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Hwang YM, Roper RT, Piekos SN, Enquobahrie DA, Hebert MF, Paquette AG, Baloni P, Price ND, Hood L, Hadlock JJ. Timing of selective serotonin reuptake inhibitor use and risk for preterm birth and related adverse events: with a consideration of the COVID-19 pandemic period. J Matern Fetal Neonatal Med 2024; 37:2313364. [PMID: 38342572 PMCID: PMC11033706 DOI: 10.1080/14767058.2024.2313364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 01/29/2024] [Indexed: 02/13/2024]
Abstract
OBJECTIVE There is uncertainty around the safety of SSRIs for treating depression during pregnancy. Nevertheless, the use of SSRIs has been gradually increasing, especially during the COVID-19 pandemic period. We aimed to (1) characterize maternal depression rate and use of SSRIs in a recent 10-year period, (2) address confounding by indication, as well as socioeconomic and environmental factors, and (3) evaluate associations of the timing of SSRI exposure in pregnancy with risk for preterm birth (PTB), low birthweight (LBW), and small for gestational age (SGA) infants among women with depression before pregnancy. METHODS We conducted propensity score-adjusted regression to calculate odds ratios (ORs) of PTB, LBW, and SGA. We accounted for maternal/pregnancy characteristics, comorbidity, depression severity, time of delivery, social vulnerability, and rural residence. RESULTS There were 50.3% and 40.3% increases in the prevalence rate of prenatal depression and prenatal SSRI prescription rate during the pandemic. We identified women with depression ≤180 days before pregnancy (n = 8406). Women with no SSRI order during pregnancy (n = 3760) constituted the unexposed group. The late SSRI exposure group consisted of women with an SSRI order after the first trimester (n = 3759). The early-only SSRI exposure group consisted of women with SSRI orders only in the first trimester (n = 887). The late SSRI exposure group had an increased risk of PTB of OR = 1.5 ([1.2,1.8]) and LBW of OR = 1.5 ([1.2,2.0]), relative to the unexposed group. Associations between late SSRI exposure and risk of PTB/LBW were similar among a subsample of patients who delivered during the pandemic. CONCLUSIONS These findings suggest an association between PTB/LBW and SSRI exposure is dependent on exposure timing during pregnancy. Small for gestational age is not associated with SSRI exposure.
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Affiliation(s)
- Yeon Mi Hwang
- Institute for Systems Biology; 401 Terry Ave N, Seattle, Washington, USA 98109
- Molecular Engineering and Sciences Institute, University of Washington; Seattle, Washington, USA
| | - Ryan T. Roper
- Institute for Systems Biology; 401 Terry Ave N, Seattle, Washington, USA 98109
| | - Samantha N. Piekos
- Institute for Systems Biology; 401 Terry Ave N, Seattle, Washington, USA 98109
| | - Daniel A. Enquobahrie
- Department of Epidemiology, School of Public Health, University of Washington; Seattle, Washington, USA
| | - Mary F. Hebert
- Department of Pharmacy, School of Pharmacy, University of Washington; Seattle, Washington, USA
| | - Alison G. Paquette
- Department of Pediatrics, School of Medicine, University of Washington; Seattle, Washington USA
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute; Seattle, Washington USA
| | - Priyanka Baloni
- School of Health Sciences, Purdue University, West Lafayette, Indiana USA
| | - Nathan D. Price
- Institute for Systems Biology; 401 Terry Ave N, Seattle, Washington, USA 98109
- Thorne HealthTech, New York, New York, USA
| | - Leroy Hood
- Institute for Systems Biology; 401 Terry Ave N, Seattle, Washington, USA 98109
- Providence St. Joseph Health; Renton, Washington, USA
| | - Jennifer J. Hadlock
- Institute for Systems Biology; 401 Terry Ave N, Seattle, Washington, USA 98109
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2
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Hwang YM, Wei Q, Piekos SN, Vemuri B, Molani S, Mease P, Hood L, Hadlock J. Maternal-fetal outcomes in patients with immune-mediated inflammatory diseases, with consideration of comorbidities: a retrospective cohort study in a large U.S. healthcare system. EClinicalMedicine 2024; 68:102435. [PMID: 38586478 PMCID: PMC10994966 DOI: 10.1016/j.eclinm.2024.102435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 12/25/2023] [Accepted: 01/10/2024] [Indexed: 04/09/2024] Open
Abstract
Background Immune-mediated inflammatory diseases (IMIDs) are likely to complicate maternal health. However, literature on patients with IMIDs undergoing pregnancy is scarce and often overlooks the presence of comorbidities. We aimed to evaluate the impact of IMIDs on adverse pregnancy outcomes after assessing and addressing any discrepancies in the distribution of covariates associated with adverse pregnancy outcomes between patients with and without IMIDs. Methods We conducted a retrospective cohort study using data from an integrated U.S. community healthcare system that provides care across Alaska, California, Montana, Oregon, New Mexico, Texas, and Washington. We used a database containing all structured data from electronic health record (EHRs) and analyzed the cohort of pregnant people who had live births from January 1, 2013, through December 31, 2022. We investigated 12 selected IMIDs: psoriasis, inflammatory bowel disease, rheumatoid arthritis, spondyloarthritis, multiple sclerosis, systemic lupus erythematosus, psoriatic arthritis, antiphospholipid syndrome, Sjögren's syndrome, vasculitides, sarcoidosis, and systemic sclerosis. We characterized patients with IMIDs prior to pregnancy (IMIDs group) based on pregnancy/maternal characteristics, comorbidities, and pre-pregnancy/prenatal immunomodulatory medications (IMMs) prescription patterns. We 1:1 propensity score matched the IMIDs cohort with people who had no IMID diagnoses prior to pregnancy (non-IMIDs cohort). Outcome measures were preterm birth (PTB), low birth weight (LBW), small for gestational age (SGA), and caesarean section. Findings Our analytic cohort had 365,075 people, of which 5784 were in the IMIDs group and 359,291 were in the non-IMIDs group. The prevalence rate of pregnancy of at least 20 weeks duration in people with a previous IMID diagnosis has doubled in the past ten years. 17% of the IMIDs group had at least one prenatal IMM prescription. Depending on the type of IMM, 48%-70% of the patients taking IMMs before pregnancy continued them throughout pregnancy. Overall, patients with one or more of these 12 IMIDs had increased risk of PTB (Relative risk (RR) = 1.1 [1.0, 1.3]; p = 0.08), LBW (RR = 1.2 [1.0, 1.4]; p = 0.02), SGA (RR = 1.1 [1.0, 1.2]; p = 0.03), and caesarean section (RR = 1.1 [1.1, 1.2], p < 0.0001) compared to a matched cohort of people without IMIDs. When adjusted for comorbidities, patients with rheumatoid arthritis (PTB RR = 1.2, p = 0.5; LBW RR = 1.1, p = 0.6) and/or inflammatory bowel disease (PTB RR = 1.2, p = 0.3; LBW RR = 1.0, p = 0.8) did not have significantly increased risk for PTB and LBW. Interpretation For patients who have been pregnant for 20 weeks or greater, the association between IMIDs and adverse pregnancy outcomes depends on both the nature of the IMID and the presence of comorbidities. Because this study was limited to pregnancies resulting in live births, results must be interpreted together with other studies on early pregnancy loss and stillbirth in patient with IMIDs. Funding National Institutes of Health.
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Affiliation(s)
- Yeon Mi Hwang
- Institute for Systems Biology, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
| | - Qi Wei
- Institute for Systems Biology, Seattle, WA, USA
| | | | - Bhargav Vemuri
- Institute for Systems Biology, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
| | | | - Philip Mease
- University of Washington, Seattle, WA, USA
- Providence Health and Services and Affiliates, WA, USA
| | - Leroy Hood
- Institute for Systems Biology, Seattle, WA, USA
| | - Jennifer Hadlock
- Institute for Systems Biology, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
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3
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Piekos SN, Hwang YM, Roper RT, Sorensen T, Price ND, Hood L, Hadlock JJ. Effect of COVID-19 vaccination and booster on maternal-fetal outcomes: a retrospective cohort study. Lancet Digit Health 2023; 5:e594-e606. [PMID: 37537121 PMCID: PMC10473855 DOI: 10.1016/s2589-7500(23)00093-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 04/18/2023] [Accepted: 05/02/2023] [Indexed: 08/05/2023]
Abstract
BACKGROUND COVID-19 in pregnant people increases the risk for poor maternal-fetal outcomes. However, COVID-19 vaccination hesitancy remains due to concerns over the vaccine's potential effects on maternal-fetal outcomes. Here we examine the impact of COVID-19 vaccination and boosters on maternal SARS-CoV-2 infections and birth outcomes. METHODS This was a retrospective multicentre cohort study on the impact of COVID-19 vaccination on maternal-fetal outcomes for people who delivered (n=106 428) at Providence St Joseph Health across seven western US states from Jan 26, 2021 to Oct 26, 2022. Cohorts were defined by vaccination status at delivery: vaccinated (n=35 926; two or more doses of mRNA-1273 Moderna or BNT162b2 Pfizer-BioNTech), unvaccinated (n=55 878), unvaccinated propensity score matched (n=16 771), boosted (n=10 927; three or more doses), vaccinated unboosted (n=13 243; two doses only), and vaccinated unboosted with propensity score matching (n=4414). We built supervised machine learning classification models, which we used to determine which people were more likely to be vaccinated or boosted at delivery. The primary outcome was maternal SARS-CoV-2 infection. COVID-19 vaccination status at delivery, COVID-19-related health care, preterm birth, stillbirth, and very low birthweight were evaluated as secondary outcomes. FINDINGS Vaccinated people were more likely to conceive later in the pandemic, have commercial insurance, be older, live in areas with lower household composition vulnerability, and have a higher BMI than unvaccinated people. Boosted people were more likely to have more days since receiving the second COVID-19 vaccine dose, conceive earlier in the pandemic, have commercial insurance, be older, and live in areas with lower household composition vulnerability than vaccinated unboosted people. Vaccinated pregnant people had lower rates of COVID-19 during pregnancy (4·0%) compared with unvaccinated matched people (5·3%; p<0·0001). COVID-19 rates were even lower in boosted people (3·2%) compared with vaccinated unboosted matched people (5·6%; p<0·0001). Vaccinated people were also less likely to have a preterm birth (7·9%; p<0·0001), stillbirth (0·3%; p<0·0002), or very low birthweight neonate (1·0%; p<0·0001) compared with unvaccinated matched people (preterm birth 9·4%; stillbirth 0·6%; very low birthweight 1·5%). Boosted people were less likely to have a stillbirth (0·3%; p<0·025) and have no differences in rates of preterm birth (7·6%; p=0·090) or very low birthweight neonates (0·8%; p=0·092) compared with vaccinated unboosted matched people (stillbirth 0·5%; preterm birth 8·4%; very low birthweight 1·1%). INTERPRETATION COVID-19 vaccination protects against adverse maternal-fetal outcomes, with booster doses conferring additional protection. Pregnant people should be high priority for vaccination and stay up to date with their COVID-19 vaccination schedule. FUNDING National Institute for Child Health & Human Development and the William O and K Carole Ellison Foundation.
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Affiliation(s)
| | | | | | - Tanya Sorensen
- Swedish Health Services, Swedish Medical Center, Seattle, WA, USA
| | - Nathan D Price
- Institute for Systems Biology, Seattle, WA, USA; Thorne HealthTech, New York, NY, USA
| | - Leroy Hood
- Institute for Systems Biology, Seattle, WA, USA
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Hwang YM, Wei Q, Piekos SN, Vemuri B, Molani S, Mease P, Hood L, Hadlock JJ. Maternal-fetal outcomes in patients with immune mediated inflammatory diseases, with consideration of comorbidities: a retrospective cohort study in a large U.S. healthcare system. medRxiv 2023:2023.08.07.23293726. [PMID: 37609126 PMCID: PMC10441487 DOI: 10.1101/2023.08.07.23293726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Background Immune-mediated inflammatory diseases (IMIDs) are likely to complicate maternal health. However, literature data on patients with IMIDs undergoing pregnancy is scarce and often overlooks the impact of comorbidities. Methods We investigated 12 selected IMIDs: psoriasis, inflammatory bowel disease, rheumatoid arthritis, spondyloarthritis, multiple sclerosis, systemic lupus erythematosus, psoriatic arthritis, antiphospholipid syndrome, Sjögren's syndrome, vasculitis, sarcoidosis, systemic sclerosis. We characterized patients with IMIDs prior to pregnancy (IMIDs group) based on pregnancy/maternal characteristics, comorbidities, and pre-pregnancy/prenatal immunomodulatory medications (IMMs) prescription patterns. We 1:1 propensity score matched the IMIDs cohort with people who had no IMID diagnoses prior to pregnancy (non-IMIDs cohort). Outcome measures were preterm birth (PTB), low birth weight (LBW), small for gestational age (SGA), and cesarean section. Findings The prevalence rate of pregnancy occurring with people with a previous IMID diagnosis has doubled in the past ten years. We identified 5,784 patients with IMIDs. 17% of the IMIDs group had at least one prenatal IMM prescription. Depending on the type of IMM, from 48% to 70% of the patients taking IMMs before pregnancy continued them throughout pregnancy. Patients with IMIDs had similar but slightly increased risks of PTB (Relative risk (RR)=1·1[1·0, 1·3]), LBW (RR=1·2 [1·0,1·4]), SGA (RR=1·1 [1·0,1·2]), and cesarean section (RR=1·1 [1·1,1·2]) compared to a matched cohort of people without IMIDs. Out of the 12 selected IMIDs, three for PTB, one for LBW, two for SGA, and six for cesarean section had results supporting increased risk. Interpretation The association between IMIDs and the increased risk of adverse pregnancy outcomes depend on both the nature of the IMID and the presence of comorbidities.
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Affiliation(s)
- Yeon Mi Hwang
- Institute for Systems Biology, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
| | - Qi Wei
- Institute for Systems Biology, Seattle, WA, USA
| | | | - Bhargav Vemuri
- Institute for Systems Biology, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
| | | | | | - Leroy Hood
- Institute for Systems Biology, Seattle, WA, USA
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Collier AE, Piekos SN, Liu A, Pattison JM, Felix F, Bailetti AA, Sedov E, Gaddam S, Zhen H, Oro AE. GRHL2 and AP2a coordinate early surface ectoderm lineage commitment during development. iScience 2023; 26:106125. [PMID: 36843855 PMCID: PMC9950457 DOI: 10.1016/j.isci.2023.106125] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/09/2022] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Ectodermal dysplasias including skin abnormalities and cleft lip/palate result from improper surface ectoderm (SE) patterning. However, the connection between SE gene regulatory networks and disease remains poorly understood. Here, we dissect human SE differentiation with multiomics and establish GRHL2 as a key mediator of early SE commitment, which acts by skewing cell fate away from the neural lineage. GRHL2 and master SE regulator AP2a balance early cell fate output, with GRHL2 facilitating AP2a binding to SE loci. In turn, AP2a restricts GRHL2 DNA binding away from de novo chromatin contacts. Integration of these regulatory sites with ectodermal dysplasia-associated genomic variants annotated within the Biomedical Data Commons identifies 55 loci previously implicated in craniofacial disorders. These include ABCA4/ARHGAP29 and NOG regulatory regions where disease-linked variants directly affect GRHL2/AP2a binding and gene transcription. These studies elucidate the logic underlying SE commitment and deepen our understanding of human oligogenic disease pathogenesis.
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Affiliation(s)
- Ann E. Collier
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
| | - Samantha N. Piekos
- Stem Cell Biology and Regenerative Medicine Graduate Program, Stanford University, Stanford, CA USA
| | - Angela Liu
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
- Stem Cell Biology and Regenerative Medicine Graduate Program, Stanford University, Stanford, CA USA
| | | | - Franco Felix
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
- Stem Cell Biology and Regenerative Medicine Graduate Program, Stanford University, Stanford, CA USA
| | | | - Egor Sedov
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
| | - Sadhana Gaddam
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
| | - Hanson Zhen
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
| | - Anthony E. Oro
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
- Stem Cell Biology and Regenerative Medicine Graduate Program, Stanford University, Stanford, CA USA
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6
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Piekos SN, Hwang YM, Roper RT, Sorensen T, Price ND, Hood L, Hadlock JJ. The effect of COVID-19 vaccination and booster on maternal-fetal outcomes: a retrospective multicenter cohort study. medRxiv 2022:2022.08.12.22278727. [PMID: 36032974 PMCID: PMC9413719 DOI: 10.1101/2022.08.12.22278727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Background COVID-19 infection in pregnant people has previously been shown to increase the risk for poor maternal-fetal outcomes. Despite this, there has been a lag in COVID-19 vaccination in pregnant people due to concerns over the potential effects of the vaccine on maternal-fetal outcomes. Here we examine the impact of COVID-19 vaccination and booster on maternal COVID-19 breakthrough infections and birth outcomes. Methods This was a retrospective multicenter cohort study on the impact of COVID-19 vaccination on maternal-fetal outcomes for people that delivered (n=86,833) at Providence St. Joseph Health across Alaska, California, Montana, Oregon, New Mexico, Texas, and Washington from January 26, 2021 through July 11, 2022. Cohorts were defined by vaccination status at time of delivery: unvaccinated (n=48,492), unvaccinated propensity score matched (n=26,790), vaccinated (n=26,792; two doses of mRNA-1273 Moderna or BNT162b2 Pfizer-BioNTech), and/or boosted (n=7,616). The primary outcome was maternal COVID-19 infection. COVID-19 vaccination status at delivery, COVID-19 infection-related health care, preterm birth (PTB), stillbirth, very low birth weight (VLBW), and small for gestational age (SGA) were evaluated as secondary outcomes. Findings Vaccinated pregnant people were significantly less likely to have a maternal COVID-19 infection than unvaccinated matched (p<0.0001) pregnant people. During a maternal COVID-19 infection, vaccinated pregnant people had similar rates of hospitalization (p=0.23), but lower rates of supplemental oxygen (p<0.05) or vasopressor (p<0.05) use than those in an unvaccinated matched cohort. Compared to an unvaccinated matched cohort, vaccinated people had significantly lower stillbirth rate (p<0.01) as well as no difference in rate of PTB (p=0.35), SGA (p=0.79), or rate of VLBW (>1,500 g; 0.31). Vaccinated people who were boosted had significantly lower rates of maternal COVID-19 infections (p<0.0001), COVID-19 related hospitalization (p<0.05), PTB (p<0.05), stillbirth (p<0.01), SGA (p<0.05), and VLBW (p<0.01), compared to vaccinated people that did not receive a third booster dose five months after completing the initial vaccination series. Interpretation COVID-19 vaccination protects against adverse maternal-fetal outcomes with booster doses conferring additional protection against COVID-19 infection. It is therefore important for pregnant people to have high priority status for vaccination, and for them to stay current with their COVID-19 vaccination schedule. Funding This study was funded by the National Institute for Child Health & Human Development and the William O. and K. Carole Ellison Foundation.
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Affiliation(s)
| | | | | | - Tanya Sorensen
- Swedish Health Services, Swedish Medical Center, Seattle, WA, USA
| | - Nathan D Price
- Institute for Systems Biology, Seattle, WA, USA
- Thorne HealthTech, New York, NY, USA
| | - Leroy Hood
- Institute for Systems Biology, Seattle, WA, USA
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7
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Piekos SN, Roper RT, Hwang YM, Sorensen T, Price ND, Hood L, Hadlock JJ. The effect of maternal SARS-CoV-2 infection timing on birth outcomes: a retrospective multicentre cohort study. Lancet Digit Health 2022; 4:e95-e104. [PMID: 35034863 PMCID: PMC8758153 DOI: 10.1016/s2589-7500(21)00250-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 09/03/2021] [Accepted: 10/13/2021] [Indexed: 12/13/2022]
Abstract
Background The impact of maternal SARS-CoV-2 infection remains unclear. In this study, we evaluated the risk of maternal SARS-CoV-2 infection on birth outcomes and how this is modulated by the pregnancy trimester in which the infection occurs. We also developed models to predict gestational age at delivery for people following a SARS-CoV-2 infection during pregnancy. Methods We did a retrospective cohort study of the impact of maternal SARS-CoV-2 infection on birth outcomes. We used clinical data from Providence St Joseph Health electronic health records for pregnant people who delivered in the USA at the Providence, Swedish, or Kadlec sites in Alaska, California, Montana, Oregon, or Washington. The SARS-CoV-2 positive cohort included people who had a positive SARS-CoV-2 PCR-based test during pregnancy, subdivided by trimester of infection. No one in this cohort had been vaccinated for COVID-19 at time of infection. The SARS-CoV-2 negative cohort were people with at least one negative SARS-CoV-2 PCR-based test and no positive tests during pregnancy. Cohorts were matched on common covariates impacting birth outcomes, and univariate and multivariate analysis were done to investigate risk factors and predict outcomes. The primary outcome was gestational age at delivery with annotation of preterm birth classification. We trained multiple supervised learning models on 24 features of the SARS-CoV-2 positive cohort to evaluate performance and feature importance for each model and discuss the impact of SARS-CoV-2 infection on gestational age at delivery. Findings Between March 5, 2020, and July 4, 2021, 73 666 pregnant people delivered, 18 335 of whom had at least one SARS-CoV-2 test during pregnancy before Feb 14, 2021. We observed 882 people infected with SARS-CoV-2 during their pregnancy (first trimester n=85; second trimester n=226; and third trimester n=571) and 19 769 people who have never tested positive for SARS-CoV-2 and received at least one negative SARS-CoV-2 test during their pregnancy. SARS-CoV-2 infection indicated an increased risk of preterm delivery (p<0·05) and stillbirth (p<0·05), accounted for primarily by first and second trimester SARS-CoV-2 infections. Gestational age at SARS-CoV-2 infection was correlated with gestational age at delivery (p<0·01) and had the greatest impact on predicting gestational age at delivery. The people in this study had mild or moderate SARS-CoV-2 infections and acute COVID-19 severity was not correlated with gestational age at delivery (p=0·31). Interpretation These results suggest that pregnant people would benefit from increased monitoring and enhanced prenatal care after first or second trimester SARS-CoV-2 infection, regardless of acute COVID-19 severity. Funding US National Institutes of Health.
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Affiliation(s)
| | | | | | - Tanya Sorensen
- Swedish Health Services, Swedish Maternal and Fetal Specialty Center, Seattle, WA, USA
| | - Nathan D Price
- Institute for Systems Biology, Seattle, WA, USA; Onegevity Health, New York, NY, USA
| | - Leroy Hood
- Institute for Systems Biology, Seattle, WA, USA
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8
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Piekos SN, Gaddam S, Bhardwaj P, Radhakrishnan P, Guha RV, Oro AE. Biomedical Data Commons (BMDC) prioritizes B-lymphocyte non-coding genetic variants in Type 1 Diabetes. PLoS Comput Biol 2021; 17:e1009382. [PMID: 34543288 PMCID: PMC8483327 DOI: 10.1371/journal.pcbi.1009382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 09/30/2021] [Accepted: 08/25/2021] [Indexed: 11/18/2022] Open
Abstract
The repurposing of biomedical data is inhibited by its fragmented and multi-formatted nature that requires redundant investment of time and resources by data scientists. This is particularly true for Type 1 Diabetes (T1D), one of the most intensely studied common childhood diseases. Intense investigation of the contribution of pancreatic β-islet and T-lymphocytes in T1D has been made. However, genetic contributions from B-lymphocytes, which are known to play a role in a subset of T1D patients, remain relatively understudied. We have addressed this issue through the creation of Biomedical Data Commons (BMDC), a knowledge graph that integrates data from multiple sources into a single queryable format. This increases the speed of analysis by multiple orders of magnitude. We develop a pipeline using B-lymphocyte multi-dimensional epigenome and connectome data and deploy BMDC to assess genetic variants in the context of Type 1 Diabetes (T1D). Pipeline-identified variants are primarily common, non-coding, poorly conserved, and are of unknown clinical significance. While variants and their chromatin connectivity are cell-type specific, they are associated with well-studied disease genes in T-lymphocytes. Candidates include established variants in the HLA-DQB1 and HLA-DRB1 and IL2RA loci that have previously been demonstrated to protect against T1D in humans and mice providing validation for this method. Others are included in the well-established T1D GRS2 genetic risk scoring method. More intriguingly, other prioritized variants are completely novel and form the basis for future mechanistic and clinical validation studies The BMDC community-based platform can be expanded and repurposed to increase the accessibility, reproducibility, and productivity of biomedical information for diverse applications including the prioritization of cell type-specific disease alleles from complex phenotypes.
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Affiliation(s)
- Samantha N. Piekos
- Program in Epithelial Biology, Stanford University, Stanford, California, United States of America
- Google Data Commons, Mountain View, California, United States of America
| | - Sadhana Gaddam
- Program in Epithelial Biology, Stanford University, Stanford, California, United States of America
| | - Pranav Bhardwaj
- Department of Statistics, Stanford University, Stanford, California, United States of America
| | | | - Ramanathan V. Guha
- Google Data Commons, Mountain View, California, United States of America
| | - Anthony E. Oro
- Program in Epithelial Biology, Stanford University, Stanford, California, United States of America
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Pattison JM, Melo SP, Piekos SN, Torkelson JL, Bashkirova E, Mumbach MR, Rajasingh C, Zhen HH, Li L, Liaw E, Alber D, Rubin AJ, Shankar G, Bao X, Chang HY, Khavari PA, Oro AE. Retinoic acid and BMP4 cooperate with p63 to alter chromatin dynamics during surface epithelial commitment. Nat Genet 2018; 50:1658-1665. [PMID: 30397335 PMCID: PMC6265075 DOI: 10.1038/s41588-018-0263-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 09/21/2018] [Indexed: 01/14/2023]
Abstract
Human embryonic stem cell (hESC) differentiation promises advances in regenerative medicine1–3, yet conversion into transplantable tissues remains poorly understood. Using our keratinocyte differentiation system, we employ a multi-dimensional genomics approach to interrogate the contributions of inductive morphogens retinoic acid (RA) and bone morphogenetic protein 4 (BMP4) and the epidermal master regulator p634,5 during surface ectoderm commitment. In contrast to other master regulators6–9, p63 effects major transcriptional changes only after morphogens alter chromatin accessibility, establishing an epigenetic landscape for p63 to modify. p63 distally closes chromatin accessibility and promotes accumulation of H3K27me3 modifications. Cohesin HiChIP10 visualizations of chromosome conformation reveal that p63 and the morphogens contribute to dynamic long-range chromatin interactions, as illustrated with TFAP2C regulation11. Our study demonstrates the unexpected dependency of p63 on morphogenetic signaling and provides novel insights into how a master regulator can specify diverse transcriptional programs based on the chromatin landscape induced by specific morphogen exposure.
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Affiliation(s)
- Jillian M Pattison
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Sandra P Melo
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA.,Agilent Technologies, Santa Clara, CA, USA
| | - Samantha N Piekos
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jessica L Torkelson
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Elizaveta Bashkirova
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA.,Columbia Stem Cell Initiative, Columbia University Medical Center, New York, NY, USA
| | - Maxwell R Mumbach
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA.,Center for Personal Dynamic Regulomes, Stanford, CA, USA
| | - Charlotte Rajasingh
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Hanson Hui Zhen
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lingjie Li
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Eric Liaw
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA.,David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Daniel Alber
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Adam J Rubin
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Gautam Shankar
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Xiaomin Bao
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA.,Departments of Molecular Sciences and Dermatology, Northwestern University, Evanston, IL, USA
| | - Howard Y Chang
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA.,Center for Personal Dynamic Regulomes, Stanford, CA, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Anthony E Oro
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA.
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