Cellular and transcriptional diversity over the course of human lactation

Nyquist, Sarah K.; Gao, Patricia; Haining, T. K. J.; Retchin, M. R.; Golan, Yarden; Drake, Riley S.; Kolb, Kellie E.; Mead, Benjamin E.; Ahituv, Nadav; Martinez, Micaela E; Shalek, Alex K.; Berger, Bonnie; Goods, Brittany A.

doi:10.1073/pnas.2121720119

Cited by 26 publications

(39 citation statements)

References 91 publications

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“…Single-cell transcriptomic analysis did not identify a cluster of stem-like cells within our breast milk cell population, nor were we able to isolate any clusters with high expression of the typical stem-like transcription factors, which is in agreement with recent publications ( 30 ). These data are not necessarily contradictory to our flow cytometry and qPCR data.…”

Section: Discussionsupporting

confidence: 92%

“…Our findings are generally aligned with those reported from the scRNA-seq analysis of two donors with gestational diabetes ( 13 ) and a longitudinal scRNA-seq lactation study ( 30 ). Differences observed might be due to the number of cells analyzed, number of donors, and/or our use of fresh rather than frozen samples.…”

Section: Discussionsupporting

confidence: 88%

“…For example, Lee et al (37) demonstrated that fresh peripheral blood mononuclear cells had a higher unique molecular identifier, higher medium genes per cell, and altered scRNA-seq cell clustering compared to cells that were freeze-thawed. Nyquist and colleagues (30) found that freezing breast milk cell samples led to a decrease in quality data and recommend processing fresh or storage at 4°C overnight. These methodological differences enabled our identification of previously unidentified subpopulations: FGFBP1 + lactocytes (cluster 2), PTPRF + lactocytes (cluster 6), and chemotactic epithelial cells (cluster 7; Fig.…”

Section: Discussionmentioning

confidence: 99%

“…( 37 ) demonstrated that fresh peripheral blood mononuclear cells had a higher unique molecular identifier, higher medium genes per cell, and altered scRNA-seq cell clustering compared to cells that were freeze-thawed. Nyquist and colleagues ( 30 ) found that freezing breast milk cell samples led to a decrease in quality data and recommend processing fresh or storage at 4°C overnight.…”

Section: Discussionmentioning

confidence: 99%

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Profiling of mature-stage human breast milk cells identifies six unique lactocyte subpopulations

et al. 2022

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Breast milk is chock-full of nutrients, immunological factors, and cells that aid infant development. Maternal cells are the least studied breast milk component, and their unique properties are difficult to identify using traditional techniques. Here, we characterized the cells in mature-stage breast milk from healthy donors at the protein, gene, and transcriptome levels. Holistic analysis of flow cytometry, quantitative polymerase chain reaction, and single-cell RNA sequencing data identified the predominant cell population as epithelial with smaller populations of macrophages and T cells. Two percent of epithelial cells expressed four stem cell markers: SOX2, TRA-1-60, NANOG, and SSEA4. Furthermore, milk contained six distinct epithelial lactocyte subpopulations, including three previously unidentified subpopulations programmed toward mucosal defense and intestinal development. Pseudotime analysis delineated the differentiation pathways of epithelial progenitors. Together, these data define healthy human maternal breast milk cells and provide a basis for their application in maternal and infant medicine.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionsupporting

confidence: 88%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Profiling of mature-stage human breast milk cells identifies six unique lactocyte subpopulations

et al. 2022

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“…Hence, the mammary gland undergoes dramatic developmental changes during pregnancy and lactation. To investigate mammary gland development, several studies have performed scRNA-seq on epithelial cells of mammary glands [12][13][14][15]. However, the development of mammary glands also requires the interplay between epithelial cells and the cells in the niche, including adipocytes, fibroblasts, and immune cells [16][17][18].…”

Section: Resultsmentioning

confidence: 99%

scCDC: a computational method for gene-specific contamination detection and correction in single-cell and single-nucleus RNA-seq data

Wang

Cen

et al. 2022

Preprint

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In droplet-based single-cell RNA-seq (scRNA-seq) and single-nucleus RNA-seq (snRNA-seq) assays, systematic contamination of ambient RNA molecules biases the estimation of genuine transcriptional levels. To correct the contamination, several computational methods have been developed. However, these methods do not distinguish the contamination-causing genes and thus either under- or over-corrected the contamination in our in-house snRNA-seq data of virgin and lactating mammary glands. Hence, we developed scCDC as the first method that specifically detects the contamination-causing genes and only corrects the expression counts of these genes. Benchmarked against existing methods on synthetic and real scRNA-seq and snRNA-seq datasets, scCDC achieved the best contamination correction accuracy with minimal data alteration. Moreover, scCDC applies to processed scRNA-seq and snRNA-seq data with empty droplets removed. In conclusion, scCDC is a flexible, accurate decontamination method that detects the contamination-causing genes, corrects the contamination, and avoids the over-correction of other genes.

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Gestational age at birth influences protein and RNA content in human milk extracellular vesicles

Vahkal,

Altosaar,

Tremblay

et al. 2023

J of Extracellular Bio

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Human milk extracellular vesicles (HM EVs) are proposed to protect against disease development in infants. This protection could in part be facilitated by the bioactive EV cargo of proteins and RNA. Notably, mothers birth infants of different gestational ages with unique needs, wherein the EV cargo of HM may diverge. We collected HM from lactating mothers within two weeks of a term or preterm birth. Following purification of EVs, proteins and mRNA were extracted for proteomics and sequencing analyses, respectively. Over 2000 protein groups were identified, and over 8000 genes were quantified. The total number of proteins and mRNA did not differ significantly between the two conditions, while functional bioinformatics of differentially expressed cargo indicated enrichment in immunoregulatory cargo for preterm HM EVs. In term HM EVs, significantly upregulated cargo was enriched in metabolism‐related functions. Based on gene expression signatures from HM‐contained single cell sequencing data, we proposed that a larger portion of preterm HM EVs are secreted by immune cells, whereas term HM EVs contain more signatures of lactocyte epithelial cells. Proposed differences in EV cargo could indicate variation in mother's milk based on infants’ gestational age and provide basis for further functional characterisation.

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Cellular and transcriptional diversity over the course of human lactation

Cited by 26 publications

References 91 publications

Profiling of mature-stage human breast milk cells identifies six unique lactocyte subpopulations

Profiling of mature-stage human breast milk cells identifies six unique lactocyte subpopulations

scCDC: a computational method for gene-specific contamination detection and correction in single-cell and single-nucleus RNA-seq data

Gestational age at birth influences protein and RNA content in human milk extracellular vesicles

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