Mutational analysis of the BMP-1 gene in patients with gastroschisis

Understanding the matrix: collagen modifications in tumors and their implications for immunotherapy

Tumors are highly complex and heterogenous ecosystems where malignant cells interact with healthy cells and the surrounding extracellular matrix (ECM). Solid tumors contain large ECM deposits that can constitute up to 60% of the tumor mass. This supports the survival and growth of cancerous cells and plays a critical role in the response to immune therapy. There is untapped potential in targeting the ECM and cell-ECM interactions to improve existing immune therapy and explore novel therapeutic strategies. The most abundant proteins in the ECM are the collagen family. There are 28 different collagen subtypes that can undergo several post-translational modifications (PTMs), which alter both their structure and functionality. Here, we review current knowledge on tumor collagen composition and the consequences of collagen PTMs affecting receptor binding, cell migration and tumor stiffness. Furthermore, we discuss how these alterations impact tumor immune responses and how collagen could be targeted to treat cancer.

Identification of risk variants related to malignant tumors in children with birth defects by whole genome sequencing

Background

Children with birth defects (BD) are more likely to develop cancer and the increased risk of cancer persists into adulthood. Prior population-based assessments have demonstrated that even non-chromosomal BDs are associated with at least two-fold increase of cancer risk. Identification of variants that are associated with malignant tumor in BD patients without chromosomal anomalies may improve our understanding of the underlying molecular mechanisms and provide clues for early cancer detection in children with BD.

Methods

In this study, whole genome sequencing (WGS) data of blood-derived DNA for 1653 individuals without chromosomal anomalies were acquired from the Kids First Data Resource Center (DRC), including 541 BD probands with at least one type of malignant tumors, 767 BD probands without malignant tumor, and 345 healthy family members who are the parents or siblings of the probands. Recurrent variants exclusively seen in cancer patients were selected and mapped to their corresponding genomic regions. The targeted genes/non-coding RNAs were further reduced using random forest and forward feature selection (ffs) models.

Results

The filtered genes/non-coding RNAs, including variants in non-coding areas, showed enrichment in cancer-related pathways. To further support the validity of these variants, blood WGS data of additional 40 independent BD probands, including 25 patients with at least one type of cancers from unrelated projects, were acquired. The counts of variants of interest identified in the Kid First data showed clear deviation in the validation dataset between BD patients with cancer and without cancer. Furthermore, a deep learning model was built to assess the predictive abilities in the 40 patients using variants of interest identified in the Kids First cohort as feature vectors. The accuracies are ~ 75%, with the noteworthy observation that variants mapped to non-coding regions provided the highest accuracy (31 out of 40 patients were labeled correctly).

Conclusion

We present for the first time a panorama of genetic variants that are associated with cancers in non-chromosomal BD patients, implying that our approach may potentially serve for the early detection of malignant tumors in patients with BD.

Fetal gastroschisis: Maternal and fetal methylation profile

OBJECTIVE

The purpose of this study was to describe the genomic deoxyribonucleic acid (DNA) methylation profile in fetuses with gastroschisis, determine whether the profile was inherited, and investigate any possible correlations with maternal risk factors.

METHOD

Genome-wide DNA methylation analysis of 96 blood samples was performed using the Illumina Human Methylation 850K BeadChip. The blood samples were collected as follows: 32 from the umbilical cord of fetuses with gastroschisis, 32 from their respective mothers, 16 from the umbilical cord of fetuses without malformation, and 16 from their respective mothers.

RESULTS

The differential DNA methylation analysis showed a significant difference between the groups. The enrichment analysis resulted in 12 sites related to T-cell activation (p = 0.0128). The sites with different methylation status contained 10 genes, three of which were related to the beta-2-microglobulin gene. The methylation profile observed in the fetuses with gastroschisis was not inherited from the mothers. In addition, there was no association between maternal urinary tract infection, smoking, and alcohol use and different methylated sites.

CONCLUSION

We established the methylation profile of gastroschisis fetuses, which differs from that of normal fetuses. The profile was not inherited and did not correlate with maternal risk factors.

Genetic variants conferring susceptibility to gastroschisis: a phenomenon restricted to the interaction with the environment?

BACKGROUND

Genes involved in gastroschisis have shown a strong interaction with environmental factors. However, less is known about its influence. We aimed to systematically review the genetic associations of gastroschisis, to summarize whether its genetic susceptibility has been restricted to the interaction with the environment, and to identify significant gaps that remain for consideration in future studies.

METHODS

Genetic association studies of gastroschisis published 1980-2017 (PubMed/MEDLINE) were independently searched by two reviewers. Significant SNP-gastroschisis associations were grouped into crude and stratified risks, whereas SNPs were assessed from two or more independent studies. Frequencies, odds ratios, and 95% confidence intervals were pooled using descriptive analysis and Chi-square test accounting for heterogeneity.

RESULTS

Seven eligible articles capturing associations of 14 SNPs from 10 genes for crude risk (including 10 and 4 SNPs with increased and decreased risk, respectively) and 30 SNPs from 14 genes for stratified risk in gastroschisis (including 37 and 14 SNPs with increased and decreased risk, respectively) were identified (Fisher's exact test, P = 0.438). The rs4961 (ADD1), rs5443 (GNB3), rs1042713, and rs1042714 (ADRB2) were significantly associated with gastroschisis.

CONCLUSIONS

Genetic susceptibility in gastroschisis is not restricted to the interaction with the environment and should not be too narrowly focused on environmental factors. We found significant associations with four SNPs from three genes related to blood pressure regulation, which supports a significant role of vascular disruption in the pathogenesis of gastroschisis. Future studies considering gene-gene or gene-environmental interactions are warranted for better understanding the etiology of gastroschisis.

Maternal smoking, xenobiotic metabolizing enzyme gene variants, and gastroschisis risk

Maternal smoking during pregnancy is one proposed risk factor for gastroschisis, but reported associations have been modest, suggesting that differences in genetic susceptibility might play a role. We included 108 non-Hispanic white and 62 Hispanic families who had infants with gastroschisis, and 1,147 non-Hispanic white and 337 Hispanic families who had liveborn infants with no major structural birth defects (controls) in these analyses. DNA was extracted from buccal cells collected from infants and mothers, and information on periconceptional smoking history was obtained from maternal interviews, as part of the National Birth Defects Prevention Study. We analyzed five polymorphisms in three genes that code for enzymes involved in metabolism of some cigarette smoke constituents (CYP1A1, CYP1A2, and NAT2). Logistic regression models were used to estimate odds ratios (ORs) and 95% confidence intervals (CIs) independently for maternal smoking and maternal and infant gene variants, and to assess joint associations of maternal smoking and maternal or infant gene variants with gastroschisis. In analyses adjusted for maternal age at delivery and stratified by maternal race-ethnicity, we identified three suggestive associations among 30 potential associations with sufficient numbers to calculate ORs: CYP1A1*2A for non-Hispanic white mothers who smoked periconceptionally (aOR = 0.38, 95% CI 0.15-0.98), and NAT2*6 for Hispanic non-smoking mothers (aOR = 2.17, 95% CI 1.12-4.19) and their infants (aOR = 2.11, 95% CI 1.00-4.48). This analysis does not support the occurrence of effect modification between periconceptional maternal smoking and most of the xenobiotic metabolizing enzyme gene variants assessed.

Gastroschisis with ceco-appendicular agenesis: a novel presentation

Gastroschisis is associated with intestinal atresia and malrotation. A few cases have been reported of appendicular agenesis associated with gastroschisis. No previous case has been reported of cecal agenesis with gastroschisis in the literature. As cecal agenesis is a very rare anomaly, its concomitant presentation with gastroschisis is extremely rare. We report a case of gastroschisis associated with ceco-appendicular agenesis. The possible embryological explanation for the presentation is discussed.

Familial recurrence of gastroschisis: literature review and data from the population-based birth registry "Mainz Model"

BACKGROUND

Familial forms of gastroschisis are considered rare. A search for these forms in a population-based birth registry in 1993 found a recurrence risk of 3.5% among first-degree relatives. Since then, similar investigations in population-based registries have led to contradictory results.

METHODS

A search of the population-based birth registry "Mainz Model" for familial cases of gastroschisis and a systematic review of the literature were performed.

RESULTS

The Mainz Model database yielded 1 familial recurrence out of 27 gastroschisis cases. From the literature, 37 affected families could be retrieved. Among 412 gastroschises from population-based registries, 10 familial recurrences have been found. These translate into a recurrence risk of 2.4%, with a strong tendency toward underestimation.

CONCLUSION

The existing data support the hypothesis that familial recurrence of gastroschisis is much more likely than previously thought.

Prenatal genomic profiling of abdominal wall defects through comparative genomic hybridization: perspectives for a new diagnostic tool

OBJECTIVES

To describe the molecular analysis through comparative genomic hybridization (CGH) of fetuses with gastroschisis, and to observe if this technique could improve the resolution of the conventional cytogenetic techniques.

METHODS

Amniotic analysis of fetuses with gastroschisis, using both conventional (G-banding) and molecular (CGH) cytogenetics assays.

RESULTS

All of the seven fetuses studied displayed a normal G-band karyotype. Six fetuses displayed a normal disomic profile through CGH and one sample has displayed ish cgh enh 3q26-->qter result (ICSN). The fetus with this imbalance of chromosome 3 was re-classified as a ruptured omphalocele, instead of gastroschisis, after birth.

CONCLUSIONS

The molecular investigation through CGH technique can improve the resolution of the conventional karyotye analysis in cases of abdominal wall defects.

Developmental roles of the BMP1/TLD metalloproteinases

The astacin family (M12A) of the metzincin subclan MA(M) of metalloproteinases has been detected in developing and mature individuals of species that range from hydra to humans. Functions of this family of metalloproteinase vary from digestive degradation of polypeptides, to biosynthetic processing of extracellular proteins, to activation of growth factors. This review will focus on a small subgroup of the astacin family; the bone morphogenetic protein 1 (BMP1)/Tolloid (TLD)-like metalloproteinases. In vertebrates, the BMP1/TLD-like metalloproteinases play key roles in regulating formation of the extracellular matrix (ECM) via biosynthetic processing of various precursor proteins into mature functional enzymes, structural proteins, and proteins involved in initiating mineralization of the ECM of hard tissues. Roles in ECM formation include: processing of the C-propeptides of procollagens types I-III, to yield the major fibrous components of vertebrate ECM; proteolytic activation of the enzyme lysyl oxidase, necessary to formation of covalent cross-links in collagen and elastic fibers; processing of NH2-terminal globular domains and C-propeptides of types V and XI procollagen chains to yield monomers that are incorporated into and control the diameters of collagen type I and II fibrils, respectively; processing of precursors for laminin 5 and collagen type VII, both of which are involved in securing epidermis to underlying dermis; and maturation of small leucine-rich proteoglycans. The BMP1/TLD-related metalloproteinases are also capable of activating the vertebrate transforming growth factor-beta (TGF-beta)-like "chalones" growth differentiation factor 8 (GDF8, also known as myostatin), and GDF11 (also known as BMP11), involved in negative feedback inhibition of muscle and neural tissue growth, respectively; by freeing them from noncovalent latent complexes with their cleaved prodomains. BMP1/TLD-like proteinases also liberate the vertebrate TGF-beta-like morphogens BMP2 and 4 and their invertebrate ortholog decapentaplegic, from latent complexes with the vertebrate extracellular antagonist chordin and its invertebrate ortholog short gastrulation (SOG), respectively. The result is formation of the BMP signaling gradients that form the dorsal-ventral axis in embryogenesis. Thus, BMP1/TLD-like proteinases appear to be key to regulating and orchestrating formation of the ECM and signaling by various TGF-beta-like proteins in morphogenetic and homeostatic events.

Incorporating genetic analyses into birth defects cluster investigations: Strategies for identifying candidate genes

BACKGROUND

Incorporating genetic analyses into birth defect cluster investigations may increase understanding of both genetic and environmental risk factors for the defect. Current constraints of most birth defect cluster investigations make candidate gene selection the most feasible approach. Here, we describe strategies for choosing candidate genes for such investigations, which will also be applicable to more general gene-environment studies.

METHODS

We reviewed publicly available web-based resources for selection of candidate genes and identification of risk factors, as well as publications on different strategies for candidate gene selection.

RESULTS

Candidate gene selection requires consideration of available gene-disease databases, previous epidemiological studies, animal model research, linkage and expression studies, and other resources. We describe general considerations for utilizing available resources, as well as provide an example of a search for candidate genes related to gastroschisis.

CONCLUSIONS

Available web resources could facilitate selection of candidate genes, but selection of optimal candidates will still require a strong understanding of genetics and the pathogenesis of the defect, as well as careful consideration of previous epidemiological studies.

Aortic carboxypeptidase-like protein is regulated by transforming growth factor β in 3T3-L1 preadipocytes

Adipogenesis is characterized by early remodeling of the extracellular matrix, allowing preadipocytes to adopt a more spherical shape and optimize lipid accumulation as they mature. Aortic carboxypeptidase-like protein (ACLP), found in collagen-rich tissues including adipose tissue, is expressed in 3T3-L1 and 3T3-F442A preadipocytes, and is downregulated during adipogenesis. We now report that ACLP is found in medium conditioned by 3T3-L1 preadipocytes. Transforming growth factor (TGF) beta, a known modulator of fibrillar matrix protein production, increased ACLP expression by 2.4+/-0.4-fold (mean+/-SE; n=3) in 3T3-L1 preadipocytes, through a mechanism that requires p42/44 MAPK activity. Addition of TGFbeta to differentiation medium, which inhibits adipogenesis, raised ACLP levels in 3T3-L1 cells. However, sustained expression of ACLP in stable clones of 3T3-L1 or 3T3-F442A preadipocytes did not interfere with adipogenesis.

Family cases of gastroschisis

The etiology of gastroschisis is still unclear. To the authors' knowledge, there are only 14 cases of familial gastroschisis in the literature. The authors add the second case of mother-and-son occurrence and a case of siblings occurrence, thereby updating the current literature for family gastroschisis.

Isolated Gastroschisis in Successive Siblings: A Case Report and Review of the Literature

BACKGROUND

Although gastroschisis occurring in siblings is rare, a number of cases have been reported. A variety of inheritance patterns and embryologic explanations have previously been suggested. Young maternal age appears to be a consistent risk factor.

CASE

At age 17 years, Melanie (pseudonym) presented at 36 weeks' gestation and delivered a boy affected by gastroschisis. This condition had not been noted at a 13-week prenatal ultrasound. At age 18 years, Melanie delivered a second son with gastroschisis. There was no history of gastroschisis or other congenital anomaly in either parent's family. Melanie denied the use of alcohol, cigarettes, street drugs, and medications. She has since delivered 2 healthy children.

CONCLUSION

There is a need for preconception counselling for women who have experienced a pregnancy complicated by gastroschisis, to discuss the low but possible risk of recurrence. Early ultrasound may allow for detection or reassurance.

Abdominal wall defects

Survival for newborns with congenital abdominal wall defects (primarily omphalocele and gastroschisis) has improved, but controversy remains regarding etiology, anatomy and embryology, the role of prenatal diagnosis and mode of delivery, and initial management. A number of recent studies have added to our knowledge and understanding of several of these topics, while several others have raised questions regarding traditional initial management of these infants. Continued improvement in the survival of these infants can be anticipated with further understanding of the in utero and antepartum diagnosis and management of infants with these common congenital abnormalities.