Pivoting COVID-19 Resources for an Equitable Mpox Vaccine Response in Louisiana.

Introduction: The first case of mpox in Louisiana was identified 2 months ahead of Southern Decadence Festival in New Orleans, the largest LGBTQ+ Pride festival in the South. With mpox case numbers reflecting racial disparities, the objective was to mount an equitable vaccination response. Methods: The Louisiana Department of Health rapidly pivoted its COVID-19 resources and strategies-specifically, using vaccine strike teams and mobile events, in-state vaccine redistribution through centralized warehousing and shipping support, and community partnerships-to now control mpox transmission. Here, the authors have evaluated state-based Immunization Information System data to examine whether the vaccination response was geographically and racially equitable. Geographic equity was measured by taking into account vaccine availability as well as uptake in areas with high Social Vulnerability Index. Results: A total of 113 providers were enrolled in the vaccination program, and 96 mobile vaccination events were held in locations frequented by at-risk populations. Racial disparities among vaccine recipients decreased over time, and vaccine availability and uptake were equitable in areas with high Social Vulnerability Indices. However, Black, female, and Hispanic/Latinx patients had significantly higher risk of not completing the 2-dose series than their counterparts. Conclusions: The mpox vaccination response in Louisiana was geographically equitable, though some demographic disparities remained.

Impact of the COVID-19 pandemic on routine childhood vaccination in 9 U.S. jurisdictions.

IMPORTANCE: Routine vaccinations are key to prevent outbreaks of vaccine-preventable diseases. However, there have been documented declines in routine childhood vaccinations in the U.S. and worldwide during the COVID-19 pandemic. OBJECTIVE: Assess how the COVID-19 pandemic impacted routine childhood vaccinations by evaluating vaccination coverage for routine childhood vaccinations for children born in 2016-2021. METHODS: Data on routine childhood vaccinations reported to CDC by nine U.S. jurisdictions via the immunization information systems (IISs) by December 31, 2022, were available for analyses. Population size for each age group was obtained from the National Center for Health Statistics' Bridging Population Estimates. MAIN OUTCOMES AND MEASURES: Vaccination coverage for routine childhood vaccinations at age three months, five months, seven months, one year, and two years was calculated by vaccine type and overall, for 4:3:1:3:3:1:4 series (≥4 doses DTaP, ≥3 doses Polio, ≥1 dose MMR, ≥3 doses Hib, ≥3 doses Hepatitis B, ≥1 dose Varicella, and ≥ 4 doses pneumococcal conjugate), for each birth cohort year and by jurisdiction. RESULTS: Overall, there was a 10.4 percentage point decrease in the 4:3:1:3:3:1:4 series in those children born in 2020 compared to those children born in 2016. As of December 31, 2022, 71.0% and 71.3% of children born in 2016 and 2017, respectively, were up to date on their routine childhood vaccinations by two years of age compared to 69.1%, 64.7% and 60.6% for children born in 2018, 2019, and 2020, respectively. CONCLUSIONS AND RELEVANCE: The decline in vaccination coverage for routine childhood vaccines is concerning. In order to protect population health, strategic efforts are needed by health care providers, schools, parents, as well as state, local, and federal governments to work together to address these declines in vaccination coverage during the COVID-19 pandemic to prevent outbreaks of vaccine preventable diseases by maintaining high levels of population immunity.

Feasibility of residential air quality monitoring to address asthma outcomes.

Improving asthma outcomes for underserved populations can be addressed through interventions to improve indoor air quality (IAQ). New protocol for measuring IAQ and health outcomes are imperative given advances in IAQ monitoring technology and challenges in conducting intervention research in homes. In this pilot study HEPA air purifiers and HEPA vacuum cleaners were provided to five homes with children with asthma. For 6 weeks, eight common components of air quality were measured using a low-cost multi-channel air quality monitoring device, with data conveyed directly from participant homes via Wi-Fi connection. In conjunction with periodic surveys on asthma control, impact of asthma on quality of life and intervention compliance, outcomes compared IAQ, home characteristics, and asthma-related measures. This pilot study demonstrates the feasibility of a protocol to evaluate a dual component intervention to improve IAQ in homes, as measured with a low-cost air quality monitoring device.

The Utility of Virtual Home Visits to Reduce Asthma Burden in Low-Income Black Communities in Louisiana During the COVID-19 Pandemic.

OBJECTIVES: The Louisiana Department of Health identified a need for greater outreach in low-income Black communities that addressed environmental asthma triggers. We piloted an asthma virtual home visit (VHV) program and evaluated its reach and ability to promote asthma self-management strategies in communities with a high prevalence of poorly controlled asthma. METHODS: Participants from Louisiana were continuously recruited into the VHV program starting in March 2021 and provided with asthma education materials. Participants reporting poorly controlled asthma and environmental triggers were also offered 3 VHVs with a respiratory therapist. All participants were asked to complete a preintervention and postintervention knowledge test, an Asthma Control Test (ACT) (maximum score = 25; scores ≤19 indicate poorly controlled asthma), and a final survey that assessed perceptions about asthma management and reduction of environmental triggers. RESULTS: As of October 2022, 147 participants were enrolled in the program, and 52 had consented to and received ≥1 VHV. Forty VHV recipients (77%) were aged <18 years, 40 (77%) were Black people, and 46 (88%) were from families with extremely low or low incomes. Asthma symptoms improved across all participants, with a median increase of 2.4 points on the ACT. Knowledge tests revealed that 86% of participants learned about ≥1 new asthma trigger; a larger percentage of VHV recipients than nonrecipients (68% vs 36%) had an improved knowledge test score postintervention. Compared with preintervention, about three-quarters of participants reported feeling more empowered to self-manage their asthma and a significant improvement in their quality of life postintervention. CONCLUSIONS: The program provided virtual asthma education to communities with a high burden of asthma and improved asthma outcomes for participants. Similar virtual models can be used to promote health equity, especially in areas with limited access to health care.

Associations of Emergency Department Visits for Asthma with Precipitation and Temperature on Thunderstorm Days: A Time-Series Analysis of Data from Louisiana, USA, 2010-2012.

BACKGROUND: Studies of thunderstorm asthma to understand risk factors using high-resolution climate data and asthma outcomes on a large scale are scarce. Moreover, thunderstorm asthma is not well studied in the United States. OBJECTIVES: We examined whether climate parameters involved in thunderstorms are associated with emergency department (ED) visits for acute asthma attacks in the United States. METHODS: We analyzed 63,789 asthma-related, daily ED visits for all age groups, and thunderstorm-associated climate data in Louisiana during 2010 through 2012. We performed time-series analyses using quasi-Poisson regression models with natural cubic splines of date, parish, holiday, day of week, season, daily maximum concentrations of ozone (O3) and fine particulate matter [PM ≤2.5µm in aerodynamic diameter (PM2.5)], and daily mean pressure, precipitation, and temperature. Because of a significant interaction effect between temperature and lightning days on asthma-related visits, we performed stratified analyses by days with/without lightning or thunderstorm (defined by any lightning and precipitation). RESULTS: On thunderstorm days, higher asthma-related ED visits were associated with higher daily mean precipitation [relative risk (RR)=1.145 per 1 g/m2/s (95% CI: 1.009, 1.300)] and lower daily mean temperature [RR=1.011 per 1°C change (1.000-1.021)] without carry-over effect to the next non-thunderstorm day. These higher risks were found mainly among children and adults <65 years of age. We observed similar results on lightning days. However, we did not find similar associations for non-thunderstorm or non-lightning days. Daily maximum O3 and PM2.5 levels were not significantly associated with asthma ED visits on thunderstorm days. DISCUSSION: Higher precipitation and lower temperature on thunderstorm days appear to contribute to asthma attacks among people with asthma, suggesting they should consider taking precautions during thunderstorms. EDs should consider preparing for a potential increase of asthma-related visits and ensuring sufficient stock of emergency medication and supplies for forecasted severe thunderstorm days. https://doi.org/10.1289/EHP10440.

Identifying Louisiana communities at the crossroads of environmental and social vulnerability, COVID-19, and asthma.

The COVID-19 pandemic has disproportionately affected the socially and environmentally vulnerable, including through indirect effects on other health conditions. Asthma is one such condition, which may be exacerbated by both prolonged adverse in-home exposures if quarantining in unhealthy homes and prolonged outdoor exposures if the ambient air quality is unhealthy or hazardous. As both are often the case in Environmental Justice (EJ) communities, here we have analyzed data at the census tract (CT) level for Louisiana to assess any correlation between social and environmental vulnerability, and health issues like COVID-19 and asthma. Higher Social Vulnerability Index (SVI), Particulate Matter less than 2.5 µm in diameter (PM2.5) and Ozone levels were associated with higher rates of cumulative COVID-19 incidence at various time points during the pandemic, as well as higher average annual asthma hospitalization rates and estimated asthma prevalence. Further, cumulative COVID-19 incidence during the first three months of the pandemic was moderately correlated with both asthma hospitalizations and estimated prevalence, suggesting similar underlying factors may be affecting both conditions. Additionally, 137 CTs were identified where social and environmental vulnerabilities co-existed, of which 75 (55%) had high estimated prevalence of asthma. These areas are likely to benefit from asthma outreach that considers both social and environmental risk factors. Fifteen out of the 137 CTs (11%) not only had higher estimated prevalence of asthma but also a high burden of COVID-19. Further research in these areas may help to elucidate any common social determinants of health that underlie both asthma and COVID-19 burdens, as well as better clarify the possible role of the environment as related to the COVID-19 burden in Louisiana.

The CURE for Cultivating Fastidious Microbes.

Course-Based Undergraduate Research Experiences (CUREs) expand the scientific educational benefits of research to large groups of students in a course setting. As part of an ongoing effort to integrate CUREs into first-year biology labs, we developed a microbiology CURE (mCURE) that uses a modified dilution-to-extinction high throughput culturing protocol for isolating abundant yet fastidious aquatic bacterioplankton during one semester. Students learn common molecular biology techniques like nucleic acid extraction, PCR, and molecular characterization; read and evaluate scientific literature; and receive training in scientific communication through written and oral exercises that incorporate social media elements. In the first three semesters, the mCUREs achieved similar cultivability success as implementation of the protocol in a standard laboratory setting. Our modular framework facilitates customization of the curriculum for use in multiple settings and we provide classroom exercises, assignments, assessment tools, and examples of student output to assist with implementation.

High-Throughput Targeted Repeat Element Bisulfite Sequencing (HT-TREBS).

High-throughput targeted repeat element bisulfite sequencing (HT-TREBS) is designed to assay the methylation level of individual retrotransposon loci of a targeted family, in a locus-specific manner, and on a genome-wide scale. Briefly, genomic DNA is sheared and ligated to Ion Torrent A adaptors (with methylated cytosines), followed by bisulfite-conversion, and amplification with primers designed to bind the targeted retrotransposon. Since the primers carry the Ion Torrent P1 adaptor as a 5'-extension, the amplified library is ready to be size-selected and sequenced on a next-generation sequencing platform. Once sequenced, each retrotransposon is mapped to a particular genomic locus, which is achieved through ensuring at least a 10-bp overlap with flanking unique sequence, followed by the calculation of methylation levels of the mapped retrotransposon using a BiQ Analyzer HT. A complete protocol for library construction as well as the bioinformatics for HT-TREBS is described in this chapter.

Intergenic and intronic DNA hypomethylated regions as putative regulators of imprinted domains.

AIM: To investigate the regulatory potential of intergenic/intronic hypomethylated regions (iHMRs) within imprinted domains. MATERIALS & METHODS: Based on the preliminary results of the histone modification and conservation profiles, we conducted reporter assays on the Peg3 and H19 domain iHMRs. The in vitro results were confirmed by the in vivo deletion of Peg3-iHMR designed to test its function in the Peg3 imprinted domain. RESULTS & CONCLUSION: Initial bioinformatic analyses suggested that some iHMRs may be noncanonical enhancers for imprinted genes. Consistent with this, Peg3- and H19-iHMRs showed context-dependent promoter and enhancer activity. Further, deletion of Peg3-iHMR resulted in allele- and sex-specific misregulation of several imprinted genes within the domain. Taken together, these results suggest that some iHMRs may function as domain-wide regulators for the associated imprinted domains.

DNA methylation variation of human-specific Alu repeats.

DNA methylation is the major repression mechanism for human retrotransposons, such as the Alu family. Here, we have determined the methylation levels associated with 5238 loci belonging to 2 Alu subfamilies, AluYa5 and AluYb8, using high-throughput targeted repeat element bisulfite sequencing (HT-TREBS). The results indicate that ∼90% of loci are repressed by high methylation levels. Of the remaining loci, many of the hypomethylated elements are found near gene promoters and show high levels of DNA methylation variation. We have characterized this variation in the context of tumorigenesis and interindividual differences. Comparison of a primary breast tumor and its matched normal tissue revealed early DNA methylation changes in ∼1% of AluYb8 elements in response to tumorigenesis. Simultaneously, AluYa5/Yb8 elements proximal to promoters also showed differences in methylation of up to one order of magnitude, even between normal individuals. Overall, the current study demonstrates that early loss of methylation occurs during tumorigenesis in a subset of young Alu elements, suggesting their potential clinical relevance. However, approaches such as deep-bisulfite-sequencing of individual loci using HT-TREBS are required to distinguish clinically relevant loci from the background observed for AluYa5/Yb8 elements in general with regard to high levels of interindividual variation in DNA methylation.

Retrotransposon-derived promoter of Mammalian Aebp2.

Variable DNA methylation in promoter regions has been implicated in altering transcriptional regulation. The current study analyzed the evolutionary origin and DNA methylation pattern of one of the promoters of Aebp2. According to the results, the first promoter of Aebp2 has been derived from retrotransposons independently in the primate and rodent lineages. DNA methylation analyses revealed that this promoter is unmethylated in sperm, methylated in mature oocytes, and partially methylated at embryonic day 10.5 (78.3%) and 14.5 (58.3%). This promoter also shows variable levels of DNA methylation among adult organs, ranging from the highest in spleen (~80%) to the lowest in tail (~50%). The results from the F1 hybrid of interspecific crossing further indicated that both alleles are equally methylated without any allele bias, also supported by its biallelic expression. Therefore, the partial methylation observed among somatic tissues is an outcome of the genome-wide resetting of DNA methylation during the implantation stage, but not of the inherited allelic methylation pattern preset during gametogenesis. Taken together, mammalian Aebp2 has adopted retrotransposons as its promoter, which displays partial DNA methylation pattern of allelic- or non-allelic origin during the different stages of development.

Locus-specific DNA methylation analysis of retrotransposons in ES, somatic and cancer cells using High-Throughput Targeted Repeat Element Bisulfite Sequencing.

DNA methylation is a major epigenetic mark associated with multiple aspects of retrotransposons within the mammalian genome. In order to study DNA methylation of a large number of retrotransposons on an individual-locus basis, we have developed a new protocol termed High-Throughput Targeted Repeat Element Bisulfite Sequencing (HT-TREBS) (Ekram and Kim, 2014 [1]). We have used this technique to characterize the locus-specific patterns of DNA methylation of 4799 members of the mouse IAP LTR (Intracisternal A Particle Long Terminal Repeat) retrotransposon family in embryonic stem, somatic and Neuro2A cells (Bakshi and Kim, 2014 [2]). Here we describe in detail the sample preparation and bioinformatics analyses used for these studies. The somatic cell data may be accessed under GEO accession number GSE49222. The ES and Neuro2A data are deposited under GEO accession number GSE60007.

AEBP2 as a transcriptional activator and its role in cell migration.

Aebp2 encodes an evolutionarily conserved zinc finger protein that has not been well studied so far, yet recent studies indicated that this gene is closely associated with the Polycomb Repressive Complex 2 (PRC2). Thus, the current study characterized the basic aspects of this gene, including alternative promoters and protein isoforms. According to the results, Aebp2 is controlled through three alternative promoters, deriving three different transcripts encoding the embryonic (32 kDa) and somatic (52 kDa) forms. Chromatin Immuno-Precipitation (ChIP) experiments revealed that AEBP2 binds to its own promoter as well as the promoters of Jarid2 and Snai2. While the embryonic form acts as a transcriptional repressor for Snai2, the somatic form functions as a transcriptional activator for Jarid2, Aebp2 and Snai2. Cell migration assays also demonstrated that the Aebp2 somatic form has an enhancing activity in cell migration. This is consistent with the functional association of Aebp2 with migratory neural crest cells. These results suggest that the two protein isoforms of AEBP2 may have opposite functions for the PcG target genes, and may play significant roles in cell migration during development.

Retrotransposon-based profiling of mammalian epigenomes: DNA methylation of IAP LTRs in embryonic stem, somatic and cancer cells.

In the current study, we have used HT-TREBS to individually analyze the DNA methylation pattern of 4799 IAP LTR retrotransposons in embryonic stem, somatic and Neuro2A cells. According to the results, half of the loci within this family show constant methylation patterns between the three cell types whereas the remaining half display variable levels of methylation. About half of the variably methylated IAP LTRs tend to be hypomethylated in ES cells, and nearly all in this group are hypomethylated in Neuro2A cells. The observed hypomethylation in both cell types occur in a non-uniform, locus-specific manner and to various degrees of severity, with some of them being easily detectible by COBRA. Overall, this study demonstrates the feasibility of HT-TREBS to study DNA methylation changes at retrotransposons in a locus-specific manner in multiple cell types and further suggests the potential utility of this technique in developing epigenetic biomarkers for tracking disease progression.

Peg3 mutational effects on reproduction and placenta-specific gene families.

Peg3 (paternally expressed gene 3) is an imprinted gene encoding a DNA-binding protein. This gene plays important roles in controlling fetal growth rates and nurturing behaviors. In the current study, a new mutant mouse model has been generated to further characterize the functions of this DNA-binding protein. Besides known phenotypes, this new mutant model also revealed potential roles of Peg3 in mammalian reproduction. Female heterozygotes produce a much smaller number of mature oocytes than the wild-type littermates, resulting in reduced litter sizes. According to genome-wide expression analyses, several placenta-specific gene families are de-repressed in the brain of Peg3 heterozygous embryos, including prolactin, cathepsin and carcinoembryonic antigen cell adhesion molecule (Ceacam) families. The observed de-repression is more pronounced in females than in males. The de-repression of several members of these gene families is observed even in the adult brain, suggesting potential defects in epigenetic setting of the placenta-specific gene families in the Peg3 mutants. Overall, these results indicate that Peg3 likely controls the transcription of several placenta-specific gene families, and further suggest that this predicted transcriptional control by Peg3 might be mediated through unknown epigenetic mechanisms.