Establishment of indicator for screening of child abuse and neglect in primary school-age children

AIM

In Japan, elementary schools are committed to early discovery of child abuse and neglect. Under Japanese law, dentists are required to be involved in child welfare and early detection of child abuse. However, the extent to which dental practitioners cooperate for prevention of child abuse with schools remains limited to date. Therefore, we undertook a community-based project that aimed to develop screening indicators to identify potentially abused children based on their oral health condition and behavioural characteristics in education settings. We have already reported on the relationship between oral health condition and child abuse. The present study established an indicator that can facilitate identification and prevention of child abuse/neglect.

METHODS

Study design: Cross-sectional study. Questionnaires were given to teachers at an elementary school to ascertain behavioural characteristics observed in children who experienced abuse.

CONCLUSION

We developed a check sheet for proper assessment, which requires as little effort as possible, and an index for screening children in need based on teaching staff's observation of students' daily behaviour in school settings. Highly selected items are advantageous as they lead to a decrease in non-response or responses, which can help in improving the accuracy of the response to each question.

Prognosis and cause of death in patients with left atrial appendage thrombus treated with or without anticoagulation therapy

Background

Thrombus in left atrial appendage (LAA) is associated with cardiogenic ischemic stroke; however, little is known about prognosis of patients with LAA thrombus detected by transoesophageal echocardiography (TOE).

Purpose

This study is to investigate the prognosis of patients with LAA thrombus and their cause of death.

Methods

Between 2005 and 2016, the patients who were performed TOE in our hospital were enrolled in this retrospective observational study. Five-year stroke free and survival curves were constructed by Kaplan-Meir method and cause of death were assessed.

Results

Among the 1263 study patients, LAA thrombus was detected in 146 (12%) patients. The patients with LAA thrombus were elder (74 y [66–79 y] vs. 70 y [62–76 y], P<0.001), than those without LAA thrombus, respectively. The prevalence of male sex (67% vs. 69%, P=0.63) were similar between the 2 groups. The prevalence of CHA2DS2-VASc score ≥2, d-dimer (1.7 mcg/ml [0.9–3.5 mcg/ml] vs. 0.8 mcg/ml [0.5–2.2 mcg/ml], P<0.001), and plasma brain natriuretic peptide (315 pg/ml [128–515 pg/ml] vs. 126 pg/ml [47–284 pg/ml], P<0.001) were higher in the patients with LAA thrombus than those without (89% vs. 78%, P=0.003). The LAA velocity was slower in the patients with LAA thrombus than those without (23 cm/s [15–34 cm/s] vs. 51 cm/s [35–72 cm/s], P<0.001). The prevalence of receiving anticoagulation therapy before (34% vs. 24%, P=0.01) and after (98% vs. 66%, P<0.001) TOE 1 month were higher in the patients with LAA thrombus than those without. The 5-year stroke free rate was lower in the patients with LAA thrombus than those without (82% vs. 93%, P<0.001); however, the 5-year survival were similar between the 2 groups (84% vs. 84%, P=0.93) (Figure). The cause of death as ischemic stroke was only 7% (1/14) and 3% (3/94), (P=0.43); the cardiac cause (14% vs. 43%, P=0.07) and the malignancy (35% vs. 29%, P=0.75) were the frequent cause of death in the patient with LAA thrombus and those without, respectively.

Conclusions

The patients who were detected thrombus in the LAA had higher incidence of ischemic stroke; however, the 5-y survival were similar. The ischemic stroke was not major cause of death in the patients with and without LAA thrombus. The higher rate of receiving anticoagulation therapy may be one of the causes of the discrepancy.

Figure 1

Funding Acknowledgement

Type of funding source: None

In Vivo Chemical Probing for G-Quadruplex Formation

While DNA inside the cells is predominantly canonical right-handed double helix, guanine-rich DNAs have potential to fold into four-stranded structures that contain stacks of G-quartets (G4 DNA quadruplex). Genome sequencing has revealed G4 sequences tend to localize at the gene control regions, especially in the promoters of oncogenes. A growing body of evidence indicates that G4 DNA quadruplexes might have important regulatory roles in genome function, highlighting the need for techniques to detect genome-wide folding of DNA into this structure. Potassium permanganate in vivo treatment of cells results in oxidizing of nucleotides in single-stranded DNA regions that accompany G4 DNA quadruplexes formation, providing an excellent probe for the conformational state of DNA inside the living cells. Here, we describe a permanganate-based methodology to detect G4 DNA quadruplex, genome-wide. This methodology combined with high-throughput sequencing provides a snapshot of the DNA conformation over the whole genome in vivo.

P4548Early drop in systolic blood pressure and worsening renal function in the elderly acute heart failure: how does heart rate interact?

Background

Renal dysfunction is a frequent finding in patients hospitalized for acute heart failure (AHF). Worsening renal function (WRF) during hospitalization was found to be related with a poor outcome independently of baseline renal function. Early drop in systolic blood pressure (SBP) has shown to predict WRF in AHF. However, there have been few studies that reported the impact of on-admission heart rate (HR) on the relationship between early SBP drop and WRF in the elderly AHF.

Purpose

We assessed the hypothesis that early SBP drop predict WRF in the elderly patients with AHF, and investigated that on-admission HR might have an interaction with that relationship.

Methods

SBP and HR were measured on admission and 6 times during 48 hours in the 245 elderly AHF inpatients (82.9±6.0 years old, male 49.4%). WRF was defined as a serum creatinine increase of ≥0.3 mg/dL by Day 5. Early drop in SBP was calculated as the difference between admission and the lowest value measured during the first 48 hour of hospitalization.

Results

Early SBP drop (51.3 vs 32.5mmHg, p<0.01) and on-admission HR (79.3 vs 89.6bpm, p<0.05) were significantly different between the group with WRF (n=36) and the group without WRF (n=209). In the multiple logistic regression analysis adjusted for the confounders including age, gender, hypertension, left ventricular ejection fraction, total cholesterol, BNP, baseline creatinine, beta-blockade use, intravenous loop diuretic, isosorbide dinitrate and carperitide use, early SBP drop (OR: 1.003, 95% CI: 1.003–1.03, p<0.04) and on-admission HR (OR: 0.98, 95% CI: 0.96–0.99, p<0.01) were significantly associated with WRF. The interaction term of early SBP drop by on-admission HR did not have a significant association with WRF (p=0.3).

Conclusions

In the elderly AHF patients, exaggerated early SBP drop and lower on-admission HR were shown as significant independent predictors of WRF. These two factors were additively associated with WRF. Too much reduction in SBP and that in HR might be harmful to renal circulation in AHF.

Carbonic anhydrase 9 expression is associated with poor prognosis, tumor proliferation, and radiosensitivity of thymic carcinomas

Introduction

Thymic epithelial tumors (TETs) comprise several histologies of thymoma and thymic carcinomas (TCs), and TC frequently metastasizes and causes death. We therefore aimed here to identify key molecules closely related to prognosis and their biological roles in high-risk TETs, particularly TCs.

Results

RNA sequence analysis demonstrated that hypoxia-related genes were highly expressed in TETs. The expression of the hypoxia-related gene CA9 was noteworthy, particularly in TCs. Immunohistochemical analysis revealed that CA9 was expressed in 81.0% of TCs and 20.7% of all TET samples. CA9 expression was significantly associated with Masaoka stage, WHO classification, and recurrence-free survival after tumor resection (P = 0.005). The down-regulation of CA9 transcription in TC cell lines by small interfering RNAs significantly inhibited CA9 expression, which inhibited proliferation and increased sensitivity to irradiation.

Conclusions

CA9 expression may serve as a significant prognostic marker of TETs and therefore represents a potential target for the development of novel drugs and radiation-sensitizing therapy designed to improve the outcomes of patients with TCs.

Materials and Methods

We performed comprehensive transcriptome sequencing of 23 TETs and physiologic thymic specimens to identify genes highly and specifically expressed in high-risk TETs, particulary TCs. We performed immunohistochemical analysis of 179 consecutive surgically resected TETs to evaluate the significance of the association of protein expression with clinicopathological features and prognosis. The biological significance of the most promising prognostic marker was further studied using the TC cell lines, Ty-82 and MP57.

Overexpression of B-cell lymphoma 6 alters gene expression profile in a myeloma cell line and is associated with decreased DNA damage response

B-cell lymphoma 6 (BCL6) attenuates DNA damage response (DDR) through gene repression and facilitates tolerance to genomic instability during immunoglobulin affinity maturation in germinal center (GC) B cells. Although BCL6 expression is repressed through normal differentiation of GC B cells into plasma cells, a recent study showed the ectopic expression of BCL6 in primary multiple myeloma (MM) cells. However, the functional roles of BCL6 in MM cells are largely unknown. Here, we report that overexpression of BCL6 in a MM cell line, KMS12PE, induced transcriptional repression of ataxia telangiectasia mutated (ATM), a DDR signaling kinase, which was associated with a reduction in γH2AX formation after DNA damage. In contrast, transcription of known targets of BCL6 in GC B cells was not affected, suggesting a cell type-specific function of BCL6. To further investigate the effects of BCL6 overexpression on the MM cell line, we undertook mRNA sequence analysis and found an upregulation in the genomic mutator activation-induced cytidine deaminase (AID) with alteration in the gene expression profile, which is suggestive of de-differentiation from plasma cells. Moreover, interleukin-6 exposure to KMS12PE led to upregulation of BCL6 and AID, downregulation of ATM, and attenuation of DDR, which were consistent with the effects of BCL6 overexpression in this MM cell line. Taken together, these results indicated that overexpression of BCL6 alters gene expression profile and confers decreased DDR in MM cells. This phenotypic change could be reproduced by interleukin-6 stimulation, suggesting an important role of external stimuli in inducing genomic instability, which is a hallmark of MM cells.

Caspase14 expression is associated with triple negative phenotypes and cancer stem cell marker expression in breast cancer patients

BACKGROUND AND OBJECTIVES

The Caspase14 (CASP14) was reported that the low expression of CASP14 in ovarian cancer and colon cancer was associated with cancer progression, on the other hand, that the CASP14 expression in breast cancer was higher than that of non-cancerous tissues. The purpose of this study is to determine the clinical significance of CASP14 in breast cancer.

METHODS

We performed immunohistochemistry for CASP14, ER, PgR, HER2, Ki67, EGFR, CK5/6, CD44, CD24, ALDH1, claudins, and androgen receptor in 222 breast cancer patients including 55 TNBC cases, and evaluated the relationship of CASP14, above-mentioned markers, and prognosis. Using public microarray database of breast cancer, the prognostic value of CASP14 was calculated.

RESULTS

High CASP14 expression was significantly associated with TNBC subtype (P = 0.015), nuclear grade (P = 0.006), Ki67, EGFR (P < 0.001, P = 0.016), ALDH1, CD44 and CD24 (P < 0.001, P < 0.001, P = 0.001) in 222 breast cancer cases, and the high expression of claudin1 (P = 0.017), and androgen receptor (P = 0.002) in TNBC cases was related to the high CASP14. According to the public database, survival in the high CASP14 breast cancer patients was shorter than low CASP14 patients.

CONCLUSIONS

High CASP14 expression is a marker of breast cancer aggressiveness in association with proliferation, TNBC phenotype, and cancer stemness.

Progress of Cell Proliferation in Striated Muscle Tissues during Development of the Mouse Tongue

The developmental stages of and places for the proliferation of tongue muscle cells have not yet been determined. To determine the stages of and places for proliferation between embryonic day (E) 9 and birth, we analyzed the expression of cyclin D1 mRNA and the immunolocalization for proliferating cell nuclear antigen (PCNA). The ratio of PCNA-positive nuclei to total nuclei (PCNA-labeling index) was obtained in the anterior, middle, and posterior regions. Cyclin D1 mRNA was highly expressed between E11 and E13, but decreased thereafter until birth. The distribution of PCNA-positive cell nuclei was consistent with that of myogenic cells in the occipital somites at E9. The PCNA-labeling index was highest at E11, then decreased until birth without a significant difference among the 3 regions. These findings suggest that some tongue muscle progenitor cells begin proliferation in the occipital somites at E9, and that the proliferation in the whole tongue region occurred most actively between E11 and E13, then decreased until birth without regional differences.

HMGN proteins modulate chromatin regulatory sites and gene expression during activation of naïve B cells

The activation of naïve B lymphocyte involves rapid and major changes in chromatin organization and gene expression; however, the complete repertoire of nuclear factors affecting these genomic changes is not known. We report that HMGN proteins, which bind to nucleosomes and affect chromatin structure and function, co-localize with, and maintain the intensity of DNase I hypersensitive sites genome wide, in resting but not in activated B cells. Transcription analyses of resting and activated B cells from wild-type and Hmgn^−/− mice, show that loss of HMGNs dampens the magnitude of the transcriptional response and alters the pattern of gene expression during the course of B-cell activation; defense response genes are most affected at the onset of activation. Our study provides insights into the biological function of the ubiquitous HMGN chromatin binding proteins and into epigenetic processes that affect the fidelity of the transcriptional response during the activation of B cell lymphocytes.

RAG Represents a Widespread Threat to the Lymphocyte Genome

The RAG1 endonuclease, together with its cofactor RAG2, is essential for V(D)J recombination but is a potent threat to genome stability. The sources of RAG1 mis-targeting and the mechanisms that have evolved to suppress it are poorly understood. Here, we report that RAG1 associates with chromatin at thousands of active promoters and enhancers in the genome of developing lymphocytes. The mouse and human genomes appear to have responded by reducing the abundance of "cryptic" recombination signals near RAG1 binding sites. This depletion operates specifically on the RSS heptamer, whereas nonamers are enriched at RAG1 binding sites. Reversing this RAG-driven depletion of cleavage sites by insertion of strong recombination signals creates an ectopic hub of RAG-mediated V(D)J recombination and chromosomal translocations. Our findings delineate rules governing RAG binding in the genome, identify areas at risk of RAG-mediated damage, and highlight the evolutionary struggle to accommodate programmed DNA damage in developing lymphocytes.

Abstract 5126: Establishment of an esophageal small cell carcinoma cell line (TYUC-1)

Background: Small cell carcinoma of the esophagus is rare and its prognosis is extremely poor. However, there is currently no in vitro model of this disease.

Methods: After obtaining written informed consent, we obtained a tumor from a 56-year-old female patient with esophageal small cell carcinoma in 2009 and transplanted it into a Severe Combined Immuno Deficiency (SCID) mouse. After successful transplantation, a tumor from the back of this mouse was minced with a sharp scissors without enzymes and was cultured in Ham F12/DMDM supplemented with 5% fetal bovine serum.

Results: Culture cells grew as adherent cells during the initial culture phase and gradually grew as floating aggregated cells. We carefully maintained these floating cells and transferred them without enzymes. These cells could passage to another flask with a split ratio of 1/10. We named these cells “TYUC-1”, and passaged them more than 85 times. The population doubling-time of TYUC-1 was approximately 30 hours. The G-band karyotype confirmed that these cells had a human origin. These cells could be transplanted to SCID mice with the same histological features of primary esophageal small cell carcinoma, and were shown to express TrkA, NGF, NSE, FGFRL1, p53, CD56, ALDH1A1, and CD44, but not CD133. A cDNA array also revealed that 9 genes were overexpressed while the expression of 33 genes was significantly lower than that in 28 esophageal squamous cell carcinoma (ESCC) cell lines. Whole exome sequencing revealed that TYUC-1 had TP53, PIK3CA, KMT2D, CACNA1H, NCOR1 and HRAS mutations. Furthermore, TYUC-1 had mutations in 128 genes, whereas 28 ESCC cell lines had no mutations in these genes.

Conclusions: We newly established TYUC-1 cells that exhibited neuroendocrine characteristics and expressed several stem cell-related molecules. These cells may be useful for understanding the characteristics of esophageal small cell carcinoma.

Citation Format: Yutaka Shimada, Tomoyuki Okumura, Yoshinori Takei, Kazuaki Watanabe, Akira Hirasawa, Arito Yamane, Masahiko Nishiyama, Takuya Nagata, Kazuhiro Tsukada, Kazuharu Shimizu. Establishment of an esophageal small cell carcinoma cell line (TYUC-1). [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5126. doi:10.1158/1538-7445.AM2015-5126

Abstract 2070: Stxbp4 suppresses APC/C mediated turnover of p63 and increases tumorigenicity and malignancy

p63 plays a pivotal role in epithelial development and maintenance of epithelial proliferative potential. The delN isoforms of p63 are thought to be involved in both basal-epidermal gene expression and maintenance of epithelial progenitor proliferative potential. It is also thought that delN versions of p63 and p73 can serve to inhibit the abilities of their TA isoform counterparts to induce cell cycle arrest and apoptosis. Consistent with this, after DNA damage or during terminal differentiation, delNp63 proteins are quickly down regulated. Although p53 is frequently mutated in human cancers, p63 mutation is rare and it overexpresses especially in squamous carcinomas, such as lung, bladder, breast, and head and neck squamous cell carcinoma. Indeed several report concluded that immuno histochemistry with delNp63 is a powerful ancillary method for classifying lung adenocarcinoma and squamous carcinoma, a distinction with important therapeutic implications. We previously reported that APC/C plays a role in ubiquitin-mediated turnover of delNp63 and that Stxbp4 suppresses the degradation of delNp63 by the APC/C and Rack1-VHL. Importantly, both Stxbp4 and APC/C degradation-resistant delNp63 suppress the terminal differentiation process in 3D organotypic culture model as well as in vitro culture. To investigate the effect and the mechanism of delNp63 for tumorigenicity and malignancy in Lung squamous carcinoma, we examined a transcriptome analysis (RNA-seq) of delNp63 and Stxbp4 with NGS (Next Generation Sequencer) and generated xenograft mice model. Thus, our study provides insight into a novel mechanism for delNp63 in regulating tumorigenicity and malignancy in squamous cell carcinoma as well as epitherial development.

Citation Format: Yukihiro Otaka, Susumu Rokudai, Kyoichi Kaira, Kimihiro Shimizu, Masashi Ito, Ami Ichihara, Reika Kawabata, Shinji Yoshiyama, Arito Yamane, Takayuki Asao, Carol Prives, Masahiko Nishiyama. Stxbp4 suppresses APC/C mediated turnover of p63 and increases tumorigenicity and malignancy. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2070. doi:10.1158/1538-7445.AM2015-2070

Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation

A key finding of the ENCODE project is that the enhancer landscape of mammalian cells undergoes marked alterations during ontogeny. However, the nature and extent of these changes are unclear. As part of the NIH Mouse Regulome Project, we here combined DNaseI hypersensitivity, ChIP-seq, and ChIA-PET technologies to map the promoter-enhancer interactomes of pluripotent ES cells and differentiated B lymphocytes. We confirm that enhancer usage varies widely across tissues. Unexpectedly, we find that this feature extends to broadly transcribed genes, including Myc and Pim1 cell-cycle regulators, which associate with an entirely different set of enhancers in ES and B cells. By means of high-resolution CpG methylomes, genome editing, and digital footprinting, we show that these enhancers recruit lineage-determining factors. Furthermore, we demonstrate that the turning on and off of enhancers during development correlates with promoter activity. We propose that organisms rely on a dynamic enhancer landscape to control basic cellular functions in a tissue-specific manner.

Global regulation of promoter melting in naive lymphocytes

Lymphocyte activation is initiated by a global increase in messenger RNA synthesis. However, the mechanisms driving transcriptome amplification during the immune response are unknown. By monitoring single-stranded DNA genome wide, we show that the genome of naive cells is poised for rapid activation. In G0, ∼90% of promoters from genes to be expressed in cycling lymphocytes are polymerase loaded but unmelted and support only basal transcription. Furthermore, the transition from abortive to productive elongation is kinetically limiting, causing polymerases to accumulate nearer to transcription start sites. Resting lymphocytes also limit the expression of the transcription factor IIH complex, including XPB and XPD helicases involved in promoter melting and open complex extension. To date, two rate-limiting steps have been shown to control global gene expression in eukaryotes: preinitiation complex assembly and polymerase pausing. Our studies identify promoter melting as a third key regulatory step and propose that this mechanism ensures a prompt lymphocyte response to invading pathogens.

A genome-wide map of CTCF multivalency redefines the CTCF code

The "CTCF code" hypothesis posits that CTCF pleiotropic functions are driven by recognition of diverse sequences through combinatorial use of its 11 zinc fingers (ZFs). This model, however, is supported by in vitro binding studies of a limited number of sequences. To study CTCF multivalency in vivo, we define ZF binding requirements at ∼50,000 genomic sites in primary lymphocytes. We find that CTCF reads sequence diversity through ZF clustering. ZFs 4-7 anchor CTCF to ∼80% of targets containing the core motif. Nonconserved flanking sequences are recognized by ZFs 1-2 and ZFs 8-11 clusters, which also stabilize CTCF broadly. Alternatively, ZFs 9-11 associate with a second phylogenetically conserved upstream motif at ∼15% of its sites. Individually, ZFs increase overall binding and chromatin residence time. Unexpectedly, we also uncovered a conserved downstream DNA motif that destabilizes CTCF occupancy. Thus, CTCF associates with a wide array of DNA modules via combinatorial clustering of its 11 ZFs.

Role of Occlusion in Masseter Muscle Acetylcholine Receptor Clustering

Nicotinic acetylcholine receptor (nAChR) clustering is a key event in the synaptogenesis of the neuromuscular junction (NMJ) for the efficient transmission of neural signals from motor neurons to skeletal muscle. The microphthalmic mouse ( mi/mi) with a mutation in the mitf gene cannot perform occlusion, because its teeth do not erupt. The present study attempted to elucidate the contribution of occlusion to the clustering of nAChR in the NMJ of the masseter, with mi/mi as a model system. In mice at 1 week of age, no significant change in the fragmentation or volume of the nAChR cluster was observed in either the masseter or gastrocnemius between breast-fed +/+ and mi/mi. In mice at 4 and 12 weeks of age, after the occlusion emerged in the +/+, excessive fragmentation and volume decline in the nAChR cluster were observed in the masseter of mi/mi fed a powdered diet compared with +/+ fed a pellet or powdered diet, whereas, in the gastrocnemius, no such differences were observed between the 2 strains. These results indicate abnormal formation of the nAChR cluster in the NMJ of the masseter of mi/mi, suggesting that occlusion is essential for the normal progress of nAChR clustering in the NMJ of the masseter.

Rif1 prevents resection of DNA breaks and promotes immunoglobulin class switching

DNA double-strand breaks (DSBs) represent a threat to the genome because they can lead to the loss of genetic information and chromosome rearrangements. The DNA repair protein p53 binding protein 1 (53BP1) protects the genome by limiting nucleolytic processing of DSBs by a mechanism that requires its phosphorylation, but whether 53BP1 does so directly is not known. Here, we identify Rap1-interacting factor 1 (Rif1) as an ATM (ataxia-telangiectasia mutated) phosphorylation-dependent interactor of 53BP1 and show that absence of Rif1 results in 5'-3' DNA-end resection in mice. Consistent with enhanced DNA resection, Rif1 deficiency impairs DNA repair in the G(1) and S phases of the cell cycle, interferes with class switch recombination in B lymphocytes, and leads to accumulation of chromosome DSBs.

53BP1 alters the landscape of DNA rearrangements and suppresses AID-induced B cell lymphoma

Deficiencies in factors that regulate the DNA damage response enhance the incidence of malignancy by destabilizing the genome. However, the precise influence of the DNA damage response on regulation of cancer-associated rearrangements is not well defined. Here we examine the genome-wide impact of tumor protein P53-binding protein 1 (53BP1) deficiency in lymphoma and translocation. While both activation-induced cytidine deaminase (AID) and 53BP1 have been associated with cancer in humans, neither AID overexpression nor loss of 53BP1 is sufficient to produce malignancy. However, the combination of 53BP1 deficiency and AID deregulation results in B cell lymphoma. Deep sequencing of the genome of 53BP1(-/-) cancer cells and translocation capture sequencing (TC-Seq) of primary 53BP1(-/-) B cells revealed that their chromosomal rearrangements differ from those found in wild-type cells in that they show increased DNA end resection. Moreover, loss of 53BP1 alters the translocatome by increasing rearrangements to intergenic regions.

RPA accumulation during class switch recombination represents 5'-3' DNA-end resection during the S-G2/M phase of the cell cycle

Activation-induced cytidine deaminase (AID) promotes chromosomal translocations by inducing DNA double-strand breaks (DSBs) at immunoglobulin (Ig) genes and oncogenes in the G1 phase. RPA is a single-stranded DNA (ssDNA)-binding protein that associates with resected DSBs in the S phase and facilitates the assembly of factors involved in homologous repair (HR), such as Rad51. Notably, RPA deposition also marks sites of AID-mediated damage, but its role in Ig gene recombination remains unclear. Here, we demonstrate that RPA associates asymmetrically with resected ssDNA in response to lesions created by AID, recombination-activating genes (RAG), or other nucleases. Small amounts of RPA are deposited at AID targets in G1 in an ATM-dependent manner. In contrast, recruitment in the S-G2/M phase is extensive, ATM independent, and associated with Rad51 accumulation. In the S-G2/M phase, RPA increases in nonhomologous-end-joining-deficient lymphocytes, where there is more extensive DNA-end resection. Thus, most RPA recruitment during class switch recombination represents salvage of unrepaired breaks by homology-based pathways during the S-G2/M phase of the cell cycle.

c-Myc is a universal amplifier of expressed genes in lymphocytes and embryonic stem cells

The c-Myc HLH-bZIP protein has been implicated in physiological or pathological growth, proliferation, apoptosis, metabolism, and differentiation at the cellular, tissue, or organismal levels via regulation of numerous target genes. No principle yet unifies Myc action due partly to an incomplete inventory and functional accounting of Myc's targets. To observe Myc target expression and function in a system where Myc is temporally and physiologically regulated, the transcriptomes and the genome-wide distributions of Myc, RNA polymerase II, and chromatin modifications were compared during lymphocyte activation and in ES cells as well. A remarkably simple rule emerged from this quantitative analysis: Myc is not an on-off specifier of gene activity, but is a nonlinear amplifier of expression, acting universally at active genes, except for immediate early genes that are strongly induced before Myc. This rule of Myc action explains the vast majority of Myc biology observed in literature.

Zinc finger transcription factor zDC is a negative regulator required to prevent activation of classical dendritic cells in the steady state

Classical dendritic cells (cDCs) process and present antigens to T cells. Under steady-state conditions, antigen presentation by cDCs induces tolerance. In contrast, during infection or inflammation, cDCs become activated, express higher levels of cell surface MHC molecules, and induce strong adaptive immune responses. We recently identified a cDC-restricted zinc finger transcription factor, zDC (also known as Zbtb46 or Btbd4), that is not expressed by other immune cell populations, including plasmacytoid DCs, monocytes, or macrophages. We define the zDC consensus DNA binding motif and the genes regulated by zDC using chromatin immunoprecipitation and deep sequencing. By deleting zDC from the mouse genome, we show that zDC is primarily a negative regulator of cDC gene expression. zDC deficiency alters the cDC subset composition in the spleen in favor of CD8(+) DCs, up-regulates activation pathways in steady-state cDCs, including elevated MHC II expression, and enhances cDC production of vascular endothelial growth factor leading to increased vascularization of skin-draining lymph nodes. Consistent with these observations, zDC protein expression is rapidly down-regulated after TLR stimulation. Thus, zDC is a TLR-responsive, cDC-specific transcriptional repressor that is in part responsible for preventing cDC maturation in the steady state.

DNA damage defines sites of recurrent chromosomal translocations in B lymphocytes

Recurrent chromosomal translocations underlie both haematopoietic and solid tumours. Their origin has been ascribed to selection of random rearrangements, targeted DNA damage, or frequent nuclear interactions between translocation partners; however, the relative contribution of each of these elements has not been measured directly or on a large scale. Here we examine the role of nuclear architecture and frequency of DNA damage in the genesis of chromosomal translocations by measuring these parameters simultaneously in cultured mouse B lymphocytes. In the absence of recurrent DNA damage, translocations between Igh or Myc and all other genes are directly related to their contact frequency. Conversely, translocations associated with recurrent site-directed DNA damage are proportional to the rate of DNA break formation, as measured by replication protein A accumulation at the site of damage. Thus, non-targeted rearrangements reflect nuclear organization whereas DNA break formation governs the location and frequency of recurrent translocations, including those driving B-cell malignancies.

The function of platelet-derived growth factor in the differentiation of mouse tongue striated muscle

OBJECTIVE

To determine the function of platelet-derived growth factor (PDGF) in the final differentiation phase of tongue striated muscle cells.

MATERIALS AND METHODS

We analyzed the expressions of PDGF-A, -B, platelet-derived growth factor receptor (PDGFR)-α, and PDGFR-β in mouse tongues between embryonic days (E) 11 and 15. Furthermore, we examined the effects of human recombinant PDGF-AB and the peptide antagonist for PDGFRs using an organ culture system of mouse embryonic tongue. Mouse tongues at E12 were cultured in BGJb medium containing human recombinant PDGF-AB for 4 days or the peptide antagonist for PDGF receptors for 8 days.

RESULTS

PDGF-A, -B, PDGFR-α, and -β were expressed in the differentiating muscle cells between E11 and 15. The human recombinant PDGF-AB induced increases in the mRNA expressions of myogenin and muscle creatine kinase (MCK) and the number of fast myosin heavy chain (fMHC)-positive cells, markers for the differentiation of muscle cells. On the other hand, the peptide antagonist for PDGFRs induced suppressions in the mRNA expressions of myogenin and MCK, and the number of fMHC-positive cells. Both the PDGF-AB and the antagonist failed to affect the expressions of cell proliferation markers.

CONCLUSION

These results suggest that PDGF functions as a positive regulator in the final differentiation phase of tongue muscle cells in mouse embryos.

Translocation-capture sequencing reveals the extent and nature of chromosomal rearrangements in B lymphocytes

Chromosomal rearrangements, including translocations, require formation and joining of DNA double strand breaks (DSBs). These events disrupt the integrity of the genome and are frequently involved in producing leukemias, lymphomas and sarcomas. Despite the importance of these events, current understanding of their genesis is limited. To examine the origins of chromosomal rearrangements we developed Translocation Capture Sequencing (TC-Seq), a method to document chromosomal rearrangements genome-wide, in primary cells. We examined over 180,000 rearrangements obtained from 400 million B lymphocytes, revealing that proximity between DSBs, transcriptional activity and chromosome territories are key determinants of genome rearrangement. Specifically, rearrangements tend to occur in cis and to transcribed genes. Finally, we find that activation-induced cytidine deaminase (AID) induces the rearrangement of many genes found as translocation partners in mature B cell lymphoma.

Ab initio study on the hydrogen desorption from MH-NH3 (M = Li, Na, K) hydrogen storage systems

The hydrogen storage system LiH + NH(3) ↔ LiNH(2) + H(2) is one of the most promising hydrogen storage systems, where the reaction yield can be increased by replacing Li in LiH with other alkali metals (Na or K) in order of Li < Na < K. In this paper, we have studied the alkali metal M (M = Li, Na, K) dependence of the reactivity of MH with NH(3) by calculating the potential barrier of the H(2) desorption process from the reaction of an M(2)H(2) cluster with an NH(3) molecule based on the ab initio structure optimization method. We have shown that the height of the potential barrier becomes lower in order of Li, Na, and K, where the difference of the potential barrier in Li and Na is relatively smaller than that in Na and K, and this tendency is consistent with the recent experimental results. We have also shown that the H-H distance of the H(2) dimer at the transition state takes larger distance and the change of the potential energy around the transition state becomes softer in order of Li, Na, and K. There are almost no M dependence in the charge of the H atom in NH(3) before the reaction, while that of the H atom in M(2)H(2) takes larger negative value in order of Li, Na, and K. We have also performed molecular dynamics simulations on the M(2)H(2)-NH(3) system and succeeded to reproduce the H(2) desorption from the reaction of Na(2)H(2) with NH(3).

Aberrant expression and mutation-inducing activity of AID in human lung cancer

BACKGROUND

Activation-induced cytidine deaminase (AID) is expressed in B lymphocytes and triggers antibody diversification. Recent reports have indicated that the constitutive expression of AID in mice causes not only lymphomas, but also cancers of some organs including the lung, prompting us to investigate the expression and effect of AID on human lung cancer.

MATERIALS AND METHODS

We examined AID mRNA expression in 17 lung cancer cell lines and 51 primary lung cancers using a quantitative RT-PCR analysis. Next, we established H1299 lung cancer cells stably overexpressing AID and performed a supF forward mutation assay. We then examined AID protein expression and p53 mutation in 129 primary lung cancers by an immunohistochemical analysis and PCR-SSCP and sequencing analyses, respectively.

RESULTS

Aberrant mRNA expression of AID was detected in 29% (5 of 17) of the lung cancer cell lines and 31% (16 of 51) of the primary lung cancers. AID-overexpressing H1299 clones showed a 5.0- to 6.1-fold higher mutation frequency than an empty vector-transfected H1299 clone, and about half of the AID-induced mutations were base substitutions, indicating that AID induces gene mutations in lung cancer cells. Furthermore, an association was found between the AID protein expression level and the p53 mutation status in an analysis of 129 primary lung cancers. A further expression analysis revealed that a portion of AID is localized at the centrosomes.

CONCLUSION

Our current findings suggest that the aberrant expression of AID may be involved in a subset of human lung cancers as a result of its mutation-inducing activity.

Activation-induced cytidine deaminase targets DNA at sites of RNA polymerase II stalling by interaction with Spt5

Activation-induced cytidine deaminase (AID) initiates antibody gene diversification by creating U:G mismatches. However, AID is not specific for antibody genes; Off-target lesions can activate oncogenes or cause chromosome translocations. Despite its importance in these transactions little is known about how AID finds its targets. We performed an shRNA screen to identify factors required for class switch recombination (CSR) of antibody loci. We found that Spt5, a factor associated with stalled RNA polymerase II (Pol II) and single stranded DNA (ssDNA), is required for CSR. Spt5 interacts with AID, it facilitates association between AID and Pol II, and AID recruitment to its Ig and non-Ig targets. ChIP-seq experiments reveal that Spt5 colocalizes with AID and stalled Pol II. Further, Spt5 accumulation at sites of Pol II stalling is predictive of AID-induced mutation. We propose that AID is targeted to sites of Pol II stalling in part via its association with Spt5.

PTIP promotes chromatin changes critical for immunoglobulin class switch recombination

Programmed genetic rearrangements in lymphocytes require transcription at antigen receptor genes to promote accessibility for initiating double-strand break (DSB) formation critical for DNA recombination and repair. Here, we showed that activated B cells deficient in the PTIP component of the MLL3 (mixed-lineage leukemia 3)-MLL4 complex display impaired trimethylation of histone 3 at lysine 4 (H3K4me3) and transcription initiation of downstream switch regions at the immunoglobulin heavy-chain (Igh) locus, leading to defective immunoglobulin class switching. We also showed that PTIP accumulation at DSBs contributes to class switch recombination (CSR) and genome stability independently of Igh switch transcription. These results demonstrate that PTIP promotes specific chromatin changes that control the accessibility of the Igh locus to CSR and suggest a nonredundant role for the MLL3-MLL4 complex in altering antibody effector function.

Regulation of microRNA expression and abundance during lymphopoiesis

Although the cellular concentration of miRNAs is critical to their function, how miRNA expression and abundance are regulated during ontogeny is unclear. We applied miRNA-, mRNA-, and ChIP-Seq to characterize the microRNome during lymphopoiesis within the context of the transcriptome and epigenome. We show that lymphocyte-specific miRNAs are either tightly controlled by polycomb group-mediated H3K27me3 or maintained in a semi-activated epigenetic state prior to full expression. Because of miRNA biogenesis, the cellular concentration of mature miRNAs does not typically reflect transcriptional changes. However, we uncover a subset of miRNAs for which abundance is dictated by miRNA gene expression. We confirm that concentration of 5p and 3p miRNA strands depends largely on free energy properties of miRNA duplexes. Unexpectedly, we also find that miRNA strand accumulation can be developmentally regulated. Our data provide a comprehensive map of immunity's microRNome and reveal the underlying epigenetic and transcriptional forces that shape miRNA homeostasis.

The in vivo pattern of binding of RAG1 and RAG2 to antigen receptor loci

The critical initial step in V(D)J recombination, binding of RAG1 and RAG2 to recombination signal sequences flanking antigen receptor V, D, and J gene segments, has not previously been characterized in vivo. Here, we demonstrate that RAG protein binding occurs in a highly focal manner to a small region of active chromatin encompassing Ig kappa and Tcr alpha J gene segments and Igh and Tcr beta J and J-proximal D gene segments. Formation of these small RAG-bound regions, which we refer to as recombination centers, occurs in a developmental stage- and lineage-specific manner. Each RAG protein is independently capable of specific binding within recombination centers. While RAG1 binding was detected only at regions containing recombination signal sequences, RAG2 binds at thousands of sites in the genome containing histone 3 trimethylated at lysine 4. We propose that recombination centers coordinate V(D)J recombination by providing discrete sites within which gene segments are captured for recombination.

Changes in the expression of myosins during postnatal development of masseter muscle in the microphthalmic mouse

In the present study, to elucidate the influences of the deficiency of teeth on the masseter muscle, we analyzed changes in the expression of MyHC isoform mRNAs during postnatal development in mi/mi mice using real-time PCR. By 8 weeks of age, MyHC I had nearly disappeared in the +/+ mice, while it was still present in the mi/mi, and the level of MyHC I mRNA in the mi/mi was 5.1-fold higher than that in the +/+ (p<0.01). The levels of MyHC IIx mRNAs in the mi/mi mice were 41 ~ 55% lower than those in the +/+ at both 3 weeks and 4 weeks of age (p<0.05). No significant difference in the expression of MyHC IIa and IIb mRNAs in the masseter muscle was found between the mi/mi and +/+. From these results, we speculate that the deficiency of teeth affects the masseter muscles during the postnatal development.

Contribution of occlusal activity to synaptogenesis in masticatory muscles

Synaptogenesis in the neuromuscular junction involves a nicotinic acetylcholine receptor (nAChR) switch and elimination. The microphthalmic mouse (mi/mi) with a mutation in the mitf gene cannot perform occlusal activity, because its teeth do not erupt. The present study attempted to elucidate the contribution of occlusal activity to synaptogenesis in masticatory muscles. In the masseter of the mi/mi, the nAChR elimination initiated, but did not progress normally, after 3 weeks of age, when the occlusal activity emerged in the +/+ mouse, whereas the nAChR switch progressed normally during the entire period of synaptogenesis. The mRNA expression patterns of nAChR subunits in the temporalis and digastric of the mi/mi differed from those in its masseter. These findings suggest that, in the masseter, occlusal activity is essential for the completion of nAChR elimination, but not for the nAChR switch, and that the contribution of occlusal activity to synaptogenesis varies among the masticatory muscles.

Restricting activation-induced cytidine deaminase tumorigenic activity in B lymphocytes

DNA breaks play an essential role in germinal centre B cells as intermediates to immunoglobulin class switching, a recombination process initiated by activation-induced cytidine deaminase (AID). Immunoglobulin gene hypermutation is likewise catalysed by AID but is believed to occur via single-strand DNA breaks. When improperly repaired, AID-mediated lesions can promote chromosomal translocations (CTs) that juxtapose the immunoglobulin loci to heterologous genomic sites, including oncogenes. Two of the most studied translocations are the t(8;14) and T(12;15), which deregulate cMyc in human Burkitt's lymphomas and mouse plasmacytomas, respectively. While a complete understanding of the aetiology of such translocations is lacking, recent studies using diverse mouse models have shed light on two important issues: (1) the extent to which non-specific or AID-mediated DNA lesions promote CTs, and (2) the safeguard mechanisms that B cells employ to prevent AID tumorigenic activity. Here we review these advances and discuss the usage of pristane-induced mouse plasmacytomas as a tool to investigate the origin of Igh-cMyc translocations and B-cell tumorigenesis.