CADM1 inhibits squamous cell carcinoma progression by reducing STAT3 activity.

Although squamous cell carcinomas (SqCCs) of the lungs, head and neck, oesophagus, and cervix account for up to 30% of cancer deaths, the mechanisms that regulate disease progression remain incompletely understood. Here, we use gene transduction and human tumor xenograft assays to establish that the tumour suppressor Cell adhesion molecule 1 (CADM1) inhibits SqCC proliferation and invasion, processes fundamental to disease progression. We determine that the extracellular domain of CADM1 mediates these effects by forming a complex with HER2 and integrin α6β4 at the cell surface that disrupts downstream STAT3 activity. We subsequently show that treating CADM1 null tumours with the JAK/STAT inhibitor ruxolitinib mimics CADM1 gene restoration in preventing SqCC growth and metastases. Overall, this study identifies a novel mechanism by which CADM1 prevents SqCC progression and suggests that screening tumours for loss of CADM1 expression will help identify those patients most likely to benefit from JAK/STAT targeted chemotherapies

Genetic Diversity in Wheat: Analysis using Diversity Arrays Technology (DArT) in bread and durum wheats

With increasing demands on the quality and quantity of food required now and in the future, improvements to current agriculture practices are required. Increased food production requires utilisation of more agricultural land, pushing crops into non- traditional areas. The need for advances in agricultural technologies are not only required for current crop varieties, but for new varieties with increased tolerance to environmental stresses. Technological improvement means better crop yields and reduced land, water, fertilizer and pesticide use. Diversity Arrays Technology (DArT) was used to study wheat diversity, specifically to identify polymorphic markers between various wheat cultivars for use in marker- assisted breeding programs. The hybridisation based technology was used to analyse various bread and durum wheat cultivars for increased understanding of genomic diversity. Analysis shows that DArT is able to discriminate between tissue samples from wheat cultivars grown under various environmental stresses with polymorphic markers identified between samples treated with differing salt, light and temperature conditions. Epigenetic diversity was analysed through methylation detection using DArT to identify a list of candidate polymorphic markers. Markers were identified using the methylation sensitive restriction enzyme McrBC to generate control and treated targets. Diversity through cultivar exploration, looking at breeding experiments between cultivars with phenotypic extremes to examine salt tolerance versus in-tolerance using DArT produced a recombinant inbred line genetic linkage map. Bulk segregant analysis was also used to group phenotypic samples. Candidate markers were identified between cultivars that can be used to genotyping tetraploid and hexaploid wheat cultivars for germplasm identification. In addition, the identification of trait-linked molecular markers, such as salt resistance, plant breeders can genotype individual plants and populations of cultivars to determine the most suitable cultivar to plant that best complements to its local environment. This eliminates the need for multiple planting cycles to optimize crop selections, and gives the plant breeder the highest possible chance for crop success (yield, quality, performance and cost)

REST mediates resolution of HIF-dependent gene expression in prolonged hypoxia

The hypoxia-inducible factor (HIF) is a key regulator of the cellular response to hypoxia which promotes oxygen delivery and metabolic adaptation to oxygen deprivation. However, the degree and duration of HIF-1α expression in hypoxia must be carefully balanced within cells in order to avoid unwanted side effects associated with excessive activity. The expression of HIF-1α mRNA is suppressed in prolonged hypoxia, suggesting that the control of HIF1A gene transcription is tightly regulated by negative feedback mechanisms. Little is known about the resolution of the HIF-1α protein response and the suppression of HIF-1α mRNA in prolonged hypoxia. Here, we demonstrate that the Repressor Element 1-Silencing Transcription factor (REST) binds to the HIF-1α promoter in a hypoxia-dependent manner. Knockdown of REST using RNAi increases the expression of HIF-1α mRNA, protein and transcriptional activity. Furthermore REST knockdown increases glucose consumption and lactate production in a HIF-1α- (but not HIF-2α-) dependent manner. Finally, REST promotes the resolution of HIF-1α protein expression in prolonged hypoxia. In conclusion, we hypothesize that REST represses transcription of HIF-1α in prolonged hypoxia, thus contributing to the resolution of the HIF-1α response

Deciphering the genomic, epigenomic, and transcriptomic landscapes of pre-invasive lung cancer lesions.

The molecular alterations that occur in cells before cancer is manifest are largely uncharted. Lung carcinoma in situ (CIS) lesions are the pre-invasive precursor to squamous cell carcinoma. Although microscopically identical, their future is in equipoise, with half progressing to invasive cancer and half regressing or remaining static. The cellular basis of this clinical observation is unknown. Here, we profile the genomic, transcriptomic, and epigenomic landscape of CIS in a unique patient cohort with longitudinally monitored pre-invasive disease. Predictive modeling identifies which lesions will progress with remarkable accuracy. We identify progression-specific methylation changes on a background of widespread heterogeneity, alongside a strong chromosomal instability signature. We observed mutations and copy number changes characteristic of cancer and chart their emergence, offering a window into early carcinogenesis. We anticipate that this new understanding of cancer precursor biology will improve early detection, reduce overtreatment, and foster preventative therapies targeting early clonal events in lung cancer

Liquid BIOpsy for MiNimal RESidual DiSease Detection in Head and Neck Squamous Cell Carcinoma (LIONESS)-a personalised circulating tumour DNA analysis in head and neck squamous cell carcinoma.

BACKGROUND: Head and neck squamous cell carcinoma (HNSCC) remain a substantial burden to global health. Cell-free circulating tumour DNA (ctDNA) is an emerging biomarker but has not been studied sufficiently in HNSCC. METHODS: We conducted a single-centre prospective cohort study to investigate ctDNA in patients with p16-negative HNSCC who received curative-intent primary surgical treatment. Whole-exome sequencing was performed on formalin-fixed paraffin-embedded (FFPE) tumour tissue. We utilised RaDaRTM, a highly sensitive personalised assay using deep sequencing for tumour-specific variants, to analyse serial pre- and post-operative plasma samples for evidence of minimal residual disease and recurrence. RESULTS: In 17 patients analysed, personalised panels were designed to detect 34 to 52 somatic variants. Data show ctDNA detection in baseline samples taken prior to surgery in 17 of 17 patients. In post-surgery samples, ctDNA could be detected at levels as low as 0.0006% variant allele frequency. In all cases with clinical recurrence to date, ctDNA was detected prior to progression, with lead times ranging from 108 to 253 days. CONCLUSIONS: This study illustrates the potential of ctDNA as a biomarker for detecting minimal residual disease and recurrence in HNSCC and demonstrates the feasibility of personalised ctDNA assays for the detection of disease prior to clinical recurrence

The prognostic value of expression of HIF1α, EGFR and VEGF-A, in localized prostate cancer for intermediate- and high-risk patients treated with radiation therapy with or without androgen deprivation therapy

<p>Abstract</p> <p>Purpose</p> <p>Androgens stimulate the production of hypoxia-inducible factor (HIF1α) and ultimately vascular endothelial growth factor (VEGF-A). Additionally, epithelial growth factor (EGF) mediates HIF1α production. Carbonic anhydrase IX (CAIX) expression is associated with tumor cell hypoxia in a variety of malignancies. This study assesses the prognostic relation between HIF1α, VEGF-A, EGF Receptor and CAIX expression by immunochemistry in diagnostic samples of patients with intermediate- and high-risk localized prostate cancer treated with radiation therapy, with or without androgen deprivation therapy (ADT).</p> <p>Materials and methods</p> <p>Between 1994 and 2004, 103 prostate cancer patients (mean age, 68.7 ± 6.2), with prostate cancer (mean PSA, 13.3 ± 3.7), were treated with radiation therapy (RT, median dose, 74 Gy). Fifty seven (55.3%) patients received ADT (median duration, 6 months; range, 0 – 24). Median follow-up was 97.6 months (range, 5.9 – 206.8).</p> <p>Results</p> <p>Higher EGFR expression was significantly (<it>p</it> = 0.04) correlated with higher Gleason scores. On univariate analysis, HIF1α nuclear expression was a significant (<it>p</it> = 0.02) prognostic factor for biological progression-free survival (bPFS). A trend towards significance (<it>p</it> = 0.05) was observed with EGFR expression and bPFS. On multivariate analysis, low HIF1α nuclear (<it>p</it> = 0.01) and high EGFR (<it>p</it> = 0.04) expression remained significant adverse prognostic factors.</p> <p>Conclusions</p> <p>Our study suggests that high nuclear expression of HIF1α and low EGFR expression in diagnostic biopsies of prostate cancer patients treated with RT ± ADT is associated with a good prognosis.</p

Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes

Long interspersed nuclear element-1 (L1) retrotransposons are mobile repetitive elements that are abundant in the human genome. L1 elements propagate through RNA intermediates. In the germ line, neighboring, nonrepetitive sequences are occasionally mobilized by the L1 machinery, a process called 3' transduction. Because 3' transductions are potentially mutagenic, we explored the extent to which they occur somatically during tumorigenesis. Studying cancer genomes from 244 patients, we found that tumors from 53% of the patients had somatic retrotranspositions, of which 24% were 3' transductions. Fingerprinting of donor L1s revealed that a handful of source L1 elements in a tumor can spawn from tens to hundreds of 3' transductions, which can themselves seed further retrotranspositions. The activity of individual L1 elements fluctuated during tumor evolution and correlated with L1 promoter hypomethylation. The 3' transductions disseminated genes, exons, and regulatory elements to new locations, most often to heterochromatic regions of the genome

Processed pseudogenes acquired somatically during cancer development

Cancer evolves by mutation, with somatic reactivation of retrotransposons being one such mutational process. Germline retrotransposition can cause processed pseudogenes, but whether this occurs somatically has not been evaluated. Here we screen sequencing data from 660 cancer samples for somatically acquired pseudogenes. We find 42 events in 17 samples, especially non-small cell lung cancer (5/27) and colorectal cancer (2/11). Genomic features mirror those of germline LINE element retrotranspositions, with frequent target-site duplications (67%), consensus TTTTAA sites at insertion points, inverted rearrangements (21%), 5a €2 truncation (74%) and polyA tails (88%). Transcriptional consequences include expression of pseudogenes from UTRs or introns of target genes. In addition, a somatic pseudogene that integrated into the promoter and first exon of the tumour suppressor gene, MGA, abrogated expression from that allele. Thus, formation of processed pseudogenes represents a new class of mutation occurring during cancer development, with potentially diverse functional consequences depending on genomic context

Clinical outcomes, Kadish-INSICA staging and therapeutic targeting of somatostatin receptor 2 in olfactory neuroblastoma

101siIntroduction: Olfactory neuroblastoma (ONB) is a rare cancer of the sinonasal region. We provide a comprehensive analysis of this malignancy with molecular and clinical trial data on a subset of our cohort to report on the potential efficacy of somatostatin receptor 2 (SSTR2)-targeting imaging and therapy. Methods: We conducted a retrospective analysis of 404 primary, locally recurrent, and metastatic olfactory neuroblastoma (ONB) patients from 12 institutions in the United States of America, United Kingdom and Europe. Clinicopathological characteristics and treatment approach were evaluated. SSTR2 expression, SSTR2-targeted imaging and the efficacy of peptide receptor radionuclide therapy [PRRT](177Lu-DOTATATE) were reported in a subset of our cohort (LUTHREE trial; NCT03454763). Results: Dural infiltration at presentation was a significant predictor of overall survival (OS) and disease-free survival (DFS) in primary cases (n = 278). Kadish-Morita staging and Dulguerov T-stage both had limitations regarding their prognostic value. Multivariable survival analysis demonstrated improved outcomes with lower stage and receipt of adjuvant radiotherapy. Prophylactic neck irradiation significantly reduces the rate of nodal recurrence. 82.4% of the cohort were positive for SSTR2; treatment of three metastatic cases with SSTR2-targeted peptide-radionuclide receptor therapy (PRRT) in the LUTHREE trial was well-tolerated and resulted in stable disease (SD). Conclusions: This study presents pertinent clinical data from the largest dataset, to date, on ONB. We identify key prognostic markers and integrate these into an updated staging system, highlight the importance of adjuvant radiotherapy across all disease stages, the utility of prophylactic neck irradiation and the potential efficacy of targeting SSTR2 to manage disease.nonenoneLechner M.; Takahashi Y.; Turri-Zanoni M.; Liu J.; Counsell N.; Hermsen M.; Kaur R.P.; Zhao T.; Ramanathan M.; Schartinger V.H.; Emanuel O.; Helman S.; Varghese J.; Dudas J.; Riechelmann H.; Sprung S.; Haybaeck J.; Howard D.; Engel N.W.; Stewart S.; Brooks L.; Pickles J.C.; Jacques T.S.; Fenton T.R.; Williams L.; Vaz F.M.; O'Flynn P.; Stimpson P.; Wang S.; Hannan S.A.; Unadkat S.; Hughes J.; Dwivedi R.; Forde C.T.; Randhawa P.; Gane S.; Joseph J.; Andrews P.J.; Royle G.; Franchi A.; Maragliano R.; Battocchio S.; Bewicke-Copley H.; Pipinikas C.; Webster A.; Thirlwell C.; Ho D.; Teschendorff A.; Zhu T.; Steele C.D.; Pillay N.; Vanhaesebroeck B.; Mohyeldin A.; Fernandez-Miranda J.; Park K.W.; Le Q.-T.; West R.B.; Saade R.; Manes R.P.; Omay S.B.; Vining E.M.; Judson B.L.; Yarbrough W.G.; Sansovini M.; Silvia N.; Grassi I.; Bongiovanni A.; Capper D.; Schuller U.; Thavaraj S.; Sandison A.; Surda P.; Hopkins C.; Ferrari M.; Mattavelli D.; Rampinelli V.; Facchetti F.; Nicolai P.; Bossi P.; Henriquez O.A.; Magliocca K.; Solares C.A.; Wise S.K.; Llorente J.L.; Patel Z.M.; Nayak J.V.; Hwang P.H.; Lacy P.D.; Woods R.; O'Neill J.P.; Jay A.; Carnell D.; Forster M.D.; Ishii M.; London N.R.; Bell D.M.; Gallia G.L.; Castelnuovo P.; Severi S.; Lund V.J.; Hanna E.Y.Lechner, M.; Takahashi, Y.; Turri-Zanoni, M.; Liu, J.; Counsell, N.; Hermsen, M.; Kaur, R. P.; Zhao, T.; Ramanathan, M.; Schartinger, V. H.; Emanuel, O.; Helman, S.; Varghese, J.; Dudas, J.; Riechelmann, H.; Sprung, S.; Haybaeck, J.; Howard, D.; Engel, N. W.; Stewart, S.; Brooks, L.; Pickles, J. C.; Jacques, T. S.; Fenton, T. R.; Williams, L.; Vaz, F. M.; O'Flynn, P.; Stimpson, P.; Wang, S.; Hannan, S. A.; Unadkat, S.; Hughes, J.; Dwivedi, R.; Forde, C. T.; Randhawa, P.; Gane, S.; Joseph, J.; Andrews, P. J.; Royle, G.; Franchi, A.; Maragliano, R.; Battocchio, S.; Bewicke-Copley, H.; Pipinikas, C.; Webster, A.; Thirlwell, C.; Ho, D.; Teschendorff, A.; Zhu, T.; Steele, C. D.; Pillay, N.; Vanhaesebroeck, B.; Mohyeldin, A.; Fernandez-Miranda, J.; Park, K. W.; Le, Q. -T.; West, R. B.; Saade, R.; Manes, R. P.; Omay, S. B.; Vining, E. M.; Judson, B. L.; Yarbrough, W. G.; Sansovini, M.; Silvia, N.; Grassi, I.; Bongiovanni, A.; Capper, D.; Schuller, U.; Thavaraj, S.; Sandison, A.; Surda, P.; Hopkins, C.; Ferrari, M.; Mattavelli, D.; Rampinelli, V.; Facchetti, F.; Nicolai, P.; Bossi, P.; Henriquez, O. A.; Magliocca, K.; Solares, C. A.; Wise, S. K.; Llorente, J. L.; Patel, Z. M.; Nayak, J. V.; Hwang, P. H.; Lacy, P. D.; Woods, R.; O'Neill, J. P.; Jay, A.; Carnell, D.; Forster, M. D.; Ishii, M.; London, N. R.; Bell, D. M.; Gallia, G. L.; Castelnuovo, P.; Severi, S.; Lund, V. J.; Hanna, E. Y

Immune surveillance in clinical regression of pre-invasive squamous cell lung cancer

Before squamous cell lung cancer develops, pre-cancerous lesions can be found in the airways. From longitudinal monitoring, we know that only half of such lesions become cancer, whereas a third spontaneously regress. While recent studies have described the presence of an active immune response in high-grade lesions, the mechanisms underpinning clinical regression of pre-cancerous lesions remain unknown. Here, we show that host immune surveillance is strongly implicated in lesion regression. Using bronchoscopic biopsies from human subjects, we find that regressive carcinoma in-situ lesions harbour more infiltrating immune cells than those that progress to cancer. Moreover, molecular profiling of these lesions identifies potential immune escape mechanisms specifically in those that progress to cancer: antigen presentation is impaired by genomic and epigenetic changes, CCL27/CCR10 signalling is upregulated, and the immunomodulator TNFSF9 is downregulated. Changes appear intrinsic to the CIS lesions as the adjacent stroma of progressive and regressive lesions are transcriptomically similar