Histone Deacetylase Complexes Promote Trinucleotide Repeat Expansions

Genetic analysis in budding yeast and in cultured human astrocytes reveals that specific histone deacetylase complexes accelerate expansion mutations in DNA triplet repeats

DSIF and RNA Polymerase II CTD Phosphorylation Coordinate the Recruitment of Rpd3S to Actively Transcribed Genes

Histone deacetylase Rpd3 is part of two distinct complexes: the large (Rpd3L) and small (Rpd3S) complexes. While Rpd3L targets specific promoters for gene repression, Rpd3S is recruited to ORFs to deacetylate histones in the wake of RNA polymerase II, to prevent cryptic initiation within genes. Methylation of histone H3 at lysine 36 by the Set2 methyltransferase is thought to mediate the recruitment of Rpd3S. Here, we confirm by ChIP–Chip that Rpd3S binds active ORFs. Surprisingly, however, Rpd3S is not recruited to all active genes, and its recruitment is Set2-independent. However, Rpd3S complexes recruited in the absence of H3K36 methylation appear to be inactive. Finally, we present evidence implicating the yeast DSIF complex (Spt4/5) and RNA polymerase II phosphorylation by Kin28 and Ctk1 in the recruitment of Rpd3S to active genes. Taken together, our data support a model where Set2-dependent histone H3 methylation is required for the activation of Rpd3S following its recruitment to the RNA polymerase II C-terminal domain

PRC1 and PRC2 Are Not Required for Targeting of H2A.Z to Developmental Genes in Embryonic Stem Cells

The essential histone variant H2A.Z localises to both active and silent chromatin sites. In embryonic stem cells (ESCs), H2A.Z is also reported to co-localise with polycomb repressive complex 2 (PRC2) at developmentally silenced genes. The mechanism of H2A.Z targeting is not clear, but a role for the PRC2 component Suz12 has been suggested. Given this association, we wished to determine if polycomb functionally directs H2A.Z incorporation in ESCs. We demonstrate that the PRC1 component Ring1B interacts with multiple complexes in ESCs. Moreover, we show that although the genomic distribution of H2A.Z co-localises with PRC2, Ring1B and with the presence of CpG islands, H2A.Z still blankets polycomb target loci in the absence of Suz12, Eed (PRC2) or Ring1B (PRC1). Therefore we conclude that H2A.Z accumulates at developmentally silenced genes in ESCs in a polycomb independent manner

lincRNAs act in the circuitry controlling pluripotency and differentiation

Although thousands of large intergenic non-coding RNAs (lincRNAs) have been identified in mammals, few have been functionally characterized, leading to debate about their biological role. To address this, we performed loss-of-function studies on most lincRNAs expressed in mouse embryonic stem (ES) cells and characterized the effects on gene expression. Here we show that knockdown of lincRNAs has major consequences on gene expression patterns, comparable to knockdown of well-known ES cell regulators. Notably, lincRNAs primarily affect gene expression in trans. Knockdown of dozens of lincRNAs causes either exit from the pluripotent state or upregulation of lineage commitment programs. We integrate lincRNAs into the molecular circuitry of ES cells and show that lincRNA genes are regulated by key transcription factors and that lincRNA transcripts bind to multiple chromatin regulatory proteins to affect shared gene expression programs. Together, the results demonstrate that lincRNAs have key roles in the circuitry controlling ES cell state.Broad InstituteHarvard UniversityNational Human Genome Research Institute (U.S.)Merkin Family Foundation for Stem Cell Researc

Volumetric imaging and morphometric analysis of breast tumor angiogenesis using a new contrast-free ultrasound technique: a feasibility study

Abstract Background There is a strong correlation between the morphological features of new tumor vessels and malignancy. However, angiogenic heterogeneity necessitates 3D microvascular data of tumor microvessels for more reliable quantification. To provide more accurate information regarding vessel morphological features and improve breast lesion characterization, we introduced a quantitative 3D high-definition microvasculature imaging (q3D-HDMI) as a new easily applicable and robust tool to morphologically characterize microvasculature networks in breast tumors using a contrast-free ultrasound-based imaging approach. Methods In this prospective study, from January 2020 through December 2021, a newly developed q3D-HDMI technique was evaluated on participants with ultrasound-identified suspicious breast lesions recommended for core needle biopsy. The morphological features of breast tumor microvessels were extracted from the q3D-HDMI. Leave-one-out cross-validation (LOOCV) was applied to test the combined diagnostic performance of multiple morphological parameters of breast tumor microvessels. Receiver operating characteristic (ROC) curves were used to evaluate the prediction performance of the generated pooled model. Results Ninety-three participants (mean age 52 ± 17 years, 91 women) with 93 breast lesions were studied. The area under the ROC curve (AUC) generated with q3D-HDMI was 95.8% (95% CI 0.901–1.000), yielding a sensitivity of 91.7% and a specificity of 98.2%, that was significantly higher than the AUC generated with the q2D-HDMI (p = 0.02). When compared to q2D-HDMI, the tumor microvessel morphological parameters obtained from q3D-HDMI provides distinctive information that increases accuracy in differentiating breast tumors. Conclusions The proposed quantitative volumetric imaging technique augments conventional breast ultrasound evaluation by increasing specificity in differentiating malignant from benign breast masses

Correlating Tumor Stiffness with Immunohistochemical Subtypes of Breast Cancers: Prognostic Value of Comb-Push Ultrasound Shear Elastography for Differentiating Luminal Subtypes.

PURPOSE:The purpose of our study is to correlate quantitatively measured tumor stiffness with immunohistochemical (IHC) subtypes of breast cancer. Additionally, the influence of prognostic histologic features (cancer grade, size, lymph node status, and histological type and grade) to the tumor elasticity and IHC profile relationship will be investigated. METHODS:Under an institutional review board (IRB) approved protocol, B-mode ultrasound (US) and comb-push ultrasound shear elastography (CUSE) were performed on 157 female patients with suspicious breast lesions. Out of 157 patients 83 breast cancer patients confirmed by pathology were included in this study. The association between CUSE mean stiffness values and the aforementioned prognostic features of the breast cancer tumors were investigated. RESULTS:Our results demonstrate that the most statistically significant difference (p = 0.0074) with mean elasticity is tumor size. When considering large tumors (size ≥ 8mm), thus minimizing the statistical significance of tumor size, a significant difference (p 20%) subtypes. CONCLUSION:Tumor size is an independent factor influencing mean elasticity. The Ki-67 proliferation index and histological grade were dependent factors influencing mean elasticity for the differentiation between luminal subtypes. Future studies on a larger group of patients may broaden the clinical significance of these findings

Granulomatous diseases of the breast and axilla: radiological findings with pathological correlation

Abstract Objectives This article reviews our experience and describes the literature findings of granulomatous diseases of the breast and axilla. Methods After approval of the Institutional Review Board was obtained, the surgical pathological records from January 2000 to January 2017 were searched for the keyword granulomatous. Clinical, imaging and histology findings were reviewed by both a fellowship-trained radiologist and a breast-imaging consultant radiologist, reviewing 127 patients (age range, 32–86 years; 126 women and 1 man). Results Most common causes of granulomatous lesions of the breast and axilla included silicone granulomas 33% (n = 42), fat necrosis 29% (n = 37) and suture granulomas 11% (n = 14). In 16% (n = 20), no cause could be found and clinical history was consistent with idiopathic granulomatous mastitis. Other granulomatous aetiologies included granulomatous infections, sarcoidosis and Sjögren’s syndrome. Causes of axillary granulomatous disease were similar to the breast; however, a case of cat-scratch disease was found that only involved the axillary lymph nodes. They can have a variable appearance on imaging and may mimic malignancy with irregular masses seen on mammography, ultrasound and magnetic resonance imaging. Fistulas to the skin and nipple retraction can suggest chronicity and a granulomatous aetiology. Combination of clinical history, laboratory and imaging findings can be diagnostic. Conclusions Granulomatous processes of the breast are rare. The diagnosis can, however, be made if there is relevant history (prior trauma, silicone breast implants, lactation), laboratory (systemic or infectious processes) and imaging findings (fistula, nipple retraction). Recognising these entities is important for establishing pathological concordance after biopsy and for preventing unnecessary treatment. Teaching points Breast granulomatous are rare but can mimic breast carcinoma on imaging Imaging with clinical and laboratory findings can correctly diagnosis specific granulomatous breast diseases Recognition of the imaging findings allows appropriate pathological concordance and treatmen

Comb-push ultrasound shear elastography of breast masses: initial results show promise.

To evaluate the performance of Comb-push Ultrasound Shear Elastography (CUSE) for classification of breast masses.CUSE is an ultrasound-based quantitative two-dimensional shear wave elasticity imaging technique, which utilizes multiple laterally distributed acoustic radiation force (ARF) beams to simultaneously excite the tissue and induce shear waves. Female patients who were categorized as having suspicious breast masses underwent CUSE evaluations prior to biopsy. An elasticity estimate within the breast mass was obtained from the CUSE shear wave speed map. Elasticity estimates of various types of benign and malignant masses were compared with biopsy results.Fifty-four female patients with suspicious breast masses from our ongoing study are presented. Our cohort included 31 malignant and 23 benign breast masses. Our results indicate that the mean shear wave speed was significantly higher in malignant masses (6 ± 1.58 m/s) in comparison to benign masses (3.65 ± 1.36 m/s). Therefore, the stiffness of the mass quantified by the Young's modulus is significantly higher in malignant masses. According to the receiver operating characteristic curve (ROC), the optimal cut-off value of 83 kPa yields 87.10% sensitivity, 82.61% specificity, and 0.88 for the area under the curve (AUC).CUSE has the potential for clinical utility as a quantitative diagnostic imaging tool adjunct to B-mode ultrasound for differentiation of malignant and benign breast masses