Composition and optical properties of (In, Ga)As nanowires grown by group-III-assisted molecular beam epitaxy

(In, Ga) alloy droplets are used to catalyse the growth of (In, Ga)As nanowires by molecular beam epitaxy on Si(111) substrates. The composition, morphology and optical properties of these nanowires can be tuned by the employed elemental fluxes. To incorporate more than 10% of In, a high In/(In+Ga) flux ratio above 0.7 is required. We report a maximum In content of almost 30% in bulk (In, Ga)As nanowires for an In/(In+Ga) flux ratio of 0.8. However, with increasing In/(In+Ga) flux ratio, the nanowire length and diameter are notably reduced. Using photoluminescence and cathodoluminescence spectroscopy on nanowires covered by a passivating (In, Al)As shell, two luminescence bands are observed. A significant segment of the nanowires shows homogeneous emission, with a wavelength corresponding to the In content in this segment, while the consumption of the catalyst droplet leads to a spectrally-shifted emission band at the top of the nanowires. The (In,Ga)As nanowires studied in this work provide a new approach for the integration of infrared emitters on Si platforms.

Bird flight behavior, collision risk and mitigation options at high-speed railway viaducts

High-speed railway (HSR) networks are rapidly expanding and are predicted to continue to grow over coming decades. However, there is scant knowledge of their environmental impacts. Their possible effects on bird mortality, particularly at viaducts, gives especial cause for concern. This work presents the results of a nine-month monitoring of bird activity in the vicinity of three HSR viaducts in Central Spain. The study focused on the effects of the infrastructure regarding bird frequentation of the site and on bird flight activity in the danger zone for collision with passing trains. The findings show (i) that bird communities may differ markedly between sites and (ii) that bird activity increases near the railway together with changes in relative species abundances. Furthermore, (iii) birds show a significant tendency to avoid flying across the danger zone, but (iv) all kinds of birds are at a real risk of collisions with trains at viaducts. The greatest danger is at viaduct extremes rather than in their central section, particularly during gusts of wind and for small or medium-sized birds. It also appears that relatively low viaducts might pose greater risk. In practical terms, these results (i) emphasise the need for thorough prior prospection of bird species present, and their flight patterns, where new viaducts are to be built, (ii) show that there is a real risk of bird collisions with trains at viaducts, which should be mitigated, with particular attention due to viaduct extremes and areas where their height is not much above the surrounding vegetation and (iii) strongly indicate the need to minimise viaduct features that may attract birds to them, for example as potential nest sites.

Genetic footprints of a rapid and large-scale range expansion: the case of cyclic common vole in Spain

In the Anthropocene, many species are rapidly shifting their ranges in response to human-driven habitat modifications. Studying patterns and genetic signatures of range shifts helps to understand how species cope with environmental disturbances and predict future shifts in the face of global environmental change. We investigated the genetic signature of a contemporary wide-range expansion observed in the Iberian common vole Microtus arvalis asturianus shortly after a colonization event. We used mtDNA and microsatellite data to investigate patterns of genetic diversity, structure, demography, and gene flow across 57 localities covering the historical range of the species and the newly colonized area. The results showed a genetic footprint more compatible with a true range expansion (i.e. the colonization of previously unoccupied areas), than with a model of "colonization from within" (i.e. local expansions from small, unnoticed populations). Genetic diversity measures indicated that the source population was likely located at the NE of the historical range, with a declining gradient of genetic diversity towards the more recently invaded areas. At the expansion front, we observed the greatest gene flow and smallest pairwise differences between nearby localities. Both natural landscape features (rivers) and recent anthropogenic barriers (roads, railways) explained a large proportion of genetic variance among populations and had a significant impact on the colonization pathways used by voles.

Exploiting flux shadowing for strain and bending engineering in core-shell nanowires

Here we report on the non-uniform shell growth of In_xGa_1-xAs on the GaAs nanowire (NW) core by molecular beam epitaxy (MBE). The growth was realized on pre-patterned silicon substrates with the pitch size (p) ranging from 0.1 μm to 10 μm. Considering the preferable bending direction with respect to the MBE cells as well as the layout of the substrate pattern, we were able to modify the strain distribution along the NW growth axis and the subsequent bending profile. For NW arrays with a high number density, the obtained bending profile of the NWs is composed of straight (barely-strained) and bent (strained) segments with different lengths which depend on the pitch size. A precise control of the bent and straight NW segment length provides a method to design NW based devices with length selective strain distribution.

Fatty acids homeostasis during fasting predicts protection from chemotherapy toxicity

Fasting exerts beneficial effects in mice and humans, including protection from chemotherapy toxicity. To explore the involved mechanisms, we collect blood from humans and mice before and after 36 or 24 hours of fasting, respectively, and measure lipid composition of erythrocyte membranes, circulating micro RNAs (miRNAs), and RNA expression at peripheral blood mononuclear cells (PBMCs). Fasting coordinately affects the proportion of polyunsaturated versus saturated and monounsaturated fatty acids at the erythrocyte membrane; and reduces the expression of insulin signaling-related genes in PBMCs. When fasted for 24 hours before and 24 hours after administration of oxaliplatin or doxorubicin, mice show a strong protection from toxicity in several tissues. Erythrocyte membrane lipids and PBMC gene expression define two separate groups of individuals that accurately predict a differential protection from chemotherapy toxicity, with important clinical implications. Our results reveal a mechanism of fasting associated with lipid homeostasis, and provide biomarkers of fasting to predict fasting-mediated protection from chemotherapy toxicity.

Fasting has been reported to protect from chemotherapy-associated toxicity. Here, the authors show that fatty acid profiles in erythrocyte membranes and gene expression from peripheral blood mononuclear cells are associated to the fasting-mediated benefits during cancer treatment in mice and patients.

Derived Neutrophil-to-Lymphocyte Ratio Predicts Pathological Complete Response to Neoadjuvant Chemotherapy in Breast Cancer

Background

Derived neutrophil-to-lymphocyte ratio (dNLR) is a biomarker associated with clinical outcome in breast cancer (BC). We analyzed the association of dNLR with pathological complete response (pCR) in triple-negative BC (TNBC) patients receiving neoadjuvant chemotherapy (CT).

Methods

This is a retrospective analysis of two randomized studies involving early stage/locally advanced TNBC patients receiving anthracycline/taxane-based CT+/−carboplatin (GEICAM/2006-03) or nab-paclitaxel/paclitaxel followed by anthracycline regimen (ETNA). dNLR was calculated as the ratio of neutrophils to the difference between total leukocytes and neutrophils in peripheral blood before CT (baseline) and at the end of treatment (EOT). Logistic regression analyses were used to explore dNLR association with pCR.

Results

In total, 308 TNBC patients were analyzed, 216 from ETNA and 92 from GEICAM/2006-03. Baseline median dNLR was 1.61 (interquartile range (IQR): 1.25–2.04) and at EOT 1.53 (IQR: 0.96–2.22). Baseline dNLR showed positive correlation with increased tumor size (p-value = 1e−04). High baseline dNLR, as continuous variable or using median cutoff, was associated with lower likelihood of pCR in univariate analysis. High EOT dNLR as continuous variable or using quartiles was also associated with lower pCR rate in uni- and multivariate analyses.

Conclusions

High baseline and EOT dNLR correlates with lower benefit from neoadjuvant CT in TNBC.

In situx-ray analysis of misfit strain and curvature of bent polytypic GaAs-InxGa1-xAs core-shell nanowires

Misfit strain in core-shell nanowires can be elastically released by nanowire bending in case of asymmetric shell growth around the nanowire core. In this work, we investigate the bending of GaAs nanowires during the asymmetric overgrowth by an In_xGa_1-xAs shell caused by avoiding substrate rotation. We observe that the nanowire bending direction depends on the nature of the substrate's oxide layer, demonstrated by Si substrates covered by native and thermal oxide layers. Further, we follow the bending evolution by time-resolvedin situx-ray diffraction measurements during the deposition of the asymmetric shell. The XRD measurements give insight into the temporal development of the strain as well as the bending evolution in the core-shell nanowire.

Psychosis and COVID-19: About a case

Introduction

Cases of psychosis are being reported in people infected by the SARS-CoV-2 virus. The relationship between psychosis and corticosteroids treatment is well known. However, there are relatively limited data so far correlating psychosis and SARS-CoV-2.

Objectives

To describe a case of manic psychosis in a 55-year-old woman treated with corticosteroids for COVID-19 infection. Discuss the etiopathogenic factors involved in psychosis in patients infected by COVID-19.

Methods

We present the case of a 55-year-old woman, without previous psychiatric history, who was admitted to psychiatry due to a psychotic episode with maniac symptoms. Three weeks earlier, the patient had been admitted to Internal Medicine for bilateral SArs-CoV2 pneumonia, under treatment with high doses of corticosteroids. The patient presents a verbose and salty speech, euphoric mood with hyperergia, subjective increase of capacities, insomnia and delusional ideation with mystical-spiritual content with delusional interpretations and auditory hallucinations. The patient comes from Ukraine and she has been living in Spain for 20 years. She works as a household assistant. The patient relates various psychosocial stressors throughout her life.

Results

Complementary diagnostic tests were without alterations. Low-dose antipsychotic treatment is prescribed, with a rapid recovery within a week. Finally, the patient showed complete insight of the episode and was discharged from the hospital being asymptomatic.

Conclusions

It would be interesting to publish the reported cases of psychosis and infection by COVID-19 as well as to investigate the etiopathogenic factors that may be contributing to the development of psychosis in patients infected by the virus.

Disclosure

No significant relationships.

Abstract PS5-22: Mutational profile from circulating tumor DNA in triple negative breast cancer: Results from the prospective registry of unresectable locally advanced or metastatic breast cancer GEICAM/2014-03 (RegistEM)

Background: The RegistEM is a non-interventional cohort study enrolling 1,867 patients (pts) (males or females) with advanced breast cancer diagnosed from January 2016 to December 2019, either after recurrence or as first diagnosis, in 38 Spanish sites. Triple negative BC (TNBC) is clinically defined based on lack of expression of both estrogen and progesterone receptors, and HER2 overexpression, and constitutes approximately 16% of BC cases. It is a particularly proliferative and aggressive BC subtype characterized by higher rates of relapse, greater metastatic potential, and shorter overall survival compared with other BC subtypes. Recent studies have shown hormone receptor status can change from the primary (P) to the recurrence tumor (M) in a proportion of cases, inducing a switch to TNBC in the recurrence, while other remains TNBC both in the P and M setting. This feature might impact survival and treatment options. Methods: We selected TNBC pts from the RegistEM study with ctDNA plasma samples available from the relapse. TNBC pts were classified into 2 groups according to clinical subtype (CS): 1) CS-converted (CS-C), with a discordant phenotype (TN subtype in M but not in P); and 2) CS-non-converted (CS-NC), with TN phenotype in P and M. To compare the mutation profiles of the 2 groups, next-generation sequencing (NGS) was performed using the AVENIO Expanded ctDNA Analysis Kit (Roche Sequencing Solutions, Inc; 77 genes; SNPs, indels, fusions and CNVs). Genomics alterations at individual level and grouped by pathway were explored for pathogenic and probably pathogenics variants. Genomics findings were correlated with clinicopathological data and outcomes, in terms of progression-free survival (PFS) and response to first line chemotherapy treatment. Kaplan-Meier estimator and Cox regression model were used to analyze PFS, and Fisher’s test to analyze contingency tables. Bonferroni correction was used for multiple testing. Results: NGS data was available from 32 (17%) TNBC pts; 22 (69%) pts CS-NC and 10 (31%) CS-C. The time from diagnosis to relapse was 29.2 months (m) for CS-NC and 60.2m for CS-C (HR=4.81, 95% confidence interval (CI) (1.59-14.59), p=0.0055; adjusted for confounders: menopausal status, grade, stage). In the metastatic setting, CS-NC had similar PFS than CS-C (8.3m CS-C vs 5.3m CS-NC; HR=1.63, 95% CI (0.71-3.72), p=0.2442). A median of 3 genomic alterations were found, similar in both groups. The most frequent somatic alterations were TP53 (50%), MAP2K1 (25%) and APC (25%). CS-C were enriched for MAP2K1 (60% vs. 9% in CS-NC; p=0.0243). No single genomic alteration was associated with outcome. Forty-percent of tumors harbored at least 1 mutation in PI3K-AKT-mTOR pathway (PIK3CA, PIK3R1, AKT1, AKT2, PTEN or MTOR genes), with similar incidence between CS-NC and CS-C. Pts with an altered PI3K-AKT-mTOR pathway had poor PFS (3.9m mutant vs 6.7m wild-type (WT); HR=3.02, 95% CI (1.4-6.56), p=0.0033) and a trend to worse response (complete or parcial response and stable disease: 23% mutant vs 77% WT, p=0.1581). CS-C tumors presented an altered MAPK-ERK pathway (mutations in KRAS, NRAS, BRAF, MAP2K1 or RAF1 genes) more frequently in comparison to CS-NC (60% vs 23%, p=0.0557), with no differences in response or PFS. Finally tumors with a high mutation allele frequency (≥mean) showed poor PFS (HR=3.64, 95% CI (1.52-8.75), p=0.0038). Conclusion: Analysis of ctDNA reveals diverse mutational spectrum in metastatic TNBC, suggesting that the presence of PI3K-AKT-mTOR pathway alterations associates with worse outcome and poor response to standard therapies. The clinical subtype conversions from luminal primary tumor are enriched in MAPK-ERK pathway alterations.

Citation Format: Angel Guerrero-Zotano, Carlos Jara, Sara López-Tarruella, César A Rodríguez, Encarna Adrover, Catalina Falo, Purificación Martínez, Silvia Antolín, Mireia Margeli, Josefina Cruz, Alvaro Rodríguez-Lescure, Vega Iranzo, César Gómez-Raposo, Jose Juan Illarramendi, Diego Malón, Jose Luis Alonso, Antonio Antón, Raquel Andrés, Jesús Herranz, Susana Bezares, Rosalía Caballero, Isabel Álvarez, Federico Rojo. Mutational profile from circulating tumor DNA in triple negative breast cancer: Results from the prospective registry of unresectable locally advanced or metastatic breast cancer GEICAM/2014-03 (RegistEM) [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS5-22.

Abstract PS2-01: Plk1 expression & efficacy of palbociclib in advanced hormonal receptor-positive breast cancer patients from PEARL study (GEICAM 2012-03)

Background: CDK 4/6 inhibitors (CDK 4/6i) with endocrine therapy (ET) combination therapy have improved outcomes in patients (pts) with hormonal receptor positive (HR+)/human epidermal growth factor receptor negative (HER2-) advanced breast cancer (ABC). However, most pts eventually develop resistance to these drugs, and one third never respond. Aside from HR positivity, predictive markers of clinical benefit from CDK 4/6i remains elusive. We aimed to identify biomarkers of response to palbociclib (PAL) and analyze potential therapeutic targets to reverse resistance. Methods: PEARL trial is a multicenter phase 3 study that assigned 601 postmenopausal HR+/HER2- ABC pts, whose disease progressed on aromatase inhibitors (AIs), to receive PAL + ET vs capecitabine (CAPE). We performed a differential gene expression analysis in pre-treatment tumors in extreme responders to PAL using the HTG EdgeSeq Oncology Biomarker Panel (HTG Molecular Diagnostics, Inc.), containing 2534 cancer related genes. Samples were subset in 2 categories: refractory (progressive disease as best response) vs sensitive (progression-free survival (PFS) within the upper quartile). Cox regression and Significance Analysis of Microarrays (SAM) analysis adjusting for multiple comparisons were performed. Results: We analyzed 455 (75.7%) pts with pre-treatment tumors available [from them, PAL + ET arm: 229 (50.3%) pts; CAPE arm: 226 (49.7%) pts]. Fifty genes (false discovery rate (FDR)<0.05) were differentially expressed in pts sensitive vs refractory to PAL (E2F target genes, epithelial-to-mesenchymal transition (EMT) and cell cycle genes, mainly). Unsupervised hierarchical clustering of pts based on the expression of these genes revealed two clusters. Cluster 1 is composed mostly of resistant tumors, highly proliferative (Ki67≥20%: 70%) with a great proportion of luminal B (59%) and non-luminal tumors (19%). Cluster 2 is composed of sensitive, low proliferative (Ki67<20%: 58%), mostly luminal A tumors (75%). There was no difference in ESR1 mutations distribution between the two clusters (Table 1). Forty genes were up-regulated and associated with resistance, including CCNE1 and PLK1 (Polo Like Kinase 1). In the whole cohort, pts with high levels (> median) of PLK1 (PLK1-high) treated with PAL, had a worse PFS in a multivariate model (5.7 months (m) vs 9.3 m of median PFS in PLK1-High vs -Low; HR=1.64, 95% CI (1.25-2.34), p=0.0008; adjusted model for confounders: age, site of disease, sites of metastasis, prior chemotherapy and Ki67). There were no differences in population treated with CAPE (9.9 m vs 9.4 m, PLK1-High vs -Low; HR=0.82, 95% CI (0.56-1.21), p=0.3189). In the METABRIC cohort, PLK1-High was associated with worse overall survival in HR+/HER2- BC but not in triple negative nor in HER2+ tumors. Among HR+/HER2- tumors, PLK1 expression was higher in luminal B and HER2-enriched intrinsic subtypes. We interrogated DepMap database and found that in BC cells lines there was an inverse correlation between PLK1 expression and effect on cell viability of CDK4 CRISPR knock-out (Pearson correlation r:0.54, p=0.009), but not of CDK6 knock-out. Also, HR+/HER2-/High Ki67 BC cell lines (HCC1428, EFM19 and MCF7) showed resistance to PAL on cell proliferation assays but sensitivity to the PLK1 inhibitor BI-2536. Conclusion: High expression of PLK1 is associated with intrinsic resistance to PAL and ET, this might be overcome with PLK1 inhibition.

Table 1PATIENT CHARACTERISTICSCluster 1Cluster 2ALLn=57n=47n=104RespondersSensitive42 (73.68%)14 (29.79%)56 (53.85%)Refractory15 (26.32%)33 (70.21%)48 (46.15%)ESR1Mutated9 (15.79%)13 (27.66%)22 (21.15%)Wild type45 (78.95%)34 (72.34%)79 (75.96%)Unknown3 (5.26%)0 (0%)3 (2.88%)PriorQTN42 (73.68%)31 (65.96%)73 (70.19%)Y15 (26.32%)16 (34.04%)31 (29.81%)SubtypeLumA43 (75.44%)10 (21.28%)53 (50.96%)LumB14 (24.56%)28 (59.57%)42 (40.38%)Non Luminal0 (0%)9 (19.15%)9 (8.65%)MetastasisOne21 (36.84%)15 (31.91%)36 (34.62%)Multiple36 (63.16%)32 (68.09%)68 (65.38%)KI67 20%KI67<2033 (57.89%)7 (14.89%)40 (38.46%)KI67≥2016 (28.07%)33 (70.21%)49 (47.12%)Unknown8 (14.04%)7 (14.89%)15 (14.42%)Objective ResponseComplete1 (1.75%)0 (0%)1 (0.96%)Partial16 (28.07%)6 (12.77%)22 (21.15%)Progressive15 (26.32%)33 (70.21%)48 (46.15%)Stable25 (43.86%)8 (17.02%)33 (31.73%)

Citation Format: Angel Guerrero- Zotano, Christoph Zielinski, Miguel Gil-Gil, Manuel Ruiz-Borrego, Eva M. Ciruelos, Montserrat Munoz, Begoña Bermejo, Mireia Margeli, Antonio Antón, Tibor Csöszi, Andrés García-Palomo, Ana Santaballa, Jose Luis Alonso, Antonio Fernández, Massimo Corsaro, Jesús Herranz, Paula López, Rosalia Caballero, Christiane Thallinger, Miguel Martin. Plk1 expression & efficacy of palbociclib in advanced hormonal receptor-positive breast cancer patients from PEARL study (GEICAM 2012-03) [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS2-01.

Beam damage of single semiconductor nanowires during X-ray nanobeam diffraction experiments

Nanoprobe X-ray diffraction (nXRD) using focused synchrotron radiation is a powerful technique to study the structural properties of individual semiconductor nanowires. However, when performing the experiment under ambient conditions, the required high X-ray dose and prolonged exposure times can lead to radiation damage. To unveil the origin of radiation damage, a comparison is made of nXRD experiments carried out on individual semiconductor nanowires in their as-grown geometry both under ambient conditions and under He atmosphere at the microfocus station of the P08 beamline at the third-generation source PETRA III. Using an incident X-ray beam energy of 9 keV and photon flux of 1010 s-1, the axial lattice parameter and tilt of individual GaAs/In0.2Ga0.8As/GaAs core-shell nanowires were monitored by continuously recording reciprocal-space maps of the 111 Bragg reflection at a fixed spatial position over several hours. In addition, the emission properties of the (In,Ga)As quantum well, the atomic composition of the exposed nanowires and the nanowire morphology were studied by cathodoluminescence spectroscopy, energy-dispersive X-ray spectroscopy and scanning electron microscopy, respectively, both prior to and after nXRD exposure. Nanowires exposed under ambient conditions show severe optical and morphological damage, which was reduced for nanowires exposed under He atmosphere. The observed damage can be largely attributed to an oxidation process from X-ray-induced ozone reactions in air. Due to the lower heat-transfer coefficient compared with GaAs, this oxide shell limits the heat transfer through the nanowire side facets, which is considered as the main channel of heat dissipation for nanowires in the as-grown geometry.

Abstract P1-10-09: The MHCII immune activation assay is prognostic for disease free survival in basal-like TNBC breast cancer patients in the GEICAM/9906 clinical trial

Background: Approximately 40% of patients with stage I-III triple-negative breast cancer (TNBC) recur after standard treatment, while the remaining 60% experience long-term disease-free survival (DFS). There are currently no clinical tests to assess the risk of recurrence in TNBC patients. We previously developed and validated an MHCII Immune Activation assay, which measures a gene expression signature that includes the major histocompatibility complex class II (MHCII) pathway genes and markers of activated tumor infiltrating lymphocytes. The MHCII Immune Activation assay was recently shown to accurately assess the risk of recurrence in Basal-like TNBC patients using FFPE tissues from an institutional cohort. A limitation of the previous study is that the patients’ treatment regimens in the institutional cohort were heterogeneous. The goal of this study was to determine if the MHCII Immune Activation assay can accurately assess the DFS in Basal-like TNBC patients who received uniform chemotherapy regimens in the context of a randomized clinical trial. Methods: The MHCII Immune Activation assay was applied to RNA isolated from 60 Basal-like TNBC FFPE specimens from the GEICAM/9906 clinical trial, a multicenter randomized phase III study evaluating adjuvant chemotherapy in node-positive operable BC patients. Thirty nine (65%) of the patients were treated with fluorouracil, epirubicin, and cyclophosphamide (FEC), and 21 (35%) patients received FEC followed by paclitaxel (FEC-P) (median follow-up 9.7 years). The MHCII Immune Activation Score was calculated from the assay using methods described previously, and patients were categorized into a High Risk of Recurrence (High ROR) group using pre-specified thresholds. The association between the MHCII Immune Activation Score and DFS was assessed using Kaplan-Meier analysis and cox proportional hazards models. Results: Across both arms, 32/60 (53.3%) patients were classified into the High ROR group based on their Low MHCII Immune Activation Scores. Patients in the High ROR group had significantly shorter DFS (Hazard Ratio (HR)=2.9 (CI95%:1.27-6.66), p-value=0.0081). Cox proportional hazard regression of the log10 transformed MHCII Immune Activation Score confirmed that MHCII Immune Activation Score is significantly associated with DFS (Wald Test p=0.0127). In the FEC arm, there were 22/39 (56.41%) patients classified into the High ROR group (Low MHCII Immune Activation Score). Patients in the High ROR group in the FEC arm showed a trend toward shorter DFS (HR=1.99 (CI95%:0.74-5.31)), but it was not significant (p-value=0.1595). In the FEC-P arm, there were 10/21 (47.62%) patients classified into the High ROR group (Low MHCII Immune Activation Score). Patients in the High ROR group in the FEC-P arm had significantly shorter DFS (HR=6.28 (CI95%:1.28-30.73), p-value=0.0111). Larger cohorts will be needed to confirm if the association between DFS and MHCII Immune Activation Score is stronger when patients are treated with chemotherapy regimens that include paclitaxel. Conclusions: The MHCII Immune Activation assay can be applied to RNA from FFPE tumor specimens to assess risk of recurrence in TNBC patients. The MHCII Immune Activation Score is associated with risk of recurrence in TNBC patients treated with uniform adjuvant chemotherapy regimens.

Citation Format: Miguel Martín, Katherine L Updike, Alvaro Rodríguez-Lescure, Lourdes Calvo, Jesús Herranz, Nuria Martín, Philip S Bernard, Katherine E Varley. The MHCII immune activation assay is prognostic for disease free survival in basal-like TNBC breast cancer patients in the GEICAM/9906 clinical trial [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P1-10-09.

Abstract P4-10-28: Identification of a specific epigenetic signature in patients showing secondary hypertension upon anti-VEGF treatment from the GEICAM/2011-04 (BRECOL) study

BACKGROUND The appearance of secondary hypertension (HTN) is one of the most common side effects of anti-angiogenic agents since it emerges in over 50% of the patients with these therapies. Independently of tumor type, in most clinical trials it was possible to observe a positive association between secondary HTN and better clinical outcome, including Progression Free Survival (PFS) and Overall Survival (OS). Preeclampsia is one of the biological models that better resembles the anti-VEGF/VEGFR action of these therapies. DNA methylation is one of the epigenetic mechanisms potentially related to variation in susceptibility to gestational HTN. The objective of our study is to define a specific epigenetic signature that could predict secondary HTN to anti-angiogenic treatment in patients that received bevacizumab in combination with chemotherapy (CT) from the BRECOL study. METHODS Patients (n=113) from BRECOL study (NCT01733628) received bevacizumab in combination with oxaliplatin or irinotecan + fluoropyrimidines for metastatic colorectal cancer (n=49), and with paclitaxel or capecitabine for metastatic breast cancer (n=64). Blood pressure (BP) was recorded with a Holter measurement (24 hours registration starting 2 hours after treatment administration). A methylation analysis was carried out on DNA obtained from pretreatment peripheral blood samples in 32 patients (28%) distributed in 4 experimental groups (8 patients / each) and classified according to their HTN history and to their BP variation upon bevacizumab plus CT: • Group A: patients with HTN history and with BP increase • Group B: patients with HTN history and with no BP increase • Group C: patients without HTN history and with BP increase • Group D: patients without HTN history and with no BP increase Analysis was realized with the “Infinium Human Methylation EPIC BeadChip” array (Illumina®) on bisulfite-converted DNA and differentially methylated sites were identified with the LIMMA (“Linear Models for Microarray Analysis”) bioinformatics tool (Bioconductor®). RESULTS Upon analysis of 850000 different methylation sites distributed all over the genome, we identified 27 (18 localized in the coding regions of the genes: FMNL2, METTL3, ACOT6, SCARNA20, PREX1, DNAI2, RAET1G, KCNJ8, GDF7, SYNPO2, CUGBP1, FRMD8, MKL2, HIF1A, TMEM177, UTP23, PXK and TNPO1; 9 localized in intergenic regions) that are differentially methylated in patients that showed secondary HTN to bevacizumab plus CT, independently of HTN history (Groups A + C vs. B + D). Based on Principal Components (PC) analysis, we defined a methylation score predictive of elevated BP. First PC (PC1) explains the 83.2% of the variability of the 27 identified methylation sites and allows to distinguish between patients that do and do not show secondary HTN. CONCLUSIONS High BP upon anti-angiogenic treatment is associated to specific DNA methylation profiles. We identified an epigenetic methylation signature putative predictive of secondary HTN to bevacizumab treatment in metastatic breast and colorectal cancer.

Citation Format: Juan de la Haba, Teresa Morales-Ruiz, Pilar García-Alfonso, Jose Ponce Lorenzo, Lourdes Calvo, Antonio Antón, Raul Marquez, Pedro Sánchez-Rovira, Ana Santaballa, Eva Ciruelos, María Victoria García-Ortiz, Teresa Roldán-Arjona, Jesús Herranz, Massimo Chiesa, Rosalía Caballero, Javier Gallego, Álvaro Rodríguez-Lescure. Identification of a specific epigenetic signature in patients showing secondary hypertension upon anti-VEGF treatment from the GEICAM/2011-04 (BRECOL) study [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-10-28.

Correlated Nanoscale Analysis of the Emission from Wurtzite versus Zincblende (In,Ga)As/GaAs Nanowire Core-Shell Quantum Wells

While the properties of wurtzite GaAs have been extensively studied during the past decade, little is known about the influence of the crystal polytype on ternary (In,Ga)As quantum well structures. We address this question with a unique combination of correlated, spatially resolved measurement techniques on core-shell nanowires that contain extended segments of both the zincblende and wurtzite polytypes. Cathodoluminescence hyperspectral imaging reveals a blue-shift of the quantum well emission energy by 75 ± 15 meV in the wurtzite polytype segment. Nanoprobe X-ray diffraction and atom probe tomography enable k·p calculations for the specific sample geometry to reveal two comparable contributions to this shift. First, there is a 30% drop in In mole fraction going from the zincblende to the wurtzite segment. Second, the quantum well is under compressive strain, which has a much stronger impact on the hole ground state in the wurtzite than in the zincblende segment. Our results highlight the role of the crystal structure in tuning the emission of (In,Ga)As quantum wells and pave the way to exploit the possibilities of three-dimensional band gap engineering in core-shell nanowire heterostructures. At the same time, we have demonstrated an advanced characterization toolkit for the investigation of semiconductor nanostructures.

Abstract P5-12-03: Genome copy number entropy as predictor of response for neoadjuvant therapy in early breast cancer

Background

Copy Number Alterations (CNAs) represent changes in the copy number of genomic segments of somatic cells due to chromosomal instability. CNAs include gene amplifications or deletions and can be involved in tumorigenesis. We analyzed CNAs data in pre- and post-treatment (ttm) tumors from patients (pts) with early breast cancer (BC) in the neoadjuvant trials GEICAM/2006-03 and GEICAM/2006-14, with the aim to identify CNAs in particular genomic regions (genetic entropy) associated with treatment response.

Methods

GEICAM/2006-03 (NCT00432172) HER2-negative pts were selectively treated according to clinical subtypes: triple negative (TN) pts were treated with standard anthracycline/taxane -based chemotherapy (AT-CT) +/- carboplatin, while luminal patients were randomized to AT-CT vs. hormonotherapy; GEICAM/2006-14 (NCT00841828) HER2+ pts received AT-CT plus anti-HER2 therapy.Shallow-whole genome Illumina sequencing DNA data from 204 paraffin-embedded tumors (100 pre- and 104 post-ttm) were segmented to obtain CNAs and recurrent altered genomic regions were defined. We used Wilcoxon test to analyze the frequency of altered regions and logistic regression analyses to explore their association with tumor response, in terms of pathological complete response (pCR) in breast and axilla. Validation of altered genes associated with therapy response was performed in the microarray gene expression-based Hatzis dataset (GSE25066) from pts receiving neoadjuvant AT-CT (1).

Results

A total of 672 regions covering the whole genome were identified upon analysis of CNAs data. Regions were categorized according to their alteration status as amplified, normal and lost. Comparative analysis of alterations revealed 11 regions significantly different (p<0.05) in pre- vs post-ttm tumors. Logistic regression analysis showed that in pre-ttm tumors specific alterations of 8 regions localized in 3 different genomic loci (11q12, 16q22 and 21q22) were significantly associated with pCR (p<0.05). Independent analyses of CNAs data with “CGH regions” and “GISTIC2.0” tools confirmed the special relevance of 2 of these 8 regions (#653 and #654), amplified in the locus 21q22.12. This locus contains 20 genes whose expression was tested in Hatzis dataset (1) (GSE25066): the analysis showed that overexpression of 5 of these 20 genes (CHAF1B, CBR1, CBR3, RCAN1 and SLC5A3) turned out to be significantly higher in the cohort of pts who reached pCR, in agreement with our findings. Some of these genes have already been described as proliferation markers (CHAF1B) or involved in treatment response (CBR1) in BC. Other genes related to BC in this genomic region are the transcription factor RUNX1 and the Lysine Methyltransferase SETD4.

Conclusions

According to our results, neoadjuvant therapy can modulate genomic aberrations landscape in BC. Our data suggest that amplification of specific genes in the genomic locus (21q22.12) is involved in the neoadjuvant therapy response in early BC.

(1): Hatzis et al., JAMA 2011, 305(18) 1873-81

Citation Format: Alba E, Rueda OM, Lluch A, Albanell J, Chin S-F, Chacón JI, Calvo L, De la Haba-Rodriguez J, Bermejo B, Ribelles N, Sánchez-Rovira P, Plazaola A, Barnadas A, Cirauqul B, Ramos M, Arcusa A, Carrasco E, Herranz J, Chiesa M, Caballero R, Santonja A, Rojo F, Caldas C. Genome copy number entropy as predictor of response for neoadjuvant therapy in early breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-12-03.

Re-interpretation of PAM50 gene expression as quantitative tumor dimensions shows utility for clinical trials: application to prognosis and response to paclitaxel in breast cancer

Background

We recently showed PAM50 gene expression data can be represented by five quantitative, orthogonal, multi-gene breast tumor traits. These novel tumor ‘dimensions’ were superior to categorical intrinsic subtypes for clustering in high-risk breast cancer pedigrees, indicating potential to represent underlying genetic susceptibilities and biological pathways. Here we explore the prognostic and predictive utility of these dimensions in a sub-study of GEICAM/9906, a Phase III randomized prospective clinical trial of paclitaxel in breast cancer.

Methods

Tumor dimensions, PC1–PC5, were calculated using pre-defined coefficients. Univariable and multivariable Cox proportional hazards (PH) models for disease-free survival (DFS) were used to identify associations between quantitative dimensions and prognosis or response to the addition of paclitaxel. Results were illustrated using Kaplan–Meier curves.

Results

Dimensions PC1 and PC5 were associated with DFS (Cox PH p = 6.7 \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\times$$\end{document}× 10⁻⁷ and p = 0.036), remaining significant after correction for standard clinical–pathological prognostic characteristics. Both dimensions were selected in the optimal multivariable model, together with nodal status and tumor size (Cox PH p = 1.4 \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\times$$\end{document}× 10⁻¹²). Interactions with treatment were identified for PC3 and PC4. Response to paclitaxel was restricted to tumors with low PC3 and PC4 (log-rank p = 0.0021). Women with tumors high for PC3 or PC4 showed no survival advantage.

Conclusions

Our proof-of-concept application of quantitative dimensions illustrated novel findings and clinical utility beyond standard clinical–pathological characteristics and categorical intrinsic subtypes for prognosis and predicting chemotherapy response. Consideration of expression data as quantitative tumor dimensions offers new potential to identify clinically important patient subsets in clinical trials and advance precision medicine.

Electronic supplementary material

The online version of this article (10.1007/s10549-018-05097-5) contains supplementary material, which is available to authorized users.

Predicting Response to Standard First-line Treatment in High-grade Serous Ovarian Carcinoma by Angiogenesis-related Genes

BACKGROUND/AIM

Predicting response to treatment in high-grade serous ovarian carcinoma (HGSOC) still remains a clinical challenge. The standard-of-care for first-line chemotherapy, based on a combination of carboplatin and paclitaxel, achieves a high response rate. However, the development of drug resistance is one of the major limitations to efficacy. Therefore, identification of biomarkers able to predict response to chemotherapy in patients with HGSOC is a critical step for prognosis and treatment of the disease. Several studies suggest that angiogenesis is an important process in the development of ovarian carcinoma and chemoresistance. The aim of this study was to identify a profile of angiogenesis-related genes as a biomarker for response to first-line chemotherapy in HGSOC.

MATERIALS AND METHODS

Formalin-fixed paraffin-embedded samples from 39 patients with HGSOC who underwent surgical cytoreduction and received a first-line chemotherapy with carboplatin and paclitaxel were included in this study. Expression levels of 82 angiogenesis-related genes were measured by quantitative real-time polymerase chain reaction using TaqMan low-density arrays.

RESULTS

Univariate analysis identified five genes [angiopoietin 1 (ANGPT1), aryl hydrocarbon receptor nuclear translocator (ARNT), CD34, epidermal growth factor (EGF) and matrix metallopeptidase 3 (MMP3)] as being statistically associated with response to treatment. Multivariable analysis by Lasso-penalized Cox regression generated a model with the combined expression of seven genes [angiotensinogen (AGT), CD34, EGF, erythropoietin receptor (EPOR), interleukin 8 (IL8), MMP3 and MMP7)]. The area under the receiver operating characteristics curve (0.679) and cross-validated Kaplan-Meier survival curves were used to estimate the accuracy of these predictors.

CONCLUSION

An angiogenesis-related gene expression profile useful for response prediction in HGSOC was identified, supporting the important role of angiogenesis in HGSOC.

Predictive value of angiogenesis-related gene profiling in patients with HER2-negative metastatic breast cancer treated with bevacizumab and weekly paclitaxel

Bevacizumab plus weekly paclitaxel improves progression-free survival (PFS) in HER2-negative metastatic breast cancer (mBC), but its use has been questioned due to the absence of a predictive biomarker, lack of benefit in overall survival (OS) and increased toxicity. We examined the baseline tumor angiogenic-related gene expression of 60 patients with mBC with the aim of finding a signature that predicts benefit from this drug.

Multivariate analysis by Lasso-penalized Cox regression generated two predictive models: one, named G-model, including 11 genes, and the other one, named GC-model, including 13 genes plus 5 clinical covariates. Both models identified patients with improved PFS (HR (Hazard Ratio) 2.57 and 4.04, respectively) and OS (HR 3.29 and 3.43, respectively). The G-model distinguished low and high risk patients in the first 6 months, whereas the GC-model maintained significance over time.

Targeting the lipid metabolic axis ACSL/SCD in colorectal cancer progression by therapeutic miRNAs: miR-19b-1 role

An abnormal acyl-CoA synthetase/stearoyl-CoA desaturase (ACSL/SCD) lipid network fuels colon cancer progression, endowing cells with invasive and migratory properties. Therapies against this metabolic network may be useful to improve clinical outcomes. Because micro-RNAs (miRNAs/miRs) are important epigenetic regulators, we investigated novel miRNAs targeting this pro-tumorigenic axis; hence to be used as therapeutic or prognostic miRNAs. Thirty-one putative common miRNAs were predicted to simultaneously target the three enzymes comprising the ACSL/SCD network. Target validation by quantitative RT-PCR, Western blotting, and luciferase assays showed miR-544a, miR-142, and miR-19b-1 as major regulators of the metabolic axis, ACSL/SCD Importantly, lower miR-19b-1 expression was associated with a decreased survival rate in colorectal cancer (CRC) patients, accordingly with ACSL/SCD involvement in patient relapse. Finally, miR-19b-1 regulated the pro-tumorigenic axis, ACSL/SCD, being able to inhibit invasion in colon cancer cells. Because its expression correlated with an increased survival rate in CRC patients, we propose miR-19b-1 as a potential noninvasive biomarker of disease-free survival and a promising therapeutic miRNA in CRC.

The transcriptional and mutational landscapes of lipid metabolism-related genes in colon cancer

Metabolic alterations encountered in tumors are well recognized and considered as a hallmark of cancer. In addition to Warburg Effect, epidemiological and experimental studies support the crucial role of lipid metabolism in colorectal cancer (CRC). The overexpression of four lipid metabolism-related genes (ABCA1, ACSL1, AGPAT1 and SCD genes) has been proposed as prognostic marker of stage II CRC (ColoLipidGene signature).

In order to explore in depth the transcriptomic and genomic scenarios of ABCA1, ACSL1, AGPAT1 and SCD genes, we performed a transcriptomic meta-analysis in more than one thousand CRC individuals. Additionally we analyzed their genomic coding sequence in 95 patients, to find variants that could orchestrate CRC prognosis.

We found that genetic variant rs3071, located on SCD gene, defines a 9.77% of stage II CRC patients with high risk of death. Moreover, individuals with upregulation of ABCA1 and AGPAT1 expression have an increased risk of CRC recurrence, independently of tumor stage.

ABCA1 emerges as one of the main contributors to signature’s prognostic effect. Indeed, both high ABCA1 expression and presence of tumoral genetic variants located in ABCA1 coding region, seem to be associated with CRC risk of death. In addition the non-synonymous polymorphism rs2230808, located on ABCA1, is associated with gene expression. Patients carrying at least one copy of minor allele showed higher levels of ABCA1 expression than patients carrying homozygous major allele.

This study broaden the prognostic value of ABCA1, ACSL1, AGPAT1 and SCD genes, independently of CRC tumor stage, leading to future precision medicine approaches and “omics”-guided therapies.

MicroRNA-661 modulates redox and metabolic homeostasis in colon cancer

Cancer cell survival and metastasis are dependent on metabolic reprogramming that is capable of increasing resistance to oxidative and energetic stress. Targeting these two processes can be crucial for cancer progression. Herein, we describe the role of microRNA‐661 (miR661) as epigenetic regulator of colon cancer (CC) cell metabolism. MicroR661 induces a global increase in reactive oxygen species, specifically in mitochondrial superoxide anions, which appears to be mediated by decreased carbohydrate metabolism and pentose phosphate pathway, and by a higher dependency on mitochondrial respiration. MicroR661 overexpression in non‐metastatic human CC cells induces an epithelial‐to‐mesenchymal transition phenotype, and a reduced tolerance to metabolic stress. This seems to be a general effect of miR661 in CC, since metastatic CC cell metabolism is also compromised upon miR661 overexpression. We propose hexose‐6‐phosphate dehydrogenase and pyruvate kinase M2 as two key players related to the observed metabolic reprogramming. Finally, the clinical relevance of miR661 expression levels in stage‐II and III CC patients is discussed. In conclusion, we propose miR661 as a potential modulator of redox and metabolic homeostasis in CC.

Quantum Dot Self-Assembly Driven by a Surfactant-Induced Morphological Instability

In strained heteroepitaxy, two-dimensional layers can exhibit a critical thickness at which three-dimensional islands self-assemble, relieving misfit strain at the cost of an increased surface area. Here we show that such a morphological phase transition can be induced on demand using surfactants. We explore Bi as a surfactant in the growth of InAs on GaAs(110), and find that the presence of surface Bi induces Stranski-Krastanov growth of 3D islands, while growth without Bi always favors 2D layer formation. Exposing a static two monolayer thick InAs layer to Bi rapidly transforms the layer into 3D islands. Density functional theory calculations reveal that Bi as well as Sb reduce the energetic cost of 3D island formation by modifying surface energies. These 3D nanostructures behave as optically active quantum dots. This work illustrates how surfactants can enable quantum dot self-assembly where it otherwise would not occur.

Self-Assembly of InAs Nanostructures on the Sidewalls of GaAs Nanowires Directed by a Bi Surfactant

Surface energies play a dominant role in the self-assembly of three-dimensional (3D) nanostructures. In this Letter, we show that using surfactants to modify surface energies can provide a means to externally control nanostructure self-assembly, enabling the synthesis of novel hierarchical nanostructures. We explore Bi as a surfactant in the growth of InAs on the {11̅0} sidewall facets of GaAs nanowires. The presence of surface Bi induces the formation of InAs 3D islands by a process resembling the Stranski-Krastanov mechanism, which does not occur in the absence of Bi on these surfaces. The InAs 3D islands nucleate at the corners of the {11̅0} facets above a critical shell thickness and then elongate along ⟨110⟩ directions in the plane of the nanowire sidewalls. Exploiting this growth mechanism, we realize a series of novel hierarchical nanostructures, ranging from InAs quantum dots on single {11̅0} nanowire facets to zigzag-shaped nanorings completely encircling nanowire cores. Photoluminescence spectroscopy and cathodoluminescence spectral line scans reveal that small surfactant-induced InAs 3D islands behave as optically active quantum dots. This work illustrates how surfactants can provide an unprecedented level of external control over nanostructure self-assembly.

Multiple chemical sensitivity: Genotypic characterization, nutritional status and quality of life in 52 patients

BACKGROUND AND OBJECTIVES

Multiple chemical sensitivity (MCS) is a chronic, multisystem syndrome of unknown etiology. The aim of the present study was to describe the nutritional status and quality of life of patients suffering from MCS, as well as to identify potential polymorphisms associated with this illness.

PATIENTS AND METHODS

A cross-sectional, descriptive study was performed on patients with a diagnosis of MCS. Data on anthropometric and body composition variables, hand muscle strength and quality of life were collected. The selection of single nucleotide polymorphisms (SNPs) was based on genes previously associated with MCS and genes involved in inflammatory and oxidative stress pathways.

RESULTS

A total of 52 patients (93.2% female), with a mean age of 50.9 (10.3) years were included in the study. Among them, based on their BMI, 48% had an inadequate nutritional status (17% were underweight and 32% were overweight or obese). Thirty percent of patients had a low muscle mass for their age, 84% had muscle strength below the tenth percentile, and 51.8% had a high fat mass percentage. Regarding quality of life, all median scores were lower than those of other illnesses assessed for every subscale assessed. Statistically significant differences between patient cases and controls were found with respect to rs1801133 (MTHFR), rs174546 (FADS1) and rs1801282 (PPARγ) polymorphisms.

CONCLUSION

A high percentage of patients had a poor nutritional status, low muscle strength and decreased muscle mass. These facts exacerbate the already-lower quality of life of these patients. Specific genetic polymorphisms associated with the syndrome or its pathogenesis were not identified.

3'UTR Polymorphism in ACSL1 Gene Correlates with Expression Levels and Poor Clinical Outcome in Colon Cancer Patients

Strong evidence suggests that lipid metabolism (LM) has an essential role in tumor growth to support special energetic and structural requirements of tumor cells. Recently, overexpression of LM-related genes, apolipoproteins related to metabolic syndrome, and ACSL/SCD network involved in fatty acid activation have been proposed as prognostic markers of colon cancer (CC). Furthermore, activation of this latter lipid network has been recently demonstrated to confer invasive and stem cell properties to tumor cells promoting tumor aggressiveness and patient relapse. With the aim of elucidating whether any genetic variation within these genes could influence basal expression levels and consequent susceptibility to relapse, we genotype, in 284 CC patients, 57 polymorphisms located in the 7 genes of these lipid networks previously associated with worse clinical outcome of CC patients (ABCA1, ACSL1, AGPAT1, APOA2, APOC1, APOC2 and SCD), some of them related to CC aggressiveness. After adjusting with clinical confounding factors and multiple comparisons, an association between genotype and disease-free survival (DFS) was shown for rs8086 in 3'-UTR of ACSL1 gene (HR 3.08; 95% CI 1.69-5.63; adjusted p = 0.046). Furthermore, the risk T/T genotype had significantly higher ACSL1 gene expression levels than patients carrying C/T or C/C genotype (means = 5.34; 3.73; 2.37 respectively; p-value (ANOVA) = 0.019), suggesting a functional role of this variant. Thus, we have identified a "risk genotype" of ACSL1 gene that confers constitutive high levels of the enzyme, which is involved in the activation of fatty acids through conversion to acyl-CoA and has been recently related to increased invasiveness of tumor cells. These results suggest that rs8086 of ACSL1 could be a promising prognostic marker in CC patients, reinforcing the relevance of LM in the progression of CC.

A link between lipid metabolism and epithelial-mesenchymal transition provides a target for colon cancer therapy

The alterations in carbohydrate metabolism that fuel tumor growth have been extensively studied. However, other metabolic pathways involved in malignant progression, demand further understanding. Here we describe a metabolic acyl-CoA synthetase/stearoyl-CoA desaturase ACSL/SCD network causing an epithelial-mesenchymal transition (EMT) program that promotes migration and invasion of colon cancer cells. The mesenchymal phenotype produced upon overexpression of these enzymes is reverted through reactivation of AMPK signaling. Furthermore, this network expression correlates with poorer clinical outcome of stage-II colon cancer patients. Finally, combined treatment with chemical inhibitors of ACSL/SCD selectively decreases cancer cell viability without reducing normal cells viability. Thus, ACSL/SCD network stimulates colon cancer progression through conferring increased energetic capacity and invasive and migratory properties to cancer cells, and might represent a new therapeutic opportunity for colon cancer treatment.

ETP-46321, a dual p110α/δ class IA phosphoinositide 3-kinase inhibitor modulates T lymphocyte activation and collagen-induced arthritis

Class IA phosphoinositide 3-kinases (PI3Ks) are essential to function of normal and tumor cells, and to modulate immune responses. T lymphocytes express high levels of p110α and p110δ class IA PI3K. Whereas the functioning of PI3K p110δ in immune and autoimmune reactions is well established, the role of p110α is less well understood. Here, a novel dual p110α/δ inhibitor (ETP-46321) and highly specific p110α (A66) or p110δ (IC87114) inhibitors have been compared concerning T cell activation in vitro, as well as the effect on responses to protein antigen and collagen-induced arthritis in vivo. In vitro activation of naive CD4(+) T lymphocytes by anti-CD3 and anti-CD28 was inhibited more effectively by the p110δ inhibitor than by the p110α inhibitor as measured by cytokine secretion (IL-2, IL-10, and IFN-γ), T-bet expression and NFAT activation. In activated CD4(+) T cells re-stimulated through CD3 and ICOS, IC87114 inhibited Akt and Erk activation, and the secretion of IL-2, IL-4, IL-17A, and IFN-γ better than A66. The p110α/δ inhibitor ETP-46321, or p110α plus p110δ inhibitors also inhibited IL-21 secretion by differentiated CD4(+) T follicular (Tfh) or IL-17-producing (Th17) helper cells. In vivo, therapeutic administration of ETP-46321 significantly inhibited responses to protein antigen as well as collagen-induced arthritis, as measured by antigen-specific antibody responses, secretion of IL-10, IL-17A or IFN-γ, or clinical symptoms. Hence, p110α as well as p110δ Class IA PI3Ks are important to immune regulation; inhibition of both subunits may be an effective therapeutic approach in inflammatory autoimmune diseases like rheumatoid arthritis.

Role of re-growth interface preparation process for spectral line-width reduction of single InAs site-controlled quantum dots

We present growth and optical characterization measurements of single InAs site-controlled quantum dots (SCQDs) grown by molecular beam epitaxy on GaAs (001) patterned substrates by atomic force microscopy oxidation lithography. InAs SCQDs directly grown on the patterned surface were used as a seed layer and strain template for the nucleation of optically active single InAs SCQDs. The preservation of the initial geometry of the engraved pattern motifs after the re-growth interface preparation process, the lack of buffer layer growth prior to InAs seed layer deposition and the development of suitable growth conditions provide us an improvement of the SCQDs' active layer optical properties while retaining a high ratio of single occupation (89%). In this work a fivefold reduction of the average optical line-width from 870 μeV to 156 μeV for InAs SCQDs located 15 nm from the re-growth interface is obtained by increasing the temperature of the initial thermal treatment step of the re-growth interface from 490 °C to 530 °C.

Clinical relevance of the differential expression of the glycosyltransferase gene GCNT3 in colon cancer

Altered glycosylation is considered a universal cancer hallmark. Mucin-type core 2 1,6-N-acetylglucosaminyltransferase enzyme (C2GnT-M), encoded by the GCNT3 gene, has been reported to be altered in tumours and to possess tumour suppressor properties. In this work, we aimed to determine the possible role of GCNT3 gene expression as prognostic marker in colon cancer. We investigated the differential expression of GCNT3 gene among tumour samples from stage II colon cancer patients by quantitative reverse-transcription polymerase chain reaction (qRT-PCR). Univariate and Multivariate Cox regression analyses were used to determine the correlation between GCNT3 expression and disease-free survival. The risk of relapse in GCNT3 low-expressing cancer patients was significantly higher than that in GCNT3 high-expressing patients in both training (Hazard Ratio (HR) 4.26, p=0.002) and validation (HR 3.06, p=0.024) series of patients, and this association was independent of clinical factors. Additionally, qRT-PCR was used to explore the modulation of GCNT3 expression by different antitumour drugs. Three chemotherapeutic agents with different mechanism of action (5-fluorouracil, bortezomib and paclitaxel) significantly induced GCNT3 expression in several cancer cells, being observed the correlation between antitumour action and GCNT3 modulation, whereas this gene was not modulated in cells that do not respond to treatment. Overall, these results indicate that low GCNT3 expression is a promising prognostic biomarker for colon cancer that could be used to identify early-stage colon cancer patients at high risk of relapse. Additionally, our results suggest that this enzyme might also constitute a biomarker to monitor tumour response to chemotherapy in cancer patients.

Genes associated with metabolic syndrome predict disease-free survival in stage II colorectal cancer patients. A novel link between metabolic dysregulation and colorectal cancer

Studies have recently suggested that metabolic syndrome and its components increase the risk of colorectal cancer. Both diseases are increasing in most countries, and the genetic association between them has not been fully elucidated. The objective of this study was to assess the association between genetic risk factors of metabolic syndrome or related conditions (obesity, hyperlipidaemia, diabetes mellitus type 2) and clinical outcome in stage II colorectal cancer patients. Expression levels of several genes related to metabolic syndrome and associated alterations were analysed by real-time qPCR in two equivalent but independent sets of stage II colorectal cancer patients. Using logistic regression models and cross-validation analysis with all tumour samples, we developed a metabolic syndrome-related gene expression profile to predict clinical outcome in stage II colorectal cancer patients. The results showed that a gene expression profile constituted by genes previously related to metabolic syndrome was significantly associated with clinical outcome of stage II colorectal cancer patients. This metabolic profile was able to identify patients with a low risk and high risk of relapse. Its predictive value was validated using an independent set of stage II colorectal cancer patients. The identification of a set of genes related to metabolic syndrome that predict survival in intermediate-stage colorectal cancer patients allows delineation of a high-risk group that may benefit from adjuvant therapy and avoid the toxic and unnecessary chemotherapy in patients classified as low risk. Our results also confirm the linkage between metabolic disorder and colorectal cancer and suggest the potential for cancer prevention and/or treatment by targeting these genes.

Genetic variation in the TP53 pathway and bladder cancer risk. a comprehensive analysis

INTRODUCTION

Germline variants in TP63 have been consistently associated with several tumors, including bladder cancer, indicating the importance of TP53 pathway in cancer genetic susceptibility. However, variants in other related genes, including TP53 rs1042522 (Arg72Pro), still present controversial results. We carried out an in depth assessment of associations between common germline variants in the TP53 pathway and bladder cancer risk.

MATERIAL AND METHODS

We investigated 184 tagSNPs from 18 genes in 1,058 cases and 1,138 controls from the Spanish Bladder Cancer/EPICURO Study. Cases were newly-diagnosed bladder cancer patients during 1998-2001. Hospital controls were age-gender, and area matched to cases. SNPs were genotyped in blood DNA using Illumina Golden Gate and TaqMan assays. Cases were subphenotyped according to stage/grade and tumor p53 expression. We applied classical tests to assess individual SNP associations and the Least Absolute Shrinkage and Selection Operator (LASSO)-penalized logistic regression analysis to assess multiple SNPs simultaneously.

RESULTS

Based on classical analyses, SNPs in BAK1 (1), IGF1R (5), P53AIP1 (1), PMAIP1 (2), SERINPB5 (3), TP63 (3), and TP73 (1) showed significant associations at p-value≤0.05. However, no evidence of association, either with overall risk or with specific disease subtypes, was observed after correction for multiple testing (p-value≥0.8). LASSO selected the SNP rs6567355 in SERPINB5 with 83% of reproducibility. This SNP provided an OR = 1.21, 95%CI 1.05-1.38, p-value = 0.006, and a corrected p-value = 0.5 when controlling for over-estimation.

DISCUSSION

We found no strong evidence that common variants in the TP53 pathway are associated with bladder cancer susceptibility. Our study suggests that it is unlikely that TP53 Arg72Pro is implicated in the UCB in white Europeans. SERPINB5 and TP63 variation deserve further exploration in extended studies.

Whole genome prediction of bladder cancer risk with the Bayesian LASSO

To build a predictive model for urothelial carcinoma of the bladder (UCB) risk combining both genomic and nongenomic data, 1,127 cases and 1,090 controls from the Spanish Bladder Cancer/EPICURO study were genotyped using the HumanHap 1M SNP array. After quality control filters, genotypes from 475,290 variants were available. Nongenomic information comprised age, gender, region, and smoking status. Three Bayesian threshold models were implemented including: (1) only genomic information, (2) only nongenomic data, and (3) both sources of information. The three models were applied to the whole population, to only nonsmokers, to male smokers, and to extreme phenotypes to potentiate the UCB genetic component. The area under the ROC curve allowed evaluating the predictive ability of each model in a 10-fold cross-validation scenario. Smoking status showed the highest predictive ability of UCB risk (AUCtest = 0.62). On the other hand, the AUC of all genetic variants was poorer (0.53). When the extreme phenotype approach was applied, the predictive ability of the genomic model improved 15%. This study represents a first attempt to build a predictive model for UCB risk combining both genomic and nongenomic data and applying state-of-the-art statistical approaches. However, the lack of genetic relatedness among individuals, the complexity of UCB etiology, as well as a relatively small statistical power, may explain the low predictive ability for UCB risk. The study confirms the difficulty of predicting complex diseases using genetic data, and suggests the limited translational potential of findings from this type of data into public health interventions.

A large-scale assessment of two-way SNP interactions in breast cancer susceptibility using 46,450 cases and 42,461 controls from the breast cancer association consortium

Part of the substantial unexplained familial aggregation of breast cancer may be due to interactions between common variants, but few studies have had adequate statistical power to detect interactions of realistic magnitude. We aimed to assess all two-way interactions in breast cancer susceptibility between 70,917 single nucleotide polymorphisms (SNPs) selected primarily based on prior evidence of a marginal effect. Thirty-eight international studies contributed data for 46,450 breast cancer cases and 42,461 controls of European origin as part of a multi-consortium project (COGS). First, SNPs were preselected based on evidence (P < 0.01) of a per-allele main effect, and all two-way combinations of those were evaluated by a per-allele (1 d.f.) test for interaction using logistic regression. Second, all 2.5 billion possible two-SNP combinations were evaluated using Boolean operation-based screening and testing, and SNP pairs with the strongest evidence of interaction (P < 10(-4)) were selected for more careful assessment by logistic regression. Under the first approach, 3277 SNPs were preselected, but an evaluation of all possible two-SNP combinations (1 d.f.) identified no interactions at P < 10(-8). Results from the second analytic approach were consistent with those from the first (P > 10(-10)). In summary, we observed little evidence of two-way SNP interactions in breast cancer susceptibility, despite the large number of SNPs with potential marginal effects considered and the very large sample size. This finding may have important implications for risk prediction, simplifying the modelling required. Further comprehensive, large-scale genome-wide interaction studies may identify novel interacting loci if the inherent logistic and computational challenges can be overcome.

FGF receptor genes and breast cancer susceptibility: results from the Breast Cancer Association Consortium

BACKGROUND

Breast cancer is one of the most common malignancies in women. Genome-wide association studies have identified FGFR2 as a breast cancer susceptibility gene. Common variation in other fibroblast growth factor (FGF) receptors might also modify risk. We tested this hypothesis by studying genotyped single-nucleotide polymorphisms (SNPs) and imputed SNPs in FGFR1, FGFR3, FGFR4 and FGFRL1 in the Breast Cancer Association Consortium.

METHODS

Data were combined from 49 studies, including 53 835 cases and 50 156 controls, of which 89 050 (46 450 cases and 42 600 controls) were of European ancestry, 12 893 (6269 cases and 6624 controls) of Asian and 2048 (1116 cases and 932 controls) of African ancestry. Associations with risk of breast cancer, overall and by disease sub-type, were assessed using unconditional logistic regression.

RESULTS

Little evidence of association with breast cancer risk was observed for SNPs in the FGF receptor genes. The strongest evidence in European women was for rs743682 in FGFR3; the estimated per-allele odds ratio was 1.05 (95% confidence interval=1.02-1.09, P=0.0020), which is substantially lower than that observed for SNPs in FGFR2.

CONCLUSION

Our results suggest that common variants in the other FGF receptors are not associated with risk of breast cancer to the degree observed for FGFR2.

High quality factor GaAs-based photonic crystal microcavities by epitaxial re-growth

We investigate L7 photonic crystal microcavities (PCMs) fabricated by epitaxial re-growth of GaAs pre-patterned substrates, containing InAs quantum dots. The resulting PCMs show hexagonal shaped nano-holes due to the development of preferential crystallographic facets during the re-growth step. Through a careful control of the fabrication processes, we demonstrate that the photonic modes are preserved throughout the process. The quality factor (Q) of the photonic modes in the re-grown PCMs strongly depends on the relative orientation between photonic lattice and crystallographic directions. The optical modes of the re-grown PCMs preserve the linear polarization and, for the most favorable orientation, a 36% of the Q measured in PCMs fabricated by the conventional procedure is observed, exhibiting values up to ~6000. The results aim to the future integration of site-controlled QDs with high-Q PCMs for quantum photonics and quantum integrated circuits.

Recurrent inactivation of STAG2 in bladder cancer is not associated with aneuploidy

Urothelial bladder cancer (UBC) is heterogeneous at the clinical, pathological, and genetic levels. Tumor invasiveness (T) and grade (G) are the main factors associated with outcome and determine patient management (1). A discovery exome sequencing screen (n=17), followed by a prevalence screen (n=60), identified new genes mutated in this tumor coding for proteins involved in chromatin modification (MLL2, ASXL2, BPTF), cell division (STAG2, SMC1A, SMC1B), and DNA repair (ATM, ERCC2, FANCA). STAG2, a subunit of cohesin, was significantly and commonly mutated/lost in UBC, mainly in tumors of low stage/grade, and its loss was associated with improved outcome. Loss of expression was often observed in chromosomally-stable tumors and STAG2 knockdown in bladder cancer cells did not increase aneuploidy. STAG2 reintroduction in non-expressing cells led to reduced colony formation. Our findings indicate that STAG2 is a novel UBC tumor suppressor acting through mechanisms that are different from its role to prevent aneuploidy.

[Basic principles for the development of biomarkers in oncology]

The accelerated expansion of the knowledge of genetic and molecular basics of cancer, together with the recent development of molecular biology techniques, have had a significant impact in the field of oncology, among other medical disciplines. So, over the last few years, we are crossing from an empiricism-based model to an evidence-based model in which drugs are adapted depending of the molecular alterations which result crucial for tumor development (both for carcinogenesis and acquisition of an aggressive phenotype leading to tumor invasion and resistance to therapy). The molecular alterations /variations offer the possibility of being detected and used as biomarkers in clinical practice. Biomarkers may have multiple applications in the field of oncology, from determining the risk to suffer the disease to prediction of response to therapy, including diagnosis, prognosis and disease monitoring, with the final aim of performing a more personalized medicine and achieving greater efficacy for the therapies selected, diminishing each therapy's own adverse events. Considering the importance biomarkers may get to have in clinical decision making, it is basic that their development is performed under straight evaluation and validation rules. In this article we review the various types of biomarkers and the basic methodological principles for their development, validation and subsequent clinical application.

Bladder cancer and seroreactivity to BK, JC and Merkel cell polyomaviruses: the Spanish bladder cancer study

An infectious etiology for bladder cancer has long been suspected. Merkel cell virus (MCV), BKV and JCV polyomaviruses are possible causative agents but data remain scarce. Therefore, we evaluated the seroresponse to these three polyomaviruses in association with bladder cancer risk. 1,135 incident bladder cancer subjects from five Spanish regions and 982 hospital controls matched by sex, age and region were included. 99% of cases were urothelial-cell carcinomas. Antibody response against MCV, BKV and JCV was measured by enzyme immunoassay using Virus-Like-Particles. Our results show a similar seroprevalence in cases and controls: 64/60% for BKV, 83/82% for MCV and 87/83% for JCV. However, among seropositive subjects, higher median seroreactivities were observed in cases compared to controls for BKV (0.84 vs. 0.70, p-value = 0.009) and MCV (1.81 vs. 0.65, p-value < 0.001). Increased bladder cancer risk was observed for BKV (OR = 1.4, 95%CI 1.04-1.8) and for MCV (OR = 1.5, 95%CI 1.2-1.9), when comparing highest to lowest seroreactivity tertiles. The associations of BKV and MCV with bladder cancer were independent of each other and neither smoking status nor disease stage and grade modified them. Furthermore, no association was observed between seroresponse to JCV and bladder cancer. Therefore, we conclude that BKV and MCV polyomavirus infection could be related to an increased bladder cancer risk.

Single photon emission from site-controlled InAs quantum dots grown on GaAs(001) patterned substrates

We present a fabrication method to produce site-controlled and regularly spaced InAs/GaAs quantum dots for applications in quantum optical information devices. The high selectivity of our epitaxial regrowth procedure can be used to allocate the quantum dots only in positions predefined by ex-situ local oxidation atomic force nanolithography. The quantum dots obtained following this fabrication process present a high optical quality which we have evaluated by microphotoluminescence and photon correlation experiments.

Site-controlled lateral arrangements of InAs quantum dots grown on GaAs(001) patterned substrates by atomic force microscopy local oxidation nanolithography

In this work, we present a fabrication process that combines atomic force microscopy (AFM) local oxidation nanolithography and molecular beam epitaxy (MBE) growth techniques in order to control both the nucleation site and number of InAs quantum dots (QDs) inside different motifs printed on GaAs(001) substrates. We find that the presence of B-type slopes (As terminated) inside the pattern motifs is the main parameter for controlling the selectivity of the pattern for InAs growth. We demonstrate that either single InAs QDs or multiple InAs QDs in a lateral arrangement (LQDAs) can be obtained, with a precise control in their position and QD number, simply by varying the fabricated oxide length along the [110] direction.