Simultaneous measurement of nascent transcriptome and translatome using 4-thiouridine metabolic RNA labeling and translating ribosome affinity purification

Regulation of gene expression in response to various biological processes, including extracellular stimulation and environmental adaptation requires nascent RNA synthesis and translation. Analysis of the coordinated regulation of dynamic RNA synthesis and translation is required to determine functional protein production. However, reliable methods for the simultaneous measurement of nascent RNA synthesis and translation at the gene level are limited. Here, we developed a novel method for the simultaneous assessment of nascent RNA synthesis and translation by combining 4-thiouridine (4sU) metabolic RNA labeling and translating ribosome affinity purification (TRAP) using a monoclonal antibody against evolutionarily conserved ribosomal P-stalk proteins. The P-stalk-mediated TRAP (P-TRAP) technique recovered endogenous translating ribosomes, allowing easy translatome analysis of various eukaryotes. We validated this method in mammalian cells by demonstrating that acute unfolded protein response (UPR) in the endoplasmic reticulum (ER) induces dynamic reprogramming of nascent RNA synthesis and translation. Our nascent P-TRAP (nP-TRAP) method may serve as a simple and powerful tool for analyzing the coordinated regulation of transcription and translation of individual genes in various eukaryotes.

A Case of Dominant Dystrophic Epidermolysis Bullosa with a G2043R Mutation in the Type VII Collagen Gene

Dear Editor, Dystrophic epidermolysis bullosa (DEB) is a subepidermal bulla, characterized by severe itching, lichenoid or nodular prurigo-like lesions, skin erosion, scars, milia, and nail dystrophy, resulting from COL7A1 mutation. Herein, we report a case of dominant DEB with a G2043R mutation in COL7A1. A-25-year-old Japanese woman was referred to our clinic for recurrent intense pruritis and hypertrophic scars on the abdomen (Figure 1, a). She presented with paper-like scars on her forehead, breast, back, buttock, and extremities (Figure 1, b) with mild toenail hypoplasia (Figure 1, c), but no symptoms on the fingernails, hair, teeth, or esophagus. She had developed erosions at the ankle joint a few days after birth. Her parents and four siblings had no related symptoms. She had been diagnosed with DEB at 11 months based on clinical and histopathological findings. Erythema, bullae, and skin ulcers had healed with scarring on the extensor surface of the lower legs at 7 years (Figure 1, d). Histopathological findings revealed subepidermal bulla with lymphocyte and eosinophil infiltration in the upper dermis (Figure 1, e). Immunofluorescence staining with type VII collagen antibody showed uneven faint localization at the basement membrane zone (Figure 1, f). Electron microscopy showed scanty and hypoplastic anchoring fibrils (Figure 1, g). Following ethical approval, informed consent was obtained in compliance with the Declaration of Helsinki guidelines, DNA was extracted from peripheral blood lymphocytes of the patient, and exome sequence analysis was performed. A heterozygous single nucleotide substitution c.6127G>A in exon 73 of COL7A1 was found, which converts glycine to arginine residue, designated p. G2043R. Since COL7A1 is a giant gene with 118 exons and 9276 base pairs, exome sequencing is convenient to determine the mutated gene. In dominant DEB, pathogenic mutations usually occur in glycine substitutions within the type VII collagen triple helix (1). The mutation impedes the trimer formation of collagen and disrupts the normal location of anchoring fibril. The particular localization of mutated collagen VII protein could vary based on the position of mutated glycine residue. In our patient, the mutated collagens were observed sparsely and unevenly at the basement membrane, but can accumulate granularly within the basal keratinocytes (2,3). G2043R mutation such as in the present case has been previously described with dominant DEB in Italian, Hungarian, Norwegian, Mexican, Scottish, Finnish, American, Chinese, and Japanese cases (1). Given the widespread geographical distribution of this mutation and its occurrence as a de novo event like in our case, G2043R can be one of the mutational hotspots in dominant DEB (1). Symptom severity in dominant DEB varies in the same mutation or intra-familial cases, and symptoms regress with age (4). The patient had severe blisters on her legs in early childhood; however, as her age increased, the hypertrophic or atrophic scars on the lower abdomen and extensor surface of her lower legs became the primary skin symptoms. It is presumed that some factor will compensate for the vulnerabilities.

Hair abnormality in Netherton syndrome observed under polarized light microscopy

BACKGROUND

Trichorrhexis invaginata, the main diagnostic feature of Netherton syndrome, is often difficult to detect, especially in adult patients.

OBJECTIVE

We sought to describe a characteristic feature of hairs in Netherton syndrome using a polarized light microscope and the underlying histopathologic changes.

METHODS

Hairs obtained from 8 patients with Netherton syndrome were observed under polarized light, and we evaluated the correlation between number of band-like patterns and disease severity.

RESULTS

Under polarized microscopy, the hair shafts of 8 patients showed a characteristic band-like pattern under polarized light that was not observed in healthy control individuals or patients with atopic dermatitis. This discontinuity of polarized light shows a band-like pattern in which the bands mostly ranged from 0.1 to 1.0 mm in width. The observed ratio of this finding was significantly higher than that of trichorrhexis invaginata observed under light microscopy, and patients with severe dermatitis tended to have a higher ratio than those with less severe dermatitis.

LIMITATIONS

Comparative examination among other congenital ichthyoses was not performed.

CONCLUSIONS

A band-like pattern in hairs with polarized light microscopy can be seen in Netherton syndrome and may have potential utility as a diagnostic marker.

Expression Changes of Structural Protein Genes May Be Related to Adaptive Skin Characteristics Specific to Humans

Human skin is morphologically and physiologically different from the skin of other primates. However, the genetic causes underlying human-specific skin characteristics remain unclear. Here, we quantitatively demonstrate that the epidermis and dermis of human skin are significantly thicker than those of three Old World monkey species. In addition, we indicate that the topography of the epidermal basement membrane zone shows a rete ridge in humans but is flat in the Old World monkey species examined. Subsequently, we comprehensively compared gene expression levels between human and nonhuman great ape skin using next-generation cDNA sequencing (RNA-Seq). We identified four structural protein genes associated with the epidermal basement membrane zone or elastic fibers in the dermis (COL18A1, LAMB2, CD151, and BGN) that were expressed significantly greater in humans than in nonhuman great apes, suggesting that these differences may be related to the rete ridge and rich elastic fibers present in human skin. The rete ridge may enhance the strength of adhesion between the epidermis and dermis in skin. This ridge, along with a thick epidermis and rich elastic fibers might contribute to the physical strength of human skin with a low amount of hair. To estimate transcriptional regulatory regions for COL18A1, LAMB2, CD151, and BGN, we examined conserved noncoding regions with histone modifications that can activate transcription in skin cells. Human-specific substitutions in these regions, especially those located in binding sites of transcription factors which function in skin, may alter the gene expression patterns and give rise to the human-specific adaptive skin characteristics.

K1 gene transformation activities in AIDS-related and classic type Kaposi's sarcoma: Correlation with clinical presentation

Kaposi's sarcoma-associated herpesvirus (KSHV) causes both AIDS-related Kaposi's sarcoma (KS) and classic KS, but their clinical presentations are different, and respective mechanisms remain to be elucidated. The KSHV K1 gene is reportedly involved in tumorigenesis through the immunoreceptor tyrosine-based activation motif (ITAM). Since we found the sequence variations in the K1 gene of KSHV isolated from AIDS-related KS and classic KS, we hypothesized that the transformation activity of the K1 gene contributes to the different clinical presentations. To evaluate our hypothesis, we compared the transformation activities of the K1 gene between AIDS-related KS and classic KS. We also analyzed ITAM activities and the downstream AKT and NF-κB. We found that the transformation activity of AIDS-related K1 was greater than that of classic K1, and that AIDS-related K1 induced higher ITAM activity than classic K1, causing more potent Akt and NF-κB activities. K1 downregulation by siRNA in AIDS-related K1 expressing cells induced a loss of transformation properties and decreased both Akt and NF-κB activities, suggesting a correlation between the transformation activity of K1 and ITAM signaling. Our study indicates that the increased transformation activity of AIDS-related K1 is associated with its clinical aggressiveness, whereas the weak transformation activity of classic type K1 is associated with a mild clinical presentation and spontaneous regression. The mechanism of spontaneous regression of classic KS may provide new therapeutic strategy to cancer.

High Prevalence of Distinct Human Herpesvirus 8 Contributes to the High Incidence of Non-acquired Immune Deficiency Syndrome-Associated Kaposi's Sarcoma in Isolated Japanese Islands

Background

Non-acquired immune deficiency syndrome (AIDS) Kaposi's sarcoma (KS) is extremely rare in Japan but highly endemic in Okinawa, especially in Miyako Islands. We aimed to elucidate the exact incidence and cause of this high prevalence.

Methods

Non-AIDS KS cases in Okinawa Prefecture over the past 31 years were reviewed, and human herpesvirus 8 (HHV8) seroprevalence in Miyako Islands was determined. We examined whole-genome sequences of 3 HHV8 strains and performed whole-exome sequencing of 4 male patients from Miyako Islands.

Results

Approximately half of the non-AIDS KS cases in Okinawa Prefecture were from Miyako Islands. The age-adjusted incidence rate was 0.87/105 per year for Miyako Islands and 0.056/105 per year for the rest of Okinawa. Human herpesvirus 8 seroprevalence was 15.4% in Miyako Islands. The 3 HHV8 genomes isolated from Miyako islanders formed a phylogenetically branch distinct from those of previously sequenced HHV8 strains and shared specific mutations in 9 proteins. These mutations were verified in Okinawan patients other than those from Miyako Islands. Whole-exome sequencing of the 4 male Miyako Islanders did not reveal shared pathogenic mutations.

Conclusions

Miyako Islands are an endemic area of non-AIDS KS. The high rate of a distinct HHV8 may contribute to the high incidence of KS in the region.

Lafutidine, a histamine H2 receptor antagonist with mucosal protective properties, attenuates 5-fluorouracil-induced intestinal mucositis in mice through activation of extrinsic primary afferent neurons

Intestinal mucositis accompanied by severe diarrhea is one of the most common side effects during cancer chemotherapy. Lafutidine, a histamine H2 receptor antagonist with mucosal protective properties via sensory afferent neurons, is used for the treatment of upper gastrointestinal diseases. The present study investigated the effects of lafutidine on 5-fluorouracil (5-FU)-induced intestinal mucositis induced in mice. Male C57BL/6 wild-type (WT), sensory deafferented mice, and transient receptor potential vanilloid subfamily 1 knockout (TRPV1KO) mice were used. Animals were administered 5-FU once daily, while lafutidine and famotidine were administered twice daily for 6 days. Repeated administration of 5-FU caused severe intestinal mucositis, characterized by shortening of villi and destruction of crypts and was accompanied by diarrhea and body weight loss. Daily administration of lafutidine reduced the severity of intestinal mucositis, diarrhea and body weight loss in a dose-dependent manner, while famotidine had no effect on intestinal mucositis. The preventive effects of lafutidine were completely abolished in sensory deafferented and TRPV1-KO mice. Lafutidine significantly suppressed 5-FU-increased MPO activity and inflammatory cytokine expression on day 6, but not apoptosis induction in intestinal crypts on day 1. Lafutidine induced Alcian Blue and PAS-positive mucus production in the small intestine. These findings suggest that lafutidine attenuates 5-FU-induced intestinal mucositis, most likely by increasing mucus production via activation of sensory afferent neurons. Furthermore, intact TRPV1 signaling is essential for the activation of sensory afferent neurons induced by lafutidine. Therefore, lafutidine is more useful than other common antacids for the treatment of intestinal mucositis during cancer chemotherapy.

Positive PD-L1 Expression Predicts Worse Outcome in Cutaneous Angiosarcoma

Purpose

Programmed death-1 (PD-1) or programmed death ligand-1 (PD-L1) targeted therapies have shown promising survival outcomes in several human neoplasms. However, it is unclear whether the expression of PD-L1 can be correlated to any clinical and pathologic variables in patients with cutaneous angiosarcoma (CA). The aim of this study was to evaluate the clinicopathological significance of PD-L1 expression in CA patients.

Materials and Methods

Data from 52 patients with CA were retrospectively reviewed. PD-L1 expression, tumor proliferation determined by Ki-67 index, and immunohistochemical evaluation of tumor-infiltrating lymphocytes, CD4+ and CD8+, were used to determine correlation with clinicopathological variables.

Results

PD-L1 was positively expressed in 40% of all patients. PD-L1 expression was significantly associated with tumor cell proliferation. Multivariate analysis confirmed that high levels of CD8+ tumor-infiltrating lymphocytes were a significant predictor in patients with clinical stage I CA and the positive expression of PD-L1 was an independent prognostic factor in predicting worse outcome.

Conclusion

PD-L1 expression is a novel pathologic marker for predicting worse outcome in patients with CA.

CD8⁺ tumor-infiltrating lymphocytes at primary sites as a possible prognostic factor of cutaneous angiosarcoma

Tumor-infiltrating lymphocytes (TILs) have been reported as a prognostic factor in various cancers and are a promising target for immunotherapy. To investigate whether TILs have any impact on the prognosis of angiosarcoma patients, 55 non-treated patients (40 patients at stage 1 with cutaneous localized tumors, 4 patients at stage 2 with lymph node metastases and 11 patients at stage 3 with distant metastases) with angiosarcoma were evaluated retrospectively by immunohistochemistry stained CD4, CD8, FOXP3 and Ki67. The Kaplan-Meier method was used to estimate overall survival with patients at stage 1. Survival differences were analyzed by the log-rank test. Patients with higher numbers of CD8(+) TILs in their primary tumors survived significantly longer compared with patients with lower values. Moreover, the number of CD8 in TILs was positively correlated with a distant metastasis-free period. The total number of primary TILs (CD4 plus CD8) and CD8(+) primary TILs of stage 3 patients with distant metastases was positively correlated with their overall survival. To evaluate whether CD8(+) effector T cells are activated or differentiated, flow cytometric analysis of peripheral blood mononuclear cells (PBMC) was performed. The percentages of CD8(+) T cells producing IFN-γ in PBMC were significantly higher in patients with angiosarcoma (n = 10) compared not only with that of healthy controls (n = 20) but also patients with advanced melanoma (n = 11). These results suggest that anti-tumor immunity is clinically relevant in angiosarcoma.

5-HT₃ receptor antagonists ameliorate 5-fluorouracil-induced intestinal mucositis by suppression of apoptosis in murine intestinal crypt cells

BACKGROUND AND PURPOSE

Chemotherapeutic agents, including 5-fluorouracil (5-FU), frequently cause intestinal mucositis resulting in severe diarrhoea and morphological mucosal damage. 5-HT₃ receptor antagonists are clinically effective in the treatment of nausea and emesis during cancer chemotherapy. Therefore we here have examined the effects of 5-HT₃ receptor antagonists on 5-FU-induced intestinal mucositis in mice.

EXPERIMENTAL APPROACH

Intestinal mucositis was induced in male C57BL/6 mice by daily administration of 5-FU (50 mg·kg⁻¹) for 5 days. Effects of 5-HT₃ receptor antagonists, ramosetron (0.01-0.1 mg·kg⁻¹) and ondansetron (5 mg·kg⁻¹), on the accompanying histology, cytokine production and apoptosis were assessed.

KEY RESULTS

Continuous administration of 5-FU to mice caused severe intestinal mucositis, which was histologically characterized by the shortening of villi and destruction of intestinal crypts, accompanied by body weight loss and diarrhoea. Daily ramosetron administration dose-dependently reduced the severity of intestinal mucositis, body weight loss and diarrhoea. Similar beneficial effects were observed with ondansetron. The number of apoptotic, caspase-3- and caspase-8-activated cells increased 24 h after the first 5-FU administration, and these responses were reduced by ramosetron. The up-regulation of TNF-α, IL-1β and IL-6 following 5-FU treatment was also attenuated by ramosetron.

CONCLUSIONS AND IMPLICATIONS

5-HT₃ receptor antagonists ameliorated 5-FU-induced intestinal mucositis in mice, and this action could result from suppression of apoptotic responses in the intestinal crypt cells via inhibition of cytokine expression. Thus, 5-HT₃ receptor antagonists may be useful for preventing not only nausea and emesis but also intestinal mucositis during 5-FU chemotherapy.