The impact of rare cancer and early-line treatments on the benefit of comprehensive genome profiling-based precision oncology

BACKGROUND

Comprehensive genome profiling (CGP) serves as a guide for suitable genomically matched therapies for patients with cancer. However, little is known about the impact of the timing and types of cancer on the therapeutic benefit of CGP.

MATERIALS AND METHODS

A single hospital-based pan-cancer prospective study (TOP-GEAR; UMIN000011141) was conducted to examine the benefit of CGP with respect to the timing and types of cancer. Patients with advanced solid tumors (>30 types) who either progressed with or without standard treatments were genotyped using a single CGP test. The subjects were followed up for a median duration of 590 days to examine therapeutic response, using progression-free survival (PFS), PFS ratio, and factors associated with therapeutic response.

RESULTS

Among the 507 patients, 62 (12.2%) received matched therapies with an overall response rate (ORR) of 32.3%. The PFS ratios (≥1.3) were observed in 46.3% (19/41) of the evaluated patients. The proportion of subjects receiving such therapies in the rare cancer cohort was lower than that in the non-rare cancer cohort (9.6% and 17.4%, respectively; P = 0.010). However, ORR of the rare cancer patients was higher than that in the non-rare cancer cohort (43.8% and 20.0%, respectively; P = 0.046). Moreover, ORR of matched therapies in the first or second line after receiving the CGP test was higher than that in the third or later lines (62.5% and 21.7%, respectively; P = 0.003). Rare cancer and early-line treatment were significantly and independently associated with ORR of matched therapies in multivariable analysis (P = 0.017 and 0.004, respectively).

CONCLUSION

Patients with rare cancer preferentially benefited from tumor mutation profiling by increasing the chances of therapeutic response to matched therapies. Early-line treatments after profiling increase the therapeutic benefit, irrespective of tumor types.

A new mathematical model of phyllotaxis to solve the genuine puzzle spiromonostichy

Arrangement of plant leaves around the stem, termed phyllotaxis, exhibits beautiful and mysterious regularities and has been one of the most attractive subjects of biological pattern formation. After the long history of studies on phyllotaxis, it is now widely accepted that the inhibitory effect of existing leaf primordia on new primordium formation determines phyllotactic patterning. However, costoid phyllotaxis unique to Costaceae of Zingiberales, displaying spiromonostichy characterized by a steep spiral with a small divergence angle, seems to disagree with the inhibitory effect-based mechanism and has remained as a "genuine puzzle". We developed a new mathematical model, hypothesizing that each leaf primordium exerts not only the inhibitory effect but also some inductive effect. Computer simulations with the new model successfully generated a spiromonostichous pattern when these two effects met a certain relationship. The obtained spiromonostichy matched the real costoid phyllotaxis observed with Costus megalobractea, particularly for the decrease of the divergence angle associated with the enlargement of the shoot apical meristem. The new model was also shown to be able to produce a one-sided distichous pattern that is seen in phyllotaxis of a few plants of Zingiberales and has never been addressed in the previous model studies. These results implicated inductive as well as inhibitory mechanisms in phyllotactic patterning, at least in Zingiberales.

Arabidopsis ASYMMETRIC LEAVES2 and Nucleolar Factors Are Coordinately Involved in the Perinucleolar Patterning of AS2 Bodies and Leaf Development

Arabidopsis ASYMMETRIC LEAVES2 (AS2) plays a key role in the formation of flat symmetric leaves. AS2 represses the expression of the abaxial gene ETTIN/AUXIN RESPONSE FACTOR3 (ETT/ARF3). AS2 interacts in vitro with the CGCCGC sequence in ETT/ARF3 exon 1. In cells of leaf primordia, AS2 localizes at peripheral regions of the nucleolus as two AS2 bodies, which are partially overlapped with chromocenters that contain condensed 45S ribosomal DNA repeats. AS2 contains the AS2/LOB domain, which consists of three sequences conserved in the AS2/LOB family: the zinc finger (ZF) motif, the ICG sequence including the conserved glycine residue, and the LZL motif. AS2 and the genes NUCLEOLIN1 (NUC1), RNA HELICASE10 (RH10), and ROOT INITIATION DEFECTIVE2 (RID2) that encode nucleolar proteins coordinately act as repressors against the expression of ETT/ARF3. Here, we examined the formation and patterning of AS2 bodies made from as2 mutants with amino acid substitutions in the ZF motif and the ICG sequence in cells of cotyledons and leaf primordia. Our results showed that the amino acid residues next to the cysteine residues in the ZF motif were essential for both the formation of AS2 bodies and the interaction with ETT/ARF3 DNA. The conserved glycine residue in the ICG sequence was required for the formation of AS2 bodies, but not for the DNA interaction. We also examined the effects of nuc1, rh10, and rid2 mutations, which alter the metabolism of rRNA intermediates and the morphology of the nucleolus, and showed that more than two AS2 bodies were observed in the nucleolus and at its periphery. These results suggested that the patterning of AS2 bodies is tightly linked to the morphology and functions of the nucleolus and the development of flat symmetric leaves in plants.

Upstream open reading frame-mediated upregulation of ANAC082 expression in response to nucleolar stress in Arabidopsis

Perturbations in ribosome biogenesis cause a type of cellular stress called nucleolar or ribosomal stress, which triggers adaptive responses in both animal and plant cells. The Arabidopsis ANAC082 transcription factor has been identified as a key mediator of the plant nucleolar stress response. The 5'-untranslated region (5'-UTR) of ANAC082 mRNA contains an upstream ORF (uORF) encoding an evolutionarily conserved amino acid sequence. Here, we report that this uORF mediates the upregulation of ANAC082 expression in response to nucleolar stress. When transgenic Arabidopsis plants containing a luciferase reporter gene under the control of the ANAC082 promoter and 5'-UTR were treated with reagents that induced nucleolar stress, expression of the reporter gene was enhanced in a uORF sequence-dependent manner. Additionally, we examined the effect of an endoplasmic reticulum (ER) stress-inducing reagent on reporter gene expression because the closest homolog of ANAC082 in Arabidopsis, ANAC103, is involved in the ER stress response. However, the ANAC082 uORF did not respond to ER stress. Interestingly, although ANAC103 has a uORF with an amino acid sequence similar to that of the ANAC082 uORF, the C-terminal sequence critical for regulation is not well conserved among ANAC103 homologs in Brassicaceae. Transient expression assays revealed that unlike the ANAC082 uORF, the ANAC103 uORF does not exert a sequence-dependent repressive effect. Altogether, our findings suggest that the ANAC082 uORF is important for the nucleolar stress response but not for the ER stress response, and that for this reason, the uORF sequence-dependent regulation was lost in ANAC103 during evolution.

Transcriptional regulation of cell proliferation competence-associated Arabidopsis genes, CDKA;1, RID1 and SRD2, by phytohormones in tissue culture

During organ regeneration, differentiated cells acquire cell proliferation competence before the re-start of cell division. In Arabidopsis thaliana (Arabidopsis), CDKA;1, a cyclin-dependent kinase, RID1, a DEAH-box RNA helicase, and SRD2, a small nuclear RNA transcription factor, are implicated in the regulation of cell proliferation competence. Here, we report phytohormonal transcriptional regulation of these cell proliferation competence-associated genes during callus initiation. We can induce the callus initiation from Arabidopsis hypocotyl explants by the culture on the auxin-containing medium. By RT-quantitative PCR analysis, we observed higher mRNA accumulation of CDKA;1, RID1, and SRD2 in culture on the auxin-containing medium than in culture on the auxin-free medium. Promoter-reporter analysis showed that the CDKA;1, RID1, and SRD2 expression was induced in the stele regions containing pericycle cells, where cell division would be resumed to make callus, by the culture in the medium containing auxin and/or cytokinin. However, the expression levels of these genes in cortical and epidermal cells, which would not originate callus cells, were variable by genes and phytohormonal conditions. We also found that the rid1-1 mutation greatly decreased the expression levels of CDKA;1 and SRD2 during callus initiation specifically at 28°C (restrictive temperature), while the srd2-1 mutation did not obviously decrease the expression levels of CDKA;1 and RID1 regardless of temperature conditions but rather even increased them at 22°C (permissive temperature). Together, our results implicated the phytohormonal and differential regulation of cell proliferation competence-associated genes in the multistep regulation of cell proliferation competence.

Enhancement of shoot regeneration by treatment with inhibitors of auxin biosynthesis and transport during callus induction in tissue culture of Arabidopsis thaliana

In two-step culture systems for efficient shoot regeneration, explants are first cultured on auxin-rich callus-inducing medium (CIM), where cells are activated to proliferate and form calli containing root-apical meristem (RAM)-type stem cells and stem cell niche, and then cultured on cytokinin-rich shoot-inducing medium (SIM), where stem cells and stem cell niche of the shoot apical meristem (SAM) are established eventually leading to shoot regeneration. In the present study, we examined the effects of inhibitors of auxin biosynthesis and polar transport in the two-step shoot regeneration culture of Arabidopsis and found that, when they were applied during CIM culture, although callus growth was repressed, shoot regeneration in the subsequent SIM culture was significantly increased. The regeneration-stimulating effect of the auxin biosynthesis inhibitor was not linked with the reduction in the endogenous indole-3-acetic acid (IAA) level. Expression of the auxin-responsive reporter indicated that auxin response was more uniform and even stronger in the explants cultured on CIM with the inhibitors than in the control explants. These results suggested that the shoot regeneration competence of calli was enhanced somehow by the perturbation of the endogenous auxin dynamics, which we discuss in terms of the transformability between RAM and SAM stem cell niches.

Transcriptome Dynamics of Epidermal Reprogramming during Direct Shoot Regeneration in Torenia fournieri

Shoot regeneration involves reprogramming of somatic cells and de novo organization of shoot apical meristems (SAMs). In the best-studied model system of shoot regeneration using Arabidopsis, regeneration is mediated by the auxin-responsive pluripotent callus formation from pericycle or pericycle-like tissues according to the lateral root development pathway. In contrast, shoot regeneration can be induced directly from fully differentiated epidermal cells of stem explants of Torenia fournieri (Torenia), without intervening the callus mass formation in culture with cytokinin; yet, its molecular mechanisms remain unaddressed. Here, we characterized this direct shoot regeneration by cytological observation and transcriptome analyses. The results showed that the gene expression profile rapidly changes upon culture to acquire a mixed signature of multiple organs/tissues, possibly associated with epidermal reprogramming. Comparison of transcriptomes between three different callus-inducing cultures (callus induction by auxin, callus induction by wounding and protoplast culture) of Arabidopsis and the Torenia stem culture identified genes upregulated in all the four culture systems as candidates of common factors of cell reprogramming. These initial changes proceeded independently of cytokinin, followed by cytokinin-dependent, transcriptional activations of nucleolar development and cell cycle. Later, SAM regulatory genes became highly expressed, leading to SAM organization in the foci of proliferating cells in the epidermal layer. Our findings revealed three distinct phases with different transcriptomic and regulatory features during direct shoot regeneration from the epidermis in Torenia, which provides a basis for further investigation of shoot regeneration in this unique culture system.

Symmetry and its transition in phyllotaxis

Symmetry is an important component of geometric beauty and regularity in both natural and cultural scenes. Plants also display various geometric patterns with some kinds of symmetry, of which the most notable example is the arrangement of leaves around the stem, i.e., phyllotaxis. In phyllotaxis, reflection symmetry, rotation symmetry, translation symmetry, corkscrew symmetry, and/or glide reflection symmetry can be seen. These phyllotactic symmetries can be dealt with the group theory. In this review, we introduce classification of phyllotactic symmetries according to the group theory and enumerate all types of phyllotaxis, not only major ones such as spiral and decussate but also minor ones such as orixate and semi-decussate, with their symmetry groups. Next, based on the mathematical model studies of phyllotactic pattern formation, we discuss transitions between phyllotaxis types different in the symmetry class with a focus on the transition into one of the least symmetric phyllotaxis, orixate, as a representative of the symmetry-breaking process. By changes of parameters of the mathematical model, the phyllotactic pattern generated can suddenly switch its symmetry class, which is not constrained by the group-subgroup relationship of symmetry. The symmetry-breaking path to orixate phyllotaxis is also accompanied by dynamic changes of the symmetry class. The viewpoint of symmetry brings a better understanding of the variety of phyllotaxis and its transition.

Temperature-dependent fasciation mutants provide a link between mitochondrial RNA processing and lateral root morphogenesis

Although mechanisms that activate organogenesis in plants are well established, much less is known about the subsequent fine-tuning of cell proliferation, which is crucial for creating properly structured and sized organs. Here we show, through analysis of temperature-dependent fasciation (TDF) mutants of Arabidopsis, root redifferentiation defective 1 (rrd1), rrd2, and root initiation defective 4 (rid4), that mitochondrial RNA processing is required for limiting cell division during early lateral root (LR) organogenesis. These mutants formed abnormally broadened (i.e. fasciated) LRs under high-temperature conditions due to extra cell division. All TDF proteins localized to mitochondria, where they were found to participate in RNA processing: RRD1 in mRNA deadenylation, and RRD2 and RID4 in mRNA editing. Further analysis suggested that LR fasciation in the TDF mutants is triggered by reactive oxygen species generation caused by defective mitochondrial respiration. Our findings provide novel clues for the physiological significance of mitochondrial activities in plant organogenesis.

Cost-effectiveness analysis for preventing hepatitis B virus reactivation-related death in Japan

Background

There is no worldwide standard recommendation for preventing hepatitis B virus (HBV) reactivation for patients with resolved infection treated with an anti-CD20 antibody for B-cell non-Hodgkin lymphoma. This study aims to compare the cost-effectiveness between two commonly used strategies to prevent HBV reactivation-related death.

Methods

The two strategies compared were prophylactic antiviral therapy (Pro NAT) and HBV DNA monitoring followed by on-demand antiviral therapy (HBV DNA monitoring) using entecavir (Entecavir, a generic drug for Baraclude). Effectiveness was defined as the prevention of death due to HBV reactivation and costs were calculated under the health insurance system of Japan as of April 2018 using Markov model. A cost-minimization analysis, one of the cost-effectiveness analyses, was applied, since the effectiveness was the same between the two strategies according to a meta-analysis. To consider the effect of uncertainty for each parameter, probabilistic sensitivity analysis (PSA) was performed. In the scenario analysis, costs were calculated using lamivudine (Zefix) or tenofovir alafenamide (Vemlidy) instead of entecavir. All analyses were done using TreeAge Pro 2019 (TreeAge Software, Inc., MA, USA).

Results

Estimated costs per patient during the 30 months after initiation of chemotherapy for lymphoma were 1,513 USD with Pro NAT and 1,265 USD with HBV DNA monitoring. A PSA revealed that HBV DNA monitoring was more consistently cost-effective compared with Pro NAT when some parameters were set randomly according to probability distributions. In our scenario analysis, costs of Pro NAT and HBV DNA monitoring were calculated as 2,762 and 1,401 USD using lamivudine, 4,857 and 1,629 USD using tenofovir alafenamide.

Conclusions

Our cost-effectiveness analysis shows that an HBV DNA monitoring strategy using entecavir should be recommended for preventing HBV reactivation-related death in Japan.

Key messages

Cost-effectiveness analysis demonstrated that HBV DNA monitoring was more cost-effective compared to Pro NAT; this result was consistent with PSA. HBV DNA monitoring strategy should be recommended to prevent HBV reactivation-related death for the patients with resolved HBV infection in Japan.

CHARACTERISATION OF RADIOPHOTOLUMINESCENCE DOSIMETRY SYSTEM FOR INDIVIDUAL MONITORING

Performance evaluation is typically assessed as part of the approval procedure to verify that a dosimetry system fulfils specified national or international type-test requirements under representative exposure conditions that are expected to mimic workplace fields from the radiological activities being monitored. The International Atomic Energy Agency Radiation Safety Technical Services Laboratory has recently implemented an integrated radiophotoluminescence (RPL) personal dosimetry system developed by Chiyoda Technol Corporation. This paper reports on the successful verification of dosimetric performance properties of the RPL dosimetry system to IEC 62387:2020, in which the badges were exposed to a range of radiation energies and angles of incidence as well as other influence parameters. Characteristics under test included the coefficient of variation, non-linearity of response due to dose dependence as well as the energy and angular response to photon and beta radiation.

Electrochemical reduction of CO2 using Germanium-Sulfide-Indium amorphous glass structures

The research in electrochemical reduction of CO₂ is shifting towards the discovery of new and novel materials. This study shows a new class of material, that of Ge-S-In chalcogenide glass, to be active for reduction of CO₂ in aqueous solutions. Experiments were conducted with bulk and particle form of the material, yielding different product for each structural form. Faradaic efficiency of upto 15% was observed in bulk form for CO production while formic acid with up to 26.1 % faradaic efficiency was measured in powder form. Chalcogenide studies have focused primarily on the photoelectrochemical reduction however these results provide a strong merit for introducing metal in chalcogenide glass structures for electrochemical reduction of CO₂. The activity for CO₂ reduction and the change in product selectivity reflects that further efforts to improve the glass structures can be undertaken in order to increase the faradaic efficiency and selectivity of the products.

Serum immunoglobulin G antibody titer to Fusobacterium nucleatum is associated with unfavorable outcome after stroke

Stroke can be a cause of death, while in non-fatal cases it is a common cause of various disabilities resulting from associated brain damage. However, whether a specific periodontal pathogen is associated with increased risk of unfavorable outcome after stroke remains unknown. We examined risk factors for unfavorable outcome following stroke occurrence, including serum antibody titers to periodontal pathogens. The enrolled cohort included 534 patients who had experienced an acute stroke, who were divided into favorable (n = 337) and unfavorable (n = 197) outcome groups according to modified ranking scale (mRS) score determined at 3 months after onset (favorable = score 0 or 1; unfavorable = score 2-6). The associations of risk factors with unfavorable outcome, including serum titers of IgG antibodies to 16 periodontal pathogens, were examined. Logistic regression analysis showed that the initial National Institutes of Health stroke scale score [odds ratio (OR) = 1·24, 95% confidence interval (CI) = 1·18-1·31, P < 0·001] and C-reactive protein (OR = 1·29, 95% CI = 1·10-1·51, P = 0·002) were independently associated with unfavorable outcome after stroke. Following adjustment with those, detection of the antibody for Fusobacterium nucleatum ATCC 10953 in serum remained an independent predictor of unfavorable outcome (OR = 3·12, 95% CI = 1·55-6·29, P = 0·002). Determination of the antibody titer to F. nucleatum ATCC 10953 in serum may be useful as a predictor of unfavorable outcome after stroke.

Mathematical model studies of the comprehensive generation of major and minor phyllotactic patterns in plants with a predominant focus on orixate phyllotaxis

Plant leaves are arranged around the stem in a beautiful geometry that is called phyllotaxis. In the majority of plants, phyllotaxis exhibits a distichous, Fibonacci spiral, decussate, or tricussate pattern. To explain the regularity and limited variety of phyllotactic patterns, many theoretical models have been proposed, mostly based on the notion that a repulsive interaction between leaf primordia determines the position of primordium initiation. Among them, particularly notable are the two models of Douady and Couder (alternate-specific form, DC1; more generalized form, DC2), the key assumptions of which are that each leaf primordium emits a constant power that inhibits new primordium formation and that this inhibitory effect decreases with distance. It was previously demonstrated by computer simulations that any major type of phyllotaxis can occur as a self-organizing stable pattern in the framework of DC models. However, several phyllotactic types remain unaddressed. An interesting example is orixate phyllotaxis, which has a tetrastichous alternate pattern with periodic repetition of a sequence of different divergence angles: 180°, 90°, −180°, and −90°. Although the term orixate phyllotaxis was derived from Orixa japonica, this type is observed in several distant taxa, suggesting that it may reflect some aspects of a common mechanism of phyllotactic patterning. Here we examined DC models regarding the ability to produce orixate phyllotaxis and found that model expansion via the introduction of primordial age-dependent changes of the inhibitory power is absolutely necessary for the establishment of orixate phyllotaxis. The orixate patterns generated by the expanded version of DC2 (EDC2) were shown to share morphological details with real orixate phyllotaxis. Furthermore, the simulation results obtained using EDC2 fitted better the natural distribution of phyllotactic patterns than did those obtained using the previous models. Our findings imply that changing the inhibitory power is generally an important component of the phyllotactic patterning mechanism.

Phyllotaxis, the beautiful geometry of plant-leaf arrangement around the stem, has long attracted the attention of researchers of biological-pattern formation. Many mathematical models, as typified by those of Douady and Couder (alternate-specific form, DC1; more generalized form, DC2), have been proposed for phyllotactic patterning, mostly based on the notion that a repulsive interaction between leaf primordia spatially regulates primordium initiation. In the framework of DC models, which assume that each primordium emits a constant power that inhibits new primordium formation and that this inhibitory effect decreases with distance, the major types (but not all types) of phyllotaxis can occur as stable patterns. Orixate phyllotaxis, which has a tetrastichous alternate pattern with a four-cycle sequence of the divergence angle, is an interesting example of an unaddressed phyllotaxis type. Here, we examined DC models regarding the ability to produce orixate phyllotaxis and found that model expansion by introducing primordial age-dependent changes of the inhibitory power is absolutely necessary for the establishment of orixate phyllotaxis. The simulation results obtained using the expanded version of DC2 (EDC2) fitted well the natural distribution of phyllotactic patterns. Our findings imply that changing the inhibitory power is generally an important component of the phyllotactic patterning mechanism.

Hepatitis B virus reactivation in patients with rheumatoid arthritis: Analysis of the National Database of Japan

This study aimed to determine the incidence and risk factors for hepatitis B virus (HBV) reactivation in patients with rheumatoid arthritis (RA) undergoing immunosuppressive therapy. The National Database of Japan, in which insurance claim data have been comprehensively accumulated, was utilized. The subjects were 76 641 RA patients who were plausibly initiated on immunosuppressive therapy from April 2013 to March 2014. Laboratory tests of the hepatitis B surface antigen, anti-hepatitis B virus surface antibody, and anti-hepatitis B virus core antibody were performed in 28.23%, 12.52% and 14.63% of patients, respectively, when the therapy was initiated. We found that HBV reactivation and fulminant hepatitis occurred in both the patients with and without HBV DNA monitoring, indicating insufficient monitoring in Japan during the study. The cumulative incidence of HBV reactivation over 24 months was 1.57% (95% confidence interval [CI] = 1.28%-1.92%) in the monitoring group, which consisted of those with resolved HBV infection. Glucocorticoid administration was a potent risk factor for HBV reactivation (hazard ratio [HR]  = 1.70, 95% CI = 1.26-2.29, P = .001 in all subjects, and HR = 1.82, 95% CI = 1.18-2.81, P = .007 in the nonmonitoring group), although it was not statistically significant in the monitoring group (HR = 1.49, 95% CI = 0.99-2.26 and P = .057). No significant risk difference was observed between single administration of methotrexate and biological drugs.

Phylogenetic and phylodynamic analyses of hepatitis C virus subtype 1a in Okinawa, Japan

Okinawa Island, located in Southern Japan, has a higher prevalence rate of hepatitis C virus subtype 1a (HCV-1a) infection than that in mainland Japan. Okinawa has a history of US military occupation after World War II. To elucidate the transmission history of HCV-1a in Okinawa, 26 whole-genome sequences were obtained from 29 patients during 2011-2016. Phylogenetic trees were reconstructed to identify the origin and characteristics of HCV-1a in Okinawa with epidemiological information. A phylogenetic tree based on whole-genome sequencing revealed that all of the samples were located below the US branches. Additionally, we identified one cluster comprised of 17 strains (Okinawa, n = 16; United States, n = 1). The majority of the patients in this cluster were people who inject drugs (PWID), indicating the presence of a people who inject drugs (PWID) cluster. Subsequently, Bayesian analyses were employed to reveal viral population dynamics. Intriguingly, a phylodynamic analysis uncovered a substantial increase in effective population size of HCV-1a from 1965 to 1980 and a slight increase in mid-2000, which were associated with an increase in illicit drug use in Okinawa. The estimated divergence time of the PWID cluster was 1967.6 (1964.2-1971.1). These findings suggest that HCV-1a was introduced into Okinawa from the United States in the late 1960s, coincident with the Vietnam War. Subsequently, HCV-1a might have spread among the Japanese population with the spread of injecting drug use. Our study provides an understanding of HCV transmission dynamics in Okinawa, as well as the key role of PWID in HCV transmission.

Effect of Lactobacillus strains on thymus and chemokine expression in keratinocytes and development of atopic dermatitis-like symptoms

Lactobacillus strains, a major group of lactic acid bacteria, are representative food microorganisms that have many potential beneficial effects via their interactions with immune and intestinal epithelial cells. However, little is known about the effect of Lactobacillus strains on atopic dermatitis via keratinocytes, which comprise the physical barrier of the skin. In this study, we report that Lactobacillus strains have a significant suppressive effect on tumour necrosis factor (TNF)-α-induced expression and production of thymus and activation-regulated chemokine (TARC), a T helper 2 cell chemokine responsible for atopic dermatitis, in human keratinocytes. An RNA interference study showed that the effect of Lactobacillus reuteri strain Japan Collection of Microorganisms (JCM) 1112, the most suppressive strain, depended on the presence of Toll-like receptor 2 and the induction of A20 (also known as TNF-α-induced protein 3) and cylindromatosis in HaCaT cells. Topical application of a water-soluble extract of homogenised JCM 1112 cells significantly suppressed the development of house dust mite-induced atopic skin lesions and TARC expression at the lesion sites in NC/Nga mice. Our study provides new insights into the use of Lactobacillus strains as suppressive agents against keratinocyte-involved atopic inflammation of the skin.

Activation of NLRP3 inflammasome in macrophages by mycoplasmal lipoproteins and lipopeptides

The NLRP3 inflammasome, an intracellular sensor consisting of the nucleotide-binding oligomerization domain-like receptor family, pyrin domain containing 3 (NLRP3), the adaptor protein apoptosis-associated speck-like protein containing a caspase-recruitment domain (ASC), and procaspase-1, plays critical roles in host defense against microbial pathogens by inducing production of interleukin-1β (IL-1β) and IL-18. Mycoplasma salivarium and Mycoplasma pneumoniae cells activated murine bone marrow-derived macrophages (BMMs) to induce production of IL-1α, IL-1β, and IL-18. The IL-1β production-inducing activities of these mycoplasmas toward BMMs from Toll-like receptor 2 (TLR2)-deficient mice were significantly attenuated compared with those from C57BL/6 mice (B6BMMs). This result suggests the possibility that their lipoproteins as TLR2 agonists are involved in the activity. Lipoproteins of M. salivarium and M. pneumoniae (MsLP and MpLP), and the M. salivarium-derived lipopeptide FSL-1 induced IL-1β production by B6BMMs, but not by BMMs from caspase-1-, NLRP3- or ASC-deficient mice. The activities of MsLP and MpLP were not downregulated by the proteinase K treatment, suggesting that the active sites are their N-terminal lipopeptide moieties. B6BMMs internalized the mycoplasmal N-terminal lipopeptide FSL-1 at least 30 min after incubation, FSL-1-containing endosomes started to fuse with the lysosomes around 2 hours, and then FSL-1 translocated into the cytosol from LAMP-1⁺ endosomes. The artificial delivery of FSL-1 into the cytosol of B6BMMs drastically enhanced the IL-1β production-inducing activity. FSL-1 as well as the representative NLRP3 inflammasome activator nigericin induced the NLRP3/ASC speck, but FSL-1 located in a compartment different from the NLRP3/ASC speck.

Low incidence of hepatitis B virus reactivation and subsequent hepatitis in patients with chronic hepatitis C receiving direct-acting antiviral therapy

To determine the clinical characteristics of hepatitis B virus (HBV) reactivation in patients undergoing interferon-free antihepatitis C virus (HCV) therapy, we examined HBV DNA in 25 HBV co-infected patients and 765 patients with resolved HBV infection during and after treatment with direct-acting antiviral agents (DAAs). Among those with HCV genotype 1, asunaprevir plus daclatasvir was administered to 160 patients, sofosbuvir (SOF) plus ledipasvir to 438 patients and paritaprevir plus ombitasvir and ritonavir to 25 patients. In total, 167 patients with genotype 2 were treated with SOF plus ribavirin. Three patients with an HBV DNA level ≥2000 IU/mL were treated with entecavir before anti-HCV therapy, without reactivation of HBV. In 3 of 22 (12%) HBV surface antigen (HBsAg)-positive patients with an HBV DNA level <2000 IU/mL, the viral load increased during treatment. However, hepatitis flare did not occur in these patients. There was no significant difference in clinical history between patients with and without HBV reactivation. Among 765 patients with resolved HBV infection, HBV reactivation occurred in 1 (0.1%) patient after initial resolution, whose HBV DNA level spontaneously decreased after DAA therapy. We compared anti-HBs titres at baseline with those at post-DAA therapy in 123 patients without HBsAg. There was no significant difference in anti-HBs levels between the two points (P = .79). In conclusion, HBV reactivation was rare in HBsAg-negative patients treated with DAA therapy. Additionally, hepatitis did not occur in HBV-reactivated patients with a baseline HBV DNA level <2000 IU/mL before DAA therapy.

Plant Nucleolar Stress Response, a New Face in the NAC-Dependent Cellular Stress Responses

The nucleolus is the most prominent nuclear domain, where the core processes of ribosome biogenesis occur vigorously. All these processes are finely orchestrated by many nucleolar factors to build precisely ribosome particles. In animal cells, perturbations of ribosome biogenesis, mostly accompanied by structural disorders of the nucleolus, cause a kind of cellular stress to induce cell cycle arrest, senescence, or apoptosis, which is called nucleolar stress response. The best-characterized pathway of this stress response involves p53 and MDM2 as key players. p53 is a crucial transcription factor that functions in response to not only nucleolar stress but also other cellular stresses such as DNA damage stress. These cellular stresses release p53 from the inhibition by MDM2, an E3 ubiquitin ligase targeting p53, in various ways, which leads to p53-dependent activation of a set of genes. In plants, genetic impairments of ribosome biogenesis factors or ribosome components have been shown to cause characteristic phenotypes, including a narrow and pointed leaf shape, implying a common signaling pathway connecting ribosomal perturbations and certain aspects of growth and development. Unlike animals, however, plants have neither p53 nor MDM2 family proteins. Then the question arises whether plant cells have a nucleolar stress response pathway. In recent years, it has been reported that several members of the plant-specific transcription factor family NAC play critical roles in the pathways responsive to various cellular stresses. In this mini review, we outline the plant cellular stress response pathways involving NAC transcription factors with reference to the p53-MDM2-dependent pathways of animal cells, and discuss the possible involvement of a plant-unique, NAC-mediated pathway in the nucleolar stress response in plants.

Evidence for a Role of ANAC082 as a Ribosomal Stress Response Mediator Leading to Growth Defects and Developmental Alterations in Arabidopsis

Ribosome-related mutants in Arabidopsis thaliana share several notable characteristics regarding growth and development, which implies the existence of a common pathway that responds to disorders in ribosome biogenesis. As a first step to explore this pathway genetically, we screened a mutagenized population of root initiation defective2 (rid2), a temperature-sensitive mutant that is impaired in pre-rRNA processing, and isolated suppressor of root initiation defective two1 (sriw1), a suppressor mutant in which the defects of cell proliferation observed in rid2 at the restrictive temperature was markedly rescued. sriw1 was identified as a missense mutation of the NAC transcription factor gene ANAC082 The sriw1 mutation greatly alleviated the developmental abnormalities of rid2 and four other tested ribosome-related mutants, including rid3 However, the impaired pre-rRNA processing in rid2 and rid3 was not relieved by sriw1 Expression of ANAC082 was localized to regions where phenotypic effects of ribosome-related mutations are readily evident and was elevated in rid2 and rid3 compared with the wild type. These findings suggest that ANAC082 acts downstream of perturbation of biogenesis of the ribosome and may mediate a set of stress responses leading to developmental alterations and cell proliferation defects.

A genetic link between epigenetic repressor AS1-AS2 and a putative small subunit processome in leaf polarity establishment of Arabidopsis

Although the DEAD-box RNA helicase family is ubiquitous in eukaryotes, its developmental role remains unelucidated. Here, we report that cooperative action between the Arabidopsis nucleolar protein RH10, an ortholog of human DEAD-box RNA helicase DDX47, and the epigenetic repressor complex of ASYMMETRIC-LEAVES1 (AS1) and AS2 (AS1-AS2) is critical to repress abaxial (ventral) genes ETT/ARF3 and ARF4, which leads to adaxial (dorsal) development in leaf primordia at shoot apices. Double mutations of rh10-1 and as2 (or as1) synergistically up-regulated the abaxial genes, which generated abaxialized filamentous leaves with loss of the adaxial domain. DDX47 is part of the small subunit processome (SSUP) that mediates rRNA biogenesis. In rh10-1 we found various defects in SSUP-related events, such as: accumulation of 35S/33S rRNA precursors; reduction in the 18S/25S ratio; and nucleolar hypertrophy. Double mutants of as2 with mutations of genes that encode other candidate SSUP-related components such as nucleolin and putative rRNA methyltransferase exhibited similar synergistic defects caused by up-regulation of ETT/ARF3 and ARF4. These results suggest a tight link between putative SSUP and AS1-AS2 in repression of the abaxial-determining genes for cell fate decisions for adaxial development.

Summary: This paper reports the importance of cooperative action between the nucleus-localized epigenetic repressor and the nucleolus-localized proteins involved in ribosomal RNA processing for polarity establishment of Arabidopsis leaves.

Effects of HLA-DPB1 genotypes on chronic hepatitis B infection in Japanese individuals

Significant associations of HLA-DP alleles with chronic hepatitis B (CHB) infection are evident in Asian and Arabian populations, including Japanese, Han Chinese, Korean, and Saudi Arabian populations. Here, significant associations between CHB infection and five DPB1 alleles (two susceptibility alleles, DPB1(*) 05:01 and (*) 09:01, and three protective alleles, DPB1(*) 02:01, (*) 04:01, and (*) 04:02) were confirmed in a population comprising of 2582 Japanese individuals. Furthermore, odds ratios for CHB were higher for those with both DPB1 susceptibility alleles than for those with only one susceptibility allele; therefore, effects of susceptibility alleles were additive for risk of CHB infection. Similarly, protective alleles showed an additive effect on protection from CHB infection. Moreover, heterozygotes of any protective allele showed stronger association with CHB than did homozygotes, suggesting that heterozygotes may bind a greater variety of hepatitis B-derived peptides, and thus present these peptides more efficiently to T-cell receptors than homozygotes. Notably, compound heterozygote of the protective allele (any one of DPB1*02:01, *04:01, and *04:02) and the susceptible allele DPB1*05:01 was significantly associated with protection against CHB infection, which indicates that one protective HLA-DPB1 molecule can provide dominant protection. Identification of the HLA-DPB1 genotypes associated with susceptibility to and protection from CHB infection is essential for future analysis of the mechanisms responsible for immune recognition of hepatitis B virus antigens by HLA-DPB1 molecules.

Expression of microRNA-155 correlates positively with the expression of Toll-like receptor 7 and modulates hepatitis B virus via C/EBP-β in hepatocytes

Effective recognition of viral infection and successive activation of antiviral innate immune responses are vital for host antiviral defence, which largely depends on multiple regulators, including Toll-like receptors (TLRs) and microRNAs. Several early reports suggest that specific TLR-mediated immune responses can control hepatitis B virus (HBV) replication and express differentially with disease outcome. Considering the versatile function of miR-155 in the TLR-mediated innate immune response, we aimed to study the association between miR-155 and TLRs and their subsequent impact on HBV replication using both a HBV-replicating stable cell line (HepG2.2.15) and HBV-infected liver biopsy and serum samples. Our results showed that miR-155 was suppressed during HBV infection and a subsequent positive correlation of miR-155 with TLR7 activation was noted. Further, ectopic expression of miR-155 in vitro reduced HBV load as evidenced from reduced viral DNA, mRNA and subsequently reduced level of secreted viral antigens (HBsAg and HBeAg). Our results further suggested that CCAAT/enhancer-binding protein-β (C/EBP-β), a positive regulator of HBV transcription, was inhibited by miR-155. Taken together, our study established a correlation between miR-155 and TLR7 during HBV infection and also demonstrated in vitro that increased miR-155 level could help to reduce HBV viral load by targeting C/EBP-β.

Activation of inflammasomes in dendritic cells and macrophages by Mycoplasma salivarium

Interleukin-1β (IL-1β) plays crucial roles in the pathogenesis of periodontal disease. It is produced after the processing of pro-IL-1β by caspase-1, which is activated by the inflammasome-a multiprotein complex comprising nucleotide-binding domain leucine-rich repeat-containing receptor (NLR), the adaptor protein apoptosis-associated speck-like protein containing a caspase-recruitment domain (ASC), and procaspase-1. Mycoplasma salivarium preferentially inhabits the gingival sulcus and the incidence and number of organisms in the oral cavity increase significantly with the progression of periodontal disease. To initially clarify the association of this organism with periodontal diseases, this study determined whether it induces IL-1β production by innate immune cells such as dendritic cells or macrophages by using Mycoplasma pneumoniae as a positive control. Both live and heat-killed M. salivarium and M. pneumoniae cells induced IL-1β production by XS106 murine dendritic cells as well as pyroptosis. The activities were significantly downregulated by silencing of caspase-1. Bone-marrow-derived macrophage (BMMs) from wild-type and NLR-containing protein 3 (NLRP3)-, ASC-, and caspase-1-deficient mice were examined for IL-1β production in response to these mycoplasmas. Live M. salivarium and M. pneumoniae cells almost completely lost the ability to induce IL-1β production by BMMs from ASC- and caspase-1-deficient mice. Their activities toward BMMs from NLRP3-deficient mice were significantly but not completely attenuated. These results suggest that live M. salivarium and M. pneumoniae cells can activate several types of inflammasomes including the NLRP3 inflammasome. Both M. salivarium and M. pneumoniae cells can activate THP-1 human monocytic cells to induce IL-1β production. Hence, the present finding that M. salivarium induces IL-1β production by dendritic cells and macrophages may suggest the association of this organism with periodontal diseases.

Cell dedifferentiation and organogenesis in vitro require more snRNA than does seedling development in Arabidopsis thaliana

Small nuclear RNA (snRNA) is a class of non-coding RNAs that processes pre-mRNA and rRNA. Transcription of abundant snRNA species is regulated by the snRNA activating protein complex (SNAPc), which is conserved among multicellular organisms including plants. SRD2, a putative subunit of SNAPc in Arabidopsis thaliana, is essential for development, and the point mutation srd2-1 causes severe defects in hypocotyl dedifferentiation and de novo meristem formation. Based on phenotypic analysis of srd2-1 mutant plants, we previously proposed that snRNA content is a limiting factor in dedifferentiation in plant cells. Here, we performed functional complementation analysis of srd2-1 using transgenic srd2-1 Arabidopsis plants harboring SRD2 homologs from Populus trichocarpa (poplar), Nicotiana tabacum (tobacco), Oryza sativa (rice), the moss Physcomitrella patens, and Homo sapiens (human) under the control of the Arabidopsis SRD2 promoter. Only rice SRD2 suppressed the faulty tissue culture responses of srd2-1, and restore the snRNA levels; however, interestingly, all SRD2 homologs except poplar SRD2 rescued the srd2-1 defects in seedling development. These findings demonstrated that cell dedifferentiation and organogenesis induced during tissue culture require higher snRNA levels than does seedling development.

Historical review of research on plant cell dedifferentiation

Plant cell dedifferentiation has long attracted interest as a key process for understanding the plasticity of plant development. In early studies, typical examples of plant cell dedifferentiation were described as physiological and cytological changes associated with wound healing or regenerative development. Subsequently, plant tissue and cell culture techniques, in which exciting progress was achieved after discovery of the hormonal control of cell proliferation and organogenesis in vitro in the 1950s, have been used extensively to study dedifferentiation. The pioneer studies of plant tissue/cell culture led to the hypothesis that many mature plant cells retain totipotency and related dedifferentiation to the initial step of the expression of totipotency. Plant tissue/cell cultures have provided experimental systems not only for physiological analysis, but also for genetic and molecular biological analysis, of dedifferentiation. More recently, proteomic, transcriptomic, and epigenetic analyses have been applied to the study of plant cell dedifferentiation. All of these works have expanded our knowledge of plant cell dedifferentiation, and current research is contributing to unraveling the molecular mechanisms. The present article provides a brief overview of the history of research on plant cell dedifferentiation.

A novel system for xylem cell differentiation in Arabidopsis thaliana

During vascular development, procambial and cambial cells give rise to xylem and phloem cells. Because the vascular tissue is deeply embedded, it has been difficult to analyze the processes of vascular development in detail. Here, we establish a novel in vitro experimental system in which vascular development is induced in Arabidopsis thaliana leaf-disk cultures using bikinin, an inhibitor of glycogen synthase kinase 3 proteins. Transcriptome analysis reveals that mesophyll cells in leaf disks synchronously turn into procambial cells and then differentiate into tracheary elements. Leaf-disk cultures from plants expressing the procambial cell markers TDR(pro):GUS and TDR(pro):YFP can be used for spatiotemporal visualization of procambial cell formation. Further analysis with the tdr mutant and TDIF (tracheary element differentiation inhibitory factor) indicates that the key signaling TDIF-TDR-GSK3s regulates xylem differentiation in leaf-disk cultures. This new culture system can be combined with analysis using the rich material resources for Arabidopsis including cell-marker lines and mutants, thus offering a powerful tool for analyzing xylem cell differentiation.

A novel system for xylem cell differentiation in Arabidopsis thaliana

During vascular development, procambial and cambial cells give rise to xylem and phloem cells. Because the vascular tissue is deeply embedded, it has been difficult to analyze the processes of vascular developmen in detail. Here, we establish a novel in vitro experimental system, in which vascular development is induced in Arabidopsis thaliana leaf-disk cultures using bikinin, an inhibitor of glycogen synthase kinase 3 proteins. Transcriptome analysis reveals that mesophyll cells in leaf disks synchronously turn into procambial cells and then differentiate into tracheary elements. Leaf-disk cultures from plants expressing the procambial cell markers TDRpro:GUS and TDRpro:YFP can be used for spatiotemporal visualization of procambial cell formation. Further analysis with the tdr mutant and TDIF indicates that the key signaling TDIF- TDR-GSK3s regulates xylem differentiation in leaf-disk cultures. This new culture system can be combined with the analysis using the rich Arabidopsis material resources including cell-marker lines and mutants, thus offering a powerful tool for analyzing xylem cell differentiation.

Molecular Cloning and Expression of aStreptomycesSarcosine Oxidase Gene inStreptomyces lividans

A genomic library of Streptomyces sp. KB210-8SY, prepared in the plasmid vector pACYC184, was screened to obtain the gene encoding sarcosine oxidase with probes based on the amino acid sequence of the protein. A plasmid pSOXS13, which was isolated from a clone identified by hybridization with the probes, contained a 8.4-kb insert of Streptomyces DNA. When the 2.0-kb MIuI/EcoRV DNA fragment of pSOXS13 was inserted into the Streptomyces vector pIJ680 and introduced into S. lividans, the transformants produced 100-fold more sarcosine oxidase intracellularly than KB210-8SY. The nucleotides of the 1.7-kb fragment containing the sarcosine oxidase gene were sequenced. An open reading frame encoded a mature sarcosine oxidase consisting of 388 amino acids, with a calculated molecular mass of 42,107 daltons.

Involvement of rRNA biosynthesis in the regulation of CUC1 gene expression and pre-meristematic cell mound formation during shoot regeneration

At an early stage of shoot regeneration from calli of Arabidopsis, pre-meristematic cell mounds develop in association with localized strong expression of CUP-SHAPED COTYLEDON (CUC) genes. Previous characterization of root initiation-defective 3 (rid3), an Arabidopsis mutant originally isolated as being temperature-sensitive for adventitious root formation, with respect to shoot regeneration implicated RID3 in the negative regulation of CUC1 expression and the restriction of cell division in pre-meristematic cell mounds. Positional cloning has identified RID3 as a WD40 repeat protein gene whose molecular function was not investigated before. Here we performed in silico analysis of RID3 and found that RID3 is orthologous to IPI3, which mediates pre-rRNA processing in Saccharomyces cerevisiae. In the rid3 mutant, rRNA precursors accumulated to a very high level in a temperature-dependent manner. This result indicates that RID3 is required for pre-rRNA processing as is IPI3. We compared rid3 with rid2, a temperature-sensitive mutant that is mutated in a putative RNA methyltransferase gene and is impaired in pre-rRNA processing, for seedling morphology, shoot regeneration, and CUC1 expression. The rid2 and rid3 seedlings shared various developmental alterations, such as a pointed-leaf phenotype, which is often observed in ribosome-related mutants. In tissue culture for the induction of shoot regeneration, both rid2 and rid3 mutations perturbed cell-mound formation and elevated CUC1 expression. Together, our findings suggest that rRNA biosynthesis may be involved in the regulation of CUC1 gene expression and pre-meristematic cell-mound formation during shoot regeneration.