Chromosomal mapping of human cytokeratin 13 gene (KRT13)

Developmental validation of an mRNA kit: A 5-dye multiplex assay designed for body-fluid identification

Identifying the sources of biosamples found at crime scenes is crucial for forensic investigations. Among the markers used for body fluid identification (BFI), mRNA has emerged as a well-studied marker because of its high specificity and remarkable stability. Despite this potential, commercially available mRNA kits specifically designed for BFI are lacking. Therefore, we developed an mRNA kit that includes 21 specific mRNA markers of body fluids, along with three housekeeping genes for BFI, to identify four forensic-relevant fluids (blood, semen, saliva, and vaginal fluids). In this study, we tested 451 single-body-fluid samples, validated the universality of the mRNA kit, and obtained a gene expression profile. We performed the validation studies in triplicates and determined the sensitivity, specificity, stability, precision, and repeatability of the mRNA kit. The sensitivity of the kit was found to be 0.1 ng. Our validation process involved the examination of 59 RNA mixtures, 60 body fluids mixtures, and 20 casework samples, which further established the reliability of the kit. Furthermore, we constructed five classifiers that can handle single-body fluids and mixtures using this kit. The classifiers output possibility values and identify the specific body fluids of interest. Our results showed the reliability and suitability of the BFI kit, and the Random Forest classifier performed the best, with 94% precision. In conclusion, we developed an mRNA kit for BFI which can be a promising tool for forensic practice.

Two new mutations in the keratin 4 gene causing oral white sponge nevus in Chinese family

OBJECTIVE

We investigated white sponge nevus (WSN) in a Chinese family, and tried to find new mutation and demonstrated that this mutation is the causative mutation for WSN in this family and this condition affects a functionally important segment of the keratin 4 protein.

MATERIALS AND METHODS

We studied the affected family with the 32-year-old female patient, her mother, her younger sister and her daughter. Pathologic examinations were performed. DNA was extracted from peripheral blood lymphocytes, K4 and K13 genes were amplified by polymerase chain reaction (PCR) and sequenced.

RESULTS

Direct sequencing of PCR products revealed two new mutations in the keratin 4 gene, the heterozygous missense mutation 1829G-->A in exon 2B, and 2324A-->G in non-coding region. No any mutation was found in the keratin 13 gene.

CONCLUSIONS

We found two new mutations in the keratin 4, which may be related with the development of WSN.

Analysis of gene expression profiles in cholesteatoma using oligonucleotide microarray

CONCLUSION

Microarray analysis may be a useful tool to identify some candidate genes related to the pathogenesis of cholesteatoma.

OBJECTIVE

The aim of this study was to investigate gene expression profiles in human cholesteatoma using an oligonucleotide chip including 10,115 genes.

MATERIALS AND METHODS

Gene expression from five cholesteatoma matrices and five normal retroauricular skins was analyzed by Macrogen human oligo-chip and the expression levels of some selected genes were also confirmed by RT-PCR.

RESULTS

In all, 1327 up-regulated or 767 down-regulated genes that were over 3 times more prominent in cholesteatoma than in skin were identified by 5 samples of microarray data. Among these up-regulated or down-regulated genes in cholesteatoma, 291 genes were identified in 3 samples or more out of 5 samples as up-regulated expression more than threefold in density and 191 genes were down-regulated more than threefold in density. RT-PCR of 21 selected genes revealed that those expression levels were higher in choleasteatoma than retroauricular skin.

Cytokeratin expression patterns for distinction of odontogenic keratocysts from dentigerous and radicular cysts

BACKGROUND

The clinical outcome of treatment of odontogenic cysts differs depending on separate entities. Particular clinical relevance must be attached to the distinction between odontogenic keratocysts, which have an evident tendency to recur, and other odontogenic cysts. The aim of this study was to evaluate cytokeratin (CK) expression patterns as an additional tool for characterization of different cysts as the histomorphologic appearance often is not decisive.

METHODS

Thirty cases of dentigerous and radicular cysts respectively as well as 15 cases of odontogenic keratocysts were considered. Expression of CK 5/6, 7, 10, 13, 17, 19 and 20 was determined in addition to Ki-67 immunohistochemically.

RESULTS

Expression of CK 17 was discernible in 93.3% of the odontogenic keratocysts, but only in 35.0% of dentigerous and radicular cysts under study (P < 0.001). CK 19 could be detected in 48.3% of dentigerous and radicular cysts, whereas odontogenic keratocysts were completely negative (P < 0.002).

CONCLUSION

Immunohistochemical detection of CK 17 and 19 seems to be a valuable additional parameter distinguishing between odontogenic keratocysts and other odontogenic--especially dentigerous--cysts which clinically are likely the most significant differential diagnoses in this context. J Oral Pathol Med (2005) 34: 558-64.

The human type I keratin gene family: characterization of new hair follicle specific members and evaluation of the chromosome 17q21.2 gene domain

In general concurrence with recent studies, bioinformatic analysis of the chromosome 17q21.2 DNA sequence found in the EBI/Genebank database shows the presence of 27 type I keratin genes and five keratin pseudogenes present on 8 contiguous Bacterial Artificial Chromosome (BAC) sequences. This constitutes the 970 kb type I keratin gene domain. Inserted into this domain is a 350 kb region harboring 32 previously characterized keratin-associated protein genes. Of the 27 keratin genes found in this region, six have not been characterized in detail. This study reports the isolation of cDNA sequences for these keratin genes, termed K25irs1-K25irs4, Ka35, and Ka36, as well as cDNA sequences for the previously reported hair keratins hHa3-I, hHa7, and hHa8. RT-PCR analysis of 14 epithelial tissues using primers for the six novel keratins, as well as for keratins 23 and 24, shows that the six novel keratins appear to be hair follicle associated. Previous expression data, coupled with evolutionary analysis studies point to K25irs1-K25irs4 probably being inner root sheath specific keratins. Ka35 and Ka36 are, based on their exon-intron structure and expression characteristics, hair keratins. In contrast, K23 and K24 appear to be epithelial keratins associated with simple/glandular or stratified, non-cornified epithelia, respectively. A literature analysis coupled with the data presented here confirms that all of the 27 keratin genes found on this domain have been characterized at the transcriptional level. Together with K18, a type I keratin gene found on the type II keratin domain, this seems to be the entire complement of functional type I keratins in humans.

Characterization of new members of the human type II keratin gene family and a general evaluation of the keratin gene domain on chromosome 12q13.13

The recent completion of a reference sequence of the human genome now allows a complete characterization of the type II keratin gene domain on chromosome 12q13.13. This, domain, approximately 780 kb in size, is present on nine bacterial artificial chromosome clones sequenced by the Human Genome Sequencing Project. The type II keratin domain contains 27 keratin genes and eight pseudogenes. Twenty-three of these genes and four pseudogenes have been previously reported. This study describes, in addition to the genomic sequencing of the K2p gene and the bioinformatic identification of four keratin pseudogenes, the characterization of cDNA corresponding to three previously undescribed keratin genes K1b, K6l, and Kb20, as well as cDNA sequences for the previously described keratin genes hHb2, hHb4, and K3. Northern analysis of the new keratins K1b, K6l, K5b, and Kb20 using mRNA of major organs as well as of specific epithelial subtypes shows singular expression of these keratins in skin, hair follicles and, for K5b and Kb20, in tongue, respectively. In addition, the obvious discrepancies between the current reference sequence of the human genome and the previously described gene/cDNA sequences for K6c, K6d, K6e, K6f, K6h are investigated, leading to the conclusion that K6c, K6d as well as K6e, K6f are probably polymorphic variants of K6a and K6h, respectively. All 26 human type II keratins found on this domain as well as K18, dtype 1 Keratin, are identified at the genomic and transcriptional level. This appears to be the total complement of functional type II keratins in humans.

A novel mutation in the keratin 4 gene causing white sponge naevus

BACKGROUND

White sponge naevus (WSN) is a rare, autosomal dominant disorder that predominantly affects noncornified stratified squamous epithelia, most commonly the buccal mucosa. Clinically, WSN manifests as thickened spongy mucosa with a white opalescent tint in the mouth and may be confused with other disorders that cause white lesions on oral mucosa. Recent studies have identified pathogenic mutations in KRT4 and KRT13, the genes encoding mucosa-specific keratins, in WSN.

OBJECTIVES

To search for possible mutations in KRT4 and KRT13.

METHODS

We report a case of WSN in a young man who presented with diffuse irregular whitish plaques involving the buccal and gingival mucosae and the tongue. Results Pathologically, the affected mucosa showed epithelial thickening, parakeratosis and extensive vacuolization of the suprabasal keratinocytes. Mutation analysis revealed a heterozygous missense mutation 1345G-->A in KRT4, predicting an amino acid change, E449K, in the 2B domain of the K4 polypeptide.

CONCLUSIONS

We report the first mutation analysis of a Taiwanese patient with WSN. Potentially this novel mutation could disrupt the stability of keratin filaments and result in WSN.

Characterization of a 300 kbp region of human DNA containing the type II hair keratin gene domain

Screening of an arrayed human genomic P1 artificial chromosome DNA library by means of the polymerase chain reaction with a specific primer pair from the human type II hair keratin hHb5 yielded two P1 artificial chromosome clones covering approximately 300 kb of genomic DNA. The contig contained six type II hair keratin genes, hHb1-hHb6, and four keratin pseudogenes psihHbA-psihHbD. This hair keratin gene domain was flanked by type II epithelial keratins K6b/K6hf and K7, respectively. The keratin genes/pseudogene are 5-14 kbp in size with intergenic distances of 5-19 kbp of DNA and do not exhibit a single direction of transcription. With one exception, type II hair keratin genes are organized into nine exons and eight introns, with strictly conserved exon-intron boundaries. The functional hair keratin genes are grouped into two distinct subclusters near the extremities of the hair keratin gene domain. One subcluster encodes the highly related hair keratins hHb1, hHb3, and hHb6; The second cluster encodes the structurally less related hair keratins hHb2, hHb4, and hHb5. Reverse transcription-polymerase chain reaction shows that all hair keratin genes are expressed in the hair follicle. Pseudogene psihHbD is also transcriptionally expressed, albeit with alterations in splicing and frameshift mutations, leading to premature stop codons in the splice forms analyzed. Evolutionary tree analysis revealed a divergence of the type II hair keratin genes from the epithelial keratins, followed by their segregation into the members of the two subclusters over time. We assume that the approximately 200 kbp DNA domain contains the entire complement of human type II hair keratin genes.

A glutamine insertion in the 1A alpha helical domain of the keratin 4 gene in a familial case of white sponge nevus

White Sponge Nevus (WSN) is a rare, autosomal dominant disorder that predominantly affects noncornified stratified squamous epithelia. Clinically, it is characterized by the presence of soft, white, and "spongy" plaques in the oral mucosa. The characteristic histopathologic features are epithelial thickening, parakeratosis, and vacuolization of the suprabasal layer of oral epithelial keratinocytes. Mutations in keratin 4 (K4) and keratin 13 (K13) genes have already been demonstrated to be responsible for WSN; the identification of new keratin mutations in a stratified squamous epithelia closely related to epidermis is of relevance for the understanding of the biochemistry of intermediate filaments, and for genotype phenotype correlations. In this study we investigated a 27-y-old, female Italian patient, affected by white asymptomatic oral plaques. Sequence analysis revealed a 3 bp (ACA) heterozygous insertion localized in the helix initiation motif of the 1A alpha helical domain of K4. We report this new K4 gene mutation and describe an amino acid insertion, in the 1A domain, responsible for a keratin disease.

Characterization of a 190-kilobase pair domain of human type I hair keratin genes

Polymerase chain reaction-based screening of an arrayed human P1 artificial chromosome (PAC) library using primer pairs specific for the human type I hair keratins hHa3-II or hHa6, led to the isolation of two PAC clones, which covered 190 kilobase pairs (kbp) of genomic DNA and contained nine human type I hair keratin genes, one transcribed hair keratin pseudogene, as well as one orphan exon. The hair keratin genes are 4-7 kbp in size, exhibit intergenic distances of 5-8 kbp, and display the same direction of transcription. With one exception, all hair keratin genes are organized into 7 exons and 6 positionally conserved introns. On the basis of sequence homologies, the genes can be grouped into three subclusters of tandemly arranged genes. One subcluster harbors the highly related genes hHa1, hHa3-I, hHa3-II, and hHa4. A second subcluster of highly related genes comprises the novel genes hHa7 and hHa8, as well as pseudogene PsihHaA, while the structurally less related genes hHa6, hHa5, and hHa2 are constituents of the third subcluster. As shown by reverse transcription-polymerase chain reaction, all hair keratin genes, including the pseudogene, are expressed in the human hair follicle. The transcribed pseudogene PsihHaA contains a premature stop codon in exon 4 and exhibits aberrant pre-mRNA splicing. Evolutionary tree construction reveals an early divergence of hair keratin genes from cytokeratin genes, followed by the segregation of the genes into the three subclusters. We suspect that the 190-kbp domain contains the entire complement of human type I hair keratin genes.

Isolation, sequence and expression of the gene encoding human keratin 13

Keratins are a family of highly homologous proteins expressed as pairs of acidic and basic forms which make intermediate filaments in epithelial cells. Keratin 13 (K13) is the major acidic keratin, which together with K4, its basic partner, is expressed in the suprabasal layers of non-cornified stratified epithelia. The mechanism which allows mucosal-specific expression of this keratin remains unknown. To provide insight into the tissue-specific expression, we have isolated the human K13 gene by screening a chromosome 17 library with a specific K13 cRNA probe. Sequence analysis of unidirectional deletions produced by transposon Tn3 has revealed that the gene is 4601 nucleotides long and contains seven introns and eight exons. When driven by the CMV promoter, the gene produced K13 protein in MCF-7 cells, which normally do not express this protein. Two transcription-start sites were identified, the major being at 61 and the minor at 63 nucleotides upstream of ATG. The upstream sequence contained a TATA box and several other putative transcription factor binding sites. A single copy of the K13 gene was detected in the human genome by Southern hybridisation and polymerase chain reaction. K13 mRNA shows differential expression in cultured keratinocytes, and in A431 cells the RNA levels remained independent of calcium concentrations in the culture medium. Characterisation of the human K13 gene will facilitate elucidation of the molecular mechanism regulating K13 expression in mucosal tissues.

Coordinate control of growth and cytokeratin 13 expression by retinoic acid

Retinoic acid (RA) modulates the growth and differentiation of various normal and malignant cells. These effects are most likely mediated by changes in gene expression. Genes whose expression is modulated by RA may be useful as markers of growth responsiveness to retinoids. Using differential cDNA cloning we identified 10 genes regulated by RA in the head and neck squamous cell carcinoma cell line MDA886Ln. Keratin (K) 13 gene expression was the gene expression most related to the degree of sensitivity of growth to RA, as K13 was not expressed in a series of RA-resistant cell lines. Our data suggest that low K13 expression may be mechanistically related to resistance to RA-induced growth inhibition.

Keratin 13 point mutation underlies the hereditary mucosal epithelial disorder white sponge nevus

Although pathogenic keratin mutations have been well characterized in inherited epidermal disorders, analogous defects in keratins expressed in non-epidermal epithelia have yet to be described. White sponge nevus (WSN) is a rare autosomal dominant disorder of non-cornifying squamous epithelial differentiation that presents clinically as bilateral white, soft, thick plaques of the oral mucosa. Less frequently the mucous membranes of the nose, esophagus, genitalia and rectum are involved. Histopathological features, including epithelial thickening, parakeratosis, extensive vacuolization of the suprabasal keratinocytes and compact aggregates of keratin intermediate filaments (KIF) in the upper spinous layers, resemble those found in epidermal disorders due to keratin defects. We analysed a multigenerational family with WSN and found cosegregation of the disease with the keratin gene cluster on chromosome 17. We identified a missense mutation in one allele of keratin 13 that leads to proline substitution for a conserved leucine. The mutation occurred within the conserved 1A region of the helical rod domain, which is critical for KIF stability and is the site of most pathogenic keratin mutations. This mutation enlarges the spectrum of keratins with disease-causing defects to include mucosally expressed keratin 13, and extends the known keratin diseases to disorders of non-cornifying stratified squamous epithelia.

Chromosomal locations of the genes for the beaded filament proteins CP 115 and CP 47

We have used the polymerase chain reaction (PCR) to amplify CP 115 and CP 47 encoding sequences from human lens cDNA samples. DNA sequence and northern blot analysis were used to confirm human origin. From the determined cDNA sequences, human-specific oligonucleotides were synthesized and assessed for the ability to amplify human genomic DNA. After empirically selecting a primer pair for each gene able to amplify human genomic DNA, and optimizing PCR conditions for human specificity, we used the PCR to screen a panel of mouse/human somatic cell hybrid DNA samples. Amplification of CP 115 or CP 47 sequences in each of the somatic cell hybrid samples was correlated with the presence/absence of human genomic DNA sequences encoding the respective gene sequences. From our results, we conclude that the gene for human CP 115 resides on chromosome 20 and the gene for human CP 47 on chromosome 3. Further mapping using somatic cell lines carrying derivatives of human chromosome 3 localize the gene for CP 47 to 3q21-25. We propose LIFL-H (Lens Intermediate Filament Like-Heavy) for CP 115 and LIFL-L (Lens Intermediate Filament Like-Light) for CP 47 as the gene symbols for these loci.