Joint whole exome sequencing and linkage analysis in a multigenerational family segregating Type 1 Diabetes

Backround: Type 1 diabetes (T1D) is a complex autoimmune disease with a strong familial segregation. On the other hand, the recent and rapid increase in incidence is a proof of the importance of environmental factor in the etiology of disease. Linkage and Genome-wide association studies had revealed almost 60 loci associated with the risk of T1D, explaining about 80% of the total heritability, mostly due to HLA locus. However, many familial T1D cases remains unexplained. Objective: To identify rare variants contributing to T1D susceptibility, we studied a Sardinian family with 9 individuals affected across 3 generations. Methods: We performed exome sequencing in 3 affected members and a healthy individual. In addition, all samples were extensively genotyped using Illumina OmniExpress beadchips for about 750K SNPs. A combined linkage analysis was carried out. Results: This combined approach identified three variants predicted to be damaging that are very rare in the general population (frequency <1%) and that are likely causing the disease

Prev Chronic Dis

BackgroundSchool-based student health screenings identify issues that may affect physical and intellectual development and are an important way to maintain student health. Nonprofit hospitals can provide a unique resource to school districts by assisting in the timely completion of school-based screenings and meet requirements of the Affordable Care Act. This case study describes the collaboration between an academic medical center and a local school district to conduct school-based health screenings.Community ContextPenn State Milton S. Hershey Medical Center and Penn State Hershey PRO Wellness Center collaborated with Lebanon School District to facilitate student health screenings, a need identified in part by a community health needs assessment.MethodsFrom June 2012 through February 2013, district-wide student health screenings were planned and implemented by teams of hospital nursing leadership, school district leadership, and school nurses. In fall 2013, students were screened through standardized procedures for height, weight, scoliosis, vision, and hearing.OutcomesIn 2 days, 3,105 students (67% of all students in the district) were screened. Letters explaining screening results were mailed to parents of all students screened. Debriefing meetings and follow-up surveys for the participating nurses provided feedback for future screenings.InterpretationThe 2-day collaborative screening event decreased the amount of time spent by school nurses in screening students throughout the year and allowed them more time in their role as school wellness champion. Additionally, parents found out early in the school year whether their child needed physician follow-up. Partnerships between school districts and hospitals to conduct student health screenings are a practical option for increasing outreach while satisfying community needs.26513441PMC465111

An integrated approach shows different use of water resources from Mediterranean maquis species in a coastal dune ecosystem

An integrated approach has been used to analyse the dependence of three Mediterranean species, A. unedo L., Q. ilex L., and P. latifolia L. co-occurring in a coastal dune ecosystem on two different water resources: groundwater and rainfed upper soil layers. The approach included leaf level gas exchanges, sap flow measurements and structural adaptations between 15 May and 31 July 2007. During this period it was possible to capture different species-specific response patterns to an environment characterized by a sandy soil, with a low water retention capacity, and the presence of a water table. The latter did not completely prevent the development of a drought response and, combined with previous studies in the same area, response differences between species have been partially attributed to different root distributions. Sap flow of A. unedo decreased rapidly with the decline of soil water content, while that of Q. ilex decreased only moderately. Midday leaf water potential of P. latifolia and A. unedo ranged between 122.2 and 122.7MPa throughout the measuring period, while in Q. ilex it decreased down to 123.4MPa at the end of the season. A. unedo was the only species that responded to drought with a decrease of its leaf area to sapwood area ratio from 23.9\ub11.2 (May) to 15.2\ub11.5 (July). While A. unedo also underwent an almost stepwise loss on hydraulic conductivity, such a loss did not occur for Q. ilex, whereas P. latifolia was able to slightly increase its hydraulic conducitivity. These differences show how different plant compartments coordinate differently between species in their responses to drought. The different responses appear to be mediated by different root distributions of the species and their relative resistances to drought are likely to depend on the duration of the periods in which water remains extractable in the upper soil layers

Single-cell Multiomics Analysis of Myelodysplastic Syndromes and Clinical Response to Hypomethylating Therapy

Multiomics; Myelodysplastic syndromes; Hypomethylating therapyMultiómica; Síndromes mielodisplásicos; Terapia hipometilanteMultiòmica; Síndromes mielodisplàstics; Teràpia hipometilantAlterations in epigenetic marks, such as DNA methylation, represent a hallmark of cancer that has been successfully exploited for therapy in myeloid malignancies. Hypomethylating agents (HMA), such as azacitidine, have become standard-of-care therapy to treat myelodysplastic syndromes (MDS), myeloid neoplasms that can evolve into acute myeloid leukemia. However, our capacity to identify who will respond to HMAs, and the duration of response, remains limited. To shed light on this question, we have leveraged the unprecedented analytic power of single-cell technologies to simultaneously map the genome and immunoproteome of MDS samples throughout clinical evolution. We were able to chart the architecture and evolution of molecular clones in precious paired bone marrow MDS samples at diagnosis and posttreatment to show that a combined imbalance of specific cell lineages with diverse mutational profiles is associated with the clinical response of patients with MDS to hypomethylating therapy. Significance: MDS are myeloid clonal hemopathies with a low 5-year survival rate, and approximately half of the cases do not respond to standard HMA therapy. Our innovative single-cell multiomics approach offers valuable biological insights and potential biomarkers associated with the demethylating agent efficacy. It also identifies vulnerabilities that can be targeted using personalized combinations of small drugs and antibodies.We thank CERCA Programme/Generalitat de Catalunya for institutional support. The Secretariat for Universities and Research of the Ministry of Business and Knowledge of the Government of Catalonia has provided funding to M. Esteller (2017 SGR1080 and 2021 SGR01494) and F. Solé (2017 SGR288 and 2021 SGR00560). M. Esteller has also received funding from the Spanish Ministry of Science and Innovation MCIN/AEI/10.13039/501100011033/EDRF “A way to make Europe” (RTI2018-094049-B-I00 and PID2021-125282OB-I00), Cellex Foundation (CEL007) and “la Caixa” Foundation (LCF/PR/HR22/00732). F. Solé has also received funding from the Instituto de Salud Carlos III (ISCIII), Spanish Ministry of Economy and Competitiveness (PI/17/00575 and PI 20/00531) and AECC/ISCIII TRANSCAN (AC18/000002). I. Campillo-Marcos is funded by a Juan de la Cierva-Formación fellowship from the Spanish Ministry of Science and Innovation MCIN/AEI/10.13039/501100011033 NextGenerationEU/PRTR (FJC2020-044658-I). G. Ferrer is the recipient of a Marie Skłodowska-Curie Action individual fellowship (H2020-MSCA-IF-2019-896403). We also thank Gema Fuerte (Mission Bio) for her support during sample processing and analysis

Glioblastoma cell fate is differentially regulated by the microenvironments of the tumour bulk and infiltrative margin

Glioblastoma recurrence originates from invasive cells at the tumour margin that escape surgical debulking, but their biology remains poorly understood. Here we generated three somatic mouse models recapitulating the main glioblastoma driver mutations to characterise margin cells. We find that, regardless of genetics, tumours converge on a common set of neural- like cellular states. However, bulk and margin display distinct neurogenic patterns and immune microenvironments. The margin is immune-cold and preferentially follows developmental-like trajectories to produce astrocyte-like cells. In contrast, injury-like programmes dominate in the bulk, are associated with immune infiltration and generate lowly-proliferative injured neural progenitor-like (iNPCs) cells. In vivo label-retention approaches further demonstrate that iNPCs account for a significant proportion of dormant glioblastoma cells and are induced by interferon signalling within T-cell niches. These findings indicate that tumour region is a major determinant of glioblastoma cell fate and therapeutic vulnerabilities identified in bulk may not extend to the margin residuum

Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data

Many functional analysis tools have been developed to extract functional and mechanistic insight from bulk transcriptome data. With the advent of single-cell RNA sequencing (scRNA-seq), it is in principle possible to do such an analysis for single cells. However, scRNA-seq data has characteristics such as drop-out events and low library sizes. It is thus not clear if functional TF and pathway analysis tools established for bulk sequencing can be applied to scRNA-seq in a meaningful way.To address this question, we perform benchmark studies on simulated and real scRNA-seq data. We include the bulk-RNA tools PROGENy, GO enrichment, and DoRothEA that estimate pathway and transcription factor (TF) activities, respectively, and compare them against the tools SCENIC/AUCell and metaVIPER, designed for scRNA-seq. For the in silico study, we simulate single cells from TF/pathway perturbation bulk RNA-seq experiments. We complement the simulated data with real scRNA-seq data upon CRISPR-mediated knock-out. Our benchmarks on simulated and real data reveal comparable performance to the original bulk data. Additionally, we show that the TF and pathway activities preserve cell type-specific variability by analyzing a mixture sample sequenced with 13 scRNA-seq protocols. We also provide the benchmark data for further use by the community.Our analyses suggest that bulk-based functional analysis tools that use manually curated footprint gene sets can be applied to scRNA-seq data, partially outperforming dedicated single-cell tools. Furthermore, we find that the performance of functional analysis tools is more sensitive to the gene sets than to the statistic used

Targeting lymphoid-derived IL-17 signaling to delay skin aging

Skin aging is characterized by structural and functional changes that contribute to age-associated frailty. This probably depends on synergy between alterations in the local niche and stem cell-intrinsic changes, underscored by proinflammatory microenvironments that drive pleotropic changes. The nature of these age-associated inflammatory cues, or how they affect tissue aging, is unknown. Based on single-cell RNA sequencing of the dermal compartment of mouse skin, we show a skew towards an IL-17-expressing phenotype of T helper cells, γδ T cells and innate lymphoid cells in aged skin. Importantly, in vivo blockade of IL-17 signaling during aging reduces the proinflammatory state of the skin, delaying the appearance of age-related traits. Mechanistically, aberrant IL-17 signals through NF-κB in epidermal cells to impair homeostatic functions while promoting an inflammatory state. Our results indicate that aged skin shows signs of chronic inflammation and that increased IL-17 signaling could be targeted to prevent age-associated skin ailments.© 2023. The Author(s)

Identification of a 3-gene model as a powerful diagnostic tool for the recognition of ALK-negative anaplastic large-cell lymphoma

16siAnaplastic large-cell lymphomas (ALCLs) are a group of clinically and biologically heterogeneous diseases including the ALK+ and ALK+ systemic forms. Whereas ALK+ ALCLs are molecularly characterized and can be readily diagnosed, specific immunophenotypic or genetic features to define ALK- ALCL are missing, and their distinction from other T-cell non-Hodgkin lymphomas (T-NHLs) remains controversial. In the present study, we undertook a transcriptional profiling meta-analysis of 309 cases, including ALCL and other primary T-NHL samples. Pathway discovery and prediction analyses defined a minimum set of genes capable of recognizing ALK- ALCL. Application of quantitative RT-PCR in independent datasets from cryopreserved and formalin-fixed paraffin-embedded samples validated a 3-gene model (TNFRSF8, BATF3, and TMOD1) able to successfully separate ALK- ALCL from peripheral T-cell lymphoma not otherwise specified, with overall accuracy near 97%. In conclusion, our data justify the possibility of translating quantitative RT-PCR protocols to routine clinical settings as a new approach to objectively dissect T-NHL and to select more appropriate therapeutic protocols. © 2012 by The American Society of Hematology.openopenAgnelli L.; Mereu E.; Pellegrino E.; Limongi T.; Kwee I.; Bergaggio E.; Ponzoni M.; Zamo A.; Iqbal J.; Piccaluga P.P.; Neri A.; Chan W.C.; Pileri S.; Bertoni F.; Inghirami G.; Piva R.Agnelli, L.; Mereu, E.; Pellegrino, E.; Limongi, T.; Kwee, I.; Bergaggio, E.; Ponzoni, M.; Zamo, A.; Iqbal, J.; Piccaluga, P. P.; Neri, A.; Chan, W. C.; Pileri, S.; Bertoni, F.; Inghirami, G.; Piva, R