Evaluation of the Normal Cochlear Second Interscalar Ridge Angle and Depth on 3D T2-Weighted Images: A Tool for the Diagnosis of Scala Communis and Incomplete Partition Type II

BACKGROUND AND PURPOSE

Cochlear malformations may be be subtle on imaging studies. The purpose of this study was to evaluate the angle and depth of the lateral second interscalar ridge or notch in ears without sensorineural hearing loss (normal ears) and compare them with ears that have a documented incomplete type II partition malformation.

MATERIALS AND METHODS

The second interscalar ridge notch angle and depth were measured on MR imaging in normal ears by a single experienced neuroradiologist. The images of normal and incomplete partition II malformation ears were then randomly mixed for 2 novice evaluators to measure both the second interscalar ridge notch angle and depth in a blinded manner. For the mixed group, interobserver agreement was calculated, normal and abnormal ear measurements were compared, and receiver operating characteristic curves were generated.

RESULTS

The 94 normal ears had a mean second interscalar ridge angle of 80.86° ± 11.4° and depth of 0.54 ± 0.14 mm with the 98th percentile for an angle of 101° and a depth of 0.3 mm. In the mixed group, agreement between the 2 readers was excellent, with significant differences for angle and depth found between normal and incomplete partition type II ears for angle and depth on average (P < .001). Receiver operating characteristic cutoffs for delineating normal from abnormal ears were similar for both readers (depth, 0.31/0.34 mm; angle, 114°/104°).

CONCLUSIONS

A measured angle of >114° and a depth of the second interscalar ridge notch of ≤0.31 mm suggest the diagnosis of incomplete partition type II malformation and scala communis. These measurements can be accurately made by novice readers.

Histone modification profiling in breast cancer cell lines highlights commonalities and differences among subtypes

Background

Epigenetic regulators are frequently mutated or aberrantly expressed in a variety of cancers, leading to altered transcription states that result in changes in cell identity, behavior, and response to therapy.

Results

To define alterations in epigenetic landscapes in breast cancers, we profiled the distributions of 8 key histone modifications by ChIP-Seq, as well as primary (GRO-seq) and steady state (RNA-Seq) transcriptomes, across 13 distinct cell lines that represent 5 molecular subtypes of breast cancer and immortalized human mammary epithelial cells.

Discussion

Using combinatorial patterns of distinct histone modification signals, we defined subtype-specific chromatin signatures to nominate potential biomarkers. This approach identified AFAP1-AS1 as a triple negative breast cancer-specific gene associated with cell proliferation and epithelial-mesenchymal-transition. In addition, our chromatin mapping data in basal TNBC cell lines are consistent with gene expression patterns in TCGA that indicate decreased activity of the androgen receptor pathway but increased activity of the vitamin D biosynthesis pathway.

Conclusions

Together, these datasets provide a comprehensive resource for histone modification profiles that define epigenetic landscapes and reveal key chromatin signatures in breast cancer cell line subtypes with potential to identify novel and actionable targets for treatment.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4533-0) contains supplementary material, which is available to authorized users.

Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis

Noncoding transcription is a defining feature of active enhancers, linking transcription factor (TF) binding to the molecular mechanisms controlling gene expression. To determine the relationship between enhancer activity and biological outcomes in breast cancers, we profiled the transcriptomes (using GRO-seq and RNA-seq) and epigenomes (using ChIP-seq) of 11 different human breast cancer cell lines representing five major molecular subtypes of breast cancer, as well as two immortalized (“normal”) human breast cell lines. In addition, we developed a robust and unbiased computational pipeline that simultaneously identifies putative subtype-specific enhancers and their cognate TFs by integrating the magnitude of enhancer transcription, TF mRNA expression levels, TF motif P-values, and enrichment of H3K4me1 and H3K27ac. When applied across the 13 different cell lines noted above, the Total Functional Score of Enhancer Elements (TFSEE) identified key breast cancer subtype-specific TFs that act at transcribed enhancers to dictate gene expression patterns determining growth outcomes, including Forkhead TFs, FOSL1, and PLAG1. FOSL1, a Fos family TF, (1) is highly enriched at the enhancers of triple negative breast cancer (TNBC) cells, (2) acts as a key regulator of the proliferation and viability of TNBC cells, but not Luminal A cells, and (3) is associated with a poor prognosis in TNBC breast cancer patients. Taken together, our results validate our enhancer identification pipeline and reveal that enhancers transcribed in breast cancer cells direct critical gene regulatory networks that promote pathogenesis.

Variants with a low allele frequency detected in genomic DNA affect the accuracy of mutation detection in cell-free DNA by next-generation sequencing

BACKGROUND

Next-generation sequencing of cell-free DNA (cfDNA) has been shown to be a useful noninvasive test for detecting mutations in solid tumors.

METHODS

Targeted gene sequencing was performed with a panel of 263 cancer-related genes for cfDNA and genomic DNA of peripheral blood mononuclear cells (PBMCs) obtained from presurgical specimens of 6 lung cancer patients, and mutation calls in these samples were compared with those of primary tumors and corresponding patient-derived xenografts (PDXs).

RESULTS

Approximately 67% of the mutations detected in the tumor samples (primary tumors and/or PDXs) were also detected in genomic DNA from PBMCs as background mutations. These background mutations consisted of germline polymorphisms and a group of mutations with low allele frequencies, mostly <10%. These variants with a low allele frequency were repeatedly detected in all types of samples from the same patients and at similarly low allele frequency levels in PBMCs from different patients; this indicated that their detection might be derived from common causes, such as homologous sequences in the human genome. Allele frequencies of mutations detected in both primary tumors and cfDNA showed 2 patterns: 1) low allele frequencies (approximately 1%-10%) in cfDNA but high allele frequencies (usually >10% or >3-fold increase) in primary tumors and further enrichment in PDXs and 2) similar allele frequencies across samples.

CONCLUSIONS

Because only a small fraction of total cfDNA might be derived from tumor cells, only mutations with the first allele frequency pattern may be regarded as tumor-specific mutations in cfDNA. Effective filtering of background mutations will be required to improve the accuracy of mutation calls in cfDNA. Cancer 2018;124:1061-9. © 2017 American Cancer Society.

Role of MR Neurography for the Diagnosis of Peripheral Trigeminal Nerve Injuries in Patients with Prior Molar Tooth Extraction

BACKGROUND AND PURPOSE

Clinical neurosensory testing is an imperfect reference standard to evaluate molar tooth extraction related peripheral trigeminal neuropathy. The purpose was to evaluate the diagnostic accuracy of MR neurography in this domain and correlation with neurosensory testing and surgery.

MATERIALS AND METHODS

In this retrospective study, nerve caliber, T2 signal intensity ratio, and contrast-to-noise ratios were recorded by 2 observers using MR neurography for bilateral branches of the peripheral trigeminal nerve, the inferior alveolar and lingual nerves. Patient demographics and correlation of the MR neurography findings with the Sunderland classification of nerve injury and intraoperative findings of surgical patients were obtained.

RESULTS

Among 42 patients, the mean ± SD age for case and control patients were 35.8 ± 10.2 years and 43.2 ± 11.5 years, respectively, with male-to-female ratios of 1:1.4 and 1:5, respectively. Case subjects (peripheral trigeminal neuropathy or injury) had significantly larger differences in nerve thickness, T2 signal intensity ratio, and contrast-to-noise ratios than control patients for the inferior alveolar nerve and lingual nerve (P = .01 and .0001, .012 and .005, and .01 and .01, respectively). Receiver operating characteristic analysis showed a significant association among differences in nerve thickness, T2 signal intensity ratio, and contrast-to-noise ratios and nerve injury (area under the curve, 0.83-0.84 for the inferior alveolar nerve and 0.77-0.78 for the lingual nerve). Interobserver agreement was good for the inferior alveolar nerve (intraclass correlation coefficient, 0.70-0.79) and good to excellent for the lingual nerve (intraclass correlation coefficient, 0.75-0.85). MR neurography correlations with respect to clinical neurosensory testing and surgical classifications were moderate to good. Pearson correlation coefficients of 0.68 and 0.81 and κ of 0.60 and 0.77 were observed for differences in nerve thickness.

CONCLUSIONS

MR neurography can be reliably used for the diagnosis of injuries to the peripheral trigeminal nerve related to molar tooth extractions, with good to excellent correlation of imaging with clinical findings and surgical results.

YEATS2 links histone acetylation to tumorigenesis of non-small cell lung cancer

Recognition of modified histones by “reader” proteins constitutes a key mechanism regulating diverse chromatin-associated processes important for normal and neoplastic development. We recently identified the YEATS domain as a novel acetyllysine-binding module; however, the functional importance of YEATS domain-containing proteins in human cancer remains largely unknown. Here, we show that the YEATS2 gene is highly amplified in human non-small cell lung cancer (NSCLC) and is required for cancer cell growth and survival. YEATS2 binds to acetylated histone H3 via its YEATS domain. The YEATS2-containing ATAC complex co-localizes with H3K27 acetylation (H3K27ac) on the promoters of actively transcribed genes. Depletion of YEATS2 or disruption of the interaction between its YEATS domain and acetylated histones reduces the ATAC complex-dependent promoter H3K9ac levels and deactivates the expression of essential genes. Taken together, our study identifies YEATS2 as a histone H3K27ac reader that regulates a transcriptional program essential for NSCLC tumorigenesis.

Histone modification recognition is an important mechanism for gene expression regulation in cancer. Here, the authors identify YEATS2 as a histone H3K27ac reader, regulating a transcriptional program essential for tumorigenesis in human non-small cell lung cancer.

Genomic characterization of human papillomavirus-positive and -negative human squamous cell cancer cell lines

Human cancer cell lines are the most frequently used preclinical models in the study of cancer biology and the development of therapeutics. Although anatomically diverse, human papillomavirus (HPV)-driven cancers have a common etiology and similar mutations that overlap with but are distinct from those found in HPV-negative cancers. Building on prior studies that have characterized subsets of head and neck squamous cell carcinoma (HNSCC) and cervical squamous cell carcinoma (CESC) cell lines separately, we performed genomic, viral gene expression, and viral integration analyses on 74 cell lines that include all readily-available HPV-positive (9 HNSCC, 8 CESC) and CESC (8 HPV-positive, 2 HPV-negative) cell lines and 55 HPV-negative HNSCC cell lines. We used over 700 human tumors for comparison. Mutation patterns in the cell lines were similar to those of human tumors. We confirmed HPV viral protein and mRNA expression in the HPV-positive cell lines. We found HPV types in three CESC cell lines that are distinct from those previously reported. We found that cell lines and tumors had similar patterns of viral gene expression; there were few sites of recurrent HPV integration. As seen in tumors, HPV integration did appear to alter host gene expression in cell lines. The HPV-positive cell lines had higher levels of p16 and lower levels of Rb protein expression than did the HPV-negative lines. Although the number of HPV-positive cell lines is limited, our results suggest that these cell lines represent suitable models for studying HNSCC and CESC, both of which are common and lethal.

MR Neurography of Greater Occipital Nerve Neuropathy: Initial Experience in Patients with Migraine

BACKGROUND AND PURPOSE

MR imaging of peripheral nerves (MR neurography) allows improved assessment of nerve anatomy and pathology. The objective of this study was to evaluate patients with unilateral occipital neuralgia using MR neurography and to assess the differences in greater occipital nerve signal and size between the symptomatic and asymptomatic sides.

MATERIALS AND METHODS

In this case-control evaluation using MR neurography, bilateral greater occipital nerve caliber, signal intensity, signal-to-noise ratios, and contrast-to-noise ratios were determined by 2 observers.

RESULTS

Among 18 subjects with unilateral occipital migraines, the average greater occipital nerve diameter for the symptomatic side was significantly greater at 1.77 ± 0.4 mm than for the asymptomatic side at 1.29 ± 0.25 mm (P = .001). The difference in nerve signal intensity between the symptomatic and asymptomatic sides was statistically significant at 269.06 ± 170.93 and 222.44 ± 170.46, respectively (P = .043). The signal-to-noise ratios on the symptomatic side were higher at 15.79 ± 4.59 compared with the asymptomatic nerve at 14.02 ± 5.23 (P = .009). Contrast-to-noise ratios were significantly higher on the symptomatic side than on the asymptomatic side at 2.57 ± 4.89 and -1.26 ± 5.02, respectively (P = .004). Intraobserver performance was good to excellent (intraclass coefficient correlation, 0.68-0.93), and interobserver performance was fair to excellent (intraclass coefficient correlation, 0.54-0.81).

CONCLUSIONS

MR neurography can be reliably used for the diagnosis of greater occipital nerve neuropathy in patients with unilateral occipital migraines with a good correlation of imaging findings to the clinical presentation.

LncPRESS1 Is a p53-Regulated LncRNA that Safeguards Pluripotency by Disrupting SIRT6-Mediated De-acetylation of Histone H3K56

Recent evidence suggests that lncRNAs play an integral regulatory role in numerous functions, including determination of cellular identity. We determined global expression (RNA-seq) and genome-wide profiles (ChIP-seq) of histone post-translational modifications and p53 binding in human embryonic stem cells (hESCs) undergoing differentiation to define a high-confidence set of 40 lncRNAs, which are p53 transcriptional targets. We focused on lncRNAs highly expressed in pluripotent hESCs and repressed by p53 during differentiation to identify lncPRESS1 as a p53-regulated transcript that maintains hESC pluripotency in concert with core pluripotency factors. RNA-seq of hESCs depleted of lncPRESS1 revealed that lncPRESS1 controls a gene network that promotes pluripotency. Further, we found that lncPRESS1 physically interacts with SIRT6 and prevents SIRT6 chromatin localization, which maintains high levels of histone H3K56 and H3K9 acetylation at promoters of pluripotency genes. In summary, we describe a p53-regulated, pluripotency-specific lncRNA that safeguards the hESC state by disrupting SIRT6 activity.

ENL links histone acetylation to oncogenic gene expression in acute myeloid leukaemia

Cancer cells are characterized by aberrant epigenetic landscapes and often exploit chromatin machinery to activate oncogenic gene expression programs¹. Recognition of modified histones by “reader” proteins constitutes a key mechanism underlying these processes; therefore, targeting such pathways holds clinical promise, as exemplified by the development of BET bromodomain inhibitors^{2, 3}. We recently identified the YEATS domain as a novel acetyllysine-binding module⁴, yet its functional importance in human cancer remains unknown. Here we show that the YEATS domain-containing protein ENL, but not its paralog AF9, is required for disease maintenance in acute myeloid leukaemia (AML). CRISPR-Cas9 mediated depletion of ENL led to anti-leukemic effects, including increased terminal myeloid differentiation and suppression of leukaemia growth in vitro and in vivo. Biochemical and crystal structural studies and ChIP-seq analyses revealed that ENL binds to acetylated histone H3, and colocalizes with H3K27ac and H3K9ac on the promoters of actively transcribed genes that are essential for leukaemias. Disrupting the interaction between the YEATS domain and histone acetylation via structure-based mutagenesis reduced RNA polymerase II recruitment to ENL target genes, leading to suppression of oncogenic gene expression programs. Importantly, disruption of ENL’s functionality further sensitized leukaemia cells to BET inhibitors. Together, our study identifies ENL as a histone acetylation reader that regulates oncogenic transcriptional programs in AML and suggests that displacement of ENL from chromatin may be a promising epigenetic therapy alone or in combination with BET inhibitors for AML.

Reconstruction with soft tissue free flaps for large defects after the resection of giant facial neurofibroma

Giant facial neurofibroma leads to disfigurement and functional and neurological deficits. Surgical resection is the mainstay of treatment and poses a great challenge to the surgeon with regard to the restoration of the defects arising from tumour resection. The cases of three male and three female patients diagnosed with giant facial neurofibroma, who underwent radical resection and reconstruction with soft tissue free flaps between 2008 and 2015, were analyzed retrospectively. Clinical data including patient sex, age, preoperative embolization of the nutrient artery, volume of blood loss, type and size of flaps used for reconstruction, and complications were recorded. Three of the six patients underwent preoperative embolization of the nutrient artery. The average volume of blood loss was 2850ml. Reconstruction was performed with anterolateral thigh flaps in four patients and latissimus dorsi myocutaneous flaps in two patients. All free flap reconstructions were successful. Partial necrosis of the scalp and wound dehiscence occurred in one patient each. All complications were managed successfully. In conclusion, the soft tissue free flap is a good choice for the coverage of defects after giant facial neurofibroma resection. Multi-disciplinary treatment should be strengthened to minimize the risks of complications, as well as improving quality of life.

Loss of the arginine methyltranserase PRMT7 causes syndromic intellectual disability with microcephaly and brachydactyly

Post-translational protein modifications exponentially expand the functional complement of proteins encoded by the human genome. One such modification is the covalent addition of a methyl group to arginine or lysine residues, which is used to regulate a substantial proportion of the proteome. Arginine and lysine methylation are catalyzed by protein arginine methyltransferase (PRMTs) and protein lysine methyltransferase proteins (PKMTs), respectively; each methyltransferase has a specific set of target substrates. Here, we report a male with severe intellectual disability, facial dysmorphism, microcephaly, short stature, brachydactyly, cryptorchidism and seizures who was found to have a homozygous 15,309 bp deletion encompassing the transcription start site of PRMT7, which we confirmed is functionally a null allele. We show that the patient's cells have decreased levels of protein arginine methylation, and that affected proteins include the essential histones, H2B and H4. Finally, we demonstrate that patient cells have altered Wnt signaling, which may have contributed to the skeletal abnormalities. Our findings confirm the recent disease association of PRMT7, expand the phenotypic manifestations of this disorder and provide insight into the molecular pathogenesis of this new condition.

HSFY and ZNF280BY show copy number variations within 17 water buffalo populations

Recent transcriptomic analysis of the bovine Y chromosome revealed abundant presence of multi-copy protein coding gene families on the male-specific region of the Y chromosome (MSY). Copy number variations (CNVs) of several MSY genes are closely related to semen quality and male reproduction in cattle. However, the CNVs of MSY genes in water buffalo are largely unknown. Therefore, this study aimed to investigate the CNVs of HSFY and ZNF280BY of 298 buffaloes from 17 populations distributed in China, Vietnam and Laos using quantitative PCR. Our results revealed that the median copy numbers of the HSFY and ZNF280BY genes were 47 (ranging from 20 to 145) and 269 (ranging from 73 to 974) respectively. In conclusion, this study indicated that HSFY and ZNF280BY showed abundant CNVs within swamp buffalo populations.

[Classification and imaging diagnosis of Lisfranc joint injuries]

OBJECTIVE

To accelerate the detection rate and accuracy of diagnosis in damage imaging of Lisfranc joint through research on the information of X-ray, CT, and MR imaging of tarsometatarsus joint (also called Lisfranc joint) damage.

METHODS

A total of 153 cases of tarsometratisus damage or Lisfranc ligamentous injury patients were chosen during November 2012 to November 2015. Lisfranc injuries were classified according to the Myerson fracture displacements classification and Nunley-Vertullo low-grade injury classification. All the treatment data was performed using SPSS 17.0 software.

RESULTS

For Myerson fracture displacements, there were 16 cases in Myerson Ⅰ type (homolateral complete), 100 cases in Myerson Ⅱ type (homolateral incomplete), and 5 cases in Myerson Ⅲ type (divergent). For the low-grade injury, there were 7 cases, 24 cases, and 1 case in Nunley-Vertullo Ⅰ, Ⅱ, Ⅲ type respectively. The probability was 14.9% (18/121) for patients that the initial survey found negative by X-ray imaging diagnosis and was confirmed by subsequent CT or MRI. It was found that the distance between the base of first (M1) and second (M2) metatarsus which was larger than 2 mm was 69.4%(84/121)from the X-ray imaging; there were small chip fractures between the base of M1 and M2 was 47.1% (57/121), and 71.2% (37/52)of small chip fractures in the inside of base of M2 from CT. On MRI, ligament disruption showed the discontinue or normal signal disappearing, and there were 15 cases in the complete disruption condition.

CONCLUSION

It should be suggested to take a CT or MRI check for the patients who have highly suspicious Lisfranc injure and the X-ray imaging diagnosis was negative, since there is a certain rate of missed diagnosis for the Lisfranc injure using X-ray imaging. For children and teenagers, the sports injuries and joint strain are common style, such as the injuries caused by jump from higher platform, football/skateboarding injures, etc. If the distance between the base of M1 and M2 is larger than 2 mm or there are small chip fractures between the M1 and M2, the patients would be suspected bone fracture or Lisfranc ligament injure. Myerson Ⅱ type is the most common Lisfranc joint injury , and MRI is best for Lisfranc ligament injury.

Characterization and adsorption of Lactobacillus virulent phage P1

Bacteriophage infection of lactic acid bacteria is considered an important problem worldwide in the food fermentation industry, as it may produce low quality or unsafe foods, cause fermentation failure, and result in economic losses. To increase current knowledge on the properties of Lactobacillus virulent phages, we evaluated the effect of divalent cations, temperature, pH, and chloramphenicol on the adsorption ability of Lactobacillus virulent phage P1. Phage P1 was isolated from the abnormal fermentation liquid of Lactobacillus plantarum IMAU10120. The results showed that this phage belonged to the Siphoviridae family. The latent period of this phage was 45min, and the burst time was 90min. Burst size was 132.88±2.37 phage counts expressed per milliliter per infective center. This phage showed good tolerance at different temperatures, but incubation at 50°C only affected its adsorption. Adsorption rate reached a maximum value between 30 and 42°C. A high adsorption value of phage infectivity was obtained from pH 6 to 8. Moreover, calcium ions promoted and increased the adsorption capacity of phage P1, but magnesium ions had negative effects. Chloramphenicol had no effect on phage adsorption. This study increased current knowledge on the characterization and biological aspects of Lactobacillus virulent phages, and may provide some basic information that can be used to design successful antiphage strategies in the food industry.

FOXR2 Interacts with MYC to Promote Its Transcriptional Activities and Tumorigenesis

By combining the results of a large-scale proteomic analysis of the human transcription factor interaction network with knowledge databases, we identified FOXR2 as one of the top-ranked candidate proto-oncogenes. Here, we show that FOXR2 forms a stable complex with MYC and MAX and subsequently regulates cell proliferation by promoting MYC's transcriptional activities. We demonstrate that FOXR2 is highly expressed in several breast, lung, and liver cancer cell lines and related patient tumor samples, while reduction of FOXR2 expression in a xenograft model inhibits tumor growth. These results indicate that FOXR2 acts with MYC to promote cancer cell proliferation, which is a potential tumor-specific target for therapeutic intervention against MYC-driven cancers.

MR Imaging of the Cervical Spine in Nonaccidental Trauma: A Tertiary Institution Experience

BACKGROUND AND PURPOSE

Cervical MR imaging has demonstrated a utility for detecting soft tissue injury in nonaccidental trauma. The purpose of this study was to identify the incidence and types of cervical spine injury on MR imaging in nonaccidental trauma and to correlate cervical spine injury with parenchymal injury on brain MR imaging and findings on head CT.

MATERIALS AND METHODS

A retrospective review of children diagnosed with nonaccidental trauma in a tertiary referral pediatric hospital over 8 years was performed. Inclusion criteria were children younger than 5 years of age, a confirmed diagnosis of nonaccidental trauma, and cervical spine MR imaging within 1 week of presentation. Brain and cervical spine MR imaging, head CT, cervical radiographs, and skeletal surveys were reviewed.

RESULTS

There were 89 patients included in this study (48 males; mean age, 9.1 months [range, 1-59 months]). Cervical spine injury on MR imaging was found in 61 patients (69%). Ligamentous injury was seen in 60 patients (67%), with interspinous ligaments being most commonly involved. Abnormal capsular fluid (atlanto-occipital and atlantoaxial) was present in 28 patients (32%). Cervical spine injury on MR imaging was significantly associated with parenchymal restricted diffusion on brain MR imaging and parenchymal injury on head CT (P = .0004 and P = .0104, respectively). Children with restricted diffusion on brain MR imaging were 6.22 (point estimate) times more likely to have cervical spine injury on MR imaging.

CONCLUSIONS

There is a high incidence of cervical spine injury in pediatric nonaccidental trauma. Positive findings may affect management and suggest a traumatic etiology.

SIRT6 deacetylates H3K18ac at pericentric chromatin to prevent mitotic errors and cellular senescence

Pericentric heterochromatin silencing at mammalian centromeres is essential for mitotic fidelity and genomic stability. Defective pericentric silencing has been observed in senescent cells, aging tissues, and mammalian tumors, but the underlying mechanisms and functional consequences of these defects are unclear. Here, we uncover an essential role of the human SIRT6 enzyme in pericentric transcriptional silencing, and we show that this function protects against mitotic defects, genomic instability, and cellular senescence. At pericentric heterochromatin, SIRT6 promotes deacetylation of a new substrate, residue K18 of histone H3 (H3K18), and inactivation of SIRT6 in cells leads to H3K18 hyperacetylation and aberrant accumulation of pericentric transcripts. Strikingly, depletion of these transcripts through RNA interference rescues the mitotic and senescence phenotypes of SIRT6-deficient cells. Together, our findings reveal a new function for SIRT6 and regulation of acetylated H3K18 at heterochromatin, and demonstrate the pathogenic role of deregulated pericentric transcription in aging- and cancer-related cellular dysfunction.

Abstract A06: Characterization of a novel p53-regulated embryonic stem cell-specific lncRNA that safeguards pluripotency

Recent work shows that long non-coding RNAs (lncRNAs), transcribed from 80% of our genomes, play important roles in gene regulation and are associated with disease pathogenesis. However, there is a broad gap in our knowledge regarding any contributions of lncRNAs in mediating p53 response or regulating stem cell state. Here, we report our discovery of lncRNAs that fine-tune p53's transcriptional outcomes in differentiating human embryonic stem cells (hESCs). By integrating RNA-Seq with p53 ChIP-Seq analyses along with active or repressive histone marks of hESCs undergoing differentiation, we defined a high-confidence set of 40 lncRNAs that are p53 transcriptional targets. We found that p53 directly regulates nuclear lncRNAs, which are either activated (HOTAIRM1) or repressed (lncPRESS-1) during hESC differentiation. Single-cell gene expression analysis during lineage-specific hESC differentiation revealed that lncPRESS-1 is a novel pluripotency-specific, p53-regulated transcript with expression tightly correlated with OCT4, NANOG and PRDM14. Loss-of-function of lncPRESS-1 results in diminished pluripotency and spontaneous differentiation of hESCs. In addition, mass cytometry-based multi-parametric analysis at a single cell level revealed that depletion of lncPRESS-1 results in overall loss of hESC pluripotency with marked induction of an ectoderm specific gene-signature. Further, we show that lncPRESS-1 physically interacts with SIRT6 and restrains its chromatin localization to maintain high levels of histone H3 Lys-56 (H3K56) and Lys-9 (H3K9) acetylation at promoters of pluripotency genes to sustain a chromatin architecture that favors pluripotency. In summary, we describe a novel pluripotency-specific lncRNA that safeguards the hESC state by disrupting SIRT6 activity. Since lncPRESS-1 is repressed by p53, we believe that cancers that harbor mutant TP53 will have robust expression of this lncRNA. Further investigations are underway to determine the disease relevance of lncPRESS-1 and correlation with p53-mutations.

Citation Format: Abhinav K. Jain, Kadir C. Akdemir, Yuanxin Xi, Ryan L. McCarthy, Kendra Allton, Bruce Aronow, Chunru Lin, Wei Li, Liuqing Yang, Michelle C. Barton. Characterization of a novel p53-regulated embryonic stem cell-specific lncRNA that safeguards pluripotency. [abstract]. In: Proceedings of the AACR Special Conference on Noncoding RNAs and Cancer: Mechanisms to Medicines ; 2015 Dec 4-7; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2016;76(6 Suppl):Abstract nr A06.

Knockout of Atg5 delays the maturation and reduces the survival of adult-generated neurons in the hippocampus

Autophagy is an evolutionarily conserved lysosomal degradation pathway that plays important roles in cell maintenance, expansion and differentiation. Removal of genes essential for autophagy from embryonic neural stem and precursor cells reduces the survival and inhibits neuronal differentiation of adult-generated neurons. No study has modified autophagy within the adult precursor cells, leaving the cell-autonomous role of autophagy in adult neurogenesis unknown. Here we demonstrate that autophagic flux exists in the adult dividing progenitor cells and their progeny in the dentate gyrus. To investigate the role of autophagy in adult hippocampal neurogenesis, we genetically deleted Autophagy-related gene 5 (Atg5) that reduced autophagic flux and the survival of the progeny of dividing progenitor cells. This significant reduction in survival of adult-generated neurons is accompanied by a delay in neuronal maturation, including a transient reduction in spine density in the absence of a change in differentiation. The delay in cell maturation and loss of progeny of the Atg5-null cells was not present in mice that lacked the essential pro-apoptotic protein Bax (Bcl-2-associated X protein), suggesting that Atg5-deficient cells die through a Bax-dependent mechanism. In addition, there was a loss of Atg5-null cells following exposure to running, suggesting that Atg5 is required for running-induced increases in neurogenesis. These findings highlight the cell-autonomous requirement of Atg5 in the survival of adult-generated neurons.