A Global Transcriptional Atlas of the Effect of Sleep Deprivation in the Mouse Frontal Cortex

Sleep deprivation (SD) has negative effects on brain function. Sleep problems are prevalent in neurodevelopmental, neurodegenerative and psychiatric disorders. Thus, understanding the molecular consequences of SD is of fundamental importance in neuroscience. In this study, we present the first simultaneous bulk and single-nuclear (sn)RNA sequencing characterization of the effects of SD in the mouse frontal cortex. We show that SD predominantly affects glutamatergic neurons, specifically in layers 4 and 5, and produces isoform switching of thousands of transcripts. At both the global and cell-type specific level, SD has a large repressive effect on transcription, down-regulating thousands of genes and transcripts; underscoring the importance of accounting for the effects of sleep loss in transcriptome studies of brain function. As a resource we provide extensive characterizations of cell types, genes, transcripts and pathways affected by SD; as well as tutorials for data analysis.

Curated single cell multimodal landmark datasets for R/Bioconductor

BACKGROUND

The majority of high-throughput single-cell molecular profiling methods quantify RNA expression; however, recent multimodal profiling methods add simultaneous measurement of genomic, proteomic, epigenetic, and/or spatial information on the same cells. The development of new statistical and computational methods in Bioconductor for such data will be facilitated by easy availability of landmark datasets using standard data classes.

RESULTS

We collected, processed, and packaged publicly available landmark datasets from important single-cell multimodal protocols, including CITE-Seq, ECCITE-Seq, SCoPE2, scNMT, 10X Multiome, seqFISH, and G&T. We integrate data modalities via the MultiAssayExperiment Bioconductor class, document and re-distribute datasets as the SingleCellMultiModal package in Bioconductor's Cloud-based ExperimentHub. The result is single-command actualization of landmark datasets from seven single-cell multimodal data generation technologies, without need for further data processing or wrangling in order to analyze and develop methods within Bioconductor's ecosystem of hundreds of packages for single-cell and multimodal data.

CONCLUSIONS

We provide two examples of integrative analyses that are greatly simplified by SingleCellMultiModal. The package will facilitate development of bioinformatic and statistical methods in Bioconductor to meet the challenges of integrating molecular layers and analyzing phenotypic outputs including cell differentiation, activity, and disease.

Dietary Fatty Acids Contribute to Maintaining the Balance between Pro-Inflammatory and Anti-Inflammatory Responses during Pregnancy

BACKGROUND

During pregnancy, the balance between pro-inflammatory and anti-inflammatory responses is essential for ensuring healthy outcomes. Dietary Fatty acids may modulate inflammation.

METHODS

We investigated the association between dietary fatty acids as profiled on red blood cells membranes and a few pro- and anti-inflammatory cytokines, including the adipokines leptin and adiponectin at ~38 weeks in 250 healthy women.

RESULTS

We found a number of associations, including, but not limited to those of adiponectin with C22:3/C22:4 (coeff -1.44; p = 0.008), C18:1 c13/c14 (coeff 1.4; p = 0.02); endotoxin with C20:1 (coeff -0.9; p = 0.03), C22:0 (coeff -0.4; p = 0.05); MCP-1 with C16:0 (coeff 0.8; p = 0.04); and ICAM-1 with C14:0 (coeff -86.8; p = 0.045). Several cytokines including leptin were associated with maternal body weight (coeff 0.9; p = 2.31 × 10^-5), smoking habits (i.e., ICAM-1 coeff 133.3; p = 0.09), or gestational diabetes (i.e., ICAM-1 coeff 688; p = 0.06).

CONCLUSIONS

In a general cohort of pregnant women, the intake of fatty acids influenced the balance between pro- and anti-inflammatory molecules together with weight gain, smoking habits, and gestational diabetes.

SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor

SUMMARY

SpatialExperiment is a new data infrastructure for storing and accessing spatially-resolved transcriptomics data, implemented within the R/Bioconductor framework, which provides advantages of modularity, interoperability, standardized operations and comprehensive documentation. Here, we demonstrate the structure and user interface with examples from the 10x Genomics Visium and seqFISH platforms, and provide access to example datasets and visualization tools in the STexampleData, TENxVisiumData and ggspavis packages.

AVAILABILITY AND IMPLEMENTATION

The SpatialExperiment, STexampleData, TENxVisiumData and ggspavis packages are available from Bioconductor. The package versions described in this manuscript are available in Bioconductor version 3.15 onwards.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

In PD-1+ human colon cancer cells NIVOLUMAB promotes survival and could protect tumor cells from conventional therapies

BACKGROUND

Colorectal cancer (CRC) is one of the most prevalent and deadly tumors worldwide. The majority of CRC is resistant to anti-programmed cell death-1 (PD-1)-based cancer immunotherapy, with approximately 15% with high-microsatellite instability, high tumor mutation burden, and intratumoral lymphocytic infiltration. Programmed death-ligand 1 (PD-L1)/PD-1 signaling was described in solid tumor cells. In melanoma, liver, and thyroid cancer cells, intrinsic PD-1 signaling activates oncogenic functions, while in lung cancer cells, it has a tumor suppressor effect. Our work aimed to evaluate the effects of the anti-PD-1 nivolumab (NIVO) on CRC cells.

METHODS

In vitro NIVO-treated human colon cancer cells (HT29, HCT116, and LoVo) were evaluated for cell growth, chemo/radiotherapeutic sensitivity, apoptosis, and spheroid growth. Total RNA-seq was assessed in 6-24 hours NIVO-treated human colon cancer cells HT29 and HCT116 as compared with NIVO-treated PES43 human melanoma cells. In vivo mice carrying HT29 xenograft were intraperitoneally treated with NIVO, OXA (oxaliplatin), and NIVO+OXA, and the tumors were characterized for growth, apoptosis, and pERK1/2/pP38. Forty-eight human primary colon cancers were evaluated for PD-1 expression through immunohistochemistry.

RESULTS

In PD-1+ human colon cancer cells, intrinsic PD-1 signaling significantly decreased proliferation and promoted apoptosis. On the contrary, NIVO promoted proliferation, reduced apoptosis, and protected PD-1+ cells from chemo/radiotherapy. Transcriptional profile of NIVO-treated HT29 and HCT116 human colon cancer cells revealed downregulation of BATF2, DRAM1, FXYD3, IFIT3, MT-TN, and TNFRSF11A, and upregulation of CLK1, DCAF13, DNAJC2, MTHFD1L, PRPF3, PSMD7, and SCFD1; the opposite regulation was described in NIVO-treated human melanoma PES43 cells. Differentially expressed genes (DEGs) were significantly enriched for interferon pathway, innate immune, cytokine-mediated signaling pathways. In vivo, NIVO promoted HT29 tumor growth, thus reducing OXA efficacy as revealed through significant Ki-67 increase, pERK1/2 and pP38 increase, and apoptotic cell reduction. Eleven out of 48 primary human colon cancer biopsies expressed PD-1 (22.9%). PD-1 expression is significantly associated with lower pT stage.

CONCLUSIONS

In PD-1+ human colon cancer cells, NIVO activates tumor survival pathways and could protect tumor cells from conventional therapies.

Psychological interventions during COVID pandemic: Telehealth for individuals with cystic fibrosis and caregivers

INTRODUCTION

Coronavirus disease 2019 (COVID-19) emerged in China, leading to worldwide morbidity and mortality, including depression and anxiety. As the pandemic spread throughout Italy, mental health concerns increased for people with cystic fibrosis (pwCF), who are at greater risk. The aim was to pilot a Telehealth Psychological Support Intervention for pwCF and caregivers to reduce stress, depression, and anxiety during the lockdown in Italy in March 2020.

METHODS

This intervention utilized cognitive behavioral skills (e.g., cognitive reframing). Participants included 16 pwCF and 14 parents, who completed four individual telehealth sessions with a psychologist. Stress ratings, Patient Health Questionnaire and General Anxiety Disorder, PHQ-8 and GAD-7, were completed, in addition to Feasibility and Satisfaction ratings.

RESULTS

Ratings of stress significantly decreased from pre- to post-testing for pwCF (paired t(14) = -4.06, p < .01) and parents (paired t = -5.2, p < .001). A large percentage of both groups scored in the clinical range for depression and anxiety at baseline (pwCF: depression/anxiety = 71%; parents: depression = 57%; anxiety = 79%); a large proportion (20%-40%) reported moderate to severe symptomatology. Significant reductions in depression for pwCF were found (pre: M = 8.0 to post: M = 4.7; paired t(14) = 2.8, p < .05) but not anxiety (pre: M = 6.9 to post: M = 5.6, t(14) = 1.2, p = NS-non-significant). Parental depression decreased for parents (pre: M = 6.4 to post: M = 5.1, t(14) = -2.5, p < .05), but not anxiety (pre: M = 8.1 to post: M = 7.9, t(14) = -0.2, p = NS). Feasibility and Satisfaction were positive.

CONCLUSION

This telehealth intervention yielded reductions in stress and depression for participants. Anxiety did not significantly decrease, possibly because COVID was ongoing. This feasible, satisfactory intervention was effective for improving mental health.

Easyreporting simplifies the implementation of Reproducible Research layers in R software

During last years "irreproducibility" became a general problem in omics data analysis due to the use of sophisticated and poorly described computational procedures. For avoiding misleading results, it is necessary to inspect and reproduce the entire data analysis as a unified product. Reproducible Research (RR) provides general guidelines for public access to the analytic data and related analysis code combined with natural language documentation, allowing third-parties to reproduce the findings. We developed easyreporting, a novel R/Bioconductor package, to facilitate the implementation of an RR layer inside reports/tools. We describe the main functionalities and illustrate the organization of an analysis report using a typical case study concerning the analysis of RNA-seq data. Then, we show how to use easyreporting in other projects to trace R functions automatically. This latter feature helps developers to implement procedures that automatically keep track of the analysis steps. Easyreporting can be useful in supporting the reproducibility of any data analysis project and shows great advantages for the implementation of R packages and GUIs. It turns out to be very helpful in bioinformatics, where the complexity of the analyses makes it extremely difficult to trace all the steps and parameters used in the study.

Rates of depression and anxiety in Italian patients with cystic fibrosis and parent caregivers: Implementation of the Mental Health Guidelines

BACKGROUND

Individuals with chronic respiratory conditions are at-risk for depression and anxiety. In the largest mental health screening study of over 6000 people with cystic fibrosis (CF) and 4000 parent caregivers (TIDES, 2014), rates of symptomatology were two to three times higher than in the general population. International guidelines recommend annual screening of mental health. This is the first study to implement these guidelines in one of the largest CF Centers in Italy.

METHODS

All individuals with CF, 12 and older (n = 167) and caregivers of children with CF (n = 186), birth to 18, were screened. Health outcome data were also collected (i.e FEV₁, BMI, pulmonary exacerbations, CF-related diabetes). Prevalence data and associations between psychological symptoms and health outcomes were examined.

RESULTS

A high percentage of patients and parent caregivers reported scored above the clinical cut-off for depression and anxiety (37%-48% of adolescents, 45%-46% of adults, 49%-66% of mothers and fathers). Most scores fell in the mild range, however, over 30% were in the moderate to severe range. Elevations in depression and anxiety were correlated. Adolescents who had more pulmonary exacerbations reported higher anxiety. Adults with recent events of hemoptysis reported higher symptoms of depression.

CONCLUSIONS

Symptoms of depression and anxiety were elevated in both individuals with CF and parents. Implementation of mental health screening was critical for identifying those in need of psychological interventions. These results strongly suggest that mental health should be integrated into physical health care for those with complex, chronic respiratory conditions, including COPD, PCD.

Chromatin and Transcriptional Response to Loss of TBX1 in Early Differentiation of Mouse Cells

The T-box transcription factor TBX1 has critical roles in the cardiopharyngeal lineage and the gene is haploinsufficient in DiGeorge syndrome, a typical developmental anomaly of the pharyngeal apparatus. Despite almost two decades of research, if and how TBX1 function triggers chromatin remodeling is not known. Here, we explored genome-wide gene expression and chromatin remodeling in two independent cellular models of Tbx1 loss of function, mouse embryonic carcinoma cells P19Cl6, and mouse embryonic stem cells (mESCs). The results of our study revealed that the loss or knockdown of TBX1 caused extensive transcriptional changes, some of which were cell type-specific, some were in common between the two models. However, unexpectedly we observed only limited chromatin changes in both systems. In P19Cl6 cells, differentially accessible regions (DARs) were not enriched in T-BOX binding motifs; in contrast, in mESCs, 34% (n = 47) of all DARs included a T-BOX binding motif and almost all of them gained accessibility in Tbx1 -/- cells. In conclusion, despite a clear transcriptional response of our cell models to loss of TBX1 in early cell differentiation, chromatin changes were relatively modest.

HiCeekR: A Novel Shiny App for Hi-C Data Analysis

The High-throughput Chromosome Conformation Capture (Hi-C) technique combines the power of the Next Generation Sequencing technologies with chromosome conformation capture approach to study the 3D chromatin organization at the genome-wide scale. Although such a technique is quite recent, many tools are already available for pre-processing and analyzing Hi-C data, allowing to identify chromatin loops, topological associating domains and A/B compartments. However, only a few of them provide an exhaustive analysis pipeline or allow to easily integrate and visualize other omic layers. Moreover, most of the available tools are designed for expert users, who have great confidence with command-line applications. In this paper, we present HiCeekR (https://github.com/lucidif/HiCeekR), a novel R Graphical User Interface (GUI) that allows researchers to easily perform a complete Hi-C data analysis. With the aid of the Shiny libraries, it integrates several R/Bioconductor packages for Hi-C data analysis and visualization, guiding the user during the entire process. Here, we describe its architecture and functionalities, then illustrate its capabilities using a publicly available dataset.

Shank3 modulates sleep and expression of circadian transcription factors

Autism Spectrum Disorder (ASD) is the most prevalent neurodevelopmental disorder in the United States and often co-presents with sleep problems. Sleep problems in ASD predict the severity of ASD core diagnostic symptoms and have a considerable impact on the quality of life of caregivers. Little is known, however, about the underlying molecular mechanisms of sleep problems in ASD. We investigated the role of Shank3, a high confidence ASD gene candidate, in sleep architecture and regulation. We show that mice lacking exon 21 of Shank3 have problems falling asleep even when sleepy. Using RNA-seq we show that sleep deprivation increases the differences in prefrontal cortex gene expression between mutants and wild types, downregulating circadian transcription factors Per3, Bhlhe41, Hlf, Tef, and Nr1d1. Shank3 mutants also have trouble regulating wheel-running activity in constant darkness. Overall, our study shows that Shank3 is an important modulator of sleep and clock gene expression.

Effects of Lumacaftor/Ivacaftor on physical activity and exercise tolerance in three adults with cystic fibrosis

The combination of the corrector lumacaftor with the potentiator ivacaftor has been approved for treatment of cystic fibrosis (CF) patients homozygous for the Phe508del CFTR mutation. There are no reports detailing the effect of lumacaftor-ivacaftor on physical activity (PA) and exercise tolerance. We performed incremental cardiopulmonary exercise testing (CPET) and we assessed PA pre- and post 2 years initiation of lumacaftor-ivacaftor in three CF adults. PA of mild intensity improved by +13% in patient 1, + 84% in patients 2 and + 89% in patient 3. Oxygen uptake increased both at anaerobic threshold and at peak exercise (patient 1 + 33%, patient 2 + 42% and patient 3 + 20%). Daily physical activities and exercise tolerance improved after two years of lumacaftor-ivacaftor therapy.

Distinct Antigen Delivery Systems Induce Dendritic Cells' Divergent Transcriptional Response: New Insights from a Comparative and Reproducible Computational Analysis

Vaccination is the most successful and cost-effective method to prevent infectious diseases. However, many vaccine antigens have poor in vivo immunogenic potential and need adjuvants to enhance immune response. The application of systems biology to immunity and vaccinology has yielded crucial insights about how vaccines and adjuvants work. We have previously characterized two safe and powerful delivery systems derived from non-pathogenic prokaryotic organisms: E2 and fd filamentous bacteriophage systems. They elicit an in vivo immune response inducing CD8+ T-cell responses, even in absence of adjuvants or stimuli for dendritic cells’ maturation. Nonetheless, a systematic and comparative analysis of the complex gene expression network underlying such activation is missing. Therefore, we compared the transcriptomes of ex vivo isolated bone marrow-derived dendritic cells exposed to these antigen delivery systems. Significant differences emerged, especially for genes involved in innate immunity, co-stimulation, and cytokine production. Results indicate that E2 drives polarization toward the Th2 phenotype, mainly mediated by Irf4, Ccl17, and Ccr4 over-expression. Conversely, fd-scαDEC-205 triggers Th1 T cells’ polarization through the induction of Il12b, Il12rb, Il6, and other molecules involved in its signal transduction. The data analysis was performed using RNASeqGUI, hence, addressing the increasing need of transparency and reproducibility of computational analysis.

Advancements in RNASeqGUI towards a Reproducible Analysis of RNA-Seq Experiments

We present the advancements and novelties recently introduced in RNASeqGUI, a graphical user interface that helps biologists to handle and analyse large data collected in RNA-Seq experiments. This work focuses on the concept of reproducible research and shows how it has been incorporated in RNASeqGUI to provide reproducible (computational) results. The novel version of RNASeqGUI combines graphical interfaces with tools for reproducible research, such as literate statistical programming, human readable report, parallel executions, caching, and interactive and web-explorable tables of results. These features allow the user to analyse big datasets in a fast, efficient, and reproducible way. Moreover, this paper represents a proof of concept, showing a simple way to develop computational tools for Life Science in the spirit of reproducible research.