Dynamic Contrast-Enhanced MRI Parameters and Normalized ADC Values Could Aid Differentiation of Skull Base Osteomyelitis from Nasopharyngeal Cancer

BACKGROUND AND PURPOSE

The skull base osteomyelitis sometimes can be difficult to distinguish from nasopharyngeal cancer. This study aimed to investigate the differences between skull base osteomyelitis and nasopharyngeal cancer using dynamic contrast-enhanced MR imaging and normalized ADC values.

MATERIALS AND METHODS

This study included 8 and 12 patients with skull base osteomyelitis and nasopharyngeal cancer, respectively, who underwent dynamic contrast-enhanced MR imaging and DWI before primary treatment. Quantitative dynamic contrast-enhanced MR imaging parameters and ADC values of the ROIs were analyzed. Normalized ADC parameters were calculated by dividing the ROIs of the lesion by that of the spinal cord.

RESULTS

The rate transfer constant between extravascular extracellular space and blood plasma per minute (Kep) was significantly lower in patients with skull base osteomyelitis than in those with nasopharyngeal cancer (median, 0.43 versus 0.57; P = .04). The optimal cutoff value of Kep was 0.48 (area under the curve, 0.78; 95% CI, 0.55-1). The normalized mean ADC was significantly higher in patients with skull base osteomyelitis than in those with nasopharyngeal cancer (median, 1.90 versus 0.87; P < .001). The cutoff value of normalized mean ADC was 1.55 (area under the curve, 0.96; 95% CI, 0.87-1). The area under the curve of the combination of dynamic contrast-enhanced MR imaging parameters (Kep and extravascular extracellular space volume per unit tissue volume) was 0.89 (95% CI, 0.73-1), and the area under the curve of the combination of dynamic contrast-enhanced MR imaging parameters and normalized mean ADC value was 0.98 (95% CI, 0.93-1).

CONCLUSIONS

Quantitative dynamic contrast-enhanced MR imaging parameters and normalized ADC values may be useful in differentiating skull base osteomyelitis and nasopharyngeal cancer. The combination of dynamic contrast-enhanced MR imaging parameters and normalized ADC values outperformed each measure in isolation.

Differentiation of Skull Base Chondrosarcomas, Chordomas, and Metastases: Utility of DWI and Dynamic Contrast-Enhanced Perfusion MR Imaging

BACKGROUND AND PURPOSE

Differentiation of skull base tumors, including chondrosarcomas, chordomas, and metastases, on conventional imaging remains a challenge. We aimed to test the utility of DWI and dynamic contrast-enhanced MR imaging for skull base tumors.

MATERIALS AND METHODS

Fifty-nine patients with chondrosarcomas, chordomas, or metastases between January 2015 and October 2021 were included in this retrospective study. Pretreatment normalized mean ADC and dynamic contrast-enhanced MR imaging parameters were calculated. The Kruskal-Wallis H test for all tumor types and the Mann-Whitney U test for each pair of tumors were used.

RESULTS

Fifteen chondrosarcomas (9 men; median age, 62 years), 14 chordomas (6 men; median age, 47 years), and 30 metastases (11 men; median age, 61 years) were included in this study. Fractional plasma volume helped distinguish all 3 tumor types (P = .003, <.001, and <.001, respectively), whereas the normalized mean ADC was useful in distinguishing chondrosarcomas from chordomas and metastases (P < .001 and P < .001, respectively); fractional volume of extracellular space, in distinguishing chondrosarcomas from metastases (P = .02); and forward volume transfer constant, in distinguishing metastases from chondrosarcomas/chondroma (P = .002 and .002, respectively) using the Kruskal-Wallis H test. The diagnostic performances of fractional plasma volume for each pair of tumors showed areas under curve of 0.86-0.99 (95% CI, 0.70-1.0); the forward volume transfer constant differentiated metastases from chondrosarcomas/chordomas with areas under curve of 0.82 and 0.82 (95% CI, 0.67-0.98), respectively; and the normalized mean ADC distinguished chondrosarcomas from chordomas/metastases with areas under curve of 0.96 and 0.95 (95% CI, 0.88-1.0), respectively.

CONCLUSIONS

DWI and dynamic contrast-enhanced MR imaging sequences can be beneficial for differentiating the 3 common skull base tumors.

Normalized Parameters of Dynamic Contrast-Enhanced Perfusion MRI and DWI-ADC for Differentiation between Posttreatment Changes and Recurrence in Head and Neck Cancer

BACKGROUND AND PURPOSE

Differentiating recurrence from benign posttreatment changes has clinical importance in the imaging follow-up of head and neck cancer. This study aimed to investigate the utility of normalized dynamic contrast-enhanced MR imaging and ADC for their differentiation.

MATERIALS AND METHODS

This study included 51 patients with a history of head and neck cancer who underwent follow-up dynamic contrast-enhanced MR imaging with DWI-ADC, of whom 25 had recurrences and 26 had benign posttreatment changes. Quantitative and semiquantitative dynamic contrast-enhanced MR imaging parameters and ADC of the ROI and reference region were analyzed. Normalized dynamic contrast-enhanced MR imaging parameters and normalized DWI-ADC parameters were calculated by dividing the ROI by the reference region.

RESULTS

Normalized plasma volume, volume transfer constant between extravascular extracellular space and blood plasma per minute (K ^trans), area under the curve, and wash-in were significantly higher in patients with recurrence than in those with benign posttreatment change (P = .003 to <.001). The normalized mean ADC was significantly lower in patients with recurrence than in those with benign posttreatment change (P < .001). The area under the receiver operating characteristic curve of the combination of normalized dynamic contrast-enhanced MR imaging parameters with significance (normalized plasma volume, normalized extravascular extracellular space volume per unit tissue volume, normalized K ^trans, normalized area under the curve, and normalized wash-in) and normalized mean ADC was 0.97 (95% CI, 0.93-1).

CONCLUSIONS

Normalized dynamic contrast-enhanced MR imaging parameters, normalized mean ADC, and their combination were effective in differentiating recurrence and benign posttreatment changes in head and neck cancer.

Prognostic Factors of Stroke-Like Migraine Attacks after Radiation Therapy (SMART) Syndrome

BACKGROUND AND PURPOSE

Prognostic factors of stroke-like migraine attacks after radiation therapy (SMART) syndrome have not been fully explored. This study aimed to assess clinical and imaging features to predict the clinical outcome of SMART syndrome.

MATERIALS AND METHODS

We retrospectively reviewed the clinical manifestations and imaging findings of 20 patients with SMART syndrome (median age, 48 years; 5 women) from January 2016 to January 2020 at 4 medical centers. Patient demographics and MR imaging features at the time of diagnosis were reviewed. This cohort was divided into 2 groups based on the degree of clinical improvement (completely versus incompletely recovered). The numeric and categoric variables were compared as appropriate.

RESULTS

There were statistically significant differences between the completely recovered group (n = 11; median age, 44 years; 2 women) and the incompletely recovered group (n = 9; median age, 55 years; 3 women) in age, months of follow-up, and the presence of steroid treatment at diagnosis (P = .028, .002, and .01, respectively). Regarding MR imaging features, there were statistically significant differences in the presence of linear subcortical WM susceptibility abnormality, restricted diffusion, and subcortical WM edematous changes in the acute SMART region (3/11 versus 8/9, P = .01; 0/11 versus 4/9, P = .026; and 2/11 versus 7/9, P = .022, respectively). Follow-up MRIs showed persistent susceptibility abnormality (11/11) and subcortical WM edematous changes (9/9), with resolution of restricted diffusion (4/4).

CONCLUSIONS

Age, use of steroid treatment at the diagnosis of SMART syndrome, and MR imaging findings of abnormal susceptibility signal, restricted diffusion, and subcortical WM change in the acute SMART region can be prognostic factors in SMART syndrome.

ADC for Differentiation between Posttreatment Changes and Recurrence in Head and Neck Cancer: A Systematic Review and Meta-analysis

BACKGROUND

Previous studies reported that the ADC values of recurrent head and neck cancer lesions are lower than those of posttreatment changes, however, the utility of ADC to differentiate them has not been definitively summarized and established.

PURPOSE

Our aim was to evaluate the diagnostic benefit of ADC calculated from diffusion-weighted imaging in differentiating recurrent lesions from posttreatment changes in head and neck cancer.

DATA SOURCES

MEDLINE, Scopus, and EMBASE data bases were searched for studies.

STUDY SELECTION

The review identified 6 prospective studies with a total of 365 patients (402 lesions) who were eligible for the meta-analysis.

DATA ANALYSIS

Forest plots were used to assess the mean difference in ADC values. Heterogeneity among the studies was evaluated using the Cochrane Q test and the I² statistic.

DATA SYNTHESIS

Among included studies, the overall mean of ADC values of recurrent lesions was 1.03 × 10^-3mm²/s and that of the posttreatment changes was 1.51 × 10^-3mm²/s. The ADC value of recurrence was significantly less than that of posttreatment changes in head and neck cancer (pooled mean difference: -0.45; 95% CI, -0.59-0.32, P < .0001) with heterogeneity among studies. The threshold of ADC values between recurrent lesions and posttreatment changes was suggested to be 1.10 × 10^-3mm²/s.

LIMITATIONS

Given the heterogeneity of the data of the study, the conclusions should be interpreted with caution.

CONCLUSIONS

The ADC values in recurrent head and neck cancers are lower than those of posttreatment changes, and the threshold of ADC values between them was suggested.

Pretreatment ADC Histogram Analysis as a Prognostic Imaging Biomarker for Patients with Recurrent Glioblastoma Treated with Bevacizumab: A Systematic Review and Meta-analysis

BACKGROUND

The mean ADC value of the lower Gaussian curve (ADC_L) derived from the bi-Gaussian curve-fitting histogram analysis has been reported as a predictive/prognostic imaging biomarker in patients with recurrent glioblastoma treated with bevacizumab; however, its systematic summary has been lacking.

PURPOSE

We applied a systematic review and meta-analysis to investigate the predictive/prognostic performance of ADC_L in patients with recurrent glioblastoma treated with bevacizumab.

DATA SOURCES

We performed a literature search using PubMed, Scopus, and EMBASE.

STUDY SELECTION

A total of 1344 abstracts were screened, of which 83 articles were considered potentially relevant. Data were finally extracted from 6 studies including 578 patients.

DATA ANALYSIS

Forest plots were generated to illustrate the hazard ratios of overall survival and progression-free survival. The heterogeneity across the studies was assessed using the Cochrane Q test and I² values.

DATA SYNTHESIS

The pooled hazard ratios for overall survival and progression-free survival in patients with an ADC_L lower than the cutoff values were 1.89 (95% CI, 1.53-2.31) and 1.98 (95% CI, 1.54-2.55) with low heterogeneity among the studies. Subgroup analysis of the bevacizumab-free cohort showed a pooled hazard ratio for overall survival of 1.20 (95% CI, 1.08-1.34) with low heterogeneity.

LIMITATIONS

The conclusions are limited by the difference in the definition of recurrence among the included studies.

CONCLUSIONS

This systematic review with meta-analysis supports the prognostic value of ADC_L in patients with recurrent glioblastoma treated with bevacizumab, with a low ADC_L demonstrating decreased overall survival and progression-free survival. On the other hand, the predictive role of ADC_L for bevacizumab treatment was not confirmed.

m6A Modified Short RNA Fragments Inhibit Cytoplasmic TLS/FUS Aggregation Induced by Hyperosmotic Stress

Translocated in LipoSarcoma/Fused in Sarcoma (TLS/FUS) is a nuclear RNA binding protein whose mutations cause amyotrophic lateral sclerosis. TLS/FUS undergoes LLPS and forms membraneless particles with other proteins and nucleic acids. Interaction with RNA alters conformation of TLS/FUS, which affects binding with proteins, but the effect of m⁶A RNA modification on the TLS/FUS–RNA interaction remains elusive. Here, we investigated the binding specificity of TLS/FUS to m⁶A RNA fragments by RNA pull down assay, and elucidated that both wild type and ALS-related TLS/FUS mutants strongly bound to m⁶A modified RNAs. TLS/FUS formed cytoplasmic foci by treating hyperosmotic stress, but the cells transfected with m⁶A-modified RNAs had a smaller number of foci. Moreover, m⁶A-modified RNA transfection resulted in the cells obtaining higher resistance to the stress. In summary, we propose TLS/FUS as a novel candidate of m⁶A recognition protein, and m⁶A-modified RNA fragments diffuse cytoplasmic TLS/FUS foci and thereby enhance cell viability.

Diagnostic Role of Diffusion-Weighted and Dynamic Contrast-Enhanced Perfusion MR Imaging in Paragangliomas and Schwannomas in the Head and Neck

BACKGROUND AND PURPOSE

Distinguishing schwannomas from paragangliomas in the head and neck and determining succinate dehydrogenase (SDH) mutation status in paragangliomas are clinically important. We aimed to assess the clinical usefulness of DWI and dynamic contrast-enhanced MR imaging in differentiating these 2 types of tumors, as well as the SDH mutation status of paragangliomas.

MATERIALS AND METHODS

This retrospective study from June 2016 to June 2020 included 42 patients with 15 schwannomas and 27 paragangliomas (10 SDH mutation-positive and 17 SDH mutation-negative). ADC values, dynamic contrast-enhanced MRI parameters, and tumor imaging characteristics were compared between the 2 tumors and between the mutation statuses of paragangliomas as appropriate. Multivariate stepwise logistic regression analysis was performed to identify significant differences in these parameters.

RESULTS

Fractional plasma volume (P ≤ .001), rate transfer constant (P = .038), time-to-maximum enhancement (P < .001), maximum signal-enhancement ratio (P < .001) and maximum concentration of contrast agent (P < .001), velocity of enhancement (P = .002), and tumor characteristics including the presence of flow voids (P = .001) and enhancement patterns (P = .027) showed significant differences between schwannomas and paragangliomas, though there was no significant difference in ADC values. In the multivariate logistic regression analysis, fractional plasma volume was identified as the most significant value for differentiation of the 2 tumor types (P = .014). ADC values were significantly higher in nonhereditary than in hereditary paragangliomas, while there was no difference in dynamic contrast-enhanced MR imaging parameters.

CONCLUSIONS

Dynamic contrast-enhanced MR imaging parameters show promise in differentiating head and neck schwannomas and paragangliomas, while DWI can be useful in detecting SDH mutation status in paragangliomas.

Assessment of MR Imaging and CT in Differentiating Hereditary and Nonhereditary Paragangliomas

BACKGROUND AND PURPOSE

Head and neck paragangliomas have been reported to be associated with mutations of the succinate dehydrogenase enzyme family. The aim of this study was to assess whether radiologic features could differentiate between paragangliomas in the head and neck positive and negative for the succinate dehydrogenase mutation.

MATERIALS AND METHODS

This single-center retrospective review from January 2015 to January 2020 included 40 patients with 48 paragangliomas (30 tumors positive for succinate dehydrogenase mutation in 23 patients and 18 tumors negative for the succinate dehydrogenase mutation in 17 patients). ADC values and tumor characteristics on CT and MR imaging were evaluated by 2 radiologists. Differences between the 2 cohorts in the diagnostic performance of ADC and normalized ADC (ratio to ADC in the medulla oblongata) values were evaluated using the independent samples t test. P < .05 was considered significant.

RESULTS

ADC_mean (1.07 [SD, 0.25]/1.04 [SD, 0.12] versus 1.31 [SD, 0.16]/1.30 [SD, 0.20]× 10^-3 mm²/s by radiologists 1 and 2; P < .001), ADC_maximum (1.49 [SD, 0.27]/1.49 [SD, 0.20] versus 2.01 [SD, 0.16]/1.87 [SD, 0.20] × 10^-3 mm²/s; P < .001), normalized ADC_mean (1.40 [SD, 0.33]/1.37 [SD, 0.16] versus 1.73 [SD, 0.22]/1.74 [SD, 0.27]; P < .001), and normalized ADC_maximum (1.95 [SD, 0.37]/1.97 [SD, 0.27] versus 2.64 [SD, 0.22]/2.48 [SD, 0.28]; P < .001) were significantly lower in succinate dehydrogenase mutation-positive than mutation-negative tumors. ADC_minimum, normalized ADC_minimum, and tumor characteristics were not statistically significant.

CONCLUSIONS

ADC is a promising imaging biomarker that can help differentiate succinate dehydrogenase mutation-positive from mutation-negative paragangliomas in the head and neck.

Direct visualization of the conformational change of FUS/TLS upon binding to promoter-associated non-coding RNA

High-speed AFM revealed the conformational change of fused in sarcoma (FUS) from a compact to an extended structure upon binding of non-coding RNA, which is supposed to allow FUS to bind to CBP/p300 for transcriptional interference. Thus, a mechanistic insight into transcription regulation by FUS and non-coding RNA is provided.

MRI Findings of Immune Checkpoint Inhibitor-Induced Hypophysitis: Possible Association with Fibrosis

BACKGROUND AND PURPOSE

Hypophysitis is one of the well-known adverse effects of immune checkpoint inhibitors. Immune checkpoint inhibitor-induced hypophysitis frequently causes irreversible hypopituitarism, which requires long-term hormone replacement. Despite the high frequency and clinical significance, characteristic MR imaging findings of immune checkpoint inhibitor-induced hypophysitis have not been established. In the present study, we aimed to review and extract the MR imaging features of immune checkpoint inhibitor-induced hypophysitis.

MATERIALS AND METHODS

This retrospective international multicenter study comprised 20 patients with melanoma who were being treated with immune checkpoint inhibitors and clinically diagnosed with immune checkpoint inhibitor-induced hypophysitis. Three radiologists evaluated the following MR imaging findings: enlargement of the pituitary gland and stalk; homogeneity of enhancement of the pituitary gland; presence/absence of a well-defined poorly enhanced area and, if present, its location, shape, and signal intensity in T2WI; and enhancement pattern in contrast-enhanced dynamic MR imaging. Clinical symptoms and hormone levels were also recorded.

RESULTS

Enlargement of the pituitary gland and stalk was observed in 12 and 20 patients, respectively. Nineteen patients showed poorly enhanced lesions (geographic hypoenhancing lesions) in the anterior lobe, and 11 of these lesions showed hypointensity on T2WI. Thyrotropin deficiency and corticotropin deficiency were observed in 19/20 and 12/17 patients, respectively, which persisted in 12/19 and 10/12 patients, respectively, throughout the study period.

CONCLUSIONS

Pituitary geographic hypoenhancing lesions in the anterior lobe of the pituitary gland are characteristic and frequent MR imaging findings of immune checkpoint inhibitor-induced hypophysitis. They reflect fibrosis and are useful in distinguishing immune checkpoint inhibitor-induced hypophysitis from other types of hypophysitis/tumors.

Long noncoding RNA pncRNA-D reduces cyclin D1 gene expression and arrests cell cycle through RNA m6A modification

pncRNA-D is an irradiation-induced 602-nt long noncoding RNA transcribed from the promoter region of the cyclin D1 (CCND1) gene. CCND1 expression is predicted to be inhibited through an interplay between pncRNA-D and RNA-binding protein TLS/FUS. Because the pncRNA-D-TLS interaction is essential for pncRNA-D-stimulated CCND1 inhibition, here we studied the possible role of RNA modification in this interaction in HeLa cells. We found that osmotic stress induces pncRNA-D by recruiting RNA polymerase II to its promoter. pncRNA-D was highly m6A-methylated in control cells, but osmotic stress reduced the methylation and also arginine methylation of TLS in the nucleus. Knockdown of the m6A modification enzyme methyltransferase-like 3 (METTL3) prolonged the half-life of pncRNA-D, and among the known m6A recognition proteins, YTH domain-containing 1 (YTHDC1) was responsible for binding m6A of pncRNA-D Knockdown of METTL3 or YTHDC1 also enhanced the interaction of pncRNA-D with TLS, and results from RNA pulldown assays implicated YTHDC1 in the inhibitory effect on the TLS-pncRNA-D interaction. CRISPR/Cas9-mediated deletion of candidate m6A site decreased the m6A level in pncRNA-D and altered its interaction with the RNA-binding proteins. Of note, a reduction in the m6A modification arrested the cell cycle at the G0/G1 phase, and pncRNA-D knockdown partially reversed this arrest. Moreover, pncRNA-D induction in HeLa cells significantly suppressed cell growth. Collectively, these findings suggest that m6A modification of the long noncoding RNA pncRNA-D plays a role in the regulation of CCND1 gene expression and cell cycle progression.

RNA sequence and length contribute to RNA-induced conformational change of TLS/FUS

Translocated in liposarcoma (TLS)/fused in sarcoma (FUS) is a multitasking DNA/RNA binding protein implicated in cancer and neurodegenerative diseases. Upon DNA damage, TLS is recruited to the upstream region of the cyclin D1 gene (CCND1) through binding to the promotor associated non-coding RNA (pncRNA) that is transcribed from and tethered at the upstream region. Binding to pncRNA is hypothesized to cause the conformational change of TLS that enables its inhibitive interaction with histone acetyltransferases and resultant repression of CCND1 expression, although no experimental proof has been obtained. Here, the closed-to-open conformational change of TLS on binding pncRNA was implied by fluorescence resonance energy transfer. A small fragment (31 nucleotides) of the full-length pncRNA (602 nucleotides) was shown to be sufficient for the conformational change of TLS. Dissection of pncRNA identified the G-rich RNA sequence that is critical for the conformational change. The length of RNA was also revealed to be critical for the conformational change. Furthermore, it was demonstrated that the conformational change of TLS is caused by another target DNA and RNA, telomeric DNA and telomeric repeat-containing RNA. The conformational change of TLS on binding target RNA/DNA is suggested to be essential for biological functions.

Arginine methylation of translocated in liposarcoma (TLS) inhibits its binding to long noncoding RNA, abrogating TLS-mediated repression of CBP/p300 activity

Translocated in liposarcoma (TLS) is an RNA-binding protein and a transcription-regulatory sensor of DNA damage. TLS binds promoter-associated noncoding RNA (pncRNA) and inhibits histone acetyltransferase (HAT) activity of CREB-binding protein (CBP)/E1A-binding protein P300 (p300) on the cyclin D1 (CCND1) gene. Although post-translational modifications of TLS, such as arginine methylation, are known to regulate TLS's nucleocytoplasmic shuttling and assembly in stress granules, its interactions with RNAs remain poorly characterized. Herein, using various biochemical assays, we confirmed the earlier observations that TLS is methylated by protein arginine methyltransferase 1 (PRMT1) in vitro The arginine methylation of TLS disrupted binding to pncRNA and also prevented binding of TLS to and inhibition of CBP/p300. This result indicated that arginine methylation of TLS abrogates both binding to pncRNA and TLS-mediated inhibition of CBP/p300 HAT activities. We also report that an arginine residue within the Arg-Gly-Gly domain of TLS, Arg-476, serves as the major determinant for binding to pncRNA. Either methylation or mutation of Arg-476 of TLS significantly decreased pncRNA binding and thereby prevented a pncRNA-induced allosteric alteration in TLS that is required for its interaction with CBP/p300. Moreover, unlike WT TLS, an R476A TLS mutant did not inhibit CCND1 promoter activity in luciferase reporter assays. Taken together, we propose the hypothesis that arginine methylation of TLS regulates both TLS-nucleic acid and TLS-protein interactions and thereby participates in transcriptional regulation.

Altered gene expression profiles of histone lysine methyltransferases and demethylases in rheumatoid arthritis synovial fibroblasts

OBJECTIVES

Aberrant histone lysine methylation (HKM) has been reported in rheumatoid arthritis (RA) synovial fibroblasts (SFs). As histone lysine methyltransferases (HKMTs) and demethylases (HKDMs) regulate HKM, these enzymes are believed to be dysregulated in RASFs. The aim of this study is to clarify whether gene expressions of HKMTs and HKDMs are altered in RASFs.

METHODS

SFs were isolated from synovial tissues obtained from RA or osteoarthritis (OA) patients during total knee joint replacement. The mRNA levels of 34 HKMTs and 22 HKDMs were examined after stimulation with tumour necrosis factor α (TNF-α) in RASFs and OASFs.

RESULTS

The gene expression of the 12 HKMTs, including MLL1, MLL3, SUV39H1, SUV39H2, PRDM2, EZH2, SETD2, NSD2, NSD3, SMYD4, DOT1, and PR-set7, that catalyse the methylation of H3K4, H3K9, H3K27, H3K36, H3K79, or H4K20 was higher after TNFα stimulation in RASFs vs. OASFs. The gene expression of the 4 HKDMs, including FBXL10, NO66, JMJD2D, and FBXL11, that catalyse the methylation of H3K4, H3K9, or H3K36 was higher after TNFα stimulation in RASFs vs. OASFs.

CONCLUSIONS

The study findings suggest that the HKM-modifying enzymes are involved in the alteration of HKM, which results in changes in the gene expression of RASFs.

Histone Methylation and STAT-3 Differentially Regulate Interleukin-6-Induced Matrix Metalloproteinase Gene Activation in Rheumatoid Arthritis Synovial Fibroblasts

OBJECTIVE

Synovial fibroblasts (SFs) produce matrix-degrading enzymes that cause joint destruction in rheumatoid arthritis (RA). Epigenetic mechanisms play a pivotal role in autoimmune diseases. This study was undertaken to elucidate the epigenetic mechanism that regulates the transcription of matrix metalloproteinases (MMPs) in RASFs.

METHODS

MMP gene expression and histone methylation profiles in the MMP promoters were examined in RASFs. The effect of WD repeat domain 5 (WDR5) silencing on histone methylation and MMP gene expression in RASFs was analyzed. MMP gene expression, surface expression of the interleukin-6 (IL-6) receptor, phosphorylation of STAT-3, and binding of STAT-3 in the MMP promoters were investigated in RASFs stimulated with IL-6.

RESULTS

The MMP-1, MMP-3, MMP-9, and MMP-13 genes were actively transcribed in RASFs. Correspondingly, the level of histone H3 trimethylated at lysine 4 (H3K4me3) was elevated, whereas that of H3K27me3 was suppressed in the MMP promoters in RASFs. The decrease in H3K4me3 via WDR5 small interfering RNA reduced the levels of messenger RNA for MMP-1, MMP-3, MMP-9, and MMP-13 in RASFs. Interestingly, IL-6 signaling significantly increased the expression of MMP-1, MMP-3, and MMP-13, but not MMP-9, in RASFs. Although the IL-6 signaling pathway was similarly active in RASFs and osteoarthritis SFs, STAT-3 bound to the MMP-1, MMP-3, and MMP-13 promoters, but not the MMP-9 promoter, after IL-6 stimulation in RASFs.

CONCLUSION

Our findings indicate that histone methylation and STAT-3 regulate spontaneous and IL-6-induced MMP gene activation in RASFs. The combination of chromatin structure and transcription factors may regulate distinct arthritogenic properties of RASFs.

Long noncoding RNA as a regulator for transcription

Investigation of noncoding RNAs is in rapid progress, especially regarding translational repression by small (short) noncoding RNAs like microRNAs with 20-25 nucleotide-lengths, while long noncoding RNAs with nucleotide length of more than two hundred are also emerging. Indeed, our analysis has revealed that a long noncoding RNA transcribed from cyclin D1 promoter of 200 and 300 nucleotides exerts transcriptional repression through its binding protein TLS instead of translational repression. Translational repression is executed by short noncoding RNAs, while transcriptional repression is mainly done by long noncoding RNAs. These long noncoding RNAs are heterogeneous molecules and employ divergent molecular mechanisms to exert transcriptional repression. In this review, I overview recent publications regarding the transcription regulation by long noncoding RNAs and explore their biological significance. In addition, the relation between a random transcriptional activity of RNA polymerase II and the origin of long noncoding RNAs is discussed.

The binding specificity of Translocated in LipoSarcoma/FUsed in Sarcoma with lncRNA transcribed from the promoter region of cyclin D1

Background

Translocated in LipoSarcoma (TLS, also known as FUsed in Sarcoma) is an RNA/DNA binding protein whose mutation cause amyotrophic lateral sclerosis. In previous study, we demonstrated that TLS binds to long noncoding RNA, promoter-associated ncRNA-D (pncRNA-D), transcribed from the 5′ upstream region of cyclin D1 (CCND1), and inhibits the expression of CCND1.

Results

In order to elucidate the binding specificity between TLS and pncRNA-D, we divided pncRNA-D into seven fragments and examined the binding with full-length TLS, TLS–RGG2–zinc finger–RGG3, and TLS–RGG3 by RNA pull down assay. As a result, TLS was able to bind to all the seven fragments, but the fragments containing reported recognition motifs (GGUG and GGU) tend to bind more solidly. The full-length TLS and TLS–RGG2–zinc finger–RGG3 showed a similar interaction with pncRNA-D, but the binding specificity of TLS–RGG3 was lower compared to the full-length TLS and TLS–RGG2–zinc finger–RGG3. Mutation in GGUG and GGU motifs dramatically decreased the binding, and unexpectedly, we could only detect weak interaction with the RNA sequence with stem loop structure.

Conclusion

The binding of TLS and pncRNA-D was affected by the presence of GGUG and GGU sequences, and the C terminal domains of TLS function in the interaction with pncRNA-D.

Electronic supplementary material

The online version of this article (doi:10.1186/s13578-016-0068-8) contains supplementary material, which is available to authorized users.

Development of a mouse monoclonal antibody for the detection of asymmetric dimethylarginine of Translocated in LipoSarcoma/FUsed in Sarcoma and its application in analyzing methylated TLS

Background

RNA-binding protein Translocated in LipoSarcoma/FUsed Sarcoma (TLS/FUS) is one of causative genes for familial amyotrophic lateral sclerosis (ALS). We previously identified that TLS was associated with protein arginine methyltransferase 1 (PRMT1), and four arginine residues within TLS (R216, R218, R242 and R394) were consistently dimethylated. Protein arginine methylation is involved in various cellular events such as signal transduction, transcriptional regulation and protein-protein interactions.

Results

To understand the biological role of arginine methylation of RNA-binding protein, we prepared and characterized a mouse monoclonal antibody against asymmetric dimethylarginine of TLS. By cloning and screening, one stable hybridoma cell clone (2B12) producing anti-asymmetric dimethylated TLS on R216 and R218 antibody was established. The monoclonal antibody 2B12 is specific for the asymmetrically dimethylated arginine peptide and does not react with the same peptide sequence containing unmodified and symmetrically dimethylated arginine residues by dot-blot analysis. 2B12 was also validated GST tagged TLS with PRMT1 by in vitro arginine methylation assays. Since methylated TLS in HeLa cells and mouse and human brain protein extracts was immunoprecipitated with 2B12, we performed RNA-binding protein immunoprecipitation assays using HeLa cell lysate and this antibody. We demonstrated that the long noncoding RNA (lncRNA) transcribed from cyclin D1 promoter binds methylated TLS.

Conclusions

A monoclonal antibody that is capable of detecting the methylarginine status of TLS will facilitate the molecular and cellular analysis of transcriptional regulation by lncRNA through methylated TLS, and can be used as a favorable tool for clinical diagnosis of ALS caused by TLS dysregulation.

Electronic supplementary material

The online version of this article (doi:10.1186/2045-3701-4-77) contains supplementary material, which is available to authorized users.

Regulation of telomere length by G-quadruplex telomere DNA- and TERRA-binding protein TLS/FUS

Mammalian telomeres comprise noncoding TTAGGG repeats in double-stranded regions with a single-stranded TTAGGG repeat 3' overhang and are bound by a multiprotein complex with a telomeric repeat-containing RNA (TERRA) containing a UUAGGG repeat as a G-quadruplex noncoding RNA. TLS/FUS is a human telomere-binding protein that was first identified as an oncogenic fusion protein in human myxoid and round-cell liposarcoma. Here, we show that the Arg-Gly-Gly domain in the C-terminal region of TLS forms a ternary complex with human telomere G-quadruplex DNA and TERRA in vitro. Furthermore, TLS binds to G-quadruplex telomere DNA in double-stranded regions and to G-quadruplex TERRA, which regulates histone modifications of telomeres and telomere length in vivo. Our findings suggest that the G-quadruplex functions as a scaffold for the telomere-binding protein, TLS, to regulate telomere length by histone modifications.

Structure of noncoding RNA is a determinant of function of RNA binding proteins in transcriptional regulation

The majority of the noncoding regions of mammalian genomes have been found to be transcribed to generate noncoding RNAs (ncRNAs), resulting in intense interest in their biological roles. During the past decade, numerous ncRNAs and aptamers have been identified as regulators of transcription. 6S RNA, first described as a ncRNA in E. coli, mimics an open promoter structure, which has a large bulge with two hairpin/stalk structures that regulate transcription through interactions with RNA polymerase. B2 RNA, which has stem-loops and unstructured single-stranded regions, represses transcription of mRNA in response to various stresses, including heat shock in mouse cells. The interaction of TLS (translocated in liposarcoma) with CBP/p300 was induced by ncRNAs that bind to TLS, and this in turn results in inhibition of CBP/p300 histone acetyltransferase (HAT) activity in human cells. Transcription regulator EWS (Ewing's sarcoma), which is highly related to TLS, and TLS specifically bind to G-quadruplex structures in vitro. The carboxy terminus containing the Arg-Gly-Gly (RGG) repeat domains in these proteins are necessary for cis-repression of transcription activation and HAT activity by the N-terminal glutamine-rich domain. Especially, the RGG domain in the carboxy terminus of EWS is important for the G-quadruplex specific binding. Together, these data suggest that functions of EWS and TLS are modulated by specific structures of ncRNAs.

Promoter-associated noncoding RNA from the CCND1 promoter

More than 90% of the human genome have been found to be transcribed and most of the transcripts are noncoding (nc) RNAs (Willingham et al., Science 309:1570-1573, 2005; ENCODE-consortium, Science 306:636-640, 2004; Carninci et al., Science 309:1559-1563, 2005; Bertone et al., Science 306:2242-2246, 2004). Studies on ncRNAs have been radically progressed mainly regarding microRNAs, piRNAs, siRNAs, and related small ncRNAs of which length are relatively short nucleotides (Fire et al., Nature 391:806-811, 1998; Filipowicz et al., Nat Rev Genet 9:102-114, 2008; Lau et al., Science 313:363-367, 2006; Brennecke et al., Science 322:1387-1392, 2008; Siomi and Siomi, Nature 457:396-404, 2009). These small RNAs play roles in regulation of translation and gene silencing while long ncRNAs with length more than 200 nucleotides have been emerging and turn out to be involved in regulation of transcription (Kapranov et al., Science 316:1484-1488, 2007; Ponting et al., Cell 136:629-641, 2009; Kurokawa et al., RNA Biol 6:233-236, 2009). Recently, we have identified novel, long ncRNAs bearing capability of repression of transcription (Wang et al., Nature 454:126-130, 2008).RNA-binding protein, translocated in liposarcoma (TLS), binds CREB-binding protein CBP/adenovirus p300 and inhibits their histone acetyltransferase (HAT) activities (Wang et al., Nature 454:126-130, 2008). The HAT inhibitory activity of TLS requires specific binding of RNA. The systematic evolution of ligands by exponential enrichment experiments with randomized sequences revealed that TLS specifically recognizes RNA oligonucleotides containing GGUG as a consensus sequence although the GGUG sequence is not an absolute requirement for the TLS binding (Lerga et al., J Biol Chem 276:6807-6816, 2001). TLS is specifically recruited to the CBP/p300-associated binding sites of the cyclin D1 gene (CCND1) and the cyclin E1 gene (CCNE1) promoters (Wang et al., Nature 454:126-130, 2008; Impey et al., Cell 119:1041-1054, 2004). Our extensive exploration for naturally occurring RNA molecule that binds TLS has indicated that long ncRNAs (promoter-associated ncRNAs: pncRNAs) transcribed from the CCND1 promoter bind TLS and inhibit the HAT activities on the sites to repress the transcription of the CCND1 gene (Wang et al., Nature 454:126-130, 2008). We have optimized RT-PCR, chromatin immunoprecipitation, RNA immunoprecipitation, and RNA gel-shift assay in order to detect these pncRNAs. The methods that we have developed successfully identified these low-abundant, long ncRNAs and provide the data showing that the CCND1 pncRNAs bind TLS and induce its HAT inhibitory activity to repress the transcription of CCND1 gene upon genotoxic stress.

Promoter-associated long noncoding RNAs repress transcription through a RNA binding protein TLS

The majority of the human genome is found to be transcribed and generates mostly noncoding (nc) RNAs that do not possess protein information. MicroRNAs are one of the well-identified small ncRNAs, but occupy merely a fraction of ncRNAs. Long (large) ncRNAs are emerging as a novel class of ncRNAs, but knowledge of these ncRNAs is far less accumulated. Long ncRNAs are tentatively classified as an ncRNA species containing more than 200 nucleotides. Recently, a long promoter-associated ncRNA (pncRNA) has been identified to be transcribed from the cyclin D1 promoter upon induction by genotoxic factors like ionizing-irradiation. The cyclin D1 pncRNA is specifically bound with an RNA-binding protein TLS (Translocated in liposarcoma) and exerts transcriptional repression through histone acetyltransferase (HAT) inhibitory activity. Analysis of TLS and the pncRNAs could provide a model for elucidating their roles inregulation of mammalian transcriptional programs. The pncRNA binding to TLS turns out to be an essential event for the HAT inhibitory activity. A key consensus sequence of the pncRNA is composed of GGUG, while not every RNA sequence bearing GGUG is targeted by TLS, suggesting that a secondary structure of the GGUG-bearing RNAs is also involved in recognition by TLS. Taken together, TLS is a unique mediator between signals of the long ncRNAs and transcription, suggesting that RNA networking functions in living cells.(1-3).

TLS and PRMT1 synergistically coactivate transcription at the survivin promoter through TLS arginine methylation

TLS (Translocated in LipoSarcoma), also termed FUS, is a multifunctional protein implicated in diverse cellular events such as maintaining genome integrity and regulating gene expression. We have focused on the role of TLS as a coregulator in transcriptional regulation. In the process of investigating TLS-binding proteins, we found that PRMT1 (protein arginine methyltransferase 1) was in complex with TLS. We analyzed the methylation status of endogenous TLS and demonstrated that TLS was arginine-methylated by PRMT1. Using mass spectrometry, we identified that four arginine residues within TLS (R216, R218, R242 and R394) were consistently dimethylated. We performed luciferase reporter assays to assess the functional consequence of TLS arginine methylation in transcriptional regulation and, interestingly, observed that TLS and PRMT1 synergistically coactivated transcription at the survivin promoter. Further analysis using a catalytic-dead PRMT1 or methylation inhibitor both showed that the synergistic transcriptional activation was mediated by TLS arginine-methylation. These results revealed a cooperative role of TLS and PRMT1 in transcriptional regulation.

Identification of RNA binding specificity for the TET-family proteins

The TET-family proteins (TAF15, EWS and TLS) are the RNA binding proteins involved in multiple levels of cellular functions. The RNA binding domain of those proteins is known as the important region for cellular functions. But little is known about the RNA binding specificity of TET-family proteins. In order to investigate the RNA binding properties of the TET-family proteins, we performed electrophoretic mobility shift assay using recombinant Flag-tagged TLS and guanine-rich and RNAs. It was found that TLS binds to human telomeric RNA in the presence of KCl, but not in the presence of LiCl.

Id4, a new candidate gene for senile osteoporosis, acts as a molecular switch promoting osteoblast differentiation

Excessive accumulation of bone marrow adipocytes observed in senile osteoporosis or age-related osteopenia is caused by the unbalanced differentiation of MSCs into bone marrow adipocytes or osteoblasts. Several transcription factors are known to regulate the balance between adipocyte and osteoblast differentiation. However, the molecular mechanisms that regulate the balance between adipocyte and osteoblast differentiation in the bone marrow have yet to be elucidated. To identify candidate genes associated with senile osteoporosis, we performed genome-wide expression analyses of differentiating osteoblasts and adipocytes. Among transcription factors that were enriched in the early phase of differentiation, Id4 was identified as a key molecule affecting the differentiation of both cell types. Experiments using bone marrow-derived stromal cell line ST2 and Id4-deficient mice showed that lack of Id4 drastically reduces osteoblast differentiation and drives differentiation toward adipocytes. On the other hand knockdown of Id4 in adipogenic-induced ST2 cells increased the expression of Pparγ2, a master regulator of adipocyte differentiation. Similar results were observed in bone marrow cells of femur and tibia of Id4-deficient mice. However the effect of Id4 on Pparγ2 and adipocyte differentiation is unlikely to be of direct nature. The mechanism of Id4 promoting osteoblast differentiation is associated with the Id4-mediated release of Hes1 from Hes1-Hey2 complexes. Hes1 increases the stability and transcriptional activity of Runx2, a key molecule of osteoblast differentiation, which results in an enhanced osteoblast-specific gene expression. The new role of Id4 in promoting osteoblast differentiation renders it a target for preventing the onset of senile osteoporosis.

Increased bone marrow adiposity is observed in the bone marrow of senile osteoporosis patients. This is caused by unbalanced differentiation of mesenchymal stem cells (MSCs) into osteoblast or adipocyte. Previous reports have indicated that several transcription factors play important roles in determining the direction of MSCs differentiation into osteoblast or adipocyte. So far, little is known about the overall dynamics and regulation of transcription factor expression changes leading to the imbalance of osteoblast and adipocyte differentiation inside the bone marrow. We have performed genome-wide gene expression analyses during the differentiation of MSCs into osteoblast or adipocyte. We identified basic helix-loop-helix transcription factor family member Id4 as a leading candidate controlling the differentiation toward adipocyte or osteoblast. Suppression of Id4 expression in MSCs repressed osteoblast differentiation and increased adipocyte differentiation. In contrast, overexpression of Id4 in MSCs promoted osteoblast differentiation and attenuated adipocyte differentiation. Moreover, Id4-mutant mice showed abnormal accumulation of lipid droplets in bone marrow and impaired bone formation activity. In summary, we have demonstrated a molecular function of Id4 in osteoblast differentiation. The findings revealed that Id4 is a molecular switch enhancing osteoblast differentiation at the expense of adipocyte differentiation.

Identification of DNA binding specificity for TLS

TLS (Translocated in liposarcoma) has been characterized as a rearranged gene in chromosomal translocations specific of human myxoid liposarcoma. The various cellular functions of TLS participating either in transcription or splicing processes are thought the involvement of an interaction of TLS with DNA and/or RNA. To investigate insight into DNA-TLS interaction, we performed Electrophoretic mobility shift assay of TLS with G-quadruplex DNA. It revealed that TLS especially bound to single stranded human telomeric DNA in the presence of potassium ion while it was not able to bind double stranded human telomeric DNA and single stranded human telomeric DNA in the presence of sodium ion.

Transcriptional regulation through noncoding RNAs and epigenetic modifications

The recognition that substantial portions of the "noncoding (nc)" regions of metazoan genomes are transcribed has generated intense interest in the potential biological roles of ncRNAs. Gene silencing has emerged as one of the major functions of short double stranded ncRNAs (22-25 nucleotides, nt) that are generated by specific processing machinery. Transcription is also regulated by other classes of ncRNAs, including long (more than 200 nt), single-stranded, polyadenylated RNA molecules. Here, we review recent studies suggesting that some ncRNAs appear to function by binding to and regulating the activities of transcriptional co-activator or co-repressor complexes. Although the extents to which these mechanisms are used remains to be established, the identification of highly conserved ncRNAs and the presence of RNA binding domains in a large number of transcriptional co-regulators raise the possibility that ncRNA/coregulator interactions play broad roles in the regulation of gene expression.

Gene expression analyses in X-linked myotubular myopathy

BACKGROUND

X-linked myotubular myopathy (XLMTM) is a severe congenital disorder characterized by marked muscle weakness and hypotonia. Myotubularin, the protein product of the causative gene, MTM1, is thought to be a phosphatase for phosphatidylinositol-3-phosphate and may be involved in membrane trafficking. Analysis of MTM1 knocked-out mice indicates that the characteristic small fibers in XLMTM muscles are due to atrophy rather than hypoplasia.

OBJECTIVE

To characterize gene expression profiling of skeletal muscles with XLMTM.

METHOD

The authors analyzed the expression of more than 4,200 genes in skeletal muscles from eight patients with XLMTM using their custom cDNA microarray.

RESULTS

In XLMTM, gene expression analysis revealed pathognomonic upregulation of transcripts for cytoskeletal and extracellular matrix proteins within or around atrophic myofibers.

CONCLUSION

Remodeling of cytoskeletal and extracellular architecture appears to contribute to atrophy and intracellular organelle disorganization in XLMTM myofibers.

Histone deacetylase inhibitors arrest polyglutamine-dependent neurodegeneration in Drosophila

Proteins with expanded polyglutamine repeats cause Huntington's disease and other neurodegenerative diseases. Transcriptional dysregulation and loss of function of transcriptional co-activator proteins have been implicated in the pathogenesis of these diseases. Huntington's disease is caused by expansion of a repeated sequence of the amino acid glutamine in the abnormal protein huntingtin (Htt). Here we show that the polyglutamine-containing domain of Htt, Htt exon 1 protein (Httex1p), directly binds the acetyltransferase domains of two distinct proteins: CREB-binding protein (CBP) and p300/CBP-associated factor (P/CAF). In cell-free assays, Httex1p also inhibits the acetyltransferase activity of at least three enzymes: p300, P/CAF and CBP. Expression of Httex1p in cultured cells reduces the level of the acetylated histones H3 and H4, and this reduction can be reversed by administering inhibitors of histone deacetylase (HDAC). In vivo, HDAC inhibitors arrest ongoing progressive neuronal degeneration induced by polyglutamine repeat expansion, and they reduce lethality in two Drosophila models of polyglutamine disease. These findings raise the possibility that therapy with HDAC inhibitors may slow or prevent the progressive neurodegeneration seen in Huntington's disease and other polyglutamine-repeat diseases, even after the onset of symptoms.

Spontaneous thrombosis of intracavernous internal carotid artery aneurysm and parent artery occlusion in patients with positive balloon test occlusion--two case reports

Two patients with giant intracavernous internal carotid artery (ICA) aneurysms were intolerant to balloon test occlusion of the ICA, and later developed spontaneous thrombosis of the aneurysm and the parent ICA without ischemic sequelae. Case 1: A 60-year-old female with a giant right intracavernous ICA aneurysm presented with right abducens nerve paresis. An unsuccessful extracranial-to-intracranial bypass graft operation was complicated by transient postoperative ophthalmoplegia. The patient did not tolerate balloon test occlusion of the right ICA after attempted bypass surgery, and was treated conservatively. The patient presented with acute onset of headache 3 years later. Case 2: A 50-year-old female with a giant right intracavernous ICA aneurysm presented with right abducens nerve paresis. The patient was managed conservatively after a positive balloon test occlusion of the right ICA. The patient suffered transient hypopituitarism and acute onset of headache 2 years later. Spontaneous thrombosis of the aneurysms and occlusion of the parent ICA were found in both patients. Neither had major hemispheric infarcts, but the first patient had asymptomatic infarcts, which were presumed to be thromboembolic in nature. Patients with intracavernous ICA aneurysms who have positive balloon test occlusions appear to develop tolerance to spontaneous and gradual occlusion of the ICA without significant sequelae. However, these patients have an increased risk of developing embolic infarctions. The role for anticoagulation and repeat hemodynamic tests remains unclear.

Defect of histone acetyltransferase activity of the nuclear transcriptional coactivator CBP in Rubinstein-Taybi syndrome

CREB-binding protein (CBP) is a transcriptional coactivator that has intrinsic histone acetyltransferase (HAT) activity. CBP is the causative gene of Rubinstein-Taybi syndrome (RTS). To investigate the relationships between CBP HAT activity and RTS, we analyzed 16 RTS patients. A microdeletion was identified in one patient by fluorescent in situ hybridization analysis. Heteroallelic mutations were identified in five patients by reverse transcriptase-polymerase chain reaction-single-strand conformation polymorphism analysis and sequencing. These included a 2 bp deletion between nucleotides 4319 and 4320, an 11 bp deletion between nucleotides 4898 and 4908, a 14 bp insertion (CCTCGGTCCTGCAC) between nucleotides 5212 and 5213, a 2 bp deletion between nucleotides 5222 and 5223, and a missense mutation from guanine (G) to cytosine (C) at nucleotide 4951 that changed codon 1378 from CGG (arginine) to CCG (proline). The identical missense mutation was introduced into the recombinant mouse CBP. It abolished the HAT activity of CBP and the ability of CBP to transactivate cyclic AMP-response element binding protein (CREB), in HAT assays and in microinjection experiments, respectively. These results suggest that the loss of the HAT activity of CBP may cause RTS, as the first example of a defect of HAT activity in a human disease. Our findings raise the possibility that treatment of RTS patients with histone deacetylase inhibitors might have beneficial effects.

Schizosaccharomyces pombe taf1+ is required for nitrogen starvation-induced sexual development and for entering the dormant GO state

Environmental change, such as nutritional starvation, induces physiological and morphological alterations that enable fission yeast cells to survive. We isolated a novel gene, taf1+, required for the response to nitrogen starvation in the fission yeast Schizosaccharomyces pombe. taf1 disruptants could not mate upon nitrogen starvation, but could upon carbon starvation. taf1 disruptants had a defect in inducing stell+ expression under nitrogen starvation conditions. Furthermore, they lost viability quickly in nitrogen-depleted medium. Unlike wild-type cells, starved taf1-cells had nuclear chromatin that were flat and adhered to the cell periphery. These results indicate that tqf1+ is required for nitrogen starvation-induced sexual development and entering the dormant G0 state.

Combinatorial roles of the nuclear receptor corepressor in transcription and development

Transcriptional repression plays crucial roles in diverse aspects of metazoan development, implying critical regulatory roles for corepressors such as N-CoR and SMRT. Altered patterns of transcription in tissues and cells derived from N-CoR gene-deleted mice and the resulting block at specific points in CNS, erythrocyte, and thymocyte development indicated that N-CoR was a required component of short-term active repression by nuclear receptors and MAD and of a subset of long-term repression events mediated by REST/NRSF. Unexpectedly, N-CoR and a specific deacetylase were also required for transcriptional activation of one class of retinoic acid response element. Together, these findings suggest that specific combinations of corepressors and histone deacetylases mediate the gene-specific actions of DNA-bound repressors in development of multiple organ systems.

Ligand-dependent interactions of coactivators steroid receptor coactivator-1 and peroxisome proliferator-activated receptor binding protein with nuclear hormone receptors can be imaged in live cells and are required for transcription

Members of the nuclear receptor superfamily are thought to activate transcription by recruitment of one or more recently identified coactivator complexes. Here we demonstrate that both peroxisome proliferator-activated receptor binding protein (PBP) and steroid receptor coactivator-1 (SRC-1) are required for ligand-dependent transcription of transiently transfected and chromosomally integrated reporter genes by the estrogen receptor (ER) and retinoic acid receptor (RAR). To examine ligand-dependent interactions between nuclear receptors and specific coactivators in living cells, these proteins were tagged with cyan (CFP) and yellow (YFP) mutants of the green fluorescent protein. Fluorescence resonance energy transfer (FRET) from the CFP to the YFP indicated interaction between the receptor and coactivator. CFP fusions to RAR or its ligand-binding domain exhibited rapid ligand-dependent FRET to YFP-tagged nuclear receptor interaction domains of the coactivators SRC-1 and PBP. The ER-ligand-binding domain, unlike RAR, also exhibited some basal interaction with coactivators in unstimulated cells that was abolished by the receptor antagonists tamoxifen or ICI182,780. Inhibition of FRET by tamoxifen but not ICI182,780 could be reversed by estradiol, whereas estradiol-enhanced FRET could not be inhibited by either antagonist, indicating that ligand effects can show varying degrees of hysteresis. These findings suggest that ligand-dependent transcriptional activities of the RAR and ER require concurrent or sequential recruitment of SRC-1 and PBP-containing coactivator complexes.

Molecular determinants of nuclear receptor-corepressor interaction

Retinoic acid and thyroid hormone receptors can act alternatively as ligand-independent repressors or ligand-dependent activators, based on an exchange of N-CoR or SMRT-containing corepressor complexes for coactivator complexes in response to ligands. We provide evidence that the molecular basis of N-CoR recruitment is similar to that of coactivator recruitment, involving cooperative binding of two helical interaction motifs within the N-CoR carboxyl terminus to both subunits of a RAR-RXR heterodimer. The N-CoR and SMRT nuclear receptor interaction motifs exhibit a consensus sequence of LXX I/H I XXX I/L, representing an extended helix compared to the coactivator LXXLL helix, which is able to interact with specific residues in the same receptor pocket required for coactivator binding. We propose a model in which discrimination of the different lengths of the coactivator and corepressor interaction helices by the nuclear receptor AF2 motif provides the molecular basis for the exchange of coactivators for corepressors, with ligand-dependent formation of the charge clamp that stabilizes LXXLL binding sterically inhibiting interaction of the extended corepressor helix.

Ruptured vertebral artery-posterior inferior cerebellar artery aneurysm associated with facial nerve paresis successfully treated with interlocking detachable coils--case report

An 81-year-old female presented with severe headache. Computed tomography revealed subarachnoid hemorrhage. She developed right facial nerve paresis on the next day. Angiography revealed a right vertebral artery-posterior inferior cerebellar artery aneurysm. The aneurysm was successfully occluded with interlocking detachable coils (IDCs) on the 7th day. Magnetic resonance (MR) imaging 1 month after IDC placement showed partially thrombosed aneurysm near the internal acoustic meatus. Ten months after the ictus, MR imaging revealed marked resolution of the intra-aneurysmal thrombus and reduction of the aneurysm size. Her facial nerve function gradually recovered during this period. Her facial nerve paresis was probably caused by acute stretching of the facial nerve by the ruptured aneurysm that was in direct contact with the nerve. Intra-aneurysmal thrombosis using coils can reduce aneurysm size and alleviate cranial nerve symptoms.

Transcriptional activation by NF-kappaB requires multiple coactivators

Nuclear factor-kappaB (NF-kappaB) plays a role in the transcriptional regulation of genes involved in inflammation and cell survival. In this report we demonstrate that NF-kappaB recruits a coactivator complex that has striking similarities to that recruited by nuclear receptors. Inactivation of either cyclic AMP response element binding protein (CREB)-binding protein (CBP), members of the p160 family of coactivators, or the CBP-associated factor (p/CAF) by nuclear antibody microinjection prevents NF-kappaB-dependent transactivation. Like nuclear receptor-dependent gene expression, NF-kappaB-dependent gene expression requires specific LXXLL motifs in one of the p160 family members, and enhancement of NF-kappaB activity requires the histone acetyltransferase (HAT) activity of p/CAF but not that of CBP. This coactivator complex is differentially recruited by members of the Rel family. The p50 homodimer fails to recruit coactivators, although the p50-p65 heterodimeric form of the transcription factor assembles the integrator complex. These findings provide new mechanistic insights into how this family of dimeric transcription factors has a differential effect on gene expression.

Factor-specific modulation of CREB-binding protein acetyltransferase activity

CREB-binding proteins (CBP) and p300 are essential transcriptional coactivators for a large number of regulated DNA-binding transcription factors, including CREB, nuclear receptors, and STATs. CBP and p300 function in part by mediating the assembly of multiprotein complexes that contain additional cofactors such as p300/CBP interacting protein (p/CIP), a member of the p160/SRC family of coactivators, and the p300/CBP associated factor p/CAF. In addition to serving as molecular scaffolds, CBP and p300 each possess intrinsic acetyltransferase activities that are required for their function as coactivators. Here we report that the adenovirus E1A protein inhibits the acetyltransferase activity of CBP on binding to the C/H3 domain, whereas binding of CREB, or a CREB/E1A fusion protein to the KIX domain, fails to inhibit CBP acetyltransferase activity. Surprisingly, p/CIP can either inhibit or stimulate CBP acetyltransferase activity depending on the specific substrate evaluated and the functional domains present in the p/CIP protein. While the CBP interaction domain of p/CIP inhibits acetylation of histones H3, H4, or high mobility group by CBP, it enhances acetylation of other substrates, such as Pit-1. These observations suggest that the acetyltransferase activities of CBP/p300 and p/CAF can be differentially modulated by factors binding to distinct regions of CBP/p300. Because these interactions are likely to result in differential effects on the coactivator functions of CBP/p300 for different classes of transcription factors, regulation of CBP/p300 acetyltransferase activity may represent a mechanism for integration of diverse signaling pathways.

Signal-specific co-activator domain requirements for Pit-1 activation

POU-domain proteins, such as the pituitary-specific factor Pit-1, are members of the homeodomain family of proteins which are important in development and homeostasis, acting constitutively or in response to signal-transduction pathways to either repress or activate the expression of specific genes. Here we show that whereas homeodomain-containing repressors such as Rpx2 seem to recruit only a co-repressor complex, the activity of Pit-1 is determined by a regulated balance between a co-repressor complex that contains N-CoR/SMRT, mSin3A/B and histone deacetylases, and a co-activator complex that includes the CREB-binding protein (CBP) and p/CAF. Activation of Pit-1 by cyclic AMP or growth factors depends on distinct amino- and carboxy-terminal domains of CBP, respectively. Furthermore, the histone acetyltransferase functions of CBP or p/CAF are required for Pit-1 function that is stimulated by cyclic AMP or growth factors, respectively. These data show that there is a switch in specific requirements for histone acetyltransferases and CBP domains in mediating the effects of different signal-transduction pathways on specific DNA-bound transcription factors.

Interactions controlling the assembly of nuclear-receptor heterodimers and co-activators

Retinoic-acid receptor-alpha (RAR-alpha) and peroxisome proliferator-activated receptor-gamma (PPAR-gamma) are members of the nuclear-receptor superfamily that bind to DNA as heterodimers with retinoid-X receptors (RXRs). PPAR-RXR heterodimers can be activated by PPAR or RXR ligands, whereas RAR-RXR heterodimers are selectively activated by RAR ligands only, because of allosteric inhibition of the binding of ligands to RXR by RAR. However, RXR ligands can potentiate the transcriptional effects of RAR ligands in cells. Transcriptional activation by nuclear receptors requires a carboxy-terminal helical region, termed activation function-2 (AF-2), that forms part of the ligand-binding pocket and undergoes a conformational change required for the recruitment of co-activator proteins, including NCoA-1/SRC-1. Here we show that allosteric inhibition of RXR results from a rotation of the RXR AF-2 helix that places it in contact with the RAR coactivator-binding site. Recruitment of an LXXLL motif of SRC-1 to RAR in response to ligand displaces the RXR AF-2 domain, allowing RXR ligands to bind and promote the binding of a second LXXLL motif from the same SRC-1 molecule. These results may partly explain the different responses of nuclear-receptor heterodimers to RXR-specific ligands.

Ligand binding and co-activator assembly of the peroxisome proliferator-activated receptor-gamma

The peroxisome proliferator-activated receptor-gamma (PPAR-gamma) is a ligand-dependent transcription factor that is important in adipocyte differentiation and glucose homeostasis and which depends on interactions with co-activators, including steroid receptor co-activating factor-1 (SRC-1). Here we present the X-ray crystal structure of the human apo-PPAR-gamma ligand-binding domain (LBD), at 2.2 A resolution; this structure reveals a large binding pocket, which may explain the diversity of ligands for PPAR-gamma. We also describe the ternary complex containing the PPAR-gamma LBD, the antidiabetic ligand rosiglitazone (BRL49653), and 88 amino acids of human SRC-1 at 2.3 A resolution. Glutamate and lysine residues that are highly conserved in LBDs of nuclear receptors form a 'charge clamp' that contacts backbone atoms of the LXXLL helices of SRC-1. These results, together with the observation that two consecutive LXXLL motifs of SRC-1 make identical contacts with both subunits of a PPAR-gamma homodimer, suggest a general mechanism for the assembly of nuclear receptors with co-activators.

Differential use of CREB binding protein-coactivator complexes

CREB binding protein (CBP) functions as an essential coactivator of transcription factors that are inhibited by the adenovirus early gene product E1A. Transcriptional activation by the signal transducer and activator of transcription-1 (STAT1) protein requires the C/H3 domain in CBP, which is the primary target of E1A inhibition. Here it was found that the C/H3 domain is not required for retinoic acid receptor (RAR) function, nor is it involved in E1A inhibition. Instead, E1A inhibits RAR function by preventing the assembly of CBP-nuclear receptor coactivator complexes, revealing differences in required CBP domains for transcriptional activation by RAR and STAT1.