A. Boussioutas - Academia.edu (original) (raw)

Papers by A. Boussioutas

Additional/Validation Microarray datasets The Ooi et al GC dataset was derived from a cohort stud... more Additional/Validation Microarray datasets The Ooi et al GC dataset was derived from a cohort study through the National Cancer Centre in Singapore as described previously [1].The Chen GC dataset comprised 90 primary tumors and 22 benign gastric tissues. Normalised log transformed data were downloaded from (http://genome

XLS file - 42KB, Probes represented in cluster 27.

Nature Communications, 2019

The contribution of mast cells in the microenvironment of solid malignancies remains controversia... more The contribution of mast cells in the microenvironment of solid malignancies remains controversial. Here we functionally assess the impact of tumor-adjacent, submucosal mast cell accumulation in murine and human intestinal-type gastric cancer. We find that genetic ablation or therapeutic inactivation of mast cells suppresses accumulation of tumor-associated macrophages, reduces tumor cell proliferation and angiogenesis, and diminishes tumor burden. Mast cells are activated by interleukin (IL)-33, an alarmin produced by the tumor epithelium in response to the inflammatory cytokine IL-11, which is required for the growth of gastric cancers in mice. Accordingly, ablation of the cognate IL-33 receptor St2 limits tumor growth, and reduces mast cell-dependent production and release of the macrophage-attracting factors Csf2, Ccl3, and Il6. Conversely, genetic or therapeutic macrophage depletion reduces tumor burden without affecting mast cell abundance. Therefore, tumor-derived IL-33 susta...

Journal of Clinical Oncology, 2011

4025 Background: Several gene expression signatures derived from supervised approaches based on h... more 4025 Background: Several gene expression signatures derived from supervised approaches based on histology, peritoneal or lymph node metastases and survival have been proposed to classify gastric adenocarcinomas and provide prognostic information. These studies had relatively small samples sizes. METHODS 7 datasets of gene expression profiles across different microarray platforms were generated in house or obtained from collaborators, namely a panel of 37 gastric cancer cell lines (GCCL) with Affymetrix U133-2Plus and 549 patients from 6 independent patient cohorts (Affymetrix U133-2plus: 197 (Singapore), 70 (Australia), Affymetrix U133AB: 31 (UK), Illumina Human-6 v2 : 65 (Korea1), Custom arrays: 90 (HK), 96 (Korea2). Unsupervised techniques were used to distinguish major intrinsic subtypes from GCCLs and distinguishing features identified using Linear models for microarray data (LIMMA). We classified patient tumors using the nearest template prediction algorithm and evaluated classification precision and correlation with patient survival. RESULTS Beginning with unsupervised techniques, 2 major intrinsic subtypes were identified from our training set (GCCL). A 171-gene signature was identified. At a false discovery rate of 0.05, our signature precisely classified 432 (78.6%) of primary tumors with 61.1% to 88.6% of tumors precisely classified in each dataset and 55% of the classified tumors belonging to the larger of 2 intrinsic subgroups. With 5 other published signatures, classification precision was < 30%. This intrinsic subtypes classification provided prognostic information with the more aggressive subgroup having inferior overall survival: median survival: 30 mths vs 71mths (HR 1.48; 95%CI: 1.14-1.92, p<0.01, univariate analysis and HR 1.39 ; 95% CI: 1.05-1.78, p=0.02 after adjusting for stage). All other published gene signatures were not prognostic. CONCLUSIONS An intrinsic signature precisely classifies gastric cancers in 6 large patient cohorts from different countries and with microarray platforms and provides better prognostic information compared to existing signatures.

Journal of gastroenterology and hepatology, Jan 6, 2016

Tumour testing of colorectal cancers (CRC) for mismatch repair (MMR) deficiency is an effective a... more Tumour testing of colorectal cancers (CRC) for mismatch repair (MMR) deficiency is an effective approach to identify carriers of germline MMR gene mutation (Lynch syndrome). The aim of this study was to identify MMR gene mutation carriers in two cohorts of population-based CRC utilising a combination of tumour and germline testing approaches. CRCs from 813 patients diagnosed with CRC <60 years of age from the Australasian Colorectal Cancer Family Registry (ACCFR) and from 826 patients from the Melbourne Collaborative Cohort Study (MCCS) were tested for MMR protein expression using immunohistochemistry (IHC), microsatellite instability (MSI), BRAF(V600E) somatic mutation and for MLH1 methylation. MMR gene mutation testing (Sanger sequencing and MLPA) was performed on germline DNA of patients with MMR-deficient tumours and a subset of MMR-proficient CRCs. Of the 813 ACCFR probands, 90 probands demonstrated tumour MMR-deficiency (11.1%) and 42 had a MMR gene germline mutation (5.2%)...

Journal of Innovative Optical Health Sciences, 2012

Real-time in vivo microscopic imaging has become a reality with the advent of confocal and nonlin... more Real-time in vivo microscopic imaging has become a reality with the advent of confocal and nonlinear endomicroscopy. These devices are best utilized in conjunction with standard white light endoscopy. We evaluated the use of fluorescence endomicroscopy in detecting microscopic abnormalities in colonic tissues. Mice of C57bl/6 strain had intraperitoneal injection with azoxymethane once every week for five weeks and littermates, not exposed to azoxymethane served as controls. After 14 weeks, intestines were imaged by fluorescence endomicroscopy. The images show obvious cellular structural differences between those two groups of mice. The difference in endomicroscopy imaging can be used for identifying tissues suspicious for neoplasia or other changes, leading to early diagnosis of gastrointestinal track of cancer.

Lecture Notes in Computer Science, 2008

Gene expression profiling provides insight into the functions of genes at a molecular level. Clus... more Gene expression profiling provides insight into the functions of genes at a molecular level. Clustering of gene expression profiles can facilitate the identification of the underlying driving biological program causing genes' co-expression. Standard clustering methods, grouping genes based on similar expression values, fail to capture weak expression correlations potentially causing genes in the same biological process to be grouped separately. We have developed a novel clustering algorithm which incorporates functional gene information from the Gene Ontology into the clustering process, resulting in more biologically meaningfull clusters. We have validated our method using a multi-cancer microarray dataset. In addition, we show the potential of such methods for the exploration of cancer etiology.

The Biology of Gastric Cancers, 2009

... Advances in the 1990s, principally from Stanford University and led by Patrick Brown, enabled... more ... Advances in the 1990s, principally from Stanford University and led by Patrick Brown, enabled researchers to robotically attach tens of thousands of ... hosts is thought to incite mucosal changes resulting in atrophic gastritis and intesti-nal metaplasia (Correa 1992; Craanen et al. ...

Tissue Antigens, 2003

DNA microarrays are used to study simultaneous gene expression in thousands of genes. This tool h... more DNA microarrays are used to study simultaneous gene expression in thousands of genes. This tool has moved beyond proof-of-principle and its integration into medical practice is slowly becoming a reality. This technology has enabled unparalleled progress into the study of complex polygenic diseases. Although cancer research introduced DNA microarrays into the medical arena other disciplines are beginning to exploit the power of this technology to advance medical research. In this review we outline aspects of the design of a microarray experiment from the choice of platform, through the experimental procedure to the analysis of the results. We review the current applications and speculate on potential applications of this technology with particular reference to transplantation medicine. DNA microarrays provide a new and powerful tool in the study of gene expression, using a robust, high-throughput methodology. This technology has been incorporated into many areas of medical research but is especially useful in complex polygenic diseases. The earliest tumor classification experiments of hematological malignancies have enabled segregation of disease subgroups based on the expression of thousands of genes (1). Similarly in the immunological arena, DNA microarrays were useful in characterizing the chronic inflammatory state in rheumatological diseases (2). The complexity of immune cell activation and recruitment lends itself to research using DNA microarrays (3). Given that most of the research using microarrays to date has centred on cancer, it is instructive to use cancer as a model describing how DNA microarray experiments are designed and carried out. In addition, this review will focus on current and likely future uses of DNA microarray technology in immunology in general, and transplantation medicine in particular. Cancer is characterized by the dysregulation of multiple cellular processes including cell cycle regulation, apoptosis, angiogenesis and organization of the cytoskeleton (4). It is becoming increasingly clear

Optics Express, 2010

A compact endomicroscope is the only solution for transferring second harmonic generation (SHG) i... more A compact endomicroscope is the only solution for transferring second harmonic generation (SHG) imaging into in vivo imaging and real time monitoring the content and structure of collagen. This is important for early diagnoses of different diseases associated with collagen change. A compact nonlinear endomicroscope using a double clad fiber (DCF) is newly employed in SHG imaging. The experiment shows the core of the DCF can maintain the linear polarization of the excitation laser beam in particular directions, and the degree of polarization of the excitation laser beam directly affects signal to noise ratio of SHG imaging. The nonlinear endomicroscope can display clear three dimensional (3D) SHG images of mouse tail tendon without the aid of contrast agents, which reveals the collagen fiber structure at different depths. The high resolution of SHG imaging from the endomicroscope shows that SHG imaging can reveal additional information about the orientation and degree of organisation of proteins and collagen fibers than two-photon-excited fluorescence imaging. Therefore SHG imaging offers endomicroscopy with additional channel of imaging for understanding more about biological phenomena.

Leukemia & Lymphoma, 2006

Multiple myeloma is strongly dependant upon the bone marrow micro-environment for growth and surv... more Multiple myeloma is strongly dependant upon the bone marrow micro-environment for growth and survival and extramedullary (EM) manifestations are uncommon, particularly gastric involvement [1 – 3]. However, extramedullary relapse is being increasingly reported following high-dose chemotherapy and autologous stem cell transplantation (AuSCT). To date, there is no recognized association between cytogenetic abnormalities and patterns of EM relapse but, as our understanding of the various cytogenetic abnormalities in myeloma improves, such associations may become evident. The most frequent translocations identified are t(11:14) and t(4:14), the latter of which is only detectable by fluorescent in situ hybridization (FISH), has a strong association with IgA isotype and conveys a poor prognosis [4,5]. Here, we report an unusual case of a patient with t(4:14) who rapidly relapsed following AuSCT with gastric and cutaneous involvement. A 58-year-old man was diagnosed with stage IIIB multiple myeloma in February 2004. At diagnosis, he had a serum monoclonal IgAl paraprotein of 38 g/l, bone marrow plasmacytosis of 41% and lytic lesions in both femora. Adverse prognostic factors included an elevated b2-microglobulin of 9.2 mg/l and complex cytogenetic abnormalities with loss of chromosome 13; 65 chromosomes, add(X)(q26), Y, 7X, 71, ?t(1:8)(p12;q24)62, add(3)(p25), 78, þ9, 713, 714, der(16), t(1:16)(q11;q11)62, 718, 719, þ20, 721, 722, þmar162 [6]/46, XY 22. FISH was not performed at this time. Treatment was initiated with infusional vincristine, doxorubicin and dexamethasone chemotherapy and monthly zoledronate, followed by high dose melphalan 200 mg/m and AuSCT. Restaging demonstrated a reduction in serum paraprotein to 1 g/l and a concomitant reduction in bone marrow plasmacytosis to51%. Post-AuSCT, the patient commenced maintenance prednisolone and thalidomide as part of a clinical trial but discontinued the thalidomide after 4 weeks due to development of a rash. Six months later the patient developed five rapidly enlarging subcutaneous nodules over his chest and abdomen. A fine needle aspirate from these revealed a plasma cell infiltrate consistent with EM myeloma. The patient was otherwise asymptomatic with normal biochemical parameters, including b2-microglobulin. However, the serum paraprotein had risen slightly to 4 g/l and a bone marrow biopsy showed a slightly increased plasmacytosis of 4% on aspirate with two discrete areas completely replaced with plasma cells on trephine. Cytogenetic analysis again showed complex abnormalities (persisting hyperdiploidy and loss of chromosome 13) with some clonal evolution evident in the form of two new anomalies (duplication of long arm of der(1:16) and trisomy 18). FISH performed at this time identified the presence of t(4:14). Shortly after restaging, the patient was admitted to hospital with abdominal pain. A computed tomography (CT) scan revealed extensive soft tissue deposits throughout the abdomen, multiple subcutaneous nodules over the chest and abdominal wall, and multiple lytic lesions within the vertebrae. The

Journal of Proteomics, 2012

The gp130(F/F) genetically engineered mouse (GEM) model reproducibly and predictably develops a g... more The gp130(F/F) genetically engineered mouse (GEM) model reproducibly and predictably develops a gastric adenoma phenotype resembling the primary lesions of human intestinal-type gastric cancer (GC). Accordingly, changes to the serum proteome of gp130(F/F) mice may uncover early-stage GC biomarkers. Here, we have employed several double and compound mutant GEM strains that display distinct phenotypes with respect to gastric tumour load and inflammatory response, thereby mimicking different states of inflammation-associated early-stage GC in humans. This allowed us to distinguish between proteomic changes associated with tumourigenesis rather than confounding systemic inflammation. The comparative proteomic workflow involved depletion of high abundance proteins, 2D-DIGE analysis and protein identification by LC-MS/MS. The differential expression of 112 2D-DIGE spots specifically correlated with the tumour-bearing phenotype, corresponding to 31 murine proteins and their 28 human orthologues. Eight proteins were selected for validation in GC patient sera versus healthy controls. Significant increases in serum apolipoprotein E and haptoglobin, and decreases in afamin and clusterin, were confirmed by ELISA. Receiver operating characteristic analysis revealed that these proteins may be more sensitive and specific discriminators of GC than the existing clinical marker CA72-4.

Gut, 2009

Barrett's oesophagus predisposes to oesophageal adenocarcinoma but the majority of patien... more Barrett's oesophagus predisposes to oesophageal adenocarcinoma but the majority of patients are undiagnosed. A novel non-endoscopic cytological screening device, called a capsule sponge, makes population-based screening for the disease a feasible option. However, due to the mixed cell population retrieved by the capsule sponge, biomarkers specific for Barrett's oesophagus are required. Three publically available microarray datasets were used to identify putative biomarkers present in Barrett's oesophagus but absent from normal oesophagus and gastric mucosa. Validation was performed by qPCR (n = 10 each of normal oesophagus, Barrett's oesophagus, gastric mucosa) and immunohistochemistry (normal oesophagus, n = 20; Barrett's oesophagus, n = 21; gastric mucosa, n = 24; duodenum, n = 18). The biomarker was then prospectively evaluated on capsule sponge specimens from 47 patients with Barrett's oesophagus and 99 healthy controls. 2/14 genes identified, dopa decarboxylase (DDC) and Trefoil factor 3 (TFF3), were confirmed by qPCR to be upregulated in Barrett's oesophagus compared to normal oesophagus (p<0.01) and gastric mucosa (p<0.01 and p<0.05, respectively). Immunohistochemistry confirmed that DDC protein expression was restricted to Barrett's oesophagus but was confined to <1% of the cells within the crypt compartment. TFF3 protein was expressed to high levels at the luminal surface of Barrett's oesophagus compared to absent expression in normal oesophagus and gastric mucosa (p<0.001). Using the capsule sponge 36/46 patients with Barrett's oesophagus (one inadequate sample) and 6/96 controls were positive for TFF3 giving a sensitivity of 78% and a specificity of 94%. TFF3 is a promising marker for Barrett's oesophagus screening since it is expressed at the luminal surface of Barrett's oesophagus but not in adjacent tissue types and may be applied to a non-endoscopic screening device.

Cancer Research, 2006

Gastric cancer is a leading cause of global cancer mortality, but comparatively little is known a... more Gastric cancer is a leading cause of global cancer mortality, but comparatively little is known about the cellular pathways regulating different aspects of the gastric cancer phenotype. To achieve a better understanding of gastric cancer at the levels of systems topology, functional modules, and constituent genes, we assembled and systematically analyzed a consensus gene coexpression meta-network of gastric cancer incorporating >300 tissue samples from four independent patient populations (the “gastrome”). We find that the gastrome exhibits a hierarchical scale-free architecture, with an internal structure comprising multiple deeply embedded modules associated with diverse cellular functions. Individual modules display distinct subtopologies, with some (cellular proliferation) being integrated within the primary network, and others (ribosomal biosynthesis) being relatively isolated. One module associated with intestinal differentiation exhibited a remarkably high degree of autono...

Familial Cancer, 2007

Patients suspected on clinical grounds to have hereditary non-polyposis colorectal cancer (HNPCC)... more Patients suspected on clinical grounds to have hereditary non-polyposis colorectal cancer (HNPCC) may be offered laboratory testing in order to confirm the diagnosis and to facilitate screening of pre-symptomatic family members. Tumours from an affected family member are usually pre-screened for microsatellite instability (MSI) and/or loss of immunohistochemical expression of mismatch repair (MMR) genes prior to germline MMR gene mutation testing. The efficiency of this triage process is compromised by the more frequent occurrence of sporadic colorectal cancer (CRC) showing high levels of MSI (MSI-H) due to epigenetic loss of MLH1 expression. Somatic BRAF mutations, most frequently V600E, have been described in a significant proportion of sporadic MSI-H CRC but not in HNPCC-associated cancers. BRAF mutation testing has therefore been proposed as a means to more definitively identify and exclude sporadic MSI-H CRC cases from germline MMR gene testing. However, the clinical validity and utility of this approach have not been previously evaluated in a familial cancer clinic setting. Testing for the V600E mutation was performed on MSI-H CRC samples from 68 individuals referred for laboratory investigation of suspected HNPCC. The V600E mutation was identified in 17 of 40 (42%) tumours showing loss of MLH1 protein expression by immunohistochemistry but in none of the 28 tumours that exhibited loss of MSH2 expression (P &amp;amp;amp;amp;amp;lt; 0.001). The assay was negative in all patients with an identified germline MMR gene mutation. Although biased by the fact that germline testing was not pursued beyond direct sequencing in many cases lacking a high clinical index of suspicion of HNPCC, BRAF V600E detection was therefore considered to be 100% specific and 48% sensitive in detecting sporadic MSI-H CRC amongst those cases showing loss of MLH1 protein expression, in a population of patients with MSI-H CRC and clinical features suggestive of HNPCC. Accordingly, we recommend the incorporation of BRAF V600E mutation testing into the laboratory algorithm for pre-screening patients with suspected HNPCC, whose CRCs show loss of expression of MLH1. In such tumours, the presence of a BRAF V600E mutation indicates the tumour is not related to HNPCC and that germline testing of MLH1 in that individual is not warranted. We also recommend that in families where the clinical suspicion of HNPCC is high, germline testing should not be performed on an individual whose CRC harbours a somatic BRAF mutation, as this may compromise identification of the familial mutation.