Bulk RNA sequencing of human pediatric lung cell populations reveals unique transcriptomic signature associated with postnatal pulmonary development

Gautam Bandyopadhyay¹, Matthew G. Jehrio¹, Cameron Baker¹, Soumyaroop Bhattacharya¹, Ravi Misra¹, Heidi L. Huyck¹, ChinYi Chu¹, Jason R. Myers¹, John Ashton¹, Steven Polter¹, Matthew Cochran¹, Timothy Bushnell¹, Jennifer Dutra¹, Philip J. Katzman¹, Gail H. Deutsch, Thomas J. Mariani¹, Gloria Pryhuber¹

¹University of Rochester Medical Center, ^*Corresponding author

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Description Postnatal lung development results in an increasingly functional organ prepared for gas exchange and pathogenic challenges. It is achieved through cellular differentiation and migration. Changes in the tissue architecture during this development process are well-documented and increasing cellular diversity associated with it are reported in recent years. Despite recent progress, transcriptomic and molecular pathways associated with human postnatal lung development are yet to be fully understood. In this study, we investigated gene expression patterns associated with healthy pediatric lung development in four major enriched cell populations (epithelial, endothelial, and nonendothelial mesenchymal cells, along with lung leukocytes) from 1-day-old to 8-yr-old organ donors with no known lung disease. For analysis, we considered the donors in four age groups [less than 30 days old neonates, 30 days to < 1 yr old infants, toddlers (1 to < 2 yr), and children 2 yr and older] and assessed differentially expressed genes (DEG). We found increasing age-associated transcriptional changes in all four major cell types in pediatric lung. Transition from neonate to infant stage showed highest number of DEG compared with the number of DEG found during infant to toddler- or toddler to older children-transitions. Profiles of differential gene expression and further pathway enrichment analyses indicate functional epithelial cell maturation and increased capability of antigen presentation and chemokine-mediated communication. Our study provides a comprehensive reference of gene expression patterns during healthy pediatric lung development that will be useful in identifying and understanding aberrant gene expression patterns associated with early life respiratory diseases. NEW & NOTEWORTHY This study presents postnatal transcriptomic changes in major cell populations in human lung, namely endothelial, epithelial, mesenchymal cells, and leukocytes. Although human postnatal lung development continues through early adulthood, our results demonstrate that greatest transcriptional changes occur in first few months of life during neonate to infant transition. These early transcriptional changes in lung parenchyma are particularly notable for functional maturation and activation of alveolar type II cell genes.

Dataset ID LMEX0000003691

Assay Type RNA-seq

Organism Human

Stages Neonate | Infant | Child | Adult

Sample Count 151

Sample Prep Lmdata:sample_type_sorted_cells

Reference Bandyopadhyay et al. (2024)

File	Description	Size
Cell Sorting Results	Cell sorting results	157.6 KB
Data Table (Normalized Counts)	Normalized counts output from deSeq2 (CPM)	26.8 MB
Data Table (Raw Counts)	Raw counts generated using STAR aligner on gencode 28. See report in RNA Extraction for further details in data processing	5.8 MB
RNA QC	RNA QC (Bioanalyzer results including RIN and concentration)	20.8 KB
RNA-seq QC	RNA-seq QC (GRC post read processing results)	5.8 MB
Sample Metadata	Sample Metadata	24.8 KB

LungMAP ID	Alt ID	Species	Sex	Race	Age	Age Group	GA at Birth	CGA	Weight	Weight Percentile	Cause of Death	Type of Death
LMSP0000000131	D008	Homo sapiens	Female	White	20 months	Child			12.25 kg	86	Trauma - Auto Accident	DBD (after brain death)
LMSP0000000134	D011	Homo sapiens	Female	White	20 months	Child	40 weeks		10.89 kg	53	Anoxic/Hypoxic Brain Injury - Drowning	DBD (after brain death)
LMSP0000000141	D018	Homo sapiens	Female	White	3 years	Child			15 kg	73	Anoxic/Hypoxic Brain Injury - Drowning	DBD (after brain death)
LMSP0000000142	D019	Homo sapiens	Male	White	1 days	Neonate	37 weeks, 3 days	37.43 weeks			Congenital Anomaly - Brain	DCD (circulatory death)
LMSP0000000145	D022	Homo sapiens	Male	Other	2 years	Child			11.79 kg	12	Trauma - Isolated Head Trauma	DBD (after brain death)
LMSP0000000035	D024	Homo sapiens	Male	Other	4 months	Infant			8.62 kg	94	Trauma - Auto Accident	DBD (after brain death)
LMSP0000000152	D031	Homo sapiens	Male	White	7 months	Infant	40 weeks		7.26 kg	7.4	Anoxic/Hypoxic Brain Injury - SIDS	DBD (after brain death)
LMSP0000000157	D036	Homo sapiens	Male	White	8 years	Child			34 kg	89	Trauma - Isolated Head Trauma	DBD (after brain death)
LMSP0000000159	D038	Homo sapiens	Female	Unknown or Not Reported	1 days	Neonate	39 weeks, 3 days	39.57 weeks	2.27 kg	1.2	Congenital Anomaly - Brain	DCD (circulatory death)
LMSP0000000162	D041	Homo sapiens	Male	White	6 days	Neonate	38 weeks, 3 days	39.14 weeks	3.24 kg	33	Anoxic/Hypoxic Brain Injury - Other	DCD (circulatory death)
LMSP0000000164	D043	Homo sapiens	Male	White	21 months	Child			9.8 kg	6.2	Trauma - Isolated Head Trauma	DBD (after brain death)
LMSP0000000165	D044	Homo sapiens	Male	White	6 days	Neonate	40 weeks, 3 days	41.57 weeks	3.63 kg	56	Anoxic/Hypoxic Brain Injury - Neonatal HIE	DCD (circulatory death)
LMSP0000000177	D056	Homo sapiens	Male	White	5 years	Child			22.23 kg	77	Trauma - Auto Accident	DBD (after brain death)
LMSP0000000184	D063	Homo sapiens	Male	African American	16 months	Child			11.2 kg	65	Trauma - Other	DBD (after brain death)
LMSP0000000192	D071	Homo sapiens	Male	White	24 years	Adult			90 kg		Toxin or Drug Exposure	DCD (circulatory death)
LMSP0000000196	D075	Homo sapiens	Male	White	4 months	Infant			6.8 kg	31	Anoxic/Hypoxic Brain Injury - SIDS	DBD (after brain death)
LMSP0000000213	D092	Homo sapiens	Female	African American	2 months	Infant	40 weeks, 3 days	49 weeks	5 kg	42	Anoxic/Hypoxic Brain Injury - SIDS	DBD (after brain death)
LMSP0000001012	D105	Homo sapiens	Female	White	6 months	Infant	40 weeks		8.7 kg	92	Trauma - Auto Accident	DBD (after brain death)
LMSP0000001017	D110	Homo sapiens	Male	Unknown or Not Reported	3 months	Infant	40 weeks, 3 days	58 weeks	7.71 kg	79	Stroke or Intracranial Hemorrhage	DBD (after brain death)
LMSP0000001020	D113	Homo sapiens	Male	African American	5 months	Infant	40 weeks	66.14 weeks	8.3 kg	65	Trauma - Other	DBD (after brain death)
LMSP0000001023	D116	Homo sapiens	Female	African American	40 years	Adult			88 kg		Anoxic/Hypoxic Brain Injury - Other	DBD (after brain death)
LMSP0000001026	D119	Homo sapiens	Male	White	13 months	Child	40 weeks		11.7 kg	91	Infection - Meningitis	DBD (after brain death)
LMSP0000001040	D133	Homo sapiens	Male	African American	11 months	Infant	40 weeks, 3 days	89.57 weeks	10.43 kg	81	Trauma - Fall from Height	DBD (after brain death)
LMSP0000001041	D134	Homo sapiens	Female	White	8 years	Child			27.5 kg	58	Trauma - Auto Accident	DBD (after brain death)
LMSP0000001043	D136	Homo sapiens	Male	White	16 months	Child			8.7 kg	3	Anoxic/Hypoxic Brain Injury - Other	DBD (after brain death)
LMSP0000001050	D143	Homo sapiens	Male	African American	3 months	Infant			6.35 kg	49	Anoxic/Hypoxic Brain Injury - SIDS	DBD (after brain death)

26 of this study's 26 samples were also assayed by 448 other LungMAP studies, across 9 modalities. Click any node to list those studies.

Shared samples by study