bims-ectoca 2022-03-20 papers

Issue of 2022‒03‒20
seven papers selected by
Ankita Daiya, Birla Institute of Technology and Science

Oncotarget. 2022 ;13 521-533

Correlation of nuclear pIGF-1R/IGF-1R and YAP/TAZ in a tissue microarray with outcomes in osteosarcoma patients.

Eric R Molina, Letitia K Chim, Salah-Eddine Lamhamedi-Cherradi, Sana Mohiuddin, David McCall, Branko Cuglievan, Sandhya Krishnan, Robert W Porter, Davis R Ingram, Wei-Lien Wang, Alexander J Lazar, David W Scott, Danh D Truong, Najat C Daw, Joseph A Ludwig, Antonios G Mikos.

Osteosarcoma (OS) is a genetically diverse bone cancer that lacks a consistent targetable mutation. Recent studies suggest the IGF/PI3K/mTOR pathway and YAP/TAZ paralogs regulate cell fate and proliferation in response to biomechanical cues within the tumor microenvironment. How this occurs and their implication upon osteosarcoma survival, remains poorly understood. Here, we show that IGF-1R can translocate into the nucleus, where it may act as part of a transcription factor complex. To explore the relationship between YAP/TAZ and total and nuclear phosphorylated IGF-1R (pIGF-1R), we evaluated sequential tumor sections from a 37-patient tissue microarray by confocal microscopy. Next, we examined the relationship between stained markers, clinical disease characteristics, and patient outcomes. The nuclear to cytoplasmic ratios (N:C ratio) of YAP and TAZ strongly correlated with nuclear pIGF-1R (r = 0.522, p = 0.001 for each pair). Kaplan-Meier analyses indicated that nuclear pIGF-1R predicted poor overall survival, a finding confirmed in the Cox proportional hazards model. Though additional investigation in a larger prospective study will be required to validate the prognostic accuracy of these markers, our results may have broad implications for the new class of YAP, TAZ, AXL, or TEAD inhibitors that have reached early phase clinical trials this year.

Keywords: IGF-1R; YAP/TAZ; mechanotransduction; nuclear IGF-1R; osteosarcoma

DOI: https://doi.org/10.18632/oncotarget.28215

FEBS J. 2022 Mar 18.

Histone deacetylase 7: a signalling hub controlling development, inflammation, metabolism and disease.

Yizhuo Wang, Rishika Abrol, Jeffrey Y W Mak, Kaustav Das Gupta, Divya Ramnath, Denuja Karunakaran, David P Fairlie, Matthew J Sweet.

Histone deacetylases (HDACs) catalyse removal of acetyl groups from lysine residues on both histone and non-histone proteins to control numerous cellular processes. Of the 11 zinc-dependent classical HDACs, HDAC4, 5, 7 and 9 are class IIa HDAC enzymes that regulate cellular and developmental processes through both enzymatic and non-enzymatic mechanisms. Over the last two decades, HDAC7 has been associated with key roles in numerous physiological and pathological processes. Molecular, cellular, in vivo and disease association studies have revealed that HDAC7 acts through multiple mechanisms to control biological processes in immune cells, osteoclasts, muscle, the endothelium and epithelium. This HDAC protein regulates gene expression, cell proliferation, cell differentiation and cell survival, and consequently controls development, angiogenesis, immune functions, inflammation and metabolism. This review focuses on the cell biology of HDAC7, including the regulation of its cellular localisation and molecular mechanisms of action, as well as its associative and causal links with cancer and inflammatory, metabolic and fibrotic diseases. We also review the development status of small molecule inhibitors targeting HDAC7 and their potential for intervention in different disease contexts.

Keywords: HDAC7; class IIa HDAC; gene regulation; immunometabolism; macrophage

DOI: https://doi.org/10.1111/febs.16437

Trends Genet. 2022 Mar 15. pii: S0168-9525(22)00038-5. [Epub ahead of print]

Chaperoning heterochromatin: new roles of FACT in chromatin silencing.

Magdalena Murawska, Sigurd Braun.

The multitasking histone chaperone FACT (FAcilitates Chromatin Transcription) contributes to actively transcribed euchromatin and repressed heterochromatin. However, its precise role in gene silencing has remained obscure. Here, we discuss new insights into the silent chromatin functions and recruitment mechanisms of FACT, and their possible implications in cell identity and cancer.

Keywords: FACT; H3K9 methylation; heterochromatin spreading; histone turnover

DOI: https://doi.org/10.1016/j.tig.2022.02.011

Comput Biol Chem. 2022 Feb 25. pii: S1476-9271(22)00028-7. [Epub ahead of print]98 107648

Discovering inhibitors of TEAD palmitate binding pocket through virtual screening and molecular dynamics simulation.

Yimin Li, Yaqi Li, Chao Ning, Jianda Yue, Cheng Zhang, Xiao He, Ying Wang, Zhonghua Liu.

Transcriptional enhanced associate domain (TEAD) proteins bind to YAP/TAZ and mediate YAP/TAZ-induced gene expression. TEADs are not only the key transcription factors and final effector of the Hippo signaling pathway, but also the proteins that regulate cell proliferation and apoptosis. Disorders of Hippo signaling pathway occur in liver cancer, breast cancer, colon cancer and other cancers. S-palmitylation can stabilize the structure of TEADs and is also a necessary condition for the binding of TEADs to YAP/TAZ. The absence of TEAD palmitoylation prevents TEADs from binding to chromatin, thereby inhibiting the transcription and expression of downstream target genes in the Hippo pathway through a dominant-negative mechanism. Therefore, disrupting the S-palmitylation of TEADs has become an attractive and very feasible method in cancer treatment. The palmitate binding pockets of TEADs are conservative, and the crystal structures of TEAD2-palmitoylation inhibitor complexes and the potential TEAD2 inhibitors are more than other TEADs, TEAD2 can be selected to be the target receptor. In this study, structure-based and ligand-based virtual screening, molecular dynamics simulations, Molecular Mechanics Poisson-Boltzmann Surface Area (MM/PBSA) calculations, residue decomposition binding energy calculations, and ADME predictions have been performed to discover 11 potential TEAD2 S-palmitylation inhibitors. ChEBML196567 and ZINC000013942794 are the most recommended, because they formed strong binding energies and stable hydrogen bonds with TEAD2 and have good drugbility and high human oral absorption. We found that it was easier to find the targeting small molecules using a combination of structure-based and ligand-based virtual screening methods. Besides, a new core structure has been found in the selected small molecules. In addition, we analyzed the binding modes of these small molecules to TEAD2, and confirmed the hot spot residues Cys380, Ser345, Tyr426, Phe428, Ile408, and Met379. AVAILABILITY OF DATA AND MATERIAL: Supplementary materials are available online.

Keywords: Hippo pathway; Molecular docking; Molecular dynamics simulation; Palmitoylation inhibitor; TEAD

DOI: https://doi.org/10.1016/j.compbiolchem.2022.107648

ACS Chem Biol. 2022 Mar 17.

Dynamic Opposition of Histone Modifications.

Ana María Garzón-Porras, Emma Chory, Berkley E Gryder.

Gene transcription does not only require writers of active histone modifications; on-site opposition by erasers is essential for many genes. Here, we propose the concept of dynamic opposition of histone modifications to explain this conundrum. We highlight the requirement of HDACs for acetylation balance at superenhancers, and the requirement of KDM5A for H4K3me3 recycling at highly active gene promoters. We propose that histone post-translational modifications regulate charge balance for biomolecular condensate formation and nucleosome turnover and form a short-term memory that informs lock-and-step checkpoints for chromatin engagement by RNA polymerase II.

DOI: https://doi.org/10.1021/acschembio.1c01000

BMC Genomics. 2022 Mar 17. 23(1): 214

Extensive evaluation of ATAC-seq protocols for native or formaldehyde-fixed nuclei.

Hao Zhang, Michael E Rice, Joseph W Alvin, Dominique Farrera-Gaffney, James J Galligan, Michael D L Johnson, Darren A Cusanovich.

BACKGROUND: The "Assay for Transposase Accessible Chromatin sequencing" (ATAC-seq) is an efficient and easy to implement protocol to measure chromatin accessibility that has been widely used in multiple applications studying gene regulation. While several modifications or variants of the protocol have been published since it was first described, there has not yet been an extensive evaluation of the effects of specific protocol choices head-to-head in a consistent experimental setting. In this study, we tested multiple protocol options for major ATAC-seq components (including three reaction buffers, two reaction temperatures, two enzyme sources, and the use of either native or fixed nuclei) in a well-characterized cell line. With all possible combinations of components, we created 24 experimental conditions with four replicates for each (a total of 96 samples). In addition, we tested the 12 native conditions in a primary sample type (mouse lung tissue) with two different input amounts. Through these extensive comparisons, we were able to observe the effect of different ATAC-seq conditions on data quality and to examine the utility and potential redundancy of various quality metrics.RESULTS: In general, native samples yielded more peaks (particularly at loci not overlapping transcription start sites) than fixed samples, and the temperature at which the enzymatic reaction was carried out had a major impact on data quality metrics for both fixed and native nuclei. However, the effect of various conditions tested was not always consistent between the native and fixed samples. For example, the Nextera and Omni buffers were largely interchangeable across all other conditions, while the THS buffer resulted in markedly different profiles in native samples. In-house and commercial enzymes performed similarly.
CONCLUSIONS: We found that the relationship between commonly used measures of library quality differed across temperature and fixation, and so evaluating multiple metrics in assessing the quality of a sample is recommended. Notably, we also found that these choices can bias the functional class of elements profiled and so we recommend evaluating several formulations in any new experiments. Finally, we hope the ATAC-seq workflow formulated in this study on crosslinked samples will help to profile archival clinical specimens.

Keywords: ATAC-seq; Chromatin accessibility; Quality control; Tn5; Transcription factor

DOI: https://doi.org/10.1186/s12864-021-08266-x

Nucleus. 2022 Dec;13(1): 129-143

Gaussian curvature dilutes the nuclear lamina, favoring nuclear rupture, especially at high strain rate.

Charlotte R Pfeifer, Michael P Tobin, Sangkyun Cho, Manasvita Vashisth, Lawrence J Dooling, Lizeth Lopez Vazquez, Emma G Ricci-De Lucca, Keiann T Simon, Dennis E Discher.

Nuclear rupture has long been associated with deficits or defects in lamins, with recent results also indicating a role for actomyosin stress, but key physical determinants of rupture remain unclear. Here, lamin-B filaments stably interact with the nuclear membrane at sites of low Gaussian curvature yet dilute at high curvature to favor rupture, whereas lamin-A depletion requires high strain-rates. Live-cell imaging of lamin-B1 gene-edited cancer cells is complemented by fixed-cell imaging of rupture in: iPS-derived progeria patients cells, cells within beating chick embryo hearts, and cancer cells with multi-site rupture after migration through small pores. Data fit a model of stiff filaments that detach from a curved surface.Rupture is modestly suppressed by inhibiting myosin-II and by hypotonic stress, which slow the strain-rates. Lamin-A dilution and rupture probability indeed increase above a threshold rate of nuclear pulling. Curvature-sensing mechanisms of proteins at plasma membranes, including Piezo1, might thus apply at nuclear membranes.Summary statement: High nuclear curvature drives lamina dilution and nuclear envelope rupture even when myosin stress is inhibited. Stiff filaments generally dilute from sites of high Gaussian curvature, providing mathematical fits of experiments.

Keywords: biophysical model; curvature; mechanobiology; myosin stress; nuclear envelope rupture; nuclear lamina

DOI: https://doi.org/10.1080/19491034.2022.2045726