Update of the keratin gene family: evolution, tissue-specific expression patterns, and relevance to clinical disorders

Intermediate filament (IntFil) genes arose during early metazoan evolution, to provide mechanical support for plasma membranes contacting/interacting with other cells and the extracellular matrix. Keratin genes comprise the largest subset of IntFil genes. Whereas the first keratin gene appeared in sponge, and three genes in arthropods, more rapid increases in keratin genes occurred in lungfish and amphibian genomes, concomitant with land animal-sea animal divergence (~ 440 to 410 million years ago). Human, mouse and zebrafish genomes contain 18, 17 and 24 non-keratin IntFil genes, respectively. Human has 27 of 28 type I “acidic” keratin genes clustered at chromosome (Chr) 17q21.2, and all 26 type II “basic” keratin genes clustered at Chr 12q13.13. Mouse has 27 of 28 type I keratin genes clustered on Chr 11, and all 26 type II clustered on Chr 15. Zebrafish has 18 type I keratin genes scattered on five chromosomes, and 3 type II keratin genes on two chromosomes. Types I and II keratin clusters—reflecting evolutionary blooms of keratin genes along one chromosomal segment—are found in all land animal genomes examined, but not fishes; such rapid gene expansions likely reflect sudden requirements for many novel paralogous proteins having divergent functions to enhance species survival following sea-to-land transition. Using data from the Genotype-Tissue Expression (GTEx) project, tissue-specific keratin expression throughout the human body was reconstructed. Clustering of gene expression patterns revealed similarities in tissue-specific expression patterns for previously described “keratin pairs” (i.e., KRT1/KRT10, KRT8/KRT18, KRT5/KRT14, KRT6/KRT16 and KRT6/KRT17 proteins). The ClinVar database currently lists 26 human disease-causing variants within the various domains of keratin proteins.

A KRT6A mutation p.Ile462Asn in a Chinese family with pachyonychia congenita, and identification of maternal mosaicism: a case report

Background Pachyonychia congenita (PC, OMIM #167200, #167210, #615726, #615728, and #615735) is a rare autosomal dominant disorder caused by keratin gene mutations in KRT6A,KRT6B,KRT6C,KRT16 or KRT17. It is characterized with nail dystrophy and palmoplantar keratoderma (PPK). The most prominent manifestation is plantar pain. This is a further unusual case of parental mosaicism in PC. Although very rare, germ cell mosaicism should be considered when providing genetic counselling for unaffected parents of a child with PC. Case presentation We report the case of a 5-year-old boy with thickening nails and oral leukokeratosis at birth. He began to develop palmoplantar keratoderma at 2 years old and his sister has similar clinical manifestation characterized with nail discoloration and thickening. A previously reported heterozygous mutation, p.Ile462Asn, was identified in KRT6A in the proband and his affected sister. SNaPshot sequencing revealed mosaicism at a level of 2.5% and 4.7% in DNA from blood and hair bulbs from the unaffected mother. HiSeq deep sequencing demonstrated low-grade mosaicism in the patient’s younger sister and parents. Conclusion These findings indicate the ability of WES and SNaPshot sequencing to detect low-frequency mosaic mutations. Although very rare, germinal mosaicism should be considered when genetic counseling is given to families with presumed spontaneous cases of PC.

A KRT6A Mutation p.Ile462Asn In A Chinese Family With Pachyonychia Congenita, And Identification of Maternal Mosaicism

Background: Pachyonychia congenita (PC, OMIM #167200, #167210, #615726, #615728, and #615735) is a rare autosomal dominant disorder caused by keratin gene mutations in KRT6A, KRT6B, KRT6C, KRT16 or KRT17. It is characterized with nail dystrophy and palmoplantar keratoderma (PPK). The most prominent manifestation is plantar pain. This is the first reported case of maternal mosaicism in PC. Although very rare, germ cell mosaicism should be considered when providing genetic counselling for unaffected parents of a child with PC. Methods: Genomic DNA was extracted from peripheral blood samples, hair bulbs, buccal smears and the father’s germ cells. The entire coding and flanking intronic sequences of 5 keratin genes were screened for mutations in every individuals of the family by Sanger sequencing. We used whole exome sequencing (WES) to search for mosaicism in the parents who had no KRT6A mutation identified by Sanger sequencing. Mosaicism was confirmed by SNaPshot sequencing and HiSeq deep sequencing.Results: A previously reported heterozygous mutation, p.Ile462Asn, was identified in KRT6A in the proband and his affected sister. The variant was detected in one sequencing read from 86 sequencing reads from DNA from the mother’s blood by WES. The mutation was not identified in DNA from the father’s blood. Frequency of reads was 47% and 49% in proband and his sister, respectively. SNaPshot sequencing revealed mosaicism at a level of 2.5% and 4.7% in DNA from blood and hair bulbs from the unaffected mother. HiSeq deep sequencing demonstrated low-grade mosaicism in the patient’s younger sister and parents.Conclusion: These findings indicate the ability of WES and SNaPshot sequencing to detect low-frequency mosaic mutations. Although very rare, germinal mosaicism should be considered when genetic counseling is given to families with presumed spontaneous cases of PC.

Diet Transition from High-Forage to High-Concentrate Alters Rumen Bacterial Community Composition, Epithelial Transcriptomes and Ruminal Fermentation Parameters in Dairy Cows

Effects of changing diet on rumen fermentation parameters, bacterial community composition, and transcriptome profiles were determined in three rumen-cannulated Holstein Friesian cows using a 3 × 4 cross-over design. Treatments include HF-1 (first high-forage diet), HC-1 (first high-concentrate diet), HC-2 (succeeding high-concentrate diet), and HF-2 (second high-forage diet as a recovery period). Animal diets contained Klein grass and concentrate at ratios of 8:2, 2:8, 2:8, and 8:2 (two weeks each), respectively. Ammonia-nitrogen and individual and total volatile fatty acid concentrations were increased significantly during HC-1 and HC-2. Rumen species richness significantly increased for HF-1 and HF-2. Bacteroidetes were dominant for all treatments, while phylum Firmicutes significantly increased during the HC period. Prevotella, Erysipelothrix, and Galbibacter significantly differed between HF and HC diet periods. Ruminococcus abundance was lower during HF feeding and tended to increase during successive HC feeding periods. Prevotella ruminicola was the predominant species for all diets. The RNA sequence analysis revealed the keratin gene as differentially expressed during the HF diet, while carbonic-anhydrase I and S100 calcium-binding protein were expressed in the HC diet. Most of these genes were highly expressed for HC-1 and HC-2. These results suggested that ruminal bacterial community composition, transcriptome profile, and rumen fermentation characteristics were altered by the diet transitions in dairy cows.

Pleiotropic Functions of FoxN1: Regulating Different Target Genes during Embryogenesis and Nymph Molting in the Brown Planthopper

FoxN1 gene belongs to the forkhead box gene family that comprises a diverse group of “winged helix” transcription factors that have been implicated in a variety of biochemical and cellular processes. In the brown planthopper (BPH), FoxN1 is highly expressed in the ovaries and newly laid eggs, where it acted as an indispensable gene through its molecular targets to regulate early embryonic development. Moreover, the results of the RNAi experiments indicated that Nilaparvata lugens FoxN1 (NlFoxN1) exhibited pleiotropism: they not only affected the embryogenesis, but also played an important role in molting. RNA-seq and RNAi were further used to reveal potential target genes of NlFoxN1 in different stages. In the eggs, ten downregulated genes were defined as potential target genes of NlFoxN1 because of the similar expression patterns and functions with NlFoxN1. Knockdown of NlFoxN1 or any of these genes prevented the development of the eggs, resulting in a zero hatchability. In the nymphs, NlFoxN1 regulated the expression of a keratin gene, type I cytoskeletal keratin 9 (NlKrt9), to participate in the formation of an intermediate filament framework. Depletion of NlFoxN1 or NlKrt9 in nymphs, BPHs failed to shed their old cuticle during nymph-to-nymph or nymph-to-adult molting and the mortality was almost 100%. Altogether, the pleiotropic roles of NlFoxN1 during embryogenesis and nymph molting were supported by the ability to coordinate the temporal and spatial gene expression of their target genes.