Whole genome resequencing reveals candidate genes for postaxial polydactyly in Large White pigs

Polydactyly is a genetic abnormality that affects both pig welfare and industry profits. Despite efforts to explore the genetic basis of pig polydactyly, progress remains limited. In this study, we analyzed a group of Large White pigs with postaxial polydactyly, including 29 cases and 79 controls from 24 families. High-depth sequencing was performed on 20 pigs, while low-depth sequencing was improved through imputation for the remaining pigs. A genome-wide association study (GWAS) and genetic differentiation were conducted using the resequencing dataset, resulting in the identification of 48 significantly associated SNPs and 27 candidate regions. The genetic differentiation regions on chromosomes 5 and 18, which harbored GWAS-identified SNPs, were delineated as confidence regions. The confidence region at Chr18: 1.850-1.925 Mb covers the fifth intron of LMBR1, a gene that contains an important regulatory element for SHH, known as ZRS. Mutations in this ZRS have been found to cause polydactyly in animals and humans. Therefore, we propose LMBR1 as a prospective candidate gene for postaxial polydactyly. These findings emphasize the importance of exploring the role of ZRS within LMBR1 in the pathogenesis of polydactyly in pigs.

RNA sequencing resolves novel DYNC2H1 variants causing short-rib thoracic dysplasia type 3: Case report

BACKGROUND

Intronic variants outside the canonical splice site are challenging to interpret and therefore likely represent an underreported cause of human disease. Autosomal recessive variants in DYNC2H1 are associated with short-rib thoracic dysplasia 3 with or without polydactyly (SRTD3), a clinically heterogeneous disease generally presenting with short ribs, shortened tubular bones, narrow thorax and acetabular roof anomalies. We describe a case of SRTD3 with compound heterozygous frameshift and intronic variants and highlight the essential role of RNA sequencing (RNA-Seq) in variant interpretation.

METHODS

Following inconclusive clinical genetic testing identifying a likely pathogenic frameshift variant and an intronic variant of uncertain significance (VUS) in DYNC2H1 in trans, the family enrolled in the Care4Rare Canada research program, where RNA-Seq studies were performed.

RESULTS

The proband presented with post-axial polydactyly of all four limbs, a significantly small chest with a pectus excavatum and anterior flaring of the ribs. RNA-Seq investigations revealed a novel splice junction as a result of the intronic VUS and significantly decreased DYNC2H1 gene expression in the proband.

CONCLUSION

This case demonstrates the diagnostic utility of RNA-Seq for variant interpretation following inconclusive clinical testing, which can ultimately lead to diagnosis for patients with rare disease.

Structural Evaluation and Conformational Dynamics of ZNF141T474I Mutation Provoking Postaxial Polydactyly Type A

Postaxial Polydactyly (PAP) is a congenital disorder of limb abnormalities characterized by posterior extra digits. Mutations in the N-terminal region of the Zinc finger protein 141 (ZNF141) gene were recently linked with PAP type A. Zinc finger proteins exhibit similarity at their N-terminal regions due to C2-H2 type Zinc finger domains, but their functional preferences vary significantly by the binding patterns of DNA. Methods: This study delineates the pathogenic association, miss-fold aggregation, and conformational paradigm of a missense variant (c.1420C > T; p.T474I) in ZNF141 gene segregating PAP through a molecular dynamics simulations approach. Results: In ZNF141 protein, helices play a crucial role by attaching three specific target DNA base pairs. In ZNF141T474I protein, H1, H3, and H6 helices attain more flexibility by acquiring loop conformation. The outward disposition of the proximal portion of H9-helix in mutant protein occurs due to the loss of prior beta-hairpins at the C terminal region of the C2-H2 domain. The loss of hydrogen bonds and exposure of hydrophobic residues to solvent and helices turning to loops cause dysfunction of ZNF141 protein. These significant changes in the stability and conformation of the mutant protein were validated using essential dynamics and cross-correlation maps, which revealed that upon point mutation, the overall motion of the proteins and the correlation between them were completely different, resulting in Postaxial polydactyly type A. Conclusions: This study provides molecular insights into the structural association of ZNF141 protein with PAP type A. Identification of active site residues and legends offers new therapeutic targets for ZNF141 protein. Further, it reiterates the functional importance of the last residue of a protein.

Quantitative Evaluation and Midterm Progress of Reconstructed Toe Thickness in Lateral Ray Polydactyly of the Foot

In lateral ray polydactyly, the reconstructed toe often tends to become thicker, but no standard evaluation criteria for this thickness are available. 57 patients (68 toes) with Hirai-Togashi classification type II, III, or IV whom we were able to follow-up for more than 6 months after the operation were underwent measurement of the "Reconstructed toe width to Third toe width ratio." In addition, 16 patients who could be followed up for 3 years through the mid-term course were evaluated for mid-term progress. At 6 months after surgery, the mean R/T ratio was 1.246. In patients who could be followed up for 3 years after surgery, the mean R/T ratios at 6 months after surgery and at 3 years were significantly decreased. This result suggests that the thickness of the reconstructed toe may become relatively thin in the long term.

Examination of Postoperative Outcomes Using Morphological and X-Ray Classifications and Selection of the Toe to Be Excised in Postaxial Polydactyly of the Foot

The treatment of postaxial polydactyly requires excision of the medial fifth or lateral sixth toe, and separation of the adjacent fourth/fifth toes if the adjacent toes exhibit skin syndactyly. Morphological changes in the retained toes and reoperation are common problems after such surgery. This study examined the effects of preoperative classifications and selecting the medial fifth or lateral sixth toe for excision on the postoperative outcomes of surgery for postaxial polydactyly. From April 2006 to March 2019, surgery for postaxial polydactyly was performed on 55 feet in 49 patients. The patients' mean age at surgery was 28.8 months. Postoperative esthetic and bone alignment scores, the reoperation rate, and postoperative dysfunction were examined. The postoperative esthetic and bone alignment evaluations were performed by examining postoperative photograph and X-ray images using original scoring systems. The surgical procedure was chosen by the surgeon-in-charge during a preoperative conference after considering the toe growth and bone alignment. In the postoperative esthetic evaluation, excising the lateral sixth toe produced significantly better outcomes than excising the medial fifth toe. The morphological classification also indicated that excising the lateral sixth toe produced better outcomes, as it resulted in the bifurcated toes being clearly independent. Interestingly, the postoperative X-ray-based bone alignment score was not correlated with the esthetic score. The reoperation rate tended to be high after medial fifth toe excision. There were no postoperative functional complications. Lateral sixth toe excision for postaxial polydactyly of the foot produces good postoperative esthetic outcomes.

Surgical Outcomes and Predictive Factors of Medial Toe Excision for Polysyndactyly of the Fifth Toe

BACKGROUND

We aimed to report surgical outcomes and analyze prognostic factors of medial toe excision for polysyndactyly of the fifth toe.

METHODS

We reviewed the details of 139 consecutive patients who underwent surgery for postaxial polydactyly of the foot from 2009 to 2018. Among these, 83 patients (90 feet) with polysyndactyly of the fifth toe, treated by medial toe excision (between the duplicated toes) and reconstruction of the fourth web space using a dorsal rectangular flap, were included. The toe alignment and stability were restored by chondroplasty and soft tissue balancing without an osteotomy. A full-thickness skin graft was performed in 52 feet. The mean age at surgery was 27.1 ± 17.5 months and the mean duration of follow-up was 42.8 ± 24.9 months.

RESULTS

At the last follow-up, a relatively small size of the reconstructed toe was observed in 19 feet (19/90, 21.1%). Proximal duplication level (metatarsal or proximal phalanx type) and preoperative hypoplasia of the remaining toe were related to the small postoperative size. Valgus deformity of the remaining toe was observed in 2 feet (2/90, 2.2%). We observed 17 cases with delayed healing or early postoperative wound infection. Among these, 7 cases (7/90, 7.8%) showed postoperative thickening or advancement of the web, which was not observed in cases without wound problems. No cases had functional disturbance or pain.

CONCLUSION

The overall surgical outcomes were satisfactory without an osteotomy. Patients with a proximal duplication level or preoperative hypoplasia of the remaining toe should be informed of its possible small size postoperatively.

LEVELS OF EVIDENCE

Level IV, retrospective case series.

Germline and Mosaic Variants in PRKACA and PRKACB Cause a Multiple Congenital Malformation Syndrome

PRKACA and PRKACB code for two catalytic subunits (Cα and Cβ) of cAMP-dependent protein kinase (PKA), a pleiotropic holoenzyme that regulates numerous fundamental biological processes such as metabolism, development, memory, and immune response. We report seven unrelated individuals presenting with a multiple congenital malformation syndrome in whom we identified heterozygous germline or mosaic missense variants in PRKACA or PRKACB. Three affected individuals were found with the same PRKACA variant, and the other four had different PRKACB mutations. In most cases, the mutations arose de novo, and two individuals had offspring with the same condition. Nearly all affected individuals and their affected offspring shared an atrioventricular septal defect or a common atrium along with postaxial polydactyly. Additional features included skeletal abnormalities and ectodermal defects of variable severity in five individuals, cognitive deficit in two individuals, and various unusual tumors in one individual. We investigated the structural and functional consequences of the variants identified in PRKACA and PRKACB through the use of several computational and experimental approaches, and we found that they lead to PKA holoenzymes which are more sensitive to activation by cAMP than are the wild-type proteins. Furthermore, expression of PRKACA or PRKACB variants detected in the affected individuals inhibited hedgehog signaling in NIH 3T3 fibroblasts, thereby providing an underlying mechanism for the developmental defects observed in these cases. Our findings highlight the importance of both Cα and Cβ subunits of PKA during human development.

Common atrium/atrioventricular canal defect and postaxial polydactyly: A mild clinical subtype of Ellis-van Creveld syndrome caused by hypomorphic mutations in the EVC gene

Clinical expression of Ellis-van Creveld syndrome (EvC) is variable and mild phenotypes have been described, including patients with mostly cardiac and limb involvement. Whether these cases are part of the EvC phenotypic spectrum or separate conditions is disputed. Herein, we describe a family with vertical transmission of atrioventricular canal defect (AVCD), common atrium, and postaxial polydactyly. Targeted sequencing of EVC, EVC2, WDR35, DYNC2LI1, and DYNC2H1 identified different compound heterozygosity in EVC genotypes in the two affected members, consisting of a nonsense (p.Arg622Ter) and a missense (p.Arg663Pro) variant in the father, and the same nonsense variant and a noncanonical splice-site in-frame change (c.1316-7A>G) in the daughter. Complementary DNA sequencing, immunoblot, and immunofluorescence experiments using patient-derived fibroblasts and Evc^-/- mouse embryonic fibroblasts showed that p.Arg622Ter is a loss-of-function mutation, whereas p.Arg663Pro and the splice-site change c.1316-7A>G are hypomorphic variants resulting in proteins that retain, in part, the ability to complex with EVC2. Our molecular and functional data demonstrate that at least in some cases the condition characterized as "common atrium/AVCD with postaxial polydactyly" is a mild form of EvC due to hypomorphic EVC mutations, further supporting the occurrence of genotype-phenotype correlations in this syndrome.

To Tie or Not to Tie: A Systematic Review of Postaxial Polydactyly and Outcomes of Suture Ligation Versus Surgical Excision

Background: Ulnar polydactyly is frequently encountered in the newborn nursery and is commonly treated with bedside suture ligation. However, growing concern about the complications associated with suture ligation has led some practitioners to advocate for primary surgical excision instead. Thus, we set out to compare outcomes of suture ligation and surgical excision by systematic appraisal of the literature. Methods: Following PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines, a systematic review was performed to identify studies published between 1950 and 2017 that described outcomes of suture ligation, surgical excision, or both. Baseline characteristics, complications, and study quality were extracted for each included article. Results: A total of 900 articles were reviewed, of which 10 studies (8 case series, 2 comparative analyses) met the inclusion criteria. There was considerable heterogeneity among the studies with respect to patient characteristics and reported outcomes. There were 2 retrospective case series of suture ligation that reported no acute complications and a variable proportion of patients with residual remnants or neuromas. Studies evaluating surgical ligation reported no acute or long-term complications, with only 1 case series reporting a small percentage of residual remnants. However, in the largest cohort analysis, the difference in complication rate was reported to be as high as 23.5% for suture ligation compared with 3% for surgical excision. Conclusions: There is a paucity of literature limiting the comparison of suture ligation and surgical excision for ulnar polydactyly. Further studies are required to determine the optimal treatment.

A GLI3 variant leading to polydactyly in heterozygotes and Pallister-Hall-like syndrome in a homozygote

Variants in transcriptional activator Gli Kruppel Family Member 3 (GLI3) have been reported to be associated with several phenotypes including Greig cephalopolysyndactyly syndrome (MIM #175700), Pallister-Hall syndrome (PHS) (MIM #146510), postaxial polydactyly types A1 (PAPA1) and B (PAPB) (MIM #174200), and preaxial polydactyly type 4 (MIM #174700). All these disorders follow an autosomal dominant pattern of inheritance. Hypothalamic hamartomas (MIM 241800) is associated with somatic variants in GLI3. We report a related couple with parents having PAPA1 and PAPB, who had a fetus with a phenotype most compatible with PHS. Molecular analyses demonstrated homozygosity for a pathogenic GLI3 variant (c.1927C > T; p. Arg643*) in the fetus and heterozygosity in the parents. The genetic analysis in this family demonstrates that heterozygosity and homozygosity for the same GLI3 variant can cause a different phenotype. Furthermore, the occurrence of Pallister-Hall-like syndrome in a homozygous patient should be taken into account in genetic counseling of families with PAPA1/PAPB.

Clinical study of 459 polydactyly cases in China, 2010 to 2014

Polydactyly is one of the most common hereditary limb malformations, involving additional digits on the hands and/or feet, which is a very attractive model to appreciate clinical and genetic heterogeneity. A high level of heterogeneity in polydactyly has been identified in different regions. However, such data of the medical literatures for Asian populations are relatively limited. This study was intended to shed light on the phenotypic manifestations of polydactyly in the recruited Chinese population and to characterize the medical literature on this condition. A total of 459 well-characterized polydactyly cases from Shanghai Children's Medical Center were recruited. Their phenotypes, inheritance patterns, and clinical heterogeneity were obtained from clinical medical records. It was found that 4.8% of cases were familial and 95.2% were sporadic. The proportions of preaxial and postaxial polydactyly types were 74.7% and 25.3%, respectively. In preaxial polydactyly, type I formed the overwhelming majority (95.9%). Among the postaxial polydactyly cases, type A was most prevalent at 69.8% and type B was witnessed in 30.2% of cases. Familial and sporadic polydactyly patients mainly had unilateral presentations. A total of 583 limbs with additional digits were recorded in the 459 subjects. Upper limb involvement was more common than lower, and right hand involvement was more common than left for preaxial polydactyly, and lower limb involvement was more common than upper in postaxial polydactyly. This cohort added useful clinical/epidemiological information to the polydactyly literature in the Chinese population and highlighted its marked clinical heterogeneity.

Review of literature: genes related to postaxial polydactyly

BACKGROUND

Postaxial polydactyly (PAP) is one of the commonest congenital malformations and usually is associated to several syndromes. There is no primary investigational strategy for PAP cases with single gene disorder in literature. PAP cases with single gene disorder can be classified according to common pathways and molecular basis. Molecular classification may help in diagnostic approach.

MATERIALS AND METHODS

All single gene disorders associated with PAP reported on PubMed and OMIM are analyzed and classified according to molecular basis.

RESULTS

Majority of genes related to cilia structure and functions are associated with PAP, so we classified them as ciliopathies and non-ciliopathies groups. Genes related to Shh-Gli3 pathway was the commonest group in non-ciliopathies.

CONCLUSION

Genes related to cilia are most commonly related to PAP due to their indirect relationship to Shh-Gli3 signaling pathway. Initially, PAP may be the only clinical finding with ciliopathies so those cases need follow up. Proper diagnosis is helpful for management and genetic counseling. Molecular approach may help to define pleiotropy.

A novel mutation (g.106737G>T) in zone of polarizing activity regulatory sequence (ZRS) causes variable limb phenotypes in Werner mesomelia

Werner mesomelia is characterized by a sequence variation in the specific region (position 404) of the enhancer ZRS of SHH. The phenotype comprises variable mesomelia, abnormalities of the thumb and great toe and supernumerary digits. We describe extensive variation in limb phenotype in a large family and report on a novel sequence variation NG_009240.1: g.106737G>T (traditional nomenclature: ZRS404G>T) in the ZRS within the LMBR1 gene. The newly recognized clinical features in this family include small thenar eminence, sandal gap, broad first metatarsals, mesoaxial polydactyly, and postaxial polydactyly. We provide information on 12 affected family members. We review the literature on how a sequence variation in ZRS may cause such diverse phenotypes.

A 1.1Mb deletion in distal 13q deletion syndrome region with congenital heart defect and postaxial polydactyly: additional support for a CHD locus at distal 13q34 region

13q deletion syndrome is a rare genetic disorder, especially for group 3 deletion (13q33-q34 deletion). Previously we described a patient with congenital heart defect and mental retardation and proposed that a distal 6Mb region might contain the causative gene of congenital heart defect. Here we present a new patient with congenital heart defects (CHD), hand and foot anomalies and mild mental retardation. We identified a 1.1Mb deletion at chromosome 13q34 with high resolution SNP-array BeadChips (HumanOmni1-Quad, Illumina, USA). This chromosome region contains ten annotated genes, including GRK1, TFDP1, RASA3 and GAS6. To our knowledge, this represents the smallest 13q34 deletion identified to date. Our study provides additional support that distal 13q34 deletion region might contain key gene(s) responsible for cardiac development.

Greenberg Skeletal Dysplasia: first reported case in the Democratic Republic of Congo

We describe the first Congolese case of Greenberg Skeletal Dysplasia. Were noted at birth a congenital hydrops, a chondrodystrophy, a severe hypoplastic face as well as an ulnar (postaxial) hexadactyly on all four limbs.