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Single-cell RNA sequencing of a PBMC sample collected from a male with 45,X/48,XYYY karyotype

ABSTRACT: We report a 14-year-old boy with mosaic 45,X/48,XYYY karyotype presenting with subtle dysmorphic features and height deficiency, requiring growth hormone therapy. Single-cell RNA sequencing revealed widespread differences in genotype distribution between 45,X and 48,XYYY immune cells, with concordant results at DNA level. Deregulation of predominantly autosomal genes was observed, including TCL1A overexpression in 45,X B-lymphocytes and other known genes associated with hematological malignancies, prompting long-term personalized hemato-oncological surveillance in the reported patient.

PROVIDER: EGAS00001005697 | EGA |

REPOSITORIES: EGA

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2214db0b-98f8-4cb8-9ac3-6def3a146ff6 - samples

Project description:Results of scRNA-seq analysis of a PBMC collected from a male with a mosaic 45,X/48,XYYY karyotype

| EGAD00001008645 | EGA

PBMC proteomics in paediatric obesity

Project description:We isolated cell lysate proteins from PBMCs obtained from 71 children and adolescents (age 5-18) with normal weight, overweight or obesity. Body composition was measured using bioelectrical impedance analysis. Nano-electrospray liquid chromatography-tandem mass spectrometry was used to measure protein abundances. Controlling for patient sex, we investigated changes in abundance depending on leukocyte counts and on percentage body fat (PBF). We show protein expression in PBMCs is altered in children with increased PBF, especially in mitochondrial proteins. These obesity-associated changes in are better explained by PBF than by purely height and weight-based metrics, supporting the utility of bioelectrical impedance analysis in obesity research.

2025-07-05 | PXD064634 | Pride

Genotyping of bone marrow from a male patient with refractory cytopenia with multilineage dysplasia and ringed sideroblasts and an abnormal karyotype

Project description:Somatic genetic copy number analysis of bone marrow from a male patient with refractory cytopenia with multilineage dysplasia and ringed sideroblasts and an abnormal karyotype, 45,XY,der(5)t(5;14)(q14;?q24),dic(17;20)(p13;q12),dic(17;20)(p11.2;q12),-18,+22[6]/45,XY,der(5)t(5;14)(q14;?q24),dic(17;20)(20pter->20p11.2::17p1?1.2->17p1?3::20q12->20q10::20q10->20q12::17p11.2->17qter),dic(17;20)(p11.2;q11.2),-18,+22[cp2]/46,XY,der(5)t(5;14)(q14;?q24),der(17)(20pter->20p13::20q11.2->20q11.2::17p13->17qter),der(17)(20pter->20p11.2::20q11.2->20q11.2::17p13->17qter),-18, 20,+22,+r[9] (Case 6, MacKinnon et al 2007, Genes Chr Cancer 46:27-36)

2010-01-09 | E-MEXP-2275 | biostudies-arrayexpress

Label-free quantitative proteomics on Nicotiana benthamiana plasmodesmal proteome following viral infection

Project description:We analyzed the PD-enriched fraction from Turnip mosaic virus (TuMV)-infected Nicotiana benthmiana (N. benthamiana) by using label-free quantitative proteomics of which 100 and 48 were significantly increased and decreased respectively when compared with mock plants.

2017-10-19 | PXD006323 | Pride

Preclinical Validation of a Microarray Method for Full Molecular Karyotyping of Blastomeres in a 24-hour Protocol

Project description:BACKGROUND: Pre-implantation genetic screening (PGS) has been used in an attempt to determine embryonic aneuploidy. Techniques that use new molecular methods to determine the karyotype of an embryo are expanding the scope of PGS. METHODS: We introduce a new method for PGS, termed “Parental Support” (PS), which leverages microarray measurements from parental DNA to “clean” single cell microarray measurements on embryonic cells and explicitly computes confidence in each copy number call. The method distinguishes mitotic and meiotic copy errors, and determines parental source of aneuploidy. RESULTS: Validation with 459 single cells of known karyotype indicated that per-cell false positive and false negative rates are roughly equivalent to the “gold standard” metaphase karyotype. The majority of the cells were run in parallel with a clinical commercial PGS service. Computed confidences were conservative and roughly concordant with accuracy. To examine ploidy in human embryos, the method was then applied to 26 disaggregated cryopreserved cleavage stage embryos, for a total of 134 single blastomeres. Only 23.1% of the embryos were euploid, though 46.2% of embryos were mosaic euploid. Mosaicism affected 57.7% of the embryos. Counts of mitotic and meiotic errors were roughly equivalent. Maternal meiotic trisomy predominated over paternal trisomy, and maternal meiotic trisomies were negatively predictive of mosaic euploid embryos. CONCLUSIONS: We have performed a major preclinical validation of a new method for PGS and found that the technology performs approximately as well as a metaphase karyotype. We also directly measured the mechanism of aneuploidy in cleavage stage human embryos and found high rates and distinct patterns of mitotic and meiotic aneuploidy.

2009-12-04 | GSE19247 | GEO

Modeling sex differences in humans using isogenic induced pluripotent stem cells (RRBS)

Project description:We developed a cellular model to study sex differences in humans. Using somatic cells from a mosaic Kleinefelter patient, we generated isogenic human induced pluripotent stem cell lines with different sex chromosome complements – 47,XXY / 46,XX / 46,XY and 45,X0.

2025-02-01 | GSE173336 | GEO

Modeling sex differences in humans using isogenic induced pluripotent stem cells

2022-11-24 | GSE145079 | GEO

Phenotypically Anchored Transcriptomics of Diverse Agrichemicals Revealed Congruent Pathways and Unique Gene Expression Signatures

Project description:Transcriptomic data for 48 hour post-fertilization (hpf) wildtype zebrafish developmentally exposed to 45 different agrichemicals.

2025-10-31 | GSE303009 | GEO

Modeling sex differences using isogenic human neural progenitor cells

2022-11-24 | GSE145118 | GEO

Intergenerational Regulation of Mosaic Supernumerary Chromosomes: Evidence for a Developmental Correction Mechanism from Clinical and Computational Models

Project description:Objective This study presents a rare case of father-to-offspring mosaic transmission of a supernumerary marker chromosome (SMC) and, through integration of literature analysis and computational modeling, proposes a novel embryonic selection-based regulatory mechanism. Methods Karyotyping and SNP-array were performed on amniotic fluid, cord blood, and parental samples. A systematic review identified 35 additional mosaic SMC transmission cases. Four computational frameworks—agent-based simulation, logistic regression, Bayesian inference, and Markov chain modeling—were used to test the hypothesis of selective regulation during early embryogenesis. Results The father carried a mosaic SMC at 11p11 (57%), transmitted to the fetus (38% in amniotic fluid, 45% in cord blood), with both individuals phenotypically normal and no pathogenic CNVs detected. Literature analysis showed consistent patterns of equal or reduced mosaicism in offspring. Modeling revealed that mild selection pressures could replicate observed retention patterns, supporting a non-random, developmentally regulated mechanism. Conclusion The combined clinical, literature-based, and computational evidence supports a model in which early embryos selectively eliminate SMC+ cells to maintain mosaicism at non-pathogenic levels. This proposed “Shepherd Mechanism” may underlie intergenerational mosaic regulation and provides a theoretical foundation for improved prenatal counseling in mosaic cases.

2025-12-10 | GSE302224 | GEO

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