Association of Food Desert Residency and Preterm Birth in the United States.

INTRODUCTION: Food deserts are a major public health concern. Inadequate access to healthy food has been associated with poor nutrition and the development of dietary related chronic conditions. OBJECTIVE: To determine the association between geographic access to nutritious food and preterm birth and whether gestational hypertension mediates this relationship. METHODS: Food access data was retrieved from the U.S. Department of Agriculture Food Access Research Atlas (2019) and used to quantify the percentage of Census tracts within each county that were food deserts: low-income tracts with limited access to grocery stores, supermarkets, or other sources of healthy, nutritious foods. These data were merged with US birth records from 2018 to 2019 by using the maternal county of residence (n = 7,533,319). We fit crude and adjusted logistic regression models with generalized estimating equations to determine the association between living in a food desert and the odds of preterm birth. We conducted a secondary within-group analysis by stratifying the fully adjusted model by race for non-Hispanic White and non-Hispanic Black birthing people. RESULTS: In the fully adjusted model, we found a dose-response relationship. As the prevalence of tract-level food deserts within counties increased, so did the likelihood of preterm birth (mid-range: odds ratio (OR) = 1.04, 95% confidence interval (C.I.) 1.01-1.07; high: OR = 1.07, 95% C.I. 1.03-1.11). Similar results were seen in the White-Black stratified models. However, a disparity remained as Black birthing people had the highest odds for preterm birth. Lastly, gestational hypertension appears to mediate the relationship between nutritious food access and preterm birth (natural indirect effect (NIE) = 1.01, 95% CI = 1.00, 1.01). CONCLUSION: It is salient, particularly for Black birthing people who experience high rates of adverse birth outcomes, that the role of food desert residency be explored within maternal and child health disparities.

Maternity Care Deserts in Louisiana and Breastfeeding Initiation.

BACKGROUND: Breastfeeding provides physical, psychological, and immunological benefits to both the mother and infant, but breastfeeding rates are suboptimal. The purpose of this study was to examine whether residing in a maternity care desert (a county with no hospital offering obstetric care and no OB/GYN or certified nurse midwife providers) was associated with lower breastfeeding rates among birthing people in Louisiana from 2019 to 2020. METHODS: Data provided by the March of Dimes were used to classify Louisiana parishes by level of access to maternity care. Using data on all live births provided by the Louisiana Office of Vital Records (n = 112,151), we fit adjusted modified Poisson regression models with generalized estimating equations and exploratory geospatial analysis to examine the association between place of residence and breastfeeding initiation and racial disparities in initiation. We conducted a secondary within-group analysis by fitting the fully adjusted model stratified by race/ethnicity for non-Hispanic white and non-Hispanic Black birthing people. RESULTS: We found that residing in a parish with limited (odds ratio [OR] = 0.87; 95% confidence interval [CI] [0.77, 0.99]) to no access (OR = 0.88; 95% CI [0.80, 0.97]) was significantly associated with lower breastfeeding initiation rates. The within-group analysis determined that both non-Hispanic Black and non-Hispanic white birthing people residing in a parish with limited or no maternity care access had lower breastfeeding initiation rates. CONCLUSION: Reducing rural and racial inequities in breastfeeding may require structural changes and investments in infrastructure to deliver pregnancy care.

Variants in ZNF365 isoform D are associated with Crohn's disease.

OBJECTIVE: Genome-wide association studies have identified multiple Crohn's disease (CD) susceptibility loci, including association with non-coding intergenic single-nucleotide polymorphisms (SNPs) at 10q21. DESIGN: To fine-map the 10q21 locus, the authors genotyped 86 SNPs in 1632 CD cases and 961 controls and performed single-marker and conditional analyses using logistic regression. RESULTS: Association with CD risk spanning 11 SNPs (p<0.001) was observed. The most significant association observed was at the non-synonymous SNP, rs7076156 (Ala62Thr), in ZNF365. The alanine allele was over-represented in CD (p=5.23×10⁻7; OR=1.39 (95% CI 1.22 to 1.58)); allele frequency of 76% in CD and 69.7% in controls). Conditional analysis on rs7076156 nullified all other significant associations, suggesting that this is the causative variant at this locus. Four isoforms of ZNF365 have previously been identified, and rs7076156 is located in an exon unique to ZNF365 isoform D. The authors demonstrated, using reverse transcription-PCR, expression of ZNF365D in intestinal resections from both CD subjects and controls. Markedly reduced mean expression levels of ZNF365D were identified in Epstein-Barr virus-transformed lymphoblastoid cell lines from CD subjects homozygous for the risk allele (Ala). A whole-genome microarray expression study further suggested that the Ala62Thr change in ZNF365 isoform D is related to differential expression of the genes ARL4A, MKKS, RRAGD, SUMF2, TDR1 and ZNF148 in CD. CONCLUSIONS: Collectively, these data support the hypothesis that the non-synonymous Ala62Thr SNP, rs7076156, underlies the association between 10q21 and CD risk and suggest that this SNP acts by altering expression of genes under the control of ZNF365 isoform D.

Fucosyltransferase 2 (FUT2) non-secretor status is associated with Crohn's disease.

Genetic variation in both innate and adaptive immune systems is associated with Crohn's disease (CD) susceptibility, but much of the heritability to CD remains unknown. We performed a genome-wide association study (GWAS) in 896 CD cases and 3204 healthy controls all of Caucasian origin as defined by multidimensional scaling. We found supportive evidence for 21 out of 40 CD loci identified in a recent CD GWAS meta-analysis, including two loci which had only nominally achieved replication (rs4807569, 19p13; rs991804, CCL2/CCL7). In addition, we identified associations with genes involved in tight junctions/epithelial integrity (ASHL, ARPC1A), innate immunity (EXOC2), dendritic cell biology [CADM1 (IGSF4)], macrophage development (MMD2), TGF-beta signaling (MAP3K7IP1) and FUT2 (a physiological trait that regulates gastrointestinal mucosal expression of blood group A and B antigens) (rs602662, P=3.4x10(-5)). Twenty percent of Caucasians are 'non-secretors' who do not express ABO antigens in saliva as a result of the FUT2 W134X allele. We demonstrated replication in an independent cohort of 1174 CD cases and 357 controls between the four primary FUT2 single nucleotide polymorphisms (SNPs) and CD (rs602662, combined P-value 4.90x10(-8)) and also association with FUT2 W143X (P=2.6x10(-5)). Further evidence of the relevance of this locus to CD pathogenesis was demonstrated by the association of the original four SNPs and CD in the recently published CD GWAS meta-analysis (rs602662, P=0.001). These findings strongly implicate this locus in CD susceptibility and highlight the role of the mucus layer in the development of CD.

Genetic epistasis of IL23/IL17 pathway genes in Crohn's disease.

BACKGROUND: The IL23/IL17 pathway is pivotal in the development of chronic mucosal inflammation seen in Crohn's disease (CD). Genetic variants in the IL23R and IL12B have been associated with CD susceptibility. We investigated 10 genes within the IL23/IL17 pathway in a case-control study of 763 CD cases and 254 healthy controls. METHODS: We identified a novel association in haplotypes in IL17A (empirical P = 0.02), IL17RA (P = 0.001), IL17RD (P = 0.001), IL12RB1 (P = 0.003), and IL12RB2 (P = 0.001) as well as confirming the association with IL12B variants (P = 0.003). RESULTS: The cumulative risk for carrying an increased number of CD risk haplotypes from genes in this pathway rises to an odds ratio of 4.3 for carrying 5 risk haplotypes. We have previously demonstrated an association between this cohort and IL23R haplotypes. Pairwise analyses suggest that there is statistical interaction between variants in IL17A and IL23R (P = 0.047) and between variants in IL17RA and IL23R (P = 0.036). Furthermore, a significant association between CD and the widely replicated IL23R variants is only seen in the presence of IL17A or IL17RA variants. CONCLUSIONS: These data support the investigation of pathways implicated in CD pathogenesis in order to identify further susceptibility genes and also suggest that important gene-gene interaction is present in CD susceptibility.(Inflamm Bowel Dis 2009).

MAGI2 genetic variation and inflammatory bowel disease.

BACKGROUND: Despite recent advances the majority of inflammatory bowel disease (IBD) susceptibility 'genes' remain undiscovered. Recent data suggest that autoimmune conditions may 'share' susceptibility loci. Epidemiological evidence indicates an association between celiac disease and IBD and both conditions demonstrate increased gut permeability. MAGI2, recently implicated in ulcerative colitis (UC) and celiac disease, encodes a scaffolding protein involved in epithelial integrity. Our aim was to test MAGI2 variants for association with IBD and also their role in determining intermediate hereditary phenotypes defined by antibody production to microbial antigens. METHODS: We genotyped 113 MAGI2 single nucleotide polymorphisms (SNPs) in 681 cases of Crohn's disease (CD), 259 UC cases, and 195 controls. RESULTS: The most significant IBD association was in intron 6 (rs2160322, P = 0.009) and both UC (P = 0.006) and CD (P = 0.03) contributed to this association. The most significant CD association was with an intron 2 haplotype (rs7785088/rs323149/rs13246026, P = 0.002). We observed highly significant associations with UC in intron 6 (rs7803276/rs7803705, P = 0.002) and also significant associations in introns 2, 6, and 20. Significant associations were seen with: immunoglobulin G (IgG) anti-Saccharomyces cerevisiae antibodies (ASCA)-positive CD in intron 3 (P = 0.003), intron 6 (P = 0.003), and intron 20 (P = 0.001); anti-CBir1-positive CD in intron 3 (P = 0.0001) and intron 6 (P = 0.008); and anti-outer membrane porin C (OmpC)-positive CD in intron 3 (P = 0.0009), and intron 9 (P = 0.007). Quantitative antibody levels were also associated with variants in intron 4 (anti-IgA ASCA, P = 0.0003 and anti-IgG ASCA, P = 0.0002). CONCLUSIONS: These findings support the significance of the epithelial barrier in IBD pathogenesis.

IL23R haplotypes provide a large population attributable risk for Crohn's disease.

BACKGROUND: The IL-23 pathway plays a pivotal role in the development of chronic mucosal inflammation seen in the inflammatory bowel diseases. Multiple studies have now established the contribution of the interleukin 23 receptor gene (IL23R) to Crohn's disease (CD) risk in general and of the IL23R R381Q variant in particular. The aim of this work was to estimate the total contribution of this gene to CD risk test using a haplotype approach. METHODS: In all, 763 CD subjects and 254 controls were genotyped for single nucleotide polymorphisms in the IL23R gene using Illumina and ABI methods. Haplotypes were assigned using PHASEv2 and tested for association with CD by chi-square and permutation. RESULTS: Haplotypes with both increased and decreased risk for CD were observed in 2 of the 4 observed blocks (Block 2 H1: 55.4% control, 64% CD, P = 0.019; H2: 64.5% control, 54.4% CD, P = 0.006; Block 3 H1: 55.8% control, 64.4% CD, P = 0.013; H2: 47.0% control, 36.6% CD, P = 0.001). The population attributable risk for these haplotypes was substantially larger than that estimated for the IL23R R381Q variant (Block 2 H1 and block 3 H1 approximately 20%, compared with approximately 4% for Block 3 H6, containing the variant). CONCLUSIONS: These observations suggest that IL23R makes a substantial contribution to CD susceptibility, larger than that estimated from the population frequency of the R381Q variant. These observations also support the expectation that finding "hits" from genomewide association studies will be but an important chapter in the story of unraveling the genetic contribution to CD, rather than the final chapter that brings clarity to all the plot twists of a complicated story.

GDF5 is a second locus for multiple-synostosis syndrome.

Multiple-synostosis syndrome is an autosomal dominant disorder characterized by progressive symphalangism, carpal/tarsal fusions, deafness, and mild facial dysmorphism. Heterozygosity for functional null mutations in the NOGGIN gene has been shown to be responsible for the disorder. However, in a cohort of six probands with multiple-synostosis syndrome, only one was found to be heterozygous for a NOGGIN mutation (W205X). Linkage studies involving the four-generation family of one of the mutation-negative patients excluded the NOGGIN locus, providing genetic evidence of locus heterogeneity. In this family, polymorphic markers flanking the GDF5 locus were found to cosegregate with the disease, and sequence analysis demonstrated that affected individuals in the family were heterozygous for a novel missense mutation that predicts an R438L substitution in the GDF5 protein. Unlike mutations that lead to haploinsufficiency for GDF5 and produce brachydactyly C, the protein encoded by the multiple-synostosis-syndrome allele was secreted as a mature GDF5 dimer. These data establish locus heterogeneity in multiple-synostosis syndrome and demonstrate that the disorder can result from mutations in either the NOGGIN or the GDF5 gene.

A transcriptional profile of human fetal cartilage.

Cartilage plays a central role in the patterning and growth of the skeletal elements, and mutations in genes expressed in cartilage are responsible for at least 250 distinct clinical conditions, the osteochondrodysplasias. While recent progress has been made in characterizing the genes that define cartilage biology, there are only limited data describing the gene expression profile of human cartilage. Here we describe the sequences and identities of 6266 clones from an 18-20-week human fetal cartilage cDNA library. Among the sequences, BLAST analysis identified 2404 individual transcripts. Of these, 1775 were defined as derived from characterized genes and the remaining 629 were classified as representing the products of uncharacterized genes. Analysis of the relative representation of each individual transcript showed that the 186 most abundant cDNAs in the library accounted for almost half (47.7%) of the clones. The most highly expressed gene was COL2A1, accounting for 4.15% of all cDNA clones. The cDNAs identified included clones derived from 27 genes which, when mutated, result in disorders of skeletal patterning, development and growth. There were cDNAs representing 22 genes encoding collagen subunits. The genes encoding the identified cDNAs represent candidates for the approximately 100 osteochondrodysplasias for which the causative gene has not yet been identified. Moreover, these data provide an extensive profile of human fetal cartilage gene expression at this developmental stage.

Mutations in the gene encoding filamin B disrupt vertebral segmentation, joint formation and skeletogenesis.

The filamins are cytoplasmic proteins that regulate the structure and activity of the cytoskeleton by cross-linking actin into three-dimensional networks, linking the cell membrane to the cytoskeleton and serving as scaffolds on which intracellular signaling and protein trafficking pathways are organized (reviewed in refs. 1,2). We identified mutations in the gene encoding filamin B in four human skeletal disorders. We found homozygosity or compound heterozygosity with respect to stop-codon mutations in autosomal recessive spondylocarpotarsal syndrome (SCT, OMIM 272460) and missense mutations in individuals with autosomal dominant Larsen syndrome (OMIM 150250) and the perinatal lethal atelosteogenesis I and III phenotypes (AOI, OMIM 108720; AOIII, OMIM 108721). We found that filamin B is expressed in human growth plate chondrocytes and in the developing vertebral bodies in the mouse. These data indicate an unexpected role in vertebral segmentation, joint formation and endochondral ossification for this ubiquitously expressed cytoskeletal protein.

Isolation of a new member of the ADP-ribosylation like factor gene family, ARL8, from a cartilage cDNA library.

ADP-ribosylation factors (ARFs) and ARF-like proteins (ARLs) are part of the ARF family within the RAS superfamily of regulatory GTPases. Guanine nucleotide binding proteins or GTPases are involved in a diverse spectrum of cellular activities, including regulating cell growth and signal transduction, organization of the cytoskeleton and regulating membrane trafficking along the exocytic and endocytic pathways. ARL proteins share 40-60% sequence identity with the ARF proteins, but ARLs can be distinguished from ARFs based on expression patterns and biological functions. We have identified a new ARL, ARL8, from a fetal cartilage cDNA library. ARL8 contains six exons and five introns, and encodes a 179 amino acid protein that shares homology to the other ARL proteins, especially ARL5. It also shows significant homology with orthologous proteins found in Mus musculus and Drosophila melanogaster. The expression pattern of the mouse ortholog revealed differential tissue expression and an alternate transcript was seen in brain that was age-dependent. ARL8 is an additional member of a family of closely related proteins that are conserved both within the family and across species.

Analysis of clones from a human cartilage cDNA library provides insight into chondrocyte gene expression and identifies novel candidate genes for the osteochondrodysplasias.

To begin to define the gene expression pattern in fetal cartilage and to identify uncharacterized candidate genes for the osteochondrodysplasias, we analyzed clones from a fetal cartilage cDNA library. Sequence analysis of 420 cDNA clones identified 210 clones derived from established genes but, for many of them, expression in cartilage had not been previously reported. Among the established genes were 14 genes known to produce skeletal abnormalities in either humans or mice when mutated. Thirty-two uncharacterized genes and their respective chromosomal positions were also identified. To further understand the expression profile of these genes in fetal cartilage, we constructed a cDNA microarray utilizing the clones. The microarray was used to determine which genes had higher expression in cartilage as compared with dedifferentiated, cultured chondrocytes. Many of the established genes, as well as five of the uncharacterized genes, had increased expression in cartilage, suggesting an important role for these genes in the differentiated state of chondrocytes. These data provide new candidate genes for the osteochondrodysplasias and demonstrate the usefulness of cartilage cDNA microarrays in expanding our understanding of the complexity of fetal cartilage gene expression.

Evidence that Smith-McCort dysplasia and Dyggve-Melchior-Clausen dysplasia are allelic disorders that result from mutations in a gene on chromosome 18q12.

Smith-McCort dysplasia is a rare autosomal recessive osteochondrodysplasia characterized by short limbs and a short trunk with a barrel-shaped chest. The radiographic phenotype includes platyspondyly, generalized abnormalities of the epiphyses and metaphyses, and a distinctive lacy appearance of the iliac crest. We performed a genomewide scan in a consanguineous family from Guam and found evidence of linkage to loci on chromosome 18q12. Analysis of a second, smaller family was also consistent with linkage to this region, producing a maximum combined two-point LOD score of 3.04 at a recombination fraction of 0 for the marker at locus D18S450. A 10.7-cM region containing the disease gene was defined by recombination events in two affected individuals in the larger family. Furthermore, all affected children in the larger family were homozygous for a subset of marker loci within this region, defining a 1.5-cM interval likely to contain the defective gene. Analysis of three small, unrelated families with Dyggve-Melchior-Clausen syndrome, a radiographically identical disorder with the additional clinical finding of mental retardation, provided evidence of linkage to the same region, a result consistent with the hypothesis that the two disorders are allelic.