Female sexual dysfunction and lower urinary tract symptoms associated with vulvovaginal atrophy symptoms: Results of the GENJA study.

OBJECTIVES: To investigate the main symptoms of female sexual dysfunction (FSD) and lower urinary tract symptoms associated with vulvovaginal atrophy (VVA) symptoms as the core symptoms of genitourinary syndrome of menopause. METHODS: We extracted the data of 4134 Japanese women aged 40-79 years who participated in the GENitourinary syndrome of menopause in JApanese women (GENJA) study. All participants responded to web-based questionnaires assessing their health situation, including the Vulvovaginal Symptoms Questionnaire, the Female Sexual Function Index (FSFI), and the Core Lower Urinary Tract Symptom Score. Multivariable regression and multivariable logistic regression analyses were applied to analyze the association between VVA symptoms and FSD, and between VVA symptoms and lower urinary tract symptoms. RESULTS: Multivariable regression analysis revealed that VVA symptoms were associated with lower scores for arousal, lubrication, orgasm, satisfaction, and pain domains in the FSFI in sexually active women (p < 0.01). Regression coefficients were higher for lubrication and pain domains than for the other domains. Multivariable logistic regression analysis revealed that women reporting VVA symptoms were more likely to have increased daytime urinary frequency, nocturia, urgency, slow stream, straining to void, feeling of incomplete emptying, bladder pain, and feeling a bulge/lump from or in the vagina (p < 0.05). Adjusted odds ratios were particularly high for straining to void, feeling of incomplete emptying, and bladder pain. CONCLUSIONS: Vulvovaginal atrophy symptoms were significantly associated with decreased lubrication and dyspareunia in FSD, and urinary symptoms of straining to void, feeling of incomplete emptying, and bladder pain.

Epidemiological study of genitourinary syndrome of menopause in Japan (GENJA study).

OBJECTIVE: This study aimed to investigate the prevalence of genitourinary syndrome of menopause (GSM) in Japan using the Japanese translation of the Vulvovaginal Symptoms Questionnaire (VSQ) with online survey. In addition, we examined the relationship between sexual activity and GSM symptoms. METHODS: An online survey on GSM was conducted with 4,134 women aged 40 to 79 years, who were registered in an online survey company. Several questionnaires with Japanese translations of linguistic validity were used in this study. GSM was defined as a condition in women older than 40 years with vulvovaginal symptoms on the VSQ. RESULTS: The percentage of postmenopausal women 40 years and older was 69.6%. The percentage of women with sexual activity was 22%. The prevalence of GSM with vulvovaginal symptoms was 11.6%, and 31.7% in sexually active women. The prevalence of GSM was associated with age and was significantly lower in the 70s age group than in other age groups. Vulvar hurting and dryness were both age-related only in the sexual activity group, with a statistically significantly higher prevalence in the 70s group than in the 40s group. The prevalence of vulvar dryness during sexual activity was significantly lower in the 40s age group. CONCLUSIONS: An online epidemiological survey of GSM was conducted for the first time in Japan using the linguistically validated Japanese translation of the VSQ. The prevalence of GSM with genital or sexual symptoms was 11.6% in Japanese women 40 years and older, and 31.7% in sexually active women.

Evaluation of Hemoglobin Response to Treatment With Enarodustat Using Pharmacometric Approach in Japanese Anemic Patients With Chronic Kidney Disease.

Enarodustat (JTZ-951) is a hypoxia-inducible factor prolyl hydroxylase inhibitor that has been approved and marketed in Japan for patients with anemia with chronic kidney disease (CKD). The pharmacometric approach was applied to assess the relationship between plasma concentrations of enarodustat and hemoglobin (Hb) levels, and to provide information regarding the optimal use of enarodustat in clinical practice by simulations based on the pharmacokinetic and pharmacodynamic (PK/PD) model that was developed. The PK/PD data of enarodusat obtained from phase 2 and phase 3 studies in Japanese patients with CKD were well described by the models: a 1-compartment model with first-order absorption and elimination for PK, and a semimechanistic model based on transit compartment model for PD. Although several factors were identified as statistically significant covariates on the PK/PD of enarodustat, model-based simulations showed that none of them had clinically relevant impacts on the treatment effect (ie, Hb levels) of enarodustat. Hence, enarodustat treatment provides the stable Hb control with the initial dose (hemodialysis-dependent CKD: 4 mg/day, non-dialysis-dependent CKD: 2 mg/day) and maintenance dose (1-8 mg/day) to the patients with varied demographic characteristics.

Enhanced visualization of female squirting.

INTRODUCTION: Squirting is the involuntary expulsion of fluid from the female urethra following stimulation of the anterior vaginal wall before or during orgasm. The mechanism underlying squirting has not been established. PURPOSE: To elucidate the mechanism of squirting. METHODS: The subjects in the current study were women who were able to squirt. They were not sex workers. A urethral catheter was inserted before sexual stimulation and the bladder was emptied. Then, a mixture of indigo carmine (10 ml) and saline (40 ml) was injected into the bladder. Sexual stimulation was provided to facilitate squirting, which was videotaped and verified. The secretions were collected in sterile cups, and prostate specific antigen (PSA) and glucose levels were measured. RESULTS: Five women (2 in the 30s, 2 in the 40s, and 1 in the 50s) participated in this study. All women were able to squirt; three squirted only with manual sexual stimulation and two with penetrative sexual stimulation. The discharged fluid was blue in all cases, confirming the bladder as the source. The fluid was PSA-positive in four patients. CONCLUSIONS: The main component of squirt fluid is urine, but may also contain fluid from Skene's glands (female prostate). This is the first report in which visualization of squirting was enhanced.

[LINGUISTIC VALIDATION OF JAPANESE VERSION OF THE VULVOVAGINAL SYMPTOMS QUESTIONNAIRE (VSQ)].

(Purpose) To translate the Vulvovaginal Symptoms Questionnaire (VSQ) into Japanese and evaluate the linguistic validation of the translated VSQ. (Methods) The translation and evaluation of the VSQ were performed through 3 steps: forward translation based on 2 urologists and discussed by another 3 urologists; the community review process, which consisted of one-on-one cognitive interviews with 20 patients by professional interviewers; backward translation by a native English speaker, which was discussed with the original author of the VSQ. (Results) The original author of the VSQ generally approved our translation. (Conclusion) The Japanese version of the VSQ was translated in a linguistically valid manner. It is equivalent to the original English questionnaire. It may provide a tool to assess sexual function for Japanese women with genitourinary syndrome of menopause.

Pharmacokinetics of Tenofovir Alafenamide, Tenofovir, and Emtricitabine Following Administration of Coformulated Emtricitabine/Tenofovir Alafenamide in Healthy Japanese Subjects.

A fixed-dose combination of tenofovir alafenamide (TAF) and emtricitabine (FTC) is available in 2 tablet strengths in Japan (FTC/TAF 200/10 mg and FTC/TAF 200/25 mg). These are used once daily in combination with other antiretroviral agents for the treatment of human immunodeficiency virus type 1 infection. The primary objective of this study was to investigate if there is any clinically relevant pharmacokinetic difference for TAF, tenofovir (TFV), and FTC between Japanese and non-Japanese with historical data. Three treatment groups were set in the study; FTC/TAF 200/10 mg in combination with darunavir (DRV) 800 mg + ritonavir (RTV) 100 mg (treatment A) or DRV/cobicistat (COBI) 800/150 mg (treatment B) and FTC/TAF 200/25 mg alone (treatment C). Especially for treatment C, it was designated for another purpose to evaluate the pharmacokinetic boosting effects of RTV and COBI on TAF bioavailability. As a result, the mean exposure of TAF among treatment groups was 125 to 154 ng/mL for Cmax and 119 to 179 ng·h/mL for AUCinf , which were comparable with the historical data in non-Japanese. The exposures of TFV and FTC were also consistent with the historical data. Therefore, no clinically relevant pharmacokinetic differences for TAF, TFV, and FTC were observed between Japanese and non-Japanese. Boosting effects of RTV and COBI on TAF bioavailability were slightly lower than we expected, less than a 2.5-fold increase, but it was within the range of exposures associated with efficacy and safety in phase 3 studies. Therefore, it was not considered clinically relevant.

Treatment outcomes of ureteral stenting for malignant extrinsic ureteral obstruction: a comparison between polymeric and metallic stents.

PURPOSE: To compare treatment outcomes, more specifically patency rate, of polymeric and metallic stents for malignant ureteral obstruction. PATIENTS AND METHODS: Between August 2007 and September 2017, we retrospectively analyzed the data of 92 patients (126 ureters) having a diagnosis of malignant extrinsic ureteral obstruction treated with indwelling ureteral stents (polymeric and full-length metallic stents). Of these patients, 35 (54 ureters) were treated with polymeric stents and 57 (72 ureters) with a Resonance® metallic stent. The observation period was censored to 1 year. Survival rate in cases of malignant ureteral obstruction was calculated, and the relationship between the causes of ureteral obstruction, the stent type, and the patency rate was evaluated. RESULTS: The median observation period was 145 days, with a median survival time of 258 days. The stent patency rate was 70.9% at 1 year, regardless of stent type. Stent occlusion was observed in 20 patients (33 ureters). According to stent type, occlusion of the polymeric and metallic stents was identified in 12 (22%) and 8 (11%) cases, respectively. The clinical features associated with stent failure were assessed. In univariate analysis, the patency rate was significantly better for the metallic stent than for the polymeric stent (1-year patency rate; 78.4%, 61.1%, respectively, HR, 2.15; 95% CI, 1.07-4.33; p=0.031). However, the patency rate among patients with abdominal dissemination, lymph node metastasis, and direct compression by tumor was not significantly different. CONCLUSION: Indwelling ureteral stents, particularly metallic stents, are effective for the treatment of malignant ureteral obstruction.

A change from gonadotropin releasing hormone antagonist to gonadotropin releasing hormone agonist therapy does not affect the oncological outcomes in hormone sensitive prostate cancer.

BACKGROUND: The aim of our retrospective study was to evaluate the 5-year survival and time to castration resistant prostate cancer in patients with hormone sensitive prostate cancer treated with the gonadotropin releasing hormone antagonist, degarelix. Another aim was to evaluate the effects of changing the treatment from degarelix to a gonadotropin releasing hormone agonist after achieving stable disease control, on the clinical and oncological outcomes. RESULTS: Our analysis was based on the data of 108 patients with prostate cancer who were treated with degarelix. Of these, the treatment was changed from degarelix to a gonadotropin releasing hormone agonist in 57 patients (changed group), and the treatment with degarelix was continued in the other 51 (continued group). The overall 5-year survival was statistically superior in the changed (96.6%) group than that in the continued (74.1%) group (p = 0.006). The 5-year cancer-specific survival was also superior in the changed (100%) group than that in the continued (84.6%) group (p = 0.027). The average time to castration resistant prostate cancer was comparable in both the changed (43.3 months) and continued (35.2 months) groups (p = 0.117). Lower serum levels of prostate specific antigen and alkaline phosphatase were maintained after changing the therapy from degarelix to a gonadotropin releasing hormone agonist. CONCLUSIONS: Degarelix is effective in the treatment of prostate cancer. Degarelix therapy can also be safely changed to a gonadotropin releasing hormone agonist without any adverse clinical or oncological effects.

CONTEXTE: L'objectif de notre étude rétrospective était d'évaluer la survie à 5 ans et le délai de transition du cancer de la prostate hormono-sensible au cancer de la prostate résistant à la castration chez des patients porteurs d'un cancer de la prostate hormono-sensible qui étaient traités par un antagoniste de la gonadolibérine, le dégarélix. Un autre objectif était d'évaluer les effets sur les résultats cliniques et oncologiques du remplacement du dégarélix par un agoniste de la gonadolibérine après obtention d'un état stable et contrôlé. RÉSULTATS: Notre analyse repose sur les données de 108 patients atteints d'un cancer de la prostate traités par dégarélix. Parmi ceux-ci, le traitement par dégarélix a été remplacé par un agoniste de la gonadolibérine chez 57 (groupe modifié), et le traitement par dégarélix a été poursuivi chez les autres patients (groupe inchangé). La survie globale à 5 ans était statistiquement plus élevée pour le groupe modifié (96.6%) que pour le groupe inchangé (74,1%; p = 0.006). Les chances de survie cancer-spécifiques à 5 ans était également plus élevées pour le groupe modifié (100%) que pour le groupe inchangé (84,6%; p = 0.027). Le délai moyen de transition du cancer de la prostate hormono-sensible au cancer de la prostate résistant à la castration était comparable dans le groupe modifié (43,3 mois) et dans le groupe inchangé (35,2 mois). Des taux sériques plus bas d'antigène spécifique de la prostate et de phosphatase alcaline ont été maintenus après le remplacement du dégarélix par un agoniste de la gonadolibérine. CONCLUSIONS: Le dégarélix est. efficace dans le traitement du cancer de la prostate. Le traitement par dégarélix peut aussi être remplacé en toute sécurité par un agoniste de la gonadolibérine sans aucun effet clinique ou oncologique indésirable. MOTS-CLÉS: Antagonistes et inhibiteurs de la gonadolibérine, Agoniste de la gonadolibérine, Cancer de la prostate, Dégarélix, Résistant à la castration.

Kamikihito improves cancer-related fatigue by restoring balance between the sympathetic and parasympathetic nervous systems.

BACKGROUND: Cancer-related fatigue is one of the most prevalent symptoms that patients with cancer experience, but the mechanisms underlying it are unknown. We aimed to quantify and mechanistically evaluate the improvement in fatigue related to administration of the Kampo medicine, Kamikihito. MATERIALS AND METHODS: Initially, we recruited outpatients with urological diseases and compared fatigue levels of 37 patients with cancer with a control group of 23 volunteers who had recovered completely from cancer or who were being treated for dysuria. Fatigue level was estimated using an autonomic function analyzer. Then, Kamikihito was administered to another 35 patients treated with hormone or antitumor therapy for prostate cancer and metastatic renal cell cancer. Subjective fatigue and other problems of the patients were assessed using the Chalder fatigue scale, the Center for Epidemiologic Studies Depression scale, and the Epworth sleepiness scale. Serum levels of derivatives of reactive oxygen species and biological antioxidant potential were also measured. RESULTS: Patients in the cancer treatment group experienced more fatigue compared with the control patients when evaluated using an autonomic function analyzer. The group of 35 patients who were administered Kamikihito showed improved scores for fatigue, depression, and sleepiness. Autonomic nervous system balance was also improved with Kamikihito administration. The Kamikihito group also had significantly lower reactive oxygen species metabolite levels and significantly higher antioxidant potential. CONCLUSIONS: Fatigue was more serious in patients with cancer than in control patients. Kamikihito rescued this fatigue and improved anxiety and sleepiness. It restored autonomic nervous system balance and antioxidant function.

Oncological outcomes classified according to metastatic lesions in the era of molecular targeted drugs for metastatic renal cancer.

Since the introduction of molecular targeted agents for the treatment of metastatic renal cell cancer (mRCC), several treatment outcomes, including those from our facilities, have been reported. However, the outcome of these drugs, classified by the metastatic organs, is not well known. The present study reported the treatment results of molecular-targeted agents as classified by the metastatic organ at Osaka City University Graduate School of Medicine. A total of 180 consecutively treated patients who had received molecular targeted agents for metastatic renal cancer for 3 or more months were retrospectively analyzed. The overall survival was calculated and compared according to the Memorial Sloan-Kettering Cancer Center (MSKCC) criteria, the number of metastatic organs, and metastatic lesions. The median overall survival of patients with mRCC treated by molecular targeted agents was 34 months. A significant difference in survival rate between groups was found according to the MSKCC criteria. Patients with single metastatic organ lived significantly longer compared with those with metastases in multiple organs. Patients with pancreatic metastasis had a good response to molecular targeted drugs. Pancreatic metastasis, the number of metastatic organs, and MSKCC criteria were independent risk factors for overall survival. Treatment of mRCC by molecularly targeted agents did not show any difference by metastatic organs except for the pancreas, although its efficacy depends on the number of metastatic organs and the MSKCC classification.

Phase 1 studies to assess the safety, tolerability and pharmacokinetics of JTE-052 (a novel Janus kinase inhibitor) ointment in Japanese healthy volunteers and patients with atopic dermatitis.

The purpose of the present two phase 1 studies was to assess the safety, tolerability and pharmacokinetics for topical application of a novel Janus kinase (JAK) inhibitor, JTE-052, in Japanese healthy adult male volunteers and Japanese adult patients with atopic dermatitis (AD). Additionally, exploratory investigation was performed on the efficacy for disease severity and pruritus score in AD patients. In the QBX1-1 study, the cutaneous safety of JTE-052 ointment by a patch test and a photo patch test was assessed in an intra-individual comparative study using placebo ointment, white petrolatum and non-application as comparators. The study demonstrated that JTE-052 ointment would be associated with a low potential for phototoxicity but had no potential for skin irritation or photoallergy. In the QBX1-2 study, it was revealed that the systemic exposure to JTE-052 in both healthy volunteers with normal skin and AD patients with inflamed skin was low in application of not only 1% but also 3% JTE-052 ointment. JTE-052 ointments of 1% and 3% were generally safe and well tolerated in both populations. In a repeated twice-daily application for 7 days, the efficacy of JTE-052 ointment to AD patients was observed with both 1% and 3% ointments in the exploratory investigations evaluated by Eczema Area and Severity Index, Investigator's Global Assessment and Numeric Rating Scale assessments. The mean scores for each assessment declined from the baseline throughout the study. These results suggest that the treatment of JTE-052 ointment is generally safe and effective in AD patients, although further large confirmatory studies are needed.

Effects of a Nutritional Protein-Rich Drink on the Pharmacokinetics of Elvitegravir, Cobicistat, Emtricitabine, Tenofovir Alafenamide, and Tenofovir Compared With a Standard Meal in Healthy Japanese Male Subjects.

This study investigated the effects of ingested meal types on the pharmacokinetics of elvitegravir (EVG), cobicistat (COBI), emtricitabine (FTC), tenofovir alafenamide (TAF), and tenofovir (TFV) following a single administration of the single-tablet regimen (STR) of EVG/COBI/FTC/TAF (150/150/200/10 mg) in Japanese HIV-negative healthy subjects (n = 12). In this open-label, randomized, 3-way crossover study, the bioequivalence of the EVG/COBI/FTC/TAF STR following ingestion of a nutritional protein-rich drink with a reference treatment of taking a standard breakfast was evaluated. Administration under fasted conditions, no food intake, resulted in decreases in the mean AUCinf and Cmax of EVG by 50% and 57%, respectively, relative to the administration with a standard breakfast, whereas the systemic exposure of EVG with a nutritional protein-rich drink was comparable to that with a standard breakfast. The mean AUCinf and Cmax of COBI, FTC, TAF, and TFV were comparable regardless of meal intake or meal types. Although the package insert of the EVG/COBI/FTC/TAF STR states that the medication is recommended to be taken with food, this study provides an additional insight into HIV-1-infected patients that a light meal like a nutritional protein-rich drink can be an alternative to a standard meal.

Outcomes of indwelling metallic stents for malignant extrinsic ureteral obstruction.

OBJECTIVES: To report the treatment outcomes of patients with extrinsic ureteral obstruction treated with metallic stents and to identify the factors predicting stent failure. METHODS: A total of 52 patients with extrinsic ureteral obstruction as a result of malignancy (66 ureters) were treated with metallic stents (Resonance® ) and included in the study. The median observation period was 118 days. RESULTS: The median survival time of these patients was 210 days, and the stent patency rate was 86.0% at 6 months and 60.0% at 1 year. Eight (15.4%) patients underwent nephrostomy as a result of stent failure. The occlusion rate of bilateral ureteral obstructed cases was significantly higher than that of unilateral cases. There was no correlation between the preoperative serum creatinine level, causes of ureteral occlusions (compression by tumor, lymph node metastasis, peritoneal dissemination), obstructed site (upper, middle, lower ureter) and stent failure. CONCLUSIONS: Metallic stents are excellent in maintaining patency compared with the conventional stents. Therefore, they can be used as first-line treatment of malignant ureteral obstructions.

FANTOM5 CAGE profiles of human and mouse samples.

In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities.

Comparative effectiveness of radical prostatectomy and curative radiotherapy in localized prostate cancer: long-term follow-up.

We sought to investigate the long-term outcomes after radical prostatectomy (RP) and external-beam radiation therapy (EBRT) for the treatment of localized prostate cancer in Japanese patients. RP and radiation therapy are curative treatments for localized prostate cancer. However, there is controversy around which treatment is superior in Japanese patients. The aim of our retrospective study was to compare the long-term clinical outcomes of each treatment. We retrospectively evaluated the overall survival (OS), cancer-specific survival (CSS) and biochemical failure-free survival (BFS) for patients who had been diagnosed with localized prostate cancer and treated with RP (n = 248) or conventional 2D or 3D-CRT EBRT (n = 182) between 1995 and 2009. The median OS was superior in the RP group compared with that in EBRT group (P < 0.001), although CSS was comparable for both treatment groups; BFS was superior for the EBRT group compared with that for the RP group (P = 0.04). Univariate analysis identified a prostate-specific antigen count (PSA)of ≥20 vs <20 mg/ml, clinical T-stage of the tumor and Gleason score as predictors for CSS. However, multivariate analysis did not identify a factor for CSS. Subgroup analysis was also performed based on clinical T stage, PSA and Gleason score, but there was no difference in each subgroup between RP and EBRT. Both treatments provided satisfactory clinical outcomes in terms of disease control in localized prostate cancer.

Prolonging survival in metastatic renal cell carcinoma patients treated with targeted anticancer agents: a single-center experience of treatment strategy modifications.

INTRODUCTION: We investigated therapeutic outcomes in consecutive patients with metastatic renal cell carcinoma treated with targeted anticancer agents from 2008 to 2014 in order to determine the efficacy of adverse event management for such agents and the best sequence in which to use them. MATERIALS AND METHODS: We analyzed 132 consecutive patients who had taken targeted anticancer agents for metastatic renal cell carcinoma. Of these, 101 patients received therapy between 2008 and 2011 (pioneer group) and 31 patients received therapy between 2011 and 2014 (contemporary group). Patients of the contemporary group were provided with aggressive adverse event management and education on such management, were treated according to a standard therapeutic strategy, and were able to receive axitinib as a second-line drug. We analyzed the incidence of hand-foot syndrome. Furthermore, we compared relative dose intensity between patients in the pioneer and contemporary groups who took sunitinib as first-line therapy. We also compared overall survival between the two groups to determine whether adverse event management improved prognosis. RESULTS: The incidence of hand-foot syndrome was significantly reduced by aggressive adverse event management. Relative dose intensity was significantly higher in the contemporary group than in the pioneer group. Median survival time was significantly longer in the contemporary group than in the pioneer group. CONCLUSION: Our results suggest that aggressive management of adverse events associated with targeted drugs, the use of sunitinib as a first-line therapy, and the availability of axitinib as a second-line therapy all contribute to prolonged survival for metastatic renal cell carcinoma patients.

Establishment of single-cell screening system for the rapid identification of transcriptional modulators involved in direct cell reprogramming.

Combinatorial interactions of transcription modulators are critical to regulate cell-specific expression and to drive direct cell reprogramming (e.g. trans-differentiation). However, the identification of key transcription modulators from myriad of candidate genes is laborious and time consuming. To rapidly identify key regulatory factors involved in direct cell reprogramming, we established a multiplex single-cell screening system using a fibroblast-to-monocyte transition model. The system implements a single-cell 'shotgun-transduction' strategy followed by nested-single-cell-polymerase chain reaction (Nesc-PCR) gene expression analysis. To demonstrate this, we simultaneously transduced 18 monocyte-enriched transcription modulators in fibroblasts followed by selection of single cells expressing monocyte-specific CD14 and HLA-DR cell-surface markers from a heterogeneous population. Highly multiplex Nesc-PCR expression analysis revealed a variety of gene combinations with a significant enrichment of SPI1 (86/86) and a novel transcriptional modulator, HCLS1 (76/86), in the CD14(+)/HLA-DR(+) single cells. We could further demonstrate the synergistic role of HCLS1 in regulating monocyte-specific gene expressions and phagocytosis in dermal fibroblasts in the presence of SPI1. This study establishes a platform for a multiplex single-cell screening of combinatorial transcription modulators to drive any direct cell reprogramming.

Unamplified cap analysis of gene expression on a single-molecule sequencer.

We report the development of a simplified cap analysis of gene expression (CAGE) protocol adapted for single-molecule sequencers that avoids second strand synthesis, ligation, digestion, and PCR. HeliScopeCAGE directly sequences the 3' end of cap trapped first-strand cDNAs. As with previous versions of CAGE, we better define transcription start sites (TSS) than known models, identify novel regions of transcription and alternative promoters, and find two major classes of TSS signal, sharp peaks and broad regions. However, using this protocol, we observe reproducible evidence of regulation at the much finer level of individual TSS positions. The libraries are quantitative over 5 orders of magnitude and highly reproducible (Pearson's correlation coefficient of 0.987). We have also scaled down the sample requirement to 5 µg of total RNA for a standard HeliScopeCAGE library and 100 ng for a low-quantity version. When the same RNA was run as 5-µg and 100-ng versions, the 100 ng was still able to detect expression for ∼60% of the 13,468 loci detected by a 5-µg library using the same threshold, allowing comparative analysis of even rare cell populations. Testing the protocol for differential gene expression measurements on triplicate HeLa and THP-1 samples, we find that the log fold change compared to Illumina microarray measurements is highly correlated (0.871). In addition, HeliScopeCAGE finds differential expression for thousands more loci including those with probes on the array. Finally, although the majority of tags are 5' associated, we also observe a low level of signal on exons that is useful for defining gene structures.

An atlas of combinatorial transcriptional regulation in mouse and man.

Combinatorial interactions among transcription factors are critical to directing tissue-specific gene expression. To build a global atlas of these combinations, we have screened for physical interactions among the majority of human and mouse DNA-binding transcription factors (TFs). The complete networks contain 762 human and 877 mouse interactions. Analysis of the networks reveals that highly connected TFs are broadly expressed across tissues, and that roughly half of the measured interactions are conserved between mouse and human. The data highlight the importance of TF combinations for determining cell fate, and they lead to the identification of a SMAD3/FLI1 complex expressed during development of immunity. The availability of large TF combinatorial networks in both human and mouse will provide many opportunities to study gene regulation, tissue differentiation, and mammalian evolution.

Development of a high-throughput method for the systematic identification of human proteins nuclear translocation potential.

BACKGROUND: Important clues to the function of novel and uncharacterized proteins can be obtained by identifying their ability to translocate in the nucleus. In addition, a comprehensive definition of the nuclear proteome undoubtedly represents a key step toward a better understanding of the biology of this organelle. Although several high-throughput experimental methods have been developed to explore the sub-cellular localization of proteins, these methods tend to focus on the predominant localizations of gene products and may fail to provide a complete catalog of proteins that are able to transiently locate into the nucleus. RESULTS: We have developed a method for examining the nuclear localization potential of human gene products at the proteome scale by adapting a mammalian two-hybrid system we have previously developed. Our system is composed of three constructs co-transfected into a mammalian cell line. First, it contains a PCR construct encoding a fusion protein composed of a tested protein, the PDZ-protein TIP-1, and the transactivation domain of TNNC2 (referred to as ACT construct). Second, our system contains a PCR construct encoding a fusion protein composed of the DNA binding domain of GAL4 and the PDZ binding domain of rhotekin (referred to as the BIND construct). Third, a GAL4-responsive luciferase reporter is used to detect the reconstitution of a transcriptionally active BIND-ACT complex through the interaction of TIP-1 and rhotekin, which indicates the ability of the tested protein to translocate into the nucleus. We validated our method in a small-scale feasibility study by comparing it to green fluorescent protein (GFP) fusion-based sub-cellular localization assays, sequence-based computational prediction of protein sub-cellular localization, and current sub-cellular localization data available from the literature for 22 gene products. CONCLUSION: Our reporter-based system can rapidly screen gene products for their ability to be translocated to the nucleus. Large-scale applications of the system presented herein should provide invaluable information for a more complete biological atlas.