Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single-cell atlas of circulating immune cells reveals a dynamic landscape over the first two months of age

ABSTRACT: Extremely premature infants (EPI), or those born prior to 30 weeks’ gestation, are highly susceptible to infection and inflammation. The impact of pre- and postnatal exposures on the immune response is poorly understood. We analyzed over 200, 000 circulating immune cells from 100-200L of whole blood collected from 25 donors including longitudinal samples from 10 EPI that were compared to healthy adults and to cord blood from term and preterm infants. We performed single-cell RNA-, T- and B-cell receptor sequencing, and phosphoprotein mass cytometry from matched samples and proteomics on dried blood spots from the same donors. Our data defined the trajectory of circulating T-, B-, myeloid and natural killer cells. Peripheral T cell development rapidly progressed over the first month of EPI’s life with an increase in the proportion of naïve CD4+, regulatory, and cycling T cells, accompanied by increased STAT5 signaling. Simultaneously, the transcription of IL2, which is essential for T cell activation and proliferation, increased in the lymphocytes. T cell repertoire diversity, clonality and gene usage increased rapidly over the first 60 days of life in EPI. CD38hi B cells were directly proportional to gestational age at birth. Interestingly, in utero exposure to inflammation (chorioamnionitis) altered the abundance, transcriptome and signaling of circulating T cells and monocytes specifically at 1 month of life in EPIs. Finally, we demonstrate the feasibility of a robust multi-omic longitudinal analysis in EPI from minute amounts of blood, developing a resource for studying the impact of early life exposures on immune development.

ORGANISM(S): Homo sapiens

PROVIDER: GSE271413 | GEO | 2025/02/05

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Genome wide blood DNA methylation measured at birth and age 7 on the EPIC array

Project description:We measured the DNA methylation levels at ~800,000 CpG sites from ethnically admixed children in CBMCs at birth and PBMCs age 7 to study the longitudinal dynamics of methylation marks. We found that self-reported race-dependent methylation levels were conserved over time, which helped to suggest that blood methylation levels are robust to environmental exposures during the first 7 years of life.

2020-06-04 | GSE132181 | GEO

Young infants display heterogeneous serological responses and extensive but reversible transcriptional changes following initial immunizations

Project description:Infants necessitate vaccinations to prevent life-threatening infections. Our understanding of the infant immune responses to routine vaccines remains limited. We analyzed two cohorts of 2-month-old infants before vaccination, one week, and one-month post-vaccination. We report remarkable heterogeneity but limited antibody responses to the different antigens. Whole-blood transcriptome analysis in an initial cohort showed marked overexpression of interferon-stimulated genes (ISGs) and to a lesser extent of inflammation-genes at day 7, which normalized one month post-vaccination. Single-cell RNA sequencing in peripheral blood mononuclear cells from a second cohort identified at baseline a predominantly naive immune landscape including ISGhi cells. On day 7, increased expression of interferon-, inflammation-, and cytotoxicity-related genes were observed in most immune cells, that reverted one month post-vaccination, when a CD8+ ISGhi and cytotoxic cluster and B cells expanded. Antibody responses were associated with baseline frequencies of plasma cells, B-cells, and monocytes, and induction of ISGs at day 7.

2023-11-09 | GSE204716 | GEO

Epigenetic profiling of children with respiratory allergy

Project description:The prevalence of respiratory allergy in children is increasing. Epigenetic changes (e.g. DNA methylation) are plausible underlying molecular mechanisms. Longitudinal birth cohorts are instrumental to study the relation between early-life environmental factors and the development of complex diseases. Our AXA Research Fund and Cefic-LRI supported project explores the hypothesis that chemical exposures during pregnancy can influence the immune system and development of allergy in children. Questionnaire data, as well as cord blood, plus blood and saliva samples at age 11 years, were collected in substudies of two longitudinal birth cohorts in Belgium (FLEHS1 & FLEHS2) and analyzed with Illumina Methylation 450K BeadChips as well as gene targeted iPLEX MassArrays analysis. The project aims to answer the following questions: 1) can we identify specific changes in epigenetic modifications on DNA from allergic compared to not-allergic children; 2) are these allergy-related epigenetic changes a result of chemical exposure during pregnancy; and 3) did the early life exposures leave an epigenetic “mark” that is maintained through childhood. If chemicals exposures and resulting predictive markers of allergic diseases can be detected early, prevention strategies, particularly in children or before pregnancy, could be developed.

2018-02-06 | GSE110128 | GEO

Premature skewing of T cell receptor clonality and delayed memory expansion in HIV-exposed infants

Project description:While preventing vertical HIV transmission has been very successful, HIV-exposed uninfected infants (iHEU) experience an elevated risk to infections compared to HIV-unexposed and uninfected infants (iHUU). Here we present a longitudinal multimodal analysis of infant immune ontogeny that highlights the impact of HIV/ARV exposure. Using mass cytometry, we show alterations in T cell memory differentiation between iHEU and iHUU being significant from week 15 of life. The altered memory T cell differentiation in iHEU was preceded by lower TCR Vβ clonotypic diversity and linked to TCR clonal depletion within the naïve T cell compartment. Compared to iHUU, iHEU had elevated CD56loCD16loPerforin+CD38+CD45RA+FcεRIγ+ NK cells at 1 month postpartum and whose abundance pre-vaccination were predictive of vaccine-induced pertussis and rotavirus antibody responses post 3 months of life. Collectively, HIV/ARV exposure disrupted the trajectory of innate and adaptive immunity from birth which may underlie relative vulnerability to infections in iHEU.

2024-02-23 | GSE256410 | GEO

Antibiotics and Immune Responses study

Project description:Blood collected from infants at week 6 and week 7 of life to profile how the transcriptome is changed following routine early life vaccination. Paired faecal metagenomic data is available for these infants under BioProject PRJNA807448 at the Sequence Read Archive.

2025-01-14 | GSE198276 | GEO

Changes in transcript expression in circulating whole blood resulting from exposure to neurotoxic doses of D-amphetamine or Heat Stroke/Hyperthermia

Project description:These experiments were designed to detect transcript (mRNA) changes in whole circulating blood in animals exposed to D-amphetamine under neurotoxic and non-neurotoxic conditions, or subjected to elevated environmental temperatures that produced a hyperthermia very similar to heat stroke. The study objectives were: 1) to detect transcript changes in blood due to life-threatening hyperthermia produced by elevated environmental temperatures (39°C, produces no or minimal neurotoxicity); 2) detect transcripts that could serve as biomarkers specific for neurotoxic amphetamine exposures and not seen with environmentally-induced hyperthermia; and 3) determine the transcript changes related to the immune system in circulating blood produced by either non-neurotoxic or neurotoxic amphetamine exposures. Amphetamine effects on gene expression are dependent on body temperature and indicate that many significant changes in genes related to the immune system occur, some likely in response to damage, even when animals remain normothermic during amphetamine exposure. Also, hyperthermia alone produces many changes in immune related genes in blood

2015-12-08 | GSE64778 | GEO

Early Angiogenic Proteins Associated with High Risk for Bronchopulmonary Dysplasia and Pulmonary Hypertension in Preterm Infants

Project description:Introduction: Early pulmonary vascular disease in preterm infants is associated with the subsequent development of bronchopulmonary dysplasia (BPD) and pulmonary hypertension (PH), however, mechanisms that contribute to or identify infants with increased susceptibility for BPD and/or PH are incompletely understood. Therefore, we tested if changes in circulating angiogenic peptides during the first week of life are associated with the later development of BPD and/or PH. We further sought to determine alternate peptides and related signalling pathways with the risk for BPD or PH. Methods: We prospectively enrolled infants with gestational age <34 weeks gestation and collected blood samples during their first week of life. BPD and PH were assessed at 36 weeks postmenstrual age. Samples were assayed for each of the 1121 peptides included in the SOMAscanTM technology, with subsequent pathway analysis. Results: Of 102 study infants, 82 had BPD and 13 had PH. Multiple angiogenic proteins (PF-4, VEGF121, ANG-1, BMP10, HGF, ANG2) were associated with the subsequent diagnosis of BPD, and FGF-19, PF-4, CTAP-III and PDGF-AA levels were associated with BPD severity. Early increases in BMP10 was strongly associated with the late risk for BPD and PH. Conclusion: We found that early alterations of circulating angiogenic peptides and others were associated with the subsequent development of BPD. We further identified peptides that were associated with BPD severity and BPD-associated PH, including BMP10. We speculate that proteomic biomarkers during the first week of life may identify infants at risk for BPD and/or PH to enhance care and research.

2020-01-15 | GSE121097 | GEO

Platelet mRNA in response to antiplatelet therapy exposure

Project description:The purpose of this study was to identify changes in platelet mRNA that result from exposure to antiplatelet therapy. A total of 84 healthy volunteers were recruited into a longitudinal study of various antiplatelet exposures with 58 completing all study visits. This was a 5 visit study where each visit was separated by ~ 4 weeks. At each Visit purified platelets using a CD45 negative selection protocol was performed in addition to platelet function testing using light transmittance aggregometry (ADP, EPI, and Collagen) and PFA100 (Col/EPI). After the baseline visit (V1), participants were randomized to receive 81mg/day or 325mg/day aspirin x 4 weeks followed by Visit 2. Participants then crossed over to the alternative dose of aspirin for 4 weeks followed by Visit 3. Between Visits 3 and 4 participants washed out their aspirin for 4 weeks. The final exposure was ticagrelor 90mg twice daily x 4 weeks until Visit 5.

2022-03-14 | GSE158765 | GEO

Systems biological assessment of the temporal dynamics of immunity to a viral infection in the first weeks and months of life

Project description:The dynamics of innate and adaptive immunity to infection in infants remain obscure. Here, we used a multi-omics approach to perform a longitudinal analysis of immunity to SARS-CoV-2 infection in infants and young children in the first weeks and months of life by analyzing blood samples collected before, during, and after infection with Omicron and Non-Omicron variants. Infection stimulated robust antibody titers that, unlike in adults, were stably maintained for >300 days. Antigen-specific memory B cell (MCB) responses were durable for 150 days but waned thereafter. Somatic hypermutation of V-genes in MCB accumulated progressively over 9 months. The innate response was characterized by upregulation of activation markers on blood innate cells, and a plasma cytokine profile distinct from that seen in adults, with no inflammatory cytokines, but an early and transient accumulation of chemokines (CXCL10, IL8, IL-18R1, CSF-1, CX3CL1), and type I IFN. The latter was strongly correlated with viral load, and expression of interferon-stimulated genes (ISGs) in myeloid cells measured by single- cell transcriptomics. Consistent with this, single-cell ATAC-seq revealed enhanced accessibility of chromatic loci targeted by interferon regulatory factors (IRFs) and reduced accessibility of AP-1 targeted loci, as well as traces of epigenetic imprinting in monocytes, during convalescence. Together, these data provide the first snapshot of immunity to infection during the initial weeks and months of life.

2023-10-12 | GSE239787 | GEO

Longitudinal Performance of Epi proColon

Project description:This study will evaluate longitudinal performance of Epi proColon with respect to test positivity, longitudinal adherence to Epi proColon screening, adherence to follow-up colonoscopy and diagnostic yield, as well as assay failure rates.

| 2249389 | ecrin-mdr-crc

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data