-629-5p. Besides, exosomal-miR-629-5p secreted from tumor cells could be transferred to endothelial cells and increased endothelial monolayers permeability by suppressing CELSR1 (a nonclassic-type cadherin), which had a low level in the endothelial cells of invasive LUAD specimens. Activating the expression of CELSR1 in endothelial cells markedly blocked the effect of miR-629-5p. Our study suggests the dual roles of miR-629-5p in tumor cells and endothelial cells for LUAD invasion, implying a therapeutic option to targeting miR-629-5p using the “one stone, two birds” strategy in LUAD.
... As they are validated, it is likely that more and more of these will be incorporated into the Genomic Test Directory to allow better classification and prognostication of disease. More challenging will be the measurement of the transcriptome, although this has proven an excellent research tool for profiling tumours; preservation of RNA of sufficient amount and quality is challenging for NHS Pathology departments, as it requires more rapid processing of frozen tissue or use of bespoke fixatives [34]. As 'genome-friendly' pathways become more standard practice, this may form part of future strategies within the Genomic Medicine Service. ...
Purpose of Review
We discuss the current state of genomic testing for cancer in the UK, how this has been impacted by whole genome sequencing (WGS) and the 100,000 Genomes Project, along with approaches to reviewing whole genome analyses.
Recent Findings
The 100,000 Genomes Project has led to the development of new pathways for tissue handling and processing, variant interpretation and clinical reporting of cancer genomic testing. To our knowledge, this is the first paper discussing the recommended review process for WGS reports by the Genomics Tumour Advisory Board.
Summary
Through wider use of WGS and next-generation sequencing technologies, the new NHS Genomic Medicine Service aims to expand precision oncology research and personalised cancer care. As research in cancer genomics progresses, the standards and guidelines for interpretation of WGS reports will continue to evolve.
... In approximately 50% of them one or more aberrations were detected [2 had SMARCB1 (SWI/ SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1)], 2 TP53 (tumor protein p53) mutations, 1 had each STK11 (serine/ threonine kinase 11), RET (ret proto-oncogene), and BRAF mutations (B-Raf proto-oncogene, serine/threonine kinase), while CCNE1 (cyclin E1) amplification was found in one patient with an additional TP53 mutation) (64). Moreover, TP53, mitogen activated protein kinase (MAPK3), RET and fibronectin genes up-regulation has been found in pNENs (65,66). Chromosomal imbalances were shown but not in parallel with a repeatable DNA-aberration pattern. ...
... continuous gains or losses were found implying a specific function of the RET protooncogene in GI-NET (67). Three genes clusters were suggested as predictors of the primary site of origin defining a decision tree (CD302 up-regulation implying ileum, PPWD1 (peptidylprolyl isomerase domain and WD repeat containing 1) down-regulation implying pancreas and ABHD14B (abhydrolase domain containing 14B) up-regulation implying stomach (66). Other genetic abnormalities included CDKN1B gene mutation (encoding p27, a cell cycle regulator) in SI-NETs and the amplification of chromosome 17q in SI-NETs and pNEN metastatic foci (68). ...
... The array-CGH displayed an enormous number of DNA aberrations [epidermal growth factor receptor (EGFR), erb-B2, E-cadherin, BIRC5 (survivin) MEN1, p53, H19, IGFII (insulin-like growth factor II), c-Myc, c-Met, cyclin D, wnt] that is known to affect tumor suppressor genes as well as proto-oncogenes, but in GEP-NENs no common aberration pattern for primaries and metastases was isolated (66). ...
Neuroendocrine neoplasms (NENs) arise from cells of the neuroendocrine system located in many sites amongst which most common are the gastrointestinal (GI) system and the lung. The efforts to assess the specific site of origin or predict the biological behavior of NENs is based upon a detailed study of neoplasm's architectural pattern, immunohistochemical, genetic and molecular profile. Immunohistochemistry is used to characterize the aggressivity of NENs, by assessing the proliferation index Ki-67, as well as the neuroendocrine differentiation by assessing chromogranin A (CgA) and CD56. Basal panels of immunohistochemical markers such as CDX-2, Isl-1, TTF-1, PAX6/8 are currently being used to allocate the neoplasms, while in dubious cases new markers are investigating. Unraveling the genetic and molecular mechanisms of NENs pathogenesis along with shedding light on the molecular heterogeneity of neoplasms and the individual patterns of molecular lesions, underlining these neoplasms may provide new tools in terms of diagnostics and therapeutics. Molecular targeted therapies (MTTs) such as everolimus and sunitinib have been the first example of druggable molecular targets implicated in NENs that have been approved for NEN treatment. New investigational drugs are developing along with genetic tests that may allow the identification of the specific subset of patients that will respond to each individual MTT. Multiparametrical molecular and genetic analysis such as the NETest and the MASTER are already in trials shedding light in a step-by-step management of NENs that allow not only the selection of an appropriate therapeutic option but also the identification of response to treatment or early relapse allowing an early amendment of the strategy. Summarizing the combination of histopathological, immunohistochemical, genetic and molecular profile of a NEN opens new horizons in the efficient management of NENs.
... In the chromosomal region 10q11.2 continuous gains or losses were found implying a specific role of the RET proto-oncogene in GI-NENs [63,64]. Moreover, in the same study, three genes cluster out of 1.760 could predict the primary site of origin defining a decision tree: if CD302 was upregulated in the metastasis with a fold change >13, the primary was considered to be the ileum, if PPWD1 was downregulated in the metastasis with a fold change <3 the primary was considered to be the pancreas and if ABHD14B was upregulated with a fold change >4 the primary was considered to be the stomach [64]. ...
... continuous gains or losses were found implying a specific role of the RET proto-oncogene in GI-NENs [63,64]. Moreover, in the same study, three genes cluster out of 1.760 could predict the primary site of origin defining a decision tree: if CD302 was upregulated in the metastasis with a fold change >13, the primary was considered to be the ileum, if PPWD1 was downregulated in the metastasis with a fold change <3 the primary was considered to be the pancreas and if ABHD14B was upregulated with a fold change >4 the primary was considered to be the stomach [64]. These three genes defined the stringent gene classifier to predict the site of primary origin among small bowel, pancreas and stomach [64]. ...
... Moreover, in the same study, three genes cluster out of 1.760 could predict the primary site of origin defining a decision tree: if CD302 was upregulated in the metastasis with a fold change >13, the primary was considered to be the ileum, if PPWD1 was downregulated in the metastasis with a fold change <3 the primary was considered to be the pancreas and if ABHD14B was upregulated with a fold change >4 the primary was considered to be the stomach [64]. These three genes defined the stringent gene classifier to predict the site of primary origin among small bowel, pancreas and stomach [64]. In a group of samples more recently taken from well preserved tissues from NENs the origin of the primaries, either in the ileum or the pancreas, was predicted with a sensitivity of 94% and 83%, and a specificity of 90 and 100%, respectively compared to a group of older and more manipulated samples, that produced sensitivities and specificities of only 48% and 64%, and 58% and 20%, respectively [63]. ...
Neuroendocrine neoplams (NENs) are mostly relatively indolent malignancies but a significant number have metastatic disease at diagnosis mainly to the liver. Although in the majority of such cases the primary origin of the tumor can be identified, in approximately 11–22% no primary tumor is found and such cases are designated as NENs of unknown primary origin (UPO). This has significant therapeutic implications with respect to potentially resectable hepatic disease and/or application of appropriate medical therapy, either chemotherapeutic agents or targeted treatment, as the response to various treatments varies according to the origin of the primary tumor. This lack of tumor specific orientated treatment may also account for the relatively poorer prognosis of NENs of UPO compared to metastatic NENs with a known primary site. In the majority of cases the primary tumors are located in the small bowel and the lung, but a number may still elude detection. Occasionally the presence of a functional syndrome may direct to the specific tissue of origin but in the majority of cases a number of biochemical, imaging, histopathological and molecular modalities are utilized to help identify the primary origin of the tumor and direct treatment accordingly. Several diagnostic algorithms have recently been developed to help localize an occult primary tumor; however, in a number of cases no lesion is identified even after prolonged follow-up. It is expected that the delineation of the molecular signature of the different NENs may help identify such cases and provide appropriate treatment.
... This limitation can be partially overcome by laser-based tissue microdissection as it allows a more precise sample preparation for further molecular analysis [2]. However, tissue microdissection is a time consuming technique and highly sensitive downstream analyses are needed [2][3][4], due to the limited number of samples. ...
In the last years, matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) became an imaging technique which has the potential to characterize complex tumor tissue. The combination with other modalities and with standard histology techniques was achieved by the use of image registration methods and enhances analysis possibilities. We analyzed an oral squamous cell carcinoma with up to 162 consecutive sections with MALDI MSI, hematoxylin and eosin (H&E) staining and immunohistochemistry (IHC) against CD31. Spatial segmentation maps of the MALDI MSI data were generated by similarity-based clustering of spectra. Next, the maps were overlaid with the H&E microscopy images and the results were interpreted by an experienced pathologist. Image registration was used to fuse both modalities and to build a three-dimensional (3D) model. To visualize structures below resolution of MALDI MSI, IHC was carried out for CD31 and results were embedded additionally. The integration of 3D MALDI MSI data with H&E and IHC images allows a correlation between histological and molecular information leading to a better understanding of the functional heterogeneity of tumors. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.
... PPWD1 encodes a WD40 domain containing peptidylprolyl isomerase. There is a reported association with neuroen- docrine tumors but not linear growth or intellectual disability [Posorski et al., 2011]. NLN encodes the oligopeptidase Neurolysin without know role in human disease. ...
Individuals with deletions of chromosome 5q12-13 have rarely been reported and have a range of phenotypes including postnatal growth restriction, intellectual disability, hyperactivity, and ocular abnormalities. Most individuals reported have large deletions or complex rearrangements which have made identifying genes responsible for these phenotypes challenging. Here we report an individual with a chromosome 5q12-13 deletion with intellectual disability, hyperactivity and restricted linear growth. Based on the location of our patient's deletion in relation to the previously reported deletions, we have narrowed the locus for postnatal growth restriction to less than 1 megabase. Further refinement of this locus with reports of additional individuals with deletions of this region will allow for better understanding of the gene(s) responsible for this phenotype. © 2015 Wiley Periodicals, Inc.
© 2015 Wiley Periodicals, Inc.
... Gene expression signatures differentiating NETs have been reported, but suffer from small sample sizes, inclusion of specimens from primary tumors and metastases, or lack of sufficient validation, and have yet to find widespread clinical application. [25][26][27] Our own group has investigated gene expression profiles of SBNETs and PNETs to identify markers that could indicate the primary site of origin. Initial studies of G protein-coupled receptor and exon expression arrays in a limited number of clinical specimens suggested that a formula based on expression of the oxytocin receptor (OXTR) and secretin receptor (SCTR) in metastases might discriminate between metastases of small bowel versus pancreatic origin. ...
... Other gene expression classifiers have included NETs where the primary sites were not verified by surgery. [26,27] The 92-gene classifier developed by Kerr et al. relies on primary site determinations made by a central pathology adjudication committee. [26] Although they applied rigorous methods to define the primary site, inclusion of biopsy specimens without surgical confirmation of the presumed primary site introduces uncertainty into classifier development and validation. ...
... Posorski et al. reported a three-gene expression signature for distinguishing gastrointestinal NETs, but this was based on expression measured in primary and metastatic NETs from only 17 patients, including samples from gastric, colonic, and unknown primaries in addition to PNETs and SBNETs. [27] Due to the low numbers of individual tumor types and lack of additional validation specimens, the value of this gene expression signature remains unproven. The much larger study by Kerr et al. determined a 92-gene expression signature to classify cancers of unknown primary based on a database of 2094 tumors of all types and validated on 790 others, including 50 neuroendocrine tumors. ...
Small bowel (SBNETs) and pancreatic neuroendocrine tumors (PNETs) often present with liver metastases. Although liver biopsy establishes a neuroendocrine diagnosis, the primary tumor site is frequently unknown without exploratory surgery. Gene expression differences in metastases may distinguish primary SBNETs and PNETs. This study sought to determine expression differences of four genes in neuroendocrine metastases and to create a gene expression algorithm to distinguish the primary site. Nodal and liver metastases from SBNETs and PNETs (n = 136) were collected at surgery under an Institutional Review Board-approved protocol. Quantitative PCR measured expression of bombesin-like receptor-3, opioid receptor kappa-1, oxytocin receptor, and secretin receptor in metastases. Logistic regression models defined an algorithm predicting the primary tumor site. Models were developed on a training set of 21 nodal metastases and performance was validated on an independent set of nodal and liver metastases. Expression of all four genes was significantly different in SBNET compared to PNET metastases. The optimal model employed expression of bombesin-like receptor-3 and opioid receptor kappa-1. When these genes did not amplify, the algorithm used oxytocin receptor and secretin receptor expression, which allowed classification of all 136 metastases with 94.1 % accuracy. In the independent liver metastasis validation set, 52/56 (92.9 %) were correctly classified. Positive predictive values were 92.5 % for SBNETs and 93.8 % for PNETs. This validated algorithm accurately distinguishes SBNET and PNET metastases based on their expression of four genes. High accuracy in liver metastases demonstrates applicability to the clinical setting. Studies assessing this algorithm's utility in prospective clinical decision-making are warranted.
... This was also reported in pancreatic NETs by Capurso et al. [10]. and ileal and pancreatic NETs by our group [11]. The findings have raised the question whether genetic signatures of NET metastases could help to identify the primary lesions, particularly, in case of liver metastases. ...
... The One-Color Microarray-based Gene Expression Analysis was performed with the Human Genome Quick Amp Labeling Kit according to the manufacturer's instructions (www.agilent.com, protocol vs. 5.7, March 2008), as previously described [11]. RNA was isolated from the tumor tissue pieces using the RNeasy Mini Kit from Qiagen. ...
... In a next step the hierarchical gene expression cluster of each metastasis was blindly compared with a previously established gene expression cluster database [11] containing the gene expression clusters of primary tumors from the ileum, stomach and pancreas. The results of the comparison were subsequently matched with the known clinical and pathological data. ...
Gastroenteropancreatic neuroendocrine tumors (NETs) often present as liver metastasis from a carcinoma of unknown primary. We recently showed that primary NETs from the pancreas, small intestine and stomach as well as their respective liver metastases differ from each other by the expression profile of the three genes CD302, PPWD1 and ABHB14B. The gene and protein expression of CD302, PPWD1, and ABHB14B was studied in abdominal NET metastases to identify the site of the respective primary tumors. Cryopreserved tissue from NET metastases collected in different institutions (group A: 29, group B: 50, group C: 132 specimens) were examined by comparative genomic hybridization (Agilent 105 K), gene expression analysis (Agilent 44 K) (groups A and B) and immunohistochemistry (group C). The data were blindly evaluated, i.e. without knowing the site of the primary. Gene expression analysis correctly revealed the primary in the ileum in 94 % of the cases of group A and in 58 % of group B. A pancreatic primary was predicted in 83 % (group A) and 20 % (group B), respectively. The combined sensitivity of group A and B was 75 % for ileal NETs and 38 % for pancreatic NETs. Immunohistochemical analysis of group C revealed an overall sensitivity of 80 %. Gene and protein expression analysis of CD302 and PPWD1 in NET metastases correctly identifies the primary in the pancreas or the ileum in 80 % of the cases, provided that the tissue is well preserved. Immunohistochemical profiling revealed CD302 as the best marker for ileal and PPWD1 for pancreatic detection.
