Identification of novel genes for secreted and membrane-anchored proteins in human keratinocytes

Construction of a novel prognostic-predicting model correlated to ovarian cancer

Background: Ovarian cancer (OC) is one of the most lethal gynecological cancers worldwide. The pathogenesis of the disease and outcomes prediction of OC patients remain largely unclear. The present study aimed to explore the key genes and biological pathways in ovarian carcinoma development, as well as construct a prognostic model to predict patients’ overall survival (OS).

Results: We identified 164 up-regulated and 80 down-regulated differentially expressed genes (DEGs) associated with OC. Gene Ontology (GO) term enrichment showed DEGs mainly correlated with spindle microtubes. For Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, cell cycle was mostly enriched for the DEGs. The protein–protein interaction (PPI) network yielded 238 nodes and 1284 edges. Top three modules and ten hub genes were further filtered and analyzed. Three candidiate drugs targeting for therapy were also selected. Thirteen OS-related genes were selected and an eight-mRNA model was present to stratify patients into high- and low-risk groups with significantly different survival.

Conclusions: The identified DEGs and biological pathways may provide new perspective on the pathogenesis and treatments of OC. The identified eight-mRNA signature has significant clinical implication for outcome prediction and tailored therapy guidance for OC patients.

Selenoprotein T: An Essential Oxidoreductase Serving as a Guardian of Endoplasmic Reticulum Homeostasis

Significance: Selenoproteins incorporate the essential nutrient selenium into their polypeptide chain. Seven members of this family reside in the endoplasmic reticulum (ER), the exact function of most of which is poorly understood. Especially, how ER-resident selenoproteins control the ER redox and ionic environment is largely unknown. Since alteration of ER function is observed in many diseases, the elucidation of the role of selenoproteins could enhance our understanding of the mechanisms involved in ER homeostasis. Recent Advances: Among selenoproteins, selenoprotein T (SELENOT) is remarkable as the most evolutionarily conserved and the only ER-resident selenoprotein whose gene knockout in mouse is lethal. Recent data indicate that SELENOT contributes to ER homeostasis: reduced expression of SELENOT in transgenic cell and animal models promotes accumulation of reactive oxygen and nitrogen species, depletion of calcium stores, activation of the unfolded protein response and impaired hormone secretion. Critical Issues: SELENOT is anchored to the ER membrane and associated with the oligosaccharyltransferase complex, suggesting that it regulates the early steps of N-glycosylation. Furthermore, it exerts a selenosulfide oxidoreductase activity carried by its thioredoxin-like domain. However, the physiological role of the redox activity of SELENOT is not fully understood. Likewise, the nature of its redox partners needs to be further characterized. Future Directions: Given the impact of ER stress in pathologies such as neurodegenerative, cardiovascular, metabolic and immune diseases, understanding the role of SELENOT and developing derived therapeutic tools such as selenopeptides to improve ER proteostasis and prevent ER stress could contribute to a better management of these diseases.

PERP-ing into diverse mechanisms of cancer pathogenesis: Regulation and role of the p53/p63 effector PERP

The tetraspan plasma membrane protein PERP (p53 apoptosis effector related to PMP22) is a lesser-known transcriptional target of p53 and p63. A member of the PMP22/GAS3/EMP membrane protein family, PERP was originally identified as a p53 target specifically trans-activated during apoptosis, but not during cell-cycle arrest. Several studies have since shown downregulation of PERP expression in numerous cancers, suggesting that PERP is a tumour suppressor protein. This review focusses on the important advances made in elucidating the mechanisms regulating PERP expression and its function as a tumour suppressor in diverse human cancers, including breast cancer and squamous cell carcinoma. Investigating PERP's role in clinically-aggressive uveal melanoma has revealed that PERP engages a positive-feedback loop with p53 to regulate its own expression, and that p63 is required beside p53 to achieve pro-apoptotic levels of PERP in this cancer. Furthermore, the recent discovery of the apoptosis-mediating interaction of PERP with SERCA2b at the plasma membrane-endoplasmic reticulum interface demonstrates a novel mechanism of PERP stabilisation, and how PERP can mediate Ca²⁺ signalling to facilitate apoptosis. The multi-faceted role of PERP in cancer, involving well-documented functions in mediating apoptosis and cell-cell adhesion is discussed, alongside PERP's emerging roles in epithelial-mesenchymal transition, and PERP crosstalk with inflammation signalling pathways, and other signalling pathways. The potential for restoring PERP expression as a means of cancer therapy is also considered.

Selenoprotein T is a key player in ER proteostasis, endocrine homeostasis and neuroprotection

Selenoprotein T (SELENOT, SELT) is a thioredoxin-like enzyme anchored at the endoplasmic reticulum (ER) membrane, whose primary structure is highly conserved during evolution. SELENOT is abundant in embryonic tissues and its activity is essential during development since its gene knockout in mice is lethal early during embryogenesis. Although its expression is repressed in most adult tissues, SELENOT remains particularly abundant in endocrine organs such as the pituitary, pancreas, thyroid and testis, suggesting an important role of this selenoprotein in hormone production. Our recent studies showed indeed that SELENOT plays a key function in insulin and corticotropin biosynthesis and release by regulating ER proteostasis. Although SELENOT expression is low or undetectable in most cerebral structures, its gene conditional knockout in brain provokes anatomical alterations that impact mice behavior. This suggests that SELENOT also plays an important role in brain development and function. In addition, SELENOT is induced after injury in brain or liver and exerts a cytoprotective effect. Thus, the data gathered during the last ten years of intense investigation of this newly discovered thioredoxin-like enzyme point to an essential function during development and in adult endocrine organs or lesioned brain, most likely by regulating ER redox circuits that control homeostasis and survival of cells with intense metabolic activity.

Selenoprotein T is a novel OST subunit that regulates UPR signaling and hormone secretion

Selenoprotein T (SelT) is a recently characterized thioredoxin-like protein whose expression is very high during development, but is confined to endocrine tissues in adulthood where its function is unknown. We report here that SelT is required for adaptation to the stressful conditions of high hormone level production in endocrine cells. Using immunofluorescence and TEM immunogold approaches, we find that SelT is expressed at the endoplasmic reticulum membrane in all hormone-producing pituitary cell types. SelT knockdown in corticotrope cells promotes unfolded protein response (UPR) and ER stress and lowers endoplasmic reticulum-associated protein degradation (ERAD) and hormone production. Using a screen in yeast for SelT-membrane protein interactions, we sort keratinocyte-associated protein 2 (KCP2), a subunit of the protein complex oligosaccharyltransferase (OST). In fact, SelT interacts not only with KCP2 but also with other subunits of the A-type OST complex which are depleted after SelT knockdown leading to POMC N-glycosylation defects. This study identifies SelT as a novel subunit of the A-type OST complex, indispensable for its integrity and for ER homeostasis, and exerting a pivotal adaptive function that allows endocrine cells to properly achieve the maturation and secretion of hormones.

Genome-wide association study for wool production traits in a Chinese Merino sheep population

Genome-wide association studies (GWAS) provide a powerful approach for identifying quantitative trait loci without prior knowledge of location or function. To identify loci associated with wool production traits, we performed a genome-wide association study on a total of 765 Chinese Merino sheep (JunKen type) genotyped with 50 K single nucleotide polymorphisms (SNPs). In the present study, five wool production traits were examined: fiber diameter, fiber diameter coefficient of variation, fineness dispersion, staple length and crimp. We detected 28 genome-wide significant SNPs for fiber diameter, fiber diameter coefficient of variation, fineness dispersion, and crimp trait in the Chinese Merino sheep. About 43% of the significant SNP markers were located within known or predicted genes, including YWHAZ, KRTCAP3, TSPEAR, PIK3R4, KIF16B, PTPN3, GPRC5A, DDX47, TCF9, TPTE2, EPHA5 and NBEA genes. Our results not only confirm the results of previous reports, but also provide a suite of novel SNP markers and candidate genes associated with wool traits. Our findings will be useful for exploring the genetic control of wool traits in sheep.

IgSF8: a developmentally and functionally regulated cell adhesion molecule in olfactory sensory neuron axons and synapses

Here, we investigated an Immunoglobulin (Ig) superfamily protein IgSF8 which is abundantly expressed in olfactory sensory neuron (OSN) axons and their developing synapses. We demonstrate that expression of IgSF8 within synaptic neuropil is transitory, limited to the period of glomerular formation. Glomerular expression decreases after synaptic maturation and compartmental glomerular organization is achieved, although expression is maintained at high levels within the olfactory nerve layer (ONL). Immunoprecipitations indicate that IgSF8 interacts with tetraspanin CD9 in the olfactory bulb (OB). CD9 is a component of tetraspanin-enriched microdomains (TEMs), specialized microdomains of the plasma membrane known to regulate cell morphology, motility, invasion, fusion and signaling, in both the nervous and immune systems, as well as in tumors. In vitro, both IgSF8 and CD9 localize to puncta within axons and growth cones of OSNs, consistent with TEM localization. When the olfactory epithelium (OE) was lesioned, forcing OSN regeneration en masse, IgSF8 was once again able to be detected in OSN axon terminals as synapses were reestablished. Finally, we halted synaptic maturation within glomeruli by unilaterally blocking functional activity and found that IgSF8 did not undergo exclusion from this subcellular compartment and instead continued to be detected in adult glomeruli. These data support the hypothesis that IgSF8 facilitates OSN synapse formation.

Keratinocyte-associated protein 2 is a bona fide subunit of the mammalian oligosaccharyltransferase

The oligosaccharyltransferase (OST) complex catalyses the N-glycosylation of polypeptides entering the endoplasmic reticulum, a process essential for the productive folding and trafficking of many secretory and membrane proteins. In eukaryotes, the OST typically comprises a homologous catalytic STT3 subunit complexed with several additional components that are usually conserved, and that often function to modulate N-glycosylation efficiency. By these criteria, the status of keratinocyte-associated protein 2 (KCP2) was unclear: it was found to co-purify with the canine OST suggesting it is part of the complex but, unlike most other subunits, no potential homologues are apparent in Saccharomyces cerevisiae. In this study we have characterised human KCP2 and show that the predominant species results from an alternative initiation of translation to form an integral membrane protein with three transmembrane spans. KCP2 localises to the endoplasmic reticulum, consistent with a role in protein biosynthesis, and has a functional KKxx retrieval signal at its cytosolic C-terminus. Native gel analysis suggests that the majority of KCP2 assembles into a distinct ~500 kDa complex that also contains several bona fide OST subunits, most notably the catalytic STT3A isoform. Co-immunoprecipitation studies confirmed a robust and specific physical interaction between KCP2 and STT3A, and revealed weaker associations with both STT3B and OST48. Taken together, these data strongly support the proposal that KCP2 is a newly identified subunit of the N-glycosylation machinery present in a subset of eukaryotes.

A functional single nucleotide polymorphism in mucin 1, at chromosome 1q22, determines susceptibility to diffuse-type gastric cancer

BACKGROUND & AIMS

Two major types of gastric cancer, intestinal and diffuse, develop through distinct mechanisms; the diffuse type is considered to be more influenced by genetic factors, although the mechanism is unknown. Our previous genome-wide association study associated 3 single nucleotide polymorphisms (SNPs) with diffuse-type gastric cancer (DGC); 1 was a functional SNP (rs2294008) in prostate stem cell antigen (PSCA), but the loci of the other 2 were not investigated.

METHODS

We performed high-density mapping to explore a linkage disequilibrium status of the 2 SNPs at chromosome 1q22. A DGC case-control study was conducted using DNA from 606 cases and 1264 controls (all Japanese individuals) and validated using DNA from Japanese (304 cases, 1465 controls) and Korean (452 cases, 372 controls) individuals. The effects of SNPs on function were analyzed by reporter assays and analyses of splice variants.

RESULTS

A region of a strong linkage disequilibrium with the 2 SNPs contained mucin 1 (MUC1) and other 4 genes and SNPs significantly associated with DGC (rs2070803: P = 4.33 × 10(-13); odds ratio [OR], 1.71 by meta-analysis of the studies on the 3 panels) but not with intestinal-type gastric cancer. Functional studies demonstrated that rs4072037 (P = 1.43 × 10(-11); OR, 1.66 by meta-analysis) in MUC1 affects promoter activity and determines the major splicing variants of MUC1 in the gastric epithelium. Individuals that carry both SNPs rs2294008 in PSCA and rs4072037 in MUC1 have a high risk for developing DGC (OR, 8.38).

CONCLUSIONS

MUC1 is the second major DGC susceptibility gene identified. The SNPs rs2070803 and rs4072037 in MUC1 might be used to identify individuals at risk for this type of gastric cancer.

Identification and cornification-related gene expression of canine keratinocyte differentiation-associated protein, Kdap

The outermost layer of skin, the epidermis, is cornified epithelial tissue composed of keratinocytes. To maintain the structure and function of the epidermis, the regulation of proliferation, differentiation, and cornification of keratinocytes is crucial, and various soluble factors secreted by keratinocytes are involved in these regulations. Previously, work has shown that keratinocytes secreted the protein Kdap (keratinocyte differentiation-associated protein) associated with the formation of cornified cell envelopes, a specialized protective barrier structure on the periphery of terminally differentiating keratinocytes. In the present report, the canine counterpart of human Kdap is identified and an attempt has been made to define its physiological role in canine keratinization. Canine Kdap (cKdap) showed structural features commonly observed in other counterparts and is secreted from transfected cells. The expression profile of cKdap mRNA, which was restrictively expressed in cornified epithelial tissues besides skin has also been determined. These findings indicate that there is a strong association between cKdap expression and cornification, which supports previous observations that Kdap is involved in the synthesis and/or degradation of cornified cell envelopes in humans and mice.

Identification and gene expression of bovine C-type lectin dectin-2

The C-type lectin receptor has been shown to recognize carbohydrate moieties of self and non-self antigens, thus serving as an innate immune receptor. Using bioinformatics and molecular cloning techniques, we isolated a bovine gene that encodes a polypeptide of 206 amino acids with structural features shared by mouse and human dectin-2, including a high homology with mouse dectin-2 (66%), a type II configuration, a short cytoplasmic domain without tyrosine-based signal motifs, a carbohydrate recognition domain, a putative N-glycosylation site, and an EPN motif involved in the Ca(2+)-dependent binding of hexose carbohydrates. These results reveal this bovine gene to be a counterpart of mouse dectin-2. Moreover, the bovine dectin-2 gene showed heterogeneity in mRNA (the generation of alternatively spliced transcript) and segmentation into six exons, which are also observed in mouse dectin-2. Inconsistent with mouse dectin-2 mRNA, the bovine counterpart is abundantly expressed by Langerhans cells compared to macrophages; however, lymph nodes showed the highest expression level of bovine dectin-2, while spleen and lung showed the highest expression levels of mouse and human dectin-2. In cattle, dectin-2 expressed by dendritic cells may be clinically involved in the recognition of invading antigens in lymph nodes.

Neuronal expression of keratinocyte-associated transmembrane protein-4, KCT-4, in mouse brain and its up-regulation by neurite outgrowth of Neuro-2a cells

One group of proteins that regulates neurite outgrowth and maintains neuronal networks is the immunoglobulin superfamily (IgSF). We previously identified a new member of the IgSF, keratinocyte-associated transmembrane protein-4 (KCT-4), by the signal sequence-trap method from primary cultured human keratinocytes. The KCT-4 mRNA has been found to be highly expressed in the adult human brain, although it is also distributed in various tissues. In the present study, to gain insight into the role of KCT-4 in the nervous system, we examined the expression profile and localization of KCT-4 mRNA in mouse brain. We also evaluated changes in KCT-4 mRNA expression in the differentiation of the neuroblastoma cell line Neuro-2a as the in vitro model of neurite outgrowth. KCT-4 mRNA was detected broadly in various regions of the adult mouse brain by RT-PCR. In situ hybridization revealed that it was expressed highly selectively by neurons but not by glial cells. Moreover, expression of KCT-4 mRNA was induced by neurite outgrowth of Neuro-2a. These data suggest that KCT-4 participates in the regulation of neurite outgrowth and maintenance of the neural network in the adult brain.

Characterization of cDNA and the genomic sequence encoding canine neural-cell adhesion molecule, CD56/N-CAM

The neural-cell adhesion molecule, CD56/N-CAM is a member of the immunoglobulin superfamily expressed by various tissues and cells, including natural killer (NK) cells. Despite the importance of CD56 as a marker for identifying NK cells in circulating blood, canine CD56 has not been identified. In the present study, we identified the canine counterparts of the 140-kDa (CD56-140) and 120-kDa (CD56-120) isoforms of human DC56. Both of amino acid sequences encoded by the canine CD56-140 and -120 cDNA showed high homology with those of human (both 96% homology), having well-conserved domains (five immunoglobulin, two fibronectin type III, and transmembrane and intracellular or glycosylphosphatidylinositol-linked domain) among various species (human, mouse, and feline). We revealed that the transcripts of canine CD56-140 and -120 arise from alternative mRNA splicing from a single gene located on canine chromosome 5. Moreover, the mRNA encoding canine CD56-140 was expressed at high levels constitutively by nervous system and endocrine tissues as has shown in other animals.

Proteomic analysis of mammalian oligosaccharyltransferase reveals multiple subcomplexes that contain Sec61, TRAP, and two potential new subunits

Oligosaccharyltransferase (OST) catalyzes the cotranslational transfer of high-mannose sugars to nascent polypeptides during N-linked glycosylation in the rough endoplasmic reticulum lumen. Nine OST subunits have been identified in yeast. However, the composition and organization of mammalian OST remain unclear. Using two-dimensional Blue Native polyacrylamide gel electrophoresis/sodium dodecyl sulfate-polyacrylamide gel electrophoresis and mass spectrometry, we now demonstrate that mammalian OST can be isolated from solubilized, actively engaged ribosomes as multiple distinct protein complexes that range in size from approximately 500 to 700 kDa. These complexes exhibit different ribosome affinities and subunit compositions. The major complex, OSTC(I), had an apparent size of approximately 500 kDa and was readily released from ribosome translocon complexes after puromycin treatment under physiological salt conditions. Two additional complexes were released only after treatment with high salt: OSTC(II) ( approximately 600 kDa) and OSTC(III) ( approximately 700 kDa). Both remained stably associated with heterotrimeric Sec61alphabetagamma, while OSTC(III) also contained the tetrameric TRAP complex. All known mammalian OST subunits (STT3-A, ribophorin I, ribophorin II, OST48, and DAD1) were present in all complexes. In addition, two previously uncharacterized proteins were also copurified with OST. Mass spectrometry identified a 17 kDa protein as DC2 which is weakly homologous to the C-terminal half of yeast Ost3p and Ost6p. The second protein (14 kDa) was tentatively identified as keratinocyte-associated protein 2 (KCP2) and has no previously known function. Our results identify two potential new subunits of mammalian OST and demonstrate a remarkable heterogeneity in OST composition that may reflect a means for controlling nascent chain glycosylation.

Transcriptional regulation of dectin-2 promoter in transgenic mouse

Despite a preeminent role of epidermal Langerhans cells (LC) in inducing primary immunity, application of gene-based modification to LC function is limited by lack of well-defined transcription regulatory units that can direct LC-specific gene expression. Previously we reported that the promoter activity of a 5'-flanking region of the dectin-2 gene (Dec2FR) is highly targeted to epidermal LC of transgenic mice bearing a Dec2FR-driven Luc gene. Using the mice, in which transcription activity of Dec2FR is measured by Luc assays, presently we characterized regulation of Dec2FR activity in leukocyte subpopulations under resting and activation status. Luc activity was highly variable in LC isolated from different skin areas and detected in other DC subset (dermal DC) but the levels were much lower than in resting LC. Activation of leukocytes markedly up-regulated Luc activity in all four subpopulations (CD11c+ splenic DC, Mac-1high peritoneal macrophages, splenic B220+ B cells, and CD3+ T cells). However, these levels remained lower than those in the resting and activated LC. These findings indicate that dectin-2 promoter activity remains targeted to epidermal LC even after activation of leukocytes, suggesting a high potential of Dec2FR to engineer LC-targeted gene expression to heighten efficacy of genetic vaccination and to manipulate phenotypes of preexisting immunity (Th1 vs. Th2).

Characterization of Kdap, A Protein Secreted by Keratinocytes

Using a signal sequence-trap we identified a human gene encoding a polypeptide of 99 amino acids with a putative signal sequence. The gene was identical to keratinocyte differentiation-associated protein (Kdap), which was reported previously by Oomizu et al (Gene 256: 19-27, 2000) to be expressed in embryonal rat epidermis at the mRNA level. In humans, we found Kdap mRNA expression to be restricted to epithelial tissue at high levels. The 12.5 kDa protein was detected in culture supernatant of keratinocytes and those transfected adenovirally with the Kdap gene. In normal skin, Kdap protein was found exclusively within lamellar granules of granular keratinocytes and in the intercellular space of the stratum corneum. By contrast, in lesional skin of patients with psoriasis, Kdap was expressed more widely throughout suprabasal keratinocytes. When induced to differentiate in vitro, keratinocytes showed marked upregulation of Kdap mRNA expression similar to that of involucrin mRNA, but with differing kinetics. Finally, a spliced variant of Kdap mRNA was generated by alternative splicing mechanisms. Our studies indicate that human Kdap resembles rat Kdap with respect to tissue and cell expression at the mRNA level and that Kdap is a low-molecular-weight protein secreted by keratinocytes. Thus Kdap may serve as a soluble regulator of keratinocyte differentiation.