Human natural killer (NK) cells in lymphoid tissues can be categorized into three subsets: CD56(bright)CD16(+), CD56(dim)CD16(+) and CD69(+)CXCR6(+) lymphoid tissue-resident (lt)NK cells. How the... Show moreHuman natural killer (NK) cells in lymphoid tissues can be categorized into three subsets: CD56(bright)CD16(+), CD56(dim)CD16(+) and CD69(+)CXCR6(+) lymphoid tissue-resident (lt)NK cells. How the three subsets are functionally and developmentally related is currently unknown. Therefore, we performed single-cell RNA sequencing combined with oligonucleotide-conjugated antibodies against CD56, CXCR6, CD117 and CD34 on fresh bone marrow NK cells. A minor CD56(dim)GzmK(+) subset was identified that shared features with CD56(bright) and CD56(dim)GzmK(-) NK cells based on transcriptome, phenotype (NKG2A(high)CD16(low)KLRG1(high)TIGIT(high)) and functional analysis in bone marrow and blood, supportive for an intermediate subset. Pseudotime analysis positioned CD56(bright), CD56(dim)GzmK(+) and CD56(dim)GzmK(-) cells in one differentiation trajectory, while ltNK cells were developmentally separated. Integrative analysis with bone marrow cells from the Human Cell Atlas did not demonstrate a developmental connection between CD34(+) progenitor and NK cells, suggesting absence of early NK cell stages in bone marrow. In conclusion, single-cell transcriptomics provide new insights on development and differentiation of human NK cells. Show less
Human natural killer (NK) cells in lymphoid tissues can be categorized into three subsets: CD56(bright)CD16(+), CD56(dim)CD16(+) and CD69(+)CXCR6(+) lymphoid tissue-resident (lt)NK cells. How the... Show moreHuman natural killer (NK) cells in lymphoid tissues can be categorized into three subsets: CD56(bright)CD16(+), CD56(dim)CD16(+) and CD69(+)CXCR6(+) lymphoid tissue-resident (lt)NK cells. How the three subsets are functionally and developmentally related is currently unknown. Therefore, we performed single-cell RNA sequencing combined with oligonucleotide-conjugated antibodies against CD56, CXCR6, CD117 and CD34 on fresh bone marrow NK cells. A minor CD56(dim)GzmK(+) subset was identified that shared features with CD56(bright) and CD56(dim)GzmK(-) NK cells based on transcriptome, phenotype (NKG2A(high)CD16(low)KLRG1(high)TIGIT(high)) and functional analysis in bone marrow and blood, supportive for an intermediate subset. Pseudotime analysis positioned CD56(bright), CD56(dim)GzmK(+) and CD56(dim)GzmK(-) cells in one differentiation trajectory, while ltNK cells were developmentally separated. Integrative analysis with bone marrow cells from the Human Cell Atlas did not demonstrate a developmental connection between CD34(+) progenitor and NK cells, suggesting absence of early NK cell stages in bone marrow. In conclusion, single-cell transcriptomics provide new insights on development and differentiation of human NK cells. Show less
Human natural killer (NK) cells in lymphoid tissues can be categorized into three subsets: CD56(bright)CD16(+), CD56(dim)CD16(+) and CD69(+)CXCR6(+) lymphoid tissue-resident (lt)NK cells. How the... Show moreHuman natural killer (NK) cells in lymphoid tissues can be categorized into three subsets: CD56(bright)CD16(+), CD56(dim)CD16(+) and CD69(+)CXCR6(+) lymphoid tissue-resident (lt)NK cells. How the three subsets are functionally and developmentally related is currently unknown. Therefore, we performed single-cell RNA sequencing combined with oligonucleotide-conjugated antibodies against CD56, CXCR6, CD117 and CD34 on fresh bone marrow NK cells. A minor CD56(dim)GzmK(+) subset was identified that shared features with CD56(bright) and CD56(dim)GzmK(-) NK cells based on transcriptome, phenotype (NKG2A(high)CD16(low)KLRG1(high)TIGIT(high)) and functional analysis in bone marrow and blood, supportive for an intermediate subset. Pseudotime analysis positioned CD56(bright), CD56(dim)GzmK(+) and CD56(dim)GzmK(-) cells in one differentiation trajectory, while ltNK cells were developmentally separated. Integrative analysis with bone marrow cells from the Human Cell Atlas did not demonstrate a developmental connection between CD34(+) progenitor and NK cells, suggesting absence of early NK cell stages in bone marrow. In conclusion, single-cell transcriptomics provide new insights on development and differentiation of human NK cells. Show less
Homberg, D.A.L. van den; Kwast, R.V.C.T. van der; Quax, P.H.A.; Nossent, A.Y. 2022
N-6-methyladenosine (m6A) is the most prevalent post-transcriptional RNA modification in eukaryotic cells. The modification is reversible and can be dynamically regulated by writer and eraser... Show moreN-6-methyladenosine (m6A) is the most prevalent post-transcriptional RNA modification in eukaryotic cells. The modification is reversible and can be dynamically regulated by writer and eraser enzymes. Alteration in the levels of these enzymes can lead to changes in mRNA stability, alternative splicing or microRNA processing, depending on the m6A-binding proteins. Dynamic regulation of mRNA m6A methylation after ischemia and hypoxia influences mRNA stability, alternative splicing and translation, contributing to heart failure. In this study, we studied vasoactive microRNA m6A methylation in fibroblasts and examined the effect of hypoxia on microRNAs methylation using m6A immunoprecipitation. Of the 19 microRNAs investigated, at least 16 contained m6A in both primary human fibroblasts and a human fibroblast cell line, suggesting vasoactive microRNAs are commonly m6A methylated in fibroblasts. More importantly, we found that mature microRNA m6A levels increased upon subjecting cells to hypoxia. By silencing different m6A writer and eraser enzymes followed by m6A immunoprecipitation, we identified METTL4, an snRNA m6A methyltransferase, to be predominantly responsible for the increase in m6A modification. Moreover, by using m6A-methylated microRNA mimics, we found that microRNA m6A directly affects downstream target mRNA repression efficacy. Our findings highlight the regulatory potential of the emerging field of microRNA modifications. Show less
Ingen, E. van; Homberg, D.A.L. van den; Bent, M.L. van der; Mei, H.L.; Papac-Milicevic, N.; Kremer, V.; ... ; Nossent, A.Y. 2021
We have previously shown that C/D box small nucleolar RNAs (snoRNAs) transcribed from the DLK1-DIO3 locus on human chromosome 14 (14q32) are associated with cardiovascular disease. DLK1-DIO3... Show moreWe have previously shown that C/D box small nucleolar RNAs (snoRNAs) transcribed from the DLK1-DIO3 locus on human chromosome 14 (14q32) are associated with cardiovascular disease. DLK1-DIO3 snoRNAs are 'orphan snoRNAs' that have no known targets. We aimed to identify RNA targets and elucidate the mechanism-of-action of human SNORD113-6 (AF357425 in mice). As AF357425-knockout cells were non-viable, we induced overexpression or inhibition of AF357425 in primary murine fibroblasts and performed RNA-Seq. We identified several pre-mRNAs with conserved AF357425/SNORD113-6 D'-seed binding sites in the last exon/3' untranslated region (3'UTR), which directed pre-mRNA processing and splice-variant-specific protein expression. We also pulled down the snoRNA-associated methyltransferase fibrillarin from AF357425-High versus AF357425-Low fibroblast lysates, followed by RNA isolation, ribosomal RNA depletion and RNA-Seq. Identifying mostly mRNAs, we subjected these to PANTHER pathway analysis and observed enrichment for genes in the integrin pathway. We confirmed 2'O-ribose methylation in six integrin pathway mRNAs (MAP2K1, ITGB3, ITGA7, PARVB, NTN4 and FLNB). Methylation and mRNA expressions were decreased while mRNA degradation was increased under AF357425/SNORD113-6 inhibition in both murine and human primary fibroblasts, but effects on protein expression were more ambiguous. Integrin signalling is crucial for cell-cell and cell-matrix interactions, and correspondingly, we observed altered human primary arterial fibroblast function upon SNORD113-6 inhibition. Show less
