The importance of data transformation in RNA-Seq preprocessing for bladder cancer subtyping

Bladder cancer; Molecular subtypes; RNA sequencingCáncer de vejiga; Subtipos moleculares; Secuenciación de ARNCàncer de bufeta; Subtipus moleculars; Seqüenciació de l'ARNObjective RNA-Seq provides an accurate quantification of gene expression levels and it is widely used for molecular subtype classification in cancer, with special importance in prognosis. However, the reliability and validity of these analyses can significantly be influenced by how data are processed. In this study we evaluate how RNA-Seq preprocessing methods influence molecular subtype classification in bladder cancer. By benchmarking various aligners, quantifiers and methods of normalization and transformation, we stress the importance of preprocessing choices for accurate and consistent subtype classification. Results Our findings highlight that log-transformation plays a crucial role in centroid-based classifiers such as consensusMIBC and TCGAclas, while distribution-free algorithms like LundTax offer robustness to preprocessing variations. Non log-transformed data resulted in low classification rates and poor agreement with reference classifications in consensusMIBC and TCGAclas classifiers. Additionally, LundTax consistently demonstrated better separation among subtypes, compared to consensusMIBC and TCGAclas, regardless of preprocessing methods. Nonetheless, the study is limited by the lack of a true reference for objective assessment of the accuracy of the assigned subtypes. Hence, future work will be necessary to determine the robustness and scalability of the obtained results.The work was supported by the following grants and agencies: Project PI19/00004 and PI22/00171, funded by Instituto de Salud Carlos III (ISCIII) and co-funded by the European Union; a grant from FIS-ISCIII (FI20/00095), 2021SGR00042 by Generalitat de Catalunya

MicroRNA expression profiling and DNA methylation signature for deregulated microRNA in cutaneous T-cell lymphoma

MicroRNAs usually regulate gene expression negatively, and aberrant expression has been involved in the development of several types of cancers. Microarray profiling of microRNA expression was performed to define a microRNA signature in a series of mycosis fungoides tumor stage (MFt, n=21) and CD30+ primary cutaneous anaplastic large cell lymphoma (CD30+ cALCL, n=11) samples in comparison with inflammatory dermatoses (ID, n=5). Supervised clustering confirmed a distinctive microRNA profile for cutaneous T-cell lymphoma (CTCL) with respect to ID. A 40 microRNA signature was found in MFt including upregulated onco-microRNAs (miR-146a, miR-142-3p/5p, miR-21, miR-181a/b, and miR-155) and downregulated tumor-suppressor microRNAs (miR-200ab/429 cluster, miR-10b, miR-193b, miR-141/200c, and miR-23b/27b). Regarding CD30+ cALCL, 39 differentially expressed microRNAs were identified. Particularly, overexpression of miR-155, miR-21, or miR-142-3p/5p and downregulation of the miR-141/200c clusters were observed. DNA methylation in microRNA gene promoters, as expression regulatory mechanism for deregulated microRNAs, was analyzed using Infinium 450K array and approximately one-third of the differentially expressed microRNAs showed significant DNA methylation differences. Two different microRNA methylation signatures for MFt and CD30+ cALCL were found. Correlation analysis showed an inverse relationship for microRNA promoter methylation and microRNA expression. These results reveal a subgroup-specific epigenetically regulated microRNA signatures for MFt and CD30+ cALCL patients

A Systematic Review of Gene Expression Studies in Critically Ill Patients with Sepsis and Community-Acquired Pneumonia

(1) Background: Sepsis is present in nearly 90% of critically ill patients with community-acquired pneumonia (CAP). This systematic review updates the information on studies that have assessed gene expression profiles in critically ill septic patients with CAP. (2) Methods: We searched for studies that satisfied the following criteria: (a) expression profile in critically ill patients with sepsis due to CAP, (b) presence of a control group, and (c) adult patients. Over-representation analysis was performed with clusterProfiler using the Hallmark and Reactome collections. (3) Results: A total of 4312 differentially expressed genes (DEGs) and sRNAs were included in the enrichment analysis. In the Hallmark collection, genes regulated by nuclear factor kappa B in response to tumor necrosis factor, genes upregulated by signal transducer and activator of transcription 5 in response to interleukin 2 stimulation, genes upregulated in response to interferon-gamma, genes defining the inflammatory response, a subgroup of genes regulated by MYC-version 1 (v1), and genes upregulated during transplant rejection were significantly enriched in critically ill septic patients with CAP. Moreover, 88 pathways were identified in the Reactome database. (4) Conclusions: This study summarizes the reported DEGs in critically ill septic patients with CAP and investigates their functional implications. The results highlight the complexity of immune responses during CAP

Dynamics of Gene Expression Profiling and Identification of High-Risk Patients for Severe COVID-19

The clinical manifestations of SARS-CoV-2 infection vary widely, from asymptomatic infection to the development of acute respiratory distress syndrome (ARDS) and death. The host response elicited by SARS-CoV-2 plays a key role in determining the clinical outcome. We hypothesized that determining the dynamic whole blood transcriptomic profile of hospitalized adult COVID-19 patients and characterizing the subgroup that develops severe disease and ARDS would broaden our understanding of the heterogeneity in clinical outcomes. We recruited 60 hospitalized patients with RT-PCR-confirmed SARS-CoV-2 infection, among whom 19 developed ARDS. Peripheral blood was collected using PAXGene RNA tubes within 24 h of admission and on day 7. There were 2572 differently expressed genes in patients with ARDS at baseline and 1149 at day 7. We found a dysregulated inflammatory response in COVID-19 ARDS patients, with an increased expression of genes related to pro-inflammatory molecules and neutrophil and macrophage activation at admission, in addition to an immune regulation loss. This led, in turn, to a higher expression of genes related to reactive oxygen species, protein polyubiquitination, and metalloproteinases in the latter stages. Some of the most significant differences in gene expression found between patients with and without ARDS corresponded to long non-coding RNA involved in epigenetic control

Cluster and Kill: the Use of Clustering-Triggered Emission Materials for Singlet Oxygen Photosensitization in Antimicrobial Photodynamic Therapy

The emergence of light-based technologies is revolutionizing modern medicine and healthcare by enabling precise disease diagnosis and treatment through various luminescent agents and imaging techniques. Despite challenges like biocompatibility, spectral tuning, and synthesis complexity, the primary issue is the aggregation-caused quenching of emission on high concentrations or physiological conditions. In light of these problems, Clustering-Triggered Emission (CTE), which involves the formation of atomic clusters to induce light absorption and the luminescence of unconventional chromophores, represents an all-in-one solution to the challenges identified. Given the potential for CTE materials to behave in ways previously only associated with conventional chromophores, it seems reasonable that highly oxidative reactive oxygen species can be formed from CTE excited states. The results demonstrate that it is possible to transfer the excess energy from the CTE long-lived excited states to molecular oxygen, thereby producing singlet oxygen. It is also noteworthy that over 99.9% of Staphylococcus aureus cells can be eradicated using fluences comparable to those used in traditional systems under violet light irradiation. Uncovering these photophysical properties of CTE opens the door to a revolutionary breakthrough that can disrupt conventional photodynamic therapy and usher in a new era of CTE-based photosensitizers.info:eu-repo/semantics/publishedVersio

Precision Oncology and Systemic Targeted Therapy in Pseudomyxoma Peritonei

Systemic targeted therapy; Pseudomyxoma PeritoneiTeràpia sistèmica dirigida; Pseudomixoma peritoneiTerapia sistémica dirigida; Pseudomixoma peritonealPurpose: Pseudomyxoma peritonei (PMP) is a rare and poorly understood malignant condition characterized by the accumulation of intra-abdominal mucin produced from peritoneal metastases. Currently, cytoreductive surgery remains the mainstay of treatment but disease recurrence and death after relapse frequently occur in patients with PMP. New therapeutic strategies are therefore urgently needed for these patients. Experimental Design: A total of 120 PMP samples from 50 patients were processed to generate a collection of 50 patient-derived organoid (PDO) and xenograft (PDX) models. Whole exome sequencing, immunohistochemistry analyses, and in vitro and in vivo drug efficacy studies were performed. Results: In this study, we have generated a collection of PMP preclinical models and identified druggable targets, including BRAFV600E, KRASG12C, and KRASG12D, that could also be detected in intra-abdominal mucin biopsies of patients with PMP using droplet digital PCR. Preclinical models preserved the histopathological markers from the original patient sample. The BRAFV600E inhibitor encorafenib reduced cell viability of BRAFV600E PMP-PDO models. Proof-of-concept in vivo experiments showed that a systemic treatment with encorafenib significantly reduced tumor growth and prolonged survival in subcutaneous and orthotopic BRAFV600E-PMP-PDX mouse models. Conclusions: Our study demonstrates for the first time that systemic targeted therapies can effectively control PMP tumors. BRAF signaling pathway inhibition represents a new therapeutic opportunity for patients with BRAFV600E PMP who have a poor prognosis. Importantly, our present data and collection of preclinical models pave the way for evaluating the efficacy of other systemic targeted therapies toward extending the promise of precision oncology to patients with PMP.The Project was funded by the PMPNet Research Project, sustained by an Accelerator Award on a project entitled Pseudomyxoma peritonei: building a European multicentric cohort to accelerate new therapeutic perspectives funded by the AECC (GEACC19004PAL; J. Martínez-Quintanilla, D. Cabot and H.G. Palmer), CRUK (A29365; J. Barriuso and O. Aziz) and AIRC (24285; M. Guaglio and M. Deraco). We thank Javier Carmona for revising the cover letter, and Fundación CELLEX for its institutional support. The graphical abstract and schematic representations were created thanks to the BioRender platform. J. Martínez-Quintanilla was granted by an individual fellowship from EU Marie Sklodowska-Curie actions (704319). H.G. Palmer was granted with a Miguel Servet contract (MSII14/ 00037). VHIO would like to acknowledge the Cellex Foundation for providing research facilities and equipment, the CERCA Programme from the Generalitat de Catalunya, the FERO Foundation, the Centro de Investigación Biomédica en Red Cáncer (CIBERONC) and the Agencia Estatal de Investigación for their support on this research as a Center of Excellence Severo Ochoa (CEX2020- 001024-S/AEI/10.13039/501100011033)

Reducing MYC's transcriptional footprint unveils a good prognostic gene signature in melanoma

MYC; Omomyc; MelanomaMYC; Omomyc; MelanomaMYC; Omomyc; MelanomaMYC's key role in oncogenesis and tumor progression has long been established for most human cancers. In melanoma, its deregulated activity by amplification of 8q24 chromosome or by upstream signaling coming from activating mutations in the RAS/RAF/MAPK pathway—the most predominantly mutated pathway in this disease—turns MYC into not only a driver but also a facilitator of melanoma progression, with documented effects leading to an aggressive clinical course and resistance to targeted therapy. Here, by making use of Omomyc, the most characterized MYC inhibitor to date that has just successfully completed a phase I clinical trial, we show for the first time that MYC inhibition in melanoma induces remarkable transcriptional modulation, resulting in severely compromised tumor growth and a clear abrogation of metastatic capacity independently of the driver mutation. By reducing MYC's transcriptional footprint in melanoma, Omomyc elicits gene expression profiles remarkably similar to those of patients with good prognosis, underlining the therapeutic potential that such an approach could eventually have in the clinic in this dismal disease.M.F.Z.-F. was supported by the Juan de la Cierva Programme of the Spanish Ministry of Economy and Competitiveness (IJCI-2014-22403) and Fundació La Marató de TV3 (grant 474/C/2019); F.G. was supported by Spanish Ministry of Science and Innovation Contratos Predoctorales de Formación en Investigación en Salud (PFIS; FI20/00274); I.G.-L. was supported by a grant from the University Teacher Training Program (FPU), Ministry of Universities (FPU20/04812); and S.M.-M. was supported by the Generalitat de Catalunya “Contractació de Personal Investigador Novell (FI-DGR)” 2016 fellowship (2016FI_B 00592). This project was funded by grants from the Spanish Ministry of Science and Innovation (Fondo de Inversión en Salud [FIS] PI19/01277, which also supported I.G.-L. and S.M.-M, and Retos-Colaboración 2019 RTC2019-007067-1), La Marató TV3, the Generalitat de Catalunya AGAUR 2017 grant SGR-3193, and the European Research Council (ERC-PoC II/3079/SYST-iMYC [813132]). We thank the rest of the Soucek laboratory for critical reading of the manuscript, and the personnel at Vall d'Hebron Research Institute (VHIR) High Technology Unit. We acknowledge Vall d'Hebron Institute of Oncology and the Cellex Foundation for providing research facilities and equipment

Genomics reveal local skin immune response key to control sarcoptic mange in Iberian ibex (Capra pyrenaica)

14 páginas, 7 tablas.Sarcoptic mange is an emerging and neglected contagious skin disease caused by the mite Sarcoptes scabiei, affecting humans, domestic animals, and wildlife. Mange is the main disease and a major concern for the management and conservation of populations of Iberian ibex (Capra pyrenaica), a medium-sized mountain ungulate endemic to the Iberian Peninsula and Northern Pyrenees. Differences in host-parasite interaction and host immune response determine mange clinical outcome, but little is known about the related differences in gene expression. This study determined blood and skin gene expressions in S. scabiei-experimentally infested Iberian ibexes.This study was funded by the Ministerio de Economía y Competitividad of the Spanish Government through the research project grants CGL2012- 40043-C02-01, CGL2012-40043-CO2-02 and CGL2016-80543-P. The research activities of JEG, JMP, RCS, FJCM and PF were partially funded by the Andalusian Government (PAIDI: RNM-118 groupPeer reviewe

Cluster and Kill: the Use of Clustering-Triggered Emission Materials for Singlet Oxygen Photosensitization in Antimicrobial Photodynamic Therapy.

The emergence of light-based technologies is revolutionizing modern medicine and healthcare by enabling precise disease diagnosis and treatment through various luminescent agents and imaging techniques. Despite challenges like biocompatibility, spectral tuning, and synthesis complexity, the primary issue is the aggregation-caused quenching of emission on high concentrations or physiological conditions. In light of these problems, Clustering-Triggered Emission (CTE), which involves the formation of atomic clusters to induce light absorption and the luminescence of unconventional chromophores, represents an all-in-one solution to the challenges identified. Given the potential for CTE materials to behave in ways previously only associated with conventional chromophores, it seems reasonable that highly oxidative reactive oxygen species can be formed from CTE excited states. The results demonstrate that it is possible to transfer the excess energy from the CTE long-lived excited states to molecular oxygen, thereby producing singlet oxygen. It is also noteworthy that over 99.9% of Staphylococcus aureus cells can be eradicated using fluences comparable to those used in traditional systems under violet light irradiation. Uncovering these photophysical properties of CTE opens the door to a revolutionary breakthrough that can disrupt conventional photodynamic therapy and usher in a new era of CTE-based photosensitizers

Homologous recombination repair status in metastatic prostate cancer by next-generation sequencing and functional immunofluorescence

Genomics; Immunofluorescence; Prostate cancerGenòmica; Immunofluorescència; Càncer de pròstataGenómica; Inmunofluorescencia; Cáncer de próstataMetastatic prostate cancer (mPC) is enriched for homologous recombination repair (HRR) gene alterations, which have prognostic and predictive value. Routine clinical implementation of next-generation sequencing (NGS) is still limited. We investigated the association between genomic and functional loss of HRR, using NGS and RAD51 immunofluorescence (RAD51-IF) in 219 primary or metastatic biopsies from 187 patients with stage IV prostate cancer. NGS showed frequent genomic alterations in TP53 (40%), AR (15%), PTEN (14%), FOXA1 (12%), MYC (10%), BRCA2 (9%), ATM (8%), and BRCA1 (2%). We pursued RAD51-IF in 206 samples; of those, 139/206 (67%) were evaluable. 21% of samples had RAD51-low score compatible with HRR deficiency (HRD). RAD51-IF showed high sensitivity (71%) and specificity (86%) for BRCA1/2 alterations. Patients with RAD51-low scores experienced longer progression-free survival (PFS) on poly(ADP-ribose) polymerase inhibitors (PARPi) or platinum chemotherapy. RAD51-IF is feasible in routine clinical samples from patients with mPC and is associated with clinically relevant HRR gene alterations.This work was funded by an Impact Award from the Department of Defense CDMRP (PC170510P1) and a grant from AstraZeneca (ESR-21-21360). The funders had no role in the design or conduction of the study and were not involved in the analysis or interpretation of results. CRIS Cancer Foundation (grant TCL_2020-10) and Fundación AECC (LABAE20019MATE) and a Department of Defense Physician Science Award to J.M. (PC220307). S.A.-G. was supported by Instituto de Salud Carlos III (FI19/00280). P.C.M. was supported by an ESMO Translational Research Fellowship, funded by BMS (any views, opinions, findings, conclusions, or recommendations expressed in this material are those solely of the authors and do not necessarily reflect those of ESMO or BMS). I.C.-S. was supported by a Prostate Cancer Foundation YIA (24YOU12). A.L.-G. was supported by an AECC grant (INVES20095LLOP), and V.S. received funding from an ERA PerMed grant (ERAPERMED2019-215). The VHIO authors would like to acknowledge the Spanish State Agency for Research (Agencia Estatal de Investigación) for its financial support as a Center of Excellence Severo Ochoa (CEX2020-001024-S/AEI/10.13039/501100011033), the Cellex Foundation for providing research facilities and equipment, and the CERCA Program from the Generalitat de Catalunya for their support of this research