Detection of chromothripsis-like patterns with a custom array platform for chronic lymphocytic leukemia

This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License.-- et al.Chronic lymphocytic leukemia (CLL) is a common disease with highly variable clinical course. Several recurrent chromosomal alterations are associated with prognosis and may guide risk-adapted therapy. We have developed a targeted genome-wide array to provide a robust tool for ascertaining abnormalities in CLL and to overcome limitations of the 4-marker fluorescence in situ hybridization (FISH). DNA from 180 CLL patients were hybridized to the qChip®Hemo array with a high density of probes covering commonly altered loci in CLL (11q22-q23, 13q14, and 17p13), nine focal regions (2p15-p16.1, 2p24.3, 2q13, 2q36.3-q37.1, 3p21.31, 8q24.21, 9p21.3, 10q24.32, and 18q21.32-q21.33) and two larger regions (6q14.1-q22.31 and 7q31.33-q33). Overall, 86% of the cases presented copy number alterations (CNA) by array. There was a high concordance of array findings with FISH (84% sensitivity, 100% specificity); all discrepancies corresponded to subclonal alterations detected only by FISH. A chromothripsis-like pattern was detected in eight cases. Three showed concomitant shattered 5p with gain of TERT along with isochromosome 17q. Presence of 11q loss was associated with shorter time to first treatment (P=0.003), whereas 17p loss, increased genomic complexity, and chromothripsis were associated with shorter overall survival (P<0.001, P=0.001, and P=0.02, respectively). In conclusion, we have validated a targeted array for the diagnosis of CLL that accurately detects, in a single experiment, all relevant CNAs, genomic complexity, chromothripsis, copy number neutral loss of heterozygosity, and CNAs not covered by the FISH panel. This test may be used as a practical tool to stratify CLL patients for routine diagnostics or clinical trials.Supported by: Fondo de Investigaciones Sanitarias, Instituto de Salud Carlos III (ISCIII), Grant numbers: PI11/01177, PI14/00571; Worldwide Cancer Research; Grant number: 12-0142; Marato de TV3; Grant number: TV3-Cancer/2013410; Generalitat de Catalunya Suport Grups de Recerca; Grant number: 2013-SGR-378; Red Tematica de Investigacion Cooperativa en Cancer (RTICC), Grant numbers: RD12/0036/0036, RD12/0036/0023, RD12/0036/0004, RD12/0036/0069; Subprograma Juan de la Cierva, Grant number: JCI-2011-10232; Miguel Servet Contract, Grant number: CP13/00159; the Spanish Ministry of Science and Innovation (MICINN) through the ISCIII —International Cancer Genome Consortium for Chronic Lymphocytic Leukemia (ICGC-CLL Genome Project); Institucio Catalana de Recerca i Estudis Avançats” (ICREA) of the Generalitat de Catalunya; European Regional Development Fund “Una manera de fer Europa”; Alexander von Humboldt Post-doctoral Fellowship.Peer Reviewe

Patient-Derived Multiple Myeloma 3D Models for Personalized Medicine—Are We There Yet?

Funding Information: This work was supported by Fundação para a Ciência e a Tecnologia (FCT), research grant number PTDC/MED-ONC/1215/2021/PT. Funding Information: The authors thank FCT and the Champalimaud Foundation for funding. Publisher Copyright: © 2022 by the authors.Despite the wide variety of existing therapies, multiple myeloma (MM) remains a disease with dismal prognosis. Choosing the right treatment for each patient remains one of the major challenges. A new approach being explored is the use of ex vivo models for personalized medicine. Two-dimensional culture or animal models often fail to predict clinical outcomes. Three-dimensional ex vivo models using patients’ bone marrow (BM) cells may better reproduce the complexity and heterogeneity of the BM microenvironment. Here, we review the strengths and limitations of currently existing patient-derived ex vivo three-dimensional MM models. We analyze their biochemical and biophysical properties, molecular and cellular characteristics, as well as their potential for drug testing and identification of disease biomarkers. Furthermore, we discuss the remaining challenges and give some insight on how to achieve a more biomimetic and accurate MM BM model. Overall, there is still a need for standardized culture methods and refined readout techniques. Including both myeloma and other cells of the BM microenvironment in a simple and reproducible three-dimensional scaffold is the key to faithfully mapping and examining the relationship between these players in MM. This will allow a patient-personalized profile, providing a powerful tool for clinical and research applications.publishersversionpublishe

Actividades experimentais nas escolas através de uma interacção com a universidade

A forma como a ciência é ensinada nas escolas afecta profundamente a percepção que os estudantes têm do mundo que os rodeia e consequentemente a escolha de uma futura carreira nas ciências. Por outro lado, a abertura da escola à comunidade envolvente, proporciona as condições para a sua participação activa na vida escolar, assim como a promoção do sucesso escolar, através da formação integral dos alunos, dotando-os das competências científicas, tecnológicas e sócio-culturais necessárias a sólidas opções futuras. A química como uma ciência de cariz experimental oferece aos estudantes uma melhor compreensão dos conceitos teóricos leccionados. Este trabalho descreve actividades experimentais realizadas no âmbito de um intercâmbio entre a Escola Secundária/3 de Barcelinhos e o Departamento de Química. Os projectos desenvolvidos foram “Museu das Ciências” na disciplina de Área Projecto do 12º ano de escolaridade. A actividade A Ciência na investigação criminal foi baseada nas oficinas apresentadas no projecto Sentidos da Ciência [1]. Estas actividades experimentais executadas em colaboração entre as escolas e a universidade contribuem para uma maior motivação dos alunos, uma formação científica mais sólida e um conhecimento mais integrado

Exploring the reactivity of formylporphyrins with 3-(diethylamino)phenol. Synthesis, spectroscopic properties and singlet oxygen generation of a new porphyrin–rosamine conjugate

The design of novel molecular structures with tunable photophysical properties is an important research field for many applications including optoelectronics, sensing and bioimaging. Porphyrin and rhodamine/rosamine derivatives are among the most studied and relevant chemosensors and imaging probes due to their attractive photophysical properties, such as high absorption coefficients and long emission wavelengths. In this work, we present the synthesis and the structural characterization of a new porphyrin–rosamine conjugate H2P3 and its related triarylmethane precursors H2P1 and H2P2. The photophysical properties of H2P1, H2P2 and H2P3, and their ability to chelate iron(III) and copper(II) ions, were evaluated by absorption and emission spectroscopy. The formation of copper(II) complexes was confirmed by electron paramagnetic resonance (EPR), which also allowed the detection of an intense and stable radical signal for the free-base H2P3. Further studies involving the addition of the 2,2,6,6-tetramethylpiperidine spin trap to derivatives H2P1, H2P2 and H2P3, showed that only H2P3 gives rise to an EPR detectable signal due to a strong generation of singlet oxygen.publishe

Quantitative comparison of DNA methylation assays for biomarker development and clinical applications

DNA methylation patterns are altered in numerous diseases and often correlate with clinically relevant information such as disease subtypes, prognosis and drug response. With suitable assays and after validation in large cohorts, such associations can be exploited for clinical diagnostics and personalized treatment decisions. Here we describe the results of a community-wide benchmarking study comparing the performance of all widely used methods for DNA methylation analysis that are compatible with routine clinical use. We shipped 32 reference samples to 18 laboratories in seven different countries. Researchers in those laboratories collectively contributed 21 locus-specific assays for an average of 27 predefined genomic regions, as well as six global assays. We evaluated assay sensitivity on low-input samples and assessed the assays' ability to discriminate between cell types. Good agreement was observed across all tested methods, with amplicon bisulfite sequencing and bisulfite pyrosequencing showing the best all-round performance. Our technology comparison can inform the selection, optimization and use of DNA methylation assays in large-scale validation studies, biomarker development and clinical diagnostics

Development of bacterial cellulose wound dressings with controlled delivery of vitamin D3

Book of Abstracts of CEB Annual Meeting 2017[Excerpt] Wounds, in particular traumatic (e.g. burns) and chronic ones, are a major cause of morbidity and impaired life quality. They often result in long hospitalization stays, taking up substantial health resources in developed countries. This proposal aims at developing a safe, easy-to-use and nonexpensive approach to efficiently address this problem, by attaining faster and proper wound healing. Recent studies showed that an antimicrobial peptide (AMP), LLKKK18, released from conjugates with dextrin embedded in a Carbopol hydrogel significantly improved burn wound healing. In addition to antimicrobial activity, this peptide stimulates vascularization, thus supporting a faster healing and tissue regeneration[1]. As such, one can hypothesize that a hydrogel comprising drugs that stimulate the expression of LL37 will improve wound healing while keeping the wound area infection-free. This work comprised the approach towards the development of a novel bacterial nanocellulose (BNC) dressing. BNC, already used clinically for the treatment of burn wounds due to the unique properties like high water holding capacity, high crystallinity, ultrafine fiber network, high resistance, high moldability and biocompatibility[2]. In this work BNC will be used as drug carriers for the controlled release of drugs, namely of vitamin D3, an inducer of an endogenous expression of AMP LL37, known for accelerating the wound healing process, and as a protective barrier against exogenous agents (dust, microorganism) that can impair wound healing. [...]info:eu-repo/semantics/publishedVersio

Process enhancement at near neutral pH of a homogeneous photo-Fenton reaction using ferricarboxylate complexes: Application to oxytetracycline degradation

This work demonstrates the application at near neutral pH of a photo-Fenton reaction mediated by ferricarboxylates on the treatment of aqueous solutions containing the antibiotic Oxytetracycline (OTC) under solar irradiation. The formation of a Fe:OTC complex after Fe2+ oxidation to Fe3+, in the presence of H2O2, showed the inconvenience of using the conventional Fe2+/H2O2/UV-Vis process at near neutral pH levels, as the complex is retained in the filter. To overcome this, a Fe3+/Oxalate/UV-Vis or Fe3+/Citrate/H2O2/UV-Vis process was proposed. The higher tendency of Fe3+ to form complexes with carboxylates avoids the formation of Fe:OTC complexes and allows for proper OTC detection along reaction times. The photo-Fenton process itself is improved by the extension of the iron solubility to higher and more practical pH values, by the increase of the quantum yield of Fe2+ production and by presenting stronger radiation absorption at wavelengths up to 580 nm. In this way, process efficiency was evaluated for different variables such as Fe3+ concentration, pH, temperature and irradiance, using a compound parabolic collector (CPC) photoreactor at lab-scale under simulated solar radiation. Reaction rates were compared in the presence of different inorganic anions and humic acids, and in two different real wastewater matrixes. Results obtained in a CPC pilot-scale plant under natural solar light, using an iron/oxalate molar rati

Synthesis of Catechol Derived Rosamine Dyes and Their Reactivity toward Biogenic Amines

Functional organic dyes play a key role in many fields, namely in biotechnology and medical diagnosis. Herein, we report two novel 2,3- and 3,4-dihydroxyphenyl substituted rosamines (3 and 4, respectively) that were successfully synthesized through a microwave-assisted protocol. The best reaction yields were obtained for rosamine 4, which also showed the most interesting photophysical properties, specially toward biogenic amines (BAs). Several amines including n- and t-butylamine, cadaverine, and putrescine cause spectral changes of 4, in UV–Vis and fluorescence spectra, which are indicative of their potential application as an effective tool to detect amines in acetonitrile solutions. In the gas phase, the probe response is more expressive for spermine and putrescine. Additionally, we found that methanolic solutions of rosamine 4 and n-butylamine undergo a pink to yellow color change over time, which has been attributed to the formation of a new compound. The latter was isolated and identified as 5 (9−aminopyronin), whose solutions exhibit a remarkable increase in fluorescence intensity together with a shift toward more energetic wavelengths. Other 9-aminopyronins 6a, 6b, 7a, and 7b were obtained from methanolic solutions of 4 with putrescine and cadaverine, demonstrating the potential of this new xanthene entity to react with primary amines.Financial support from PT national funds (FCT/MCTES, Fundação para a Ciência e a Tecnologia and Ministério da Ciência, Tecnologia e Ensino Superior) through the project PTDC/QUI-QOR/29426/2017. The research team would like to thank the projects UIDB/50006/2020, PTDC/QUI-QIN/28142/2017 and Grant BU263P18 (from the Junta de Castilla y León, Consejería de Educación y Cultura y Fondo Social Europeo). F. M. -S. gratefully acknowledges FCT (Portugal’s Foundation for Science and Technology) within grant DFA/BD/9136/2020. A.M.G.S. and A.L. thank FCT for the program DL 57/2016 – Norma transitória

Carbon on the Northwest European Shelf: Contemporary Budget and Future Influences

A carbon budget for the northwest European continental shelf seas (NWES) was synthesized using available estimates for coastal, pelagic and benthic carbon stocks and flows. Key uncertainties were identified and the effect of future impacts on the carbon budget were assessed. The water of the shelf seas contains between 210 and 230 Tmol of carbon and absorbs between 1.3 and 3.3 Tmol from the atmosphere annually. Off-shelf transport and burial in the sediments account for 60–100 and 0–40% of carbon outputs from the NWES, respectively. Both of these fluxes remain poorly constrained by observations and resolving their magnitudes and relative importance is a key research priority. Pelagic and benthic carbon stocks are dominated by inorganic carbon. Shelf sediments contain the largest stock of carbon, with between 520 and 1600 Tmol stored in the top 0.1 m of the sea bed. Coastal habitats such as salt marshes and mud flats contain large amounts of carbon per unit area but their total carbon stocks are small compared to pelagic and benthic stocks due to their smaller spatial extent. The large pelagic stock of carbon will continue to increase due to the rising concentration of atmospheric CO2, with associated pH decrease. Pelagic carbon stocks and flows are also likely to be significantly affected by increasing acidity and temperature, and circulation changes but the net impact is uncertain. Benthic carbon stocks will be affected by increasing temperature and acidity, and decreasing oxygen concentrations, although the net impact of these interrelated changes on carbon stocks is uncertain and a major knowledge gap. The impact of bottom trawling on benthic carbon stocks is unique amongst the impacts we consider in that it is widespread and also directly manageable, although its net effect on the carbon budget is uncertain. Coastal habitats are vulnerable to sea level rise and are strongly impacted by management decisions. Local, national and regional actions have the potential to protect or enhance carbon storage, but ultimately global governance, via controls on emissions, has the greatest potential to influence the long-term fate of carbon stocks in the northwestern European continental shelf

DNA hypomethylation affects cancer-related biological functions and genes relevant in neuroblastoma pathogenesis

Neuroblastoma (NB) pathogenesis has been reported to be closely associated with numerous genetic alterations. However, underlying DNA methylation patterns have not been extensively studied in this developmental malignancy. Here, we generated microarray-based DNA methylation profiles of primary neuroblastic tumors. Stringent supervised differential methylation analyses allowed us to identify epigenetic changes characteristic for NB tumors as well as for clinical and biological subtypes of NB. We observed that gene-specific loss of DNA methylation is more prevalent than promoter hypermethylation. Remarkably, such hypomethylation affected cancer-related biological functions and genes relevant to NB pathogenesis such as CCND1, SPRR3, BTC, EGF and FGF6. In particular, differential methylation in CCND1 affected mostly an evolutionary conserved functionally relevant 3′ untranslated region, suggesting that hypomethylation outside promoter regions may play a role in NB pathogenesis. Hypermethylation targeted genes involved in cell development and proliferation such as RASSF1A, POU2F2 or HOXD3, among others. The results derived from this study provide new candidate epigenetic biomarkers associated with NB as well as insights into the molecular pathogenesis of this tumor, which involves a marked gene-specific hypomethylation