Database on monoclonal antibodies to Cytokeratins

Antibody sequences assembly method based on weighted de Bruijn graph

With the development of next-generation protein sequencing technologies, sequence assembly algorithm has become a key technology for de novo sequencing process. At present, the existing methods can address the assembly of an unknown single protein chain. However, for monoclonal antibodies with light and heavy chains, the assembly is still an unsolved question. To address this problem, we propose a new assembly method, DBAS, which integrates the quality scores and sequence alignment scores from de novo sequencing peptides into a weighted de Bruijn graph to assemble the final protein sequences. The established method is used to assembling sequences from two datasets with mixed light and heavy chains from antibodies. The results show that the DBAS can assemble long antibody sequences for both mixed light and heavy chains and single chains. In addition, DBAS is able to distinguish the light and heavy chains by using BLAST sequence alignment. The results show that the algorithm has good performance for both target sequence coverage and contig assembly accuracy.

Genome-wide association study of body mass index in subjects with alcohol dependence

Outcomes related to disordered metabolism are common in alcohol dependence (AD). To investigate alterations in the regulation of body mass that occur in the context of AD, we performed a genome-wide association study (GWAS) of body mass index (BMI) in African Americans (AAs) and European Americans (EAs) with AD. Subjects were recruited for genetic studies of AD or drug dependence and evaluated using the Semi-structured Assessment for Drug Dependence and Alcoholism. We investigated a total of 2587 AAs and 2959 EAs with DSM-IV AD diagnosis. In the stage 1 sample (N = 4137), we observed three genome-wide significant (GWS) single-nucleotide polymorphism associations, rs200889048 (P = 8.98 * 10-12 ) and rs12490016 (P = 1.44 * 10-8 ) in EAs and rs1630623 (P = 5.14 * 10-9 ) in AAs and EAs meta-analyzed. In the stage 2 sample (N = 1409), we replicated 278, 253 and 168 of the stage 1 suggestive loci (P < 5*10-4 ) in AAs, EAs, and AAs and EAs meta-analyzed, respectively. A meta-analysis of stage 1 and stage 2 samples (N = 5546) identified two additional GWS signals: rs28562191 in EAs (P = 4.46 * 10-8 ) and rs56950471 in AAs (P = 1.57 * 10-9 ). Three of the GWS loci identified (rs200889048, rs12490016 and rs1630623) were not previously reported by GWAS of BMI in the general population, and two of them raise interesting hypotheses: rs12490016-a regulatory variant located within LINC00880, where there are other GWAS-identified variants associated with birth size, adiposity in newborns and bulimia symptoms, which also interact with social stress in relation to birth size; rs1630623-a regulatory variant related to ALDH1A1, a gene involved in alcohol metabolism and adipocyte plasticity. These loci offer molecular insights regarding the regulatory mechanisms of body mass in the context of AD.

Histologic and immunohistochemical evaluation of mirror image biopsies in oral squamous cell carcinoma

BACKGROUND AND OBJECTIVE

The concept of field cancerization has frequently been quoted to explain the occurrence of multiple primary cancers in the head and neck region and recurrence following complete excision of the original tumor. The main objective is to study the occurrence of field changes in mirror image biopsy in relation to histopathological changes in the oral mucosa among oral cancer patients using hematoxylin and eosin and to study the expression pattern of cytokeratin, Ki-67 and p53 in oral squamous cell carcinoma and mirror image biopsy.

MATERIALS AND METHODS

A pilot study of 15 patients clinically diagnosed with carcinoma lesion and their corresponding mirror image sites were taken and stained using immunohistochemistry method for the expression of cytokeratin, Ki-67 and p53.

RESULTS

Primary tumors showed strong positive staining for cytokeratin throughout both the epithelium and malignant epithelial islands but absence of staining for Ki-67 and p53.

CONCLUSION

CK may be useful in predicting epithelial differentiation and Ki-67 and p53 act as weak indicators of malignant disease progression in oral tissues.

Широкое многообразие кератинов человека

А review presents systematic data about the diversity of human keratins. The results of numerous studies concerning the structure and functions of keratins, their distribution in various cells and tissues were summarized. The role of these proteins in the development of human hereditary diseases, as well as modern approaches in use keratins in immunohistochemistry and perspectives of their further studies are discussed.

Keratins in oral cancer: necessity of mass spectrometry for validation of antibody based identifications

Keratins are intermediate filament family proteins which are predominantly expressed in the epithelial cells. Most of the studies which evaluate the status of keratins in clinical samples of the oral cavity are based on the identification of their presence and localization by immunohistochemistry using monoclonal antibodies. It is very well known that many monoclonal/polyclonal antibodies show cross-reactivity with the other closely related or non-related proteins. This cross-reactivity might be the result of epitope similarity, but it is not always necessary. Therefore studies done with only antibody based techniques can mislead interpretation unless they are validated with additional techniques like mass-spectrometry. In this investigation we have evaluated the status of keratin 18 in cancer of buccal mucosa using 1DE, 2DE and western blotting with monoclonal antibody to keratin 18. The patterns emerging showed aberrant as well as differential expression of K18 in adjacent normal versus tumor tissue samples of buccal mucosa. Mass spectrometry analysis of the immunodetected spots however revealed that it is keratin 13. Thus this study emphasizes the necessity of validation of antibody based findings when dealing with proteins of a large family having similarity/homology in amino acid sequence.

Increased expression of CK8 and CK18 in leukoplakia, oral submucous fibrosis, and oral squamous cell carcinoma: an immunohistochemistry study

OBJECTIVE

Oral squamous cell carcinoma (OSCC) may be preceded by potentially malignant disorders such as leukoplakia and oral submucous fibrosis (OSF) and has a greater than normal risk of malignant transformation. Very little is known of cytokeratin (CK) alterations in OSF, leukoplakia, and OSCC. The aim of this study was to evaluate and compare the expression of CK8 and CK18 in normal oral mucosa, oral epithelial dysplasia, OSF, and OSCC by immunohistochemistry.

STUDY DESIGN

Paraffin-embedded normal (n = 10), dysplasia (n = 10), OSF (n = 10), and OSCC (n = 10) tissues were stained with CK8 and CK18 by immunohistochemistry.

RESULTS

Increased expression of CK8 and CK18 was seen in dysplasia, OSF, and OSCC. Staining pattern and intensity showed variations, with intensity of staining in basal and suprabasal layers for CK8 and CK18.

CONCLUSIONS

Intensity of staining in the basal layer for CK18 was statistical significant, suggesting CK8 and CK18 as surrogate markers of malignant transformation.

Novel keratins identified by quantitative proteomic analysis as the major cytoskeletal proteins of equine (Equus caballus) hoof lamellar tissue

The dermo-epidermal interface that connects the equine distal phalanx to the cornified hoof wall withstands great biomechanical demands, but is also a region where structural failure often ensues as a result of laminitis. The cytoskeleton in this region maintains cell structure and facilitates intercellular adhesion, making it likely to be involved in laminitis pathogenesis, although it is poorly characterized in the equine hoof lamellae. The objective of the present study was to identify and quantify the cytoskeletal proteins present in the epidermal and dermal lamellae of the equine hoof by proteomic techniques. Protein was extracted from the mid-dorsal epidermal and dermal lamellae from the front feet of 5 Standardbred geldings and 1 Thoroughbred stallion. Mass spectrometry-based spectral counting techniques, PAGE, and immunoblotting were used to identify and quantify cytoskeletal proteins, and indirect immunofluorescence was used for cellular localization of K14 and K124 (where K refers to keratin). Proteins identified by spectral counting analysis included 3 actin microfilament proteins; 30 keratin proteins along with vimentin, desmin, peripherin, internexin, and 2 lamin intermediate filament proteins; and 6 tubulin microtubule proteins. Two novel keratins, K42 and K124, were identified as the most abundant cytoskeletal proteins (22.0 ± 3.2% and 23.3 ± 4.2% of cytoskeletal proteins, respectively) in equine hoof lamellae. Immunoreactivity to K14 was localized to the basal cell layer, and that to K124 was localized to basal and suprabasal cells in the secondary epidermal lamellae. Abundant proteins K124, K42, K14, K5, and α(1)-actin were identified on 1- and 2-dimensional polyacrylamide gels and aligned with the results of previous studies. Results of the present study provide the first comprehensive analysis of cytoskeletal proteins present in the equine lamellae by using mass spectrometry-based techniques for protein quantification and identification.

Sheep (Ovis aries) airway epithelial cells support ovine herpesvirus 2 lytic replication in vivo

Ovine herpesvirus 2 (OvHV-2) is the causative agent of sheep-associated malignant catarrhal fever (SA-MCF), a frequently fatal disease of some members of the order Artiodactyla. OvHV-2 is carried as a lifelong subclinical infection in sheep (Ovis aries). To date OvHV-2 has not been propagated in vitro and this has hampered studies of viral pathogenesis and efforts to develop a vaccine to protect animals from SA-MCF. Lytic OvHV-2 replication occurs in the lungs of experimentally infected sheep at early times post-inoculation (PI) and in the nasal cavities of naturally infected sheep during virus shedding episodes. Identification of specific cell types supporting lytic virus replication in vivo provides information that can be used in the development of an in vitro propagation system for the virus. Using fluorescence immunohistochemical techniques, we identified lytically infected alveolar epithelial cells in the lungs of sheep early during infection. Lytically infected epithelial cells were also detected in samples of nasal secretions collected from naturally infected sheep during episodes of virus shedding. This is the first reported identification in the natural reservoir species of specific cell types that support OvHV-2 lytic replication in vivo.

Immunonanoparticles − an effective tool to impair harmful proteolysis in invasive breast tumor cells

Breast cancer cells exhibit excessive proteolysis, which is responsible for extensive extracellular matrix degradation, invasion and metastasis. Besides other proteases, lysosomal cysteine protease cathepsin B has been implicated in these processes and the impairment of its intracellular activity was suggested to reduce harmful proteolysis and hence diminish progression of breast tumors. Here, we present an effective system composed of poly(D,L-lactide-coglycolide) nanoparticles, a specific anti-cytokeratin monoclonal IgG and cystatin, a potent protease inhibitor, that can neutralize the excessive intracellular proteolytic activity as well as invasive potential of breast tumor cells. The delivery system distinguishes between breast and other cells due to the monoclonal antibody specifically recognizing cytokeratines on the membrane of breast tumor cells. Bound nanoparticles are rapidly internalized by means of endocytosis releasing the inhibitor cargo within the lysosomes. This enables intracellular cathepsin B proteolytic activity to be inhibited, reducing the invasive and metastatic potential of tumor cells without affecting proteolytic functions in normal cells and processes. This approach may be applied for treatment of breast and other tumors in which intracellular proteolytic activity is a part of the process of malignant progression.

Quantitating tissue specificity of human genes to facilitate biomarker discovery

We describe a method to identify candidate cancer biomarkers by analyzing numeric approximations of tissue specificity of human genes. These approximations were calculated by analyzing predicted tissue expression distributions of genes derived from mapping expressed sequence tags (ESTs) to the human genome sequence using a binary indexing algorithm. Tissue-specificity values facilitated high-throughput analysis of the human genes and enabled the identification of genes highly specific to different tissues. Tissue expression distributions for several genes were compared to estimates obtained from other public gene expression datasets and experimentally validated using quantitative RT-PCR on RNA isolated from several human tissues. Our results demonstrate that most human genes ( approximately 98%) are expressed in many tissues (low specificity), and only a small number of genes possess very specific tissue expression profiles. These genes comprise a rich dataset from which novel therapeutic targets and novel diagnostic serum biomarkers may be selected.

Cytokeratin profile in mucoepidermoid carcinoma is not related to its histological grading of malignancy

The objective of this experiment was to determine the relationship between the expression of cytokeratins (CKs) and histologic grading in MEC. Eleven cases of MEC were selected and graded as low, intermediate and high-grade tumors. The expression of CKs 7, 8, 10, 13 and 14 was assessed immunohistochemically using streptavidin-biotin complex method. The results showed that the studied CKs were expressed in most cases of MEC, independently of histologic grading. Nonetheless, low-grade tumors demonstrated intense staining of CK 7 and 8; additionally, CK 10 and 13 were more pronounced in this grade. The immunoexpression was variable according to cellular type and organization pattern of the tumor. Mucous cells were positive for CK 7 and 8; epidermoid cells were stained for CK 10, 13 and 14; CK 7, 8, 10 and 14 were observed in intermediate cells, and CK 7 was occasionally seen in clear cells. Cystic structures and duct-like elements in MEC were positive for CK 7 and 8, whereas solid nests showed positivity for all CKs. These results suggest that expression profile of these proteins does not reflect the biological behavior of MCE, however, it guides the detection of cellular types and differential diagnosis from other salivary gland tumors.

Proteomic analysis of nasal cells from cystic fibrosis patients and non-cystic fibrosis control individuals: search for novel biomarkers of cystic fibrosis lung disease

Potential biological markers for cystic fibrosis (CF) lung disease were identified by comparative proteomics profiling of nasal cells from deletion of phenylalanine residue 508 (F508del)-homozygous CF patients and non-CF controls. From the non-CF 2-DE gels, 65 spots were identified by MS, and a reference 2-DE map was thus established. The majority of those correspond to ubiquitously expressed proteins. Consistent with the epithelial origin of this tissue, some of the identified proteins are epithelial markers (e.g. cytokeratins, palate lung and nasal epithelium clone protein (PLUNC), and squamous cell carcinoma antigen 1). Comparison of this protein profile with the one similarly obtained for CF nasal cells revealed a set of differentially expressed proteins. These included proteins related to chronic inflammation and some others involved in oxidative stress injury. Alterations were also observed in the levels of cytoskeleton proteins, being probably implicated with cytoskeleton organization changes described to occur in CF-airways. Lower levels were found for some mitochondrial proteins suggesting an altered mitochondrial metabolism in CF. Differential expression was also found for two more enzymes that have not been previously associated to CF. Further studies will clarify the involvement of such proteins in CF pathophysiology and whether they are targets for CF therapy.

Cytokeratin expression in oral submucous fibrosis--an immunohistochemical study

BACKGROUND

Oral submucous fibrosis (OSF) is a pre-malignant condition caused by habitual use of areca nut, affecting the oro-pharynx and characterized by progressive fibrosis. Alteration of cytokeratin (CK) expression has been documented in leukoplakia and oral cancer (OC). However, very little is known of CK alterations in OSF. The present study was carried out to characterize the CK profile in OSF and ascertain if this could be used as a surrogate marker for malignant transformation.

METHODS

Paraffin-embedded tissues of OSF (n = 50), normal (n = 10) and OC (n = 10) were stained with pancytokeratin (PanCK), high molecular weight cytokeratin (HMWCK), CKs 18, 14, 8, 5, 4 and 1 by immunohistochemistry.

RESULTS

Significant difference in the CK staining pattern was seen between normal, OSF and cancer. Significant changes in OSF included increased intensity of staining for PanCK and HMWCK, aberrant expression of CK8 and decreased expression of CKs 5 and 14.

CONCLUSION

Cytokeratin profile of OSF was significantly different from normals for PanCK, HMWCK, CK8, 5 and 14 suggesting their potential to be used as surrogate markers of malignant transformation. Further studies will help in better defining the nature and clinical implications of these alterations.

Utilization of fresh human tympanic membranes for structural analysis and cytokeratin immunocytochemistry implementing resin techniques

CONCLUSIONS

The results of this study have demonstrated for the first time that tympanic membrane (TM) structure is preserved following removal of fresh, normal tissue from patients undergoing surgery. Greater clarity has been demonstrated using resin sections than in previous studies on paraffin sections. Of particular note, cytokeratin (CK) immunocytochemistry was successfully performed on resin sections, which has not been previously reported. This may have potential applications for future work involving tissues that express CKs.

OBJECTIVES

To analyse the structure of normal, fresh human TM specimens after surgical removal and to evaluate their CK immunocytochemistry using resin techniques, neither of which have been demonstrated previously.

MATERIAL AND METHODS

Seven TM specimens were removed during surgery and then preserved in a modified Karnovsky's fixative. Semi-thin and thin sections were examined by means of light and electron microscopy, respectively. For comparison purposes, paraffin block-embedded specimens were also sectioned. CK immunocytochemistry was performed on semi-thin sections using standard immunoperoxidase techniques, with expression being demonstrated using light microscopy.

RESULTS

The three-layer architecture of the TM was preserved. The morphology of the TM was vastly superior in the semi-thin resin sections than in the thicker paraffin sections. The outer, middle and inner layers were clearly demonstrated. The integrity of the outer epithelial layer was maintained, with an outer keratinizing stratum corneum and underlying stratum granulosum, stratum spinosum and stratum basale layers resting on the basal lamina. The thin inner mucosal layer was also viable, consisting of simple squamous or cuboidal cells. Preservation of the middle lamina propria was achieved, with demonstration of the outer radial and inner circular fibres. CK immunocytochemistry utilizing resin techniques provided excellent staining of CK 7 and 8 in the inner layer, with positive staining of CK 5 and 10 in the outer layer.