Remodeling Proteins Research Articles

MiR-145 from Bone Marrow Mesenchymal Stem Cells (BMSC) Improves Cardiac Function After Myocardial Infarction in Rat with Diabetes

This study assesses the role of miR-145 from BMSC in the cardiac function after MI in rat with diabetes. Rat with T1DM model was established and then were treated with PBS, DM-BMSC with overexpression of miR-145, BMSC with the knockdown of miR-145 respectively after twenty-four hours followed by analysis of the remodeling of vessels and protein, mRNA expressions. miR-145 in DM-BMSC was significantly reduced compared with control group and DM-BMSC prolonged the survival rate of rats. The formation of blood capillary and axon growth in DM-BMSC was increased and decreased in BMSC with knockdown of miR-145. The therapeutic action of DM-BMSC could be improved notably and remodeling of vessels and protein was increased. Smad1 was a target gene of miR-145. In conclusion, cardiac function and neurological recovery in MI is improved by miR-145 through targeting Smad1 expression, indicating that miR-145 might be a novel target for the treatment of MI.

Abstract B010: Determining the role of BRD9 in human hematopoietic stem cell aging

Abstract Aging is the number one non-modifiable risk factor for cancer, including myeloid malignancies, such as Acute Myeloid leukemia (AML). Intrinsic changes within hematopoietic stem cells (HSC) with aging contribute to HSC dysfunction and may predispose to leukemia. We have previously shown that aged human HSC present a reduction of H3K27ac at active promoters and enhancers of genes associated with immune and cancer pathways. Concurrent with this epigenetic deregulation there is deregulation of immune-associated genes and downregulation of the bromodomain containing protein-9 (BRD9). This protein is a component of the non-canonical BAF (nc-BAF) chromatin remodeling complex, which binds to both active enhancers and promoters. Notably alteration of BRD9 has been shown to perturb immune and cancer associated pathways, with BRD9 regulating interferon-stimulated genes. However, little is known about the role of this protein in human hematopoiesis. Therefore, we hypothesize that chromatin remodeling due to loss of BRD9 with HSC aging leads to reduction of H3K27ac at active enhancers and promoters, contributing to HSC dysfunction. To investigate this, we treated human CD34+ hematopoietic stem and progenitor cells (HSPC) with dBRD9-A (100 nM) a chemical degrader of BRD9. Loss of BRD9 resulted in enhanced myeloid differentiation in vitro with a concurrent block in erythroid differentiation. Interestingly, amongst the myeloid populations upregulated with loss of BRD9 were monocytic myeloid derived suppressor cells (M-MDSC), immunosuppressive cells that are involved both in cancer pathogenesis and aging. Treatment with the BRD9 bromodomain specific inhibitor, I-BRD9 (1 µM), suggests that while the role of BRD9 in myeloid differentiation is largely bromodomain independent, the bromodomain may regulate erythroid differentiation. Similarly, loss of BRD9 leads to more myeloid biased colonies, suggesting that loss of BRD9 may recapitulate certain features of aged HSC. At the transcriptional level, RNA-seq revealed that loss of BRD9 resulted in few, but important differentially expressed genes, including downregulation of MPO, LIF, EPX, and GZMB (FDR < 0.05). However, gene set enrichment analysis showed that both bromodomain inhibition and loss of BRD9 resulted in downregulation of interferon and STAT3 associated genes, which are known BRD9 targets. Chromatin profiling of H3K27ac with CUT&RUN in young HSPC showed that with loss of BRD9, there is a reduction of H3K27ac at active enhancers that we had previously observed have loss of H3K27ac with human HSC aging (n=2). These active enhancers are associated with immune signaling and regulate hematopoietic transcription factors such as KLF6, RUNX1/2/3, and HIF1A. In conclusion, we have found that the chromatin remodeling protein BRD9 contributes to the reprogramming of age-associated enhancers and regulates human myeloid and erythroid differentiation in vitro, and that its loss may result in an expansion of M-MDSC, which has implications for age-related disorders such as immune dysfunction and cancer. Citation Format: Emmalee R. Adelman, Maria E. Figueroa. Determining the role of BRD9 in human hematopoietic stem cell aging. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr B010.

Multi-omics profiling visualizes dynamics of cardiac development and functions

Cardiogenesis is a tightly regulated dynamic process through a continuum of differentiation and proliferation events. Key factors and pathways governing this process remain incompletely understood. Here, we investigate mice hearts from embryonic day 10.5 to postnatal week 8 and dissect developmental changes in phosphoproteome-, proteome-, metabolome-, and transcriptome-encompassing cardiogenesis and cardiac maturation. We identify mitogen-activated protein kinases as core kinases involved in transcriptional regulation by mediating the phosphorylation of chromatin remodeling proteins during early cardiogenesis. We construct the reciprocal regulatory network of transcription factors (TFs) and identify a series of TFs controlling early cardiogenesis involved in cycling-dependent proliferation. After birth, we identify cardiac resident macrophages with high arachidonic acid metabolism activities likely involved in the clearance of injured apoptotic cardiomyocytes. Together, our comprehensive multi-omics data offer a panoramic view of cardiac development and maturation that provides a resource for further in-depth functional exploration.

CHD4 plays a critical role in arsenite-induced oxidative damage in human urothelial carcinoma.

Inorganic arsenic (iAs), a known human carcinogen, induces oxidative DNA damage and epigenetic silencing of tumor suppressor genes related to tumor progression. Chromodomain-helicase-DNA-binding protein 4 (CHD4) is a chromatin remodeling protein that acts on DNA repair and DNA methylation under oxidative damage in malignancies, but the role of CHD4 in arsenical urothelial carcinoma (UC) is unidentified. Our purpose was to observe CHD4-related repair effects on As-stimulated oxidative damage in human UC. The markers of oxidative DNA damage 8-hydroxy-2'-deoxyguanosine (8-OHdG) and CHD4 were investigated by immunohistochemistry in 45 UC tissues from non-blackfoot disease (BFD) areas and BFD areas respectively. The cellular mechanisms of CHD4 involved in the oxidative DNA repair and DNA methylation were evaluated by immunocytochemistry and western blot. The expressions of CHD4 and 8-OHdG were significantly increased in UC patients from the As-exposed areas. The underlying mechanism of CHD4-mediated DNA repair and DNA methylation involved the activation of zinc finger MYND-type containing 8 (ZMYND8) and DNA methyltransferase (DNMTs) in SV-HUC-1, T24 and BFTC-905 cells. These results highlight the potential clinical significance of CHD4 in UCs from BFD areas. The CHD4-mediated oxidative DNA repair and epigenetic DNA methylation in UC cells stimulated by arsenic was revealed. CHD4 might be used as a prognostic indicator in arsenical UC.

Dual Role of ACBD6 in the Acylation Remodeling of Lipids and Proteins.

The transfer of acyl chains to proteins and lipids from acyl-CoA donor molecules is achieved by the actions of diverse enzymes and proteins, including the acyl-CoA binding domain-containing protein ACBD6. N-myristoyl-transferase (NMT) enzymes catalyze the covalent attachment of a 14-carbon acyl chain from the relatively rare myristoyl-CoA to the N-terminal glycine residue of myr-proteins. The interaction of the ankyrin-repeat domain of ACBD6 with NMT produces an active enzymatic complex for the use of myristoyl-CoA protected from competitive inhibition by acyl donor competitors. The absence of the ACBD6/NMT complex in ACBD6.KO cells increased the sensitivity of the cells to competitors and significantly reduced myristoylation of proteins. Protein palmitoylation was not altered in those cells. The specific defect in myristoyl-transferase activity of the ACBD6.KO cells provided further evidence of the essential functional role of the interaction of ACBD6 with the NMT enzymes. Acyl-CoAs bound to the acyl-CoA binding domain of ACBD6 are acyl donors for the lysophospholipid acyl-transferase enzymes (LPLAT), which acylate single acyl-chain lipids, such as the bioactive molecules LPA and LPC. Whereas the formation of acyl-CoAs was not altered in ACBD6.KO cells, lipid acylation processes were significantly reduced. The defect in PC formation from LPC by the LPCAT enzymes resulted in reduced lipid droplets content. The diversity of the processes affected by ACBD6 highlight its dual function as a carrier and a regulator of acyl-CoA dependent reactions. The unique role of ACBD6 represents an essential common feature of (acyl-CoA)-dependent modification pathways controlling the lipid and protein composition of human cell membranes.

Abstract C075: The loss of ATRX induces a sex-specific progression of pancreatic ductal adenocarcinoma in the presence of oncogenic KRASG12D

Abstract Introduction: Pancreatic ductal adenocarcinoma (PDAC) is currently the third leading cause of cancer-related deaths primarily due to a lack of effective early screening and the tumor microenvironment increasing resistance to chemotherapy. Somatic mutation in oncogenic KRASG12D appears in 97% of PDAC patients, however, the addition of environmental and epigenetic stressors are required to promote PDAC initiation and progression from acinar cells. We are elucidating the mechanism by which a loss of α-thalassemia, mental-retardation, X-linked (ATRX), a SWI/SNF chromatin remodeling protein, potentiates acinar cells to develop neoplastic lesions in females. Young et al. have confirmed that female mice with a loss of Atrx, combined with KRASG12D, have shown increased acinar-to-duct cell metaplasia (ADM), increased fibrosis, inflammation, and pancreatic intraepithelial neoplasias (PanINs) lesions relative to mice expressing KRASG12D and Atrx. I hypothesize that a loss of ATRX function increases sensitivity to KRASG12D in PDAC by affecting DNA damage and repair pathways and altering gene expression in acinar cells in a sex-specific fashion. Methods: Mice with an acinar-specific Atrx deletion and oncogenic KRASG12D expression were generated by mating to mice targeting an inducible creERT to the Ptf11α gene (PtflacreERT). Mice were gavaged with tamoxifen and pancreatic injury was induced in these mice (Ptf11αcreERT KRASLSLG12DAtrxfl/fl) with cerulein 10 days later. Mice are monitored for two and five weeks following cerulein treatment and pancreatic tissue was collected for molecular, biochemical, and histological analysis. In addition, pre-neoplastic pancreatic organoid cultures +/- ATRX expression were generated to assess differences in growth rates and chemotherapy resistance. Results: Preliminary results have shown increased sensitivity to chronic pancreatitis is predicted to be observed specifically in KRASG12D Atrx-/- female pancreatic tissue and derived organoids. Conversely, a protective effect stimulated by a loss of ATRX is observed in KRASG12D Atrx-/- male mice, indicated by less ADM/PanIN lesions and greater acinar cells. Discussion: A healthier prognosis in Atrx-/-, KRAS activated male mice suggests that the interaction between ATRX and various scaffold proteins (PRC2, DAXX, EZH2, etc.) alters chromosomal architecture, possibly altering gene expression via X chromosome inactivation or reactivation. Sex-specific differences in pancreatic tissue phenotype of Atrx-/- mice are predicted to arise from differential effects of ATRX in triggering acinar cell genomic instability in female mice to prevent the resolution of dsDNA breaks via non-homologous end joining to sensitize acinar cells to oncogenic KRAS. Future experiments will focus on establishing pre-neoplastic organoid lines derived from inflamed murine pancreata to elucidate the signalling pathway of ATRX that likely stimulates a differential gene and protein expression involved in a better prognosis in KRASG12D activated, Atrx-/- male mice. Citation Format: Aswin Sureshkumar, Phyo Win, Christopher Pin. The loss of ATRX induces a sex-specific progression of pancreatic ductal adenocarcinoma in the presence of oncogenic KRASG12D [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr C075.

TMIC-81. INCREASED LEVEL OF IGFBP2 PROMOTES TUMOR METASTASIS IN SHH MEDULLOBLASTOMA

Abstract Medulloblastoma (MB) is the most common pediatric brain malignancy. MB comprises 5 major subgroups known as WNT, SHH p53wt, SHH p53mut, Group 3 and Group 4. Among the four MB subgroups SHH group is the most dominant molecular subgroup in infants and adults. These tumors are proposed to arise from cerebellar granule neuron precursors (CGNPs), whose developmental expansion requires SHH signaling from the neighboring Purkinje neurons. Previous reports suggest that SHH group features a unique tumor microenvironment compared with other MB groups. To better understand how SHH MB cells interact with Tumor Microenvironment, we performed cytokine array analysis of culture media from SHH group Patient Tumor cells, spontaneous SHH MB mouse tumor cells and SHH MB cell lines. Further, confirmed these results using ELISA, Western blot, and immunofluorescence from human SHH MB cell lines, Smo/A1 mouse tumor primary cells and PZp53Med cell lines. In continuation to the observation of IGFBP2 expression in various cell types in single cell analysis, we analyzed the presence of IGFBP2 in astrocytes using Smo/A1 mouse tumor Immunohistochemistry. Our data showed increased levels of IGFBP2 produced by SHH MB cell lines compared to others. We analyzed the role of IGFBP2 in SHH MB tumor growth and metastasis. IGFBP2 knock-down stable cell lines showed phenotypic changes including reduced cell proliferation, cell migration and EMT. Further western blot analysis of IGFBP2 KD cells showed reduced expression of EMT markers also reduced the activation of STAT3. Our preliminary in vitro data suggest IGFBP2 exerts it metastasis-promoting role in SHH MB by regulating the expression of EMT marker proteins and matrix remodeling proteins. Further functional studies suggest that in SHH MB, IGFBP2 may regulate a STAT3-mediated EMT program to metastasize. These findings provide a strong rationale for further pursuing how IGFBP2 promotes medulloblastoma tumor cell growth and migration in vivo.

Abstract 10655: Collagen Remodeling, Inflammatory Biomarkers and Fatty Acid Regulation in Understanding the Molecular Pathogenesis of Atrial Fibrillation

Introduction: Atrial Fibrillation (AF) is the most common cardiac arrythmia in the world. Structural remodeling, inflammatory pathways and fatty acid dysregulation are believed to play a role in the development of AF. Hypothesis: This study explored different biomarkers in the blood of AF patients and a control population to determine if there was a significant difference between the two groups. Methods: Sandwich ELISA kits were used to quantify the collagen remodeling proteins, various inflammatory biomarkers and liver type fatty acid binding protein (L-FABP) in the clinically diagnosed AF population (n=78) and the control population (n=50). Non-stratified fatty acids (NEFAs) were measured using an enzymatic colorimetric kit from Wako Diagnostics. Statistical analyses were performed using GraphPad Prism. Results: We found significant upregulation in all the biomarkers in the AF cohort was noted in comparison to the control group. The collagen remodeling biomarkers included MMP-1, MMP-2, TIMP-1, TIMP-2, PICP, PINP, PIIICP, PIIINP and ICTP. All the collagen remodeling biomarkers were significantly higher in AF patients compared to the control group. The inflammatory biomarker TNFa was also elevated in AF compared to the control group. The fatty acid dysregulation biomarkers, L-FABP and NEFAs, were elevated in AF patients as well. Spearman correlation analyses yielded significant correlations between L-FABP and TIMP-1 (r=0.47, p<0.001), NEFA and TIMP-2 (r=0.41, p=0.002), NEFA and ICTP (r=0.41, p=0.002), and NEFA and PIIINP (r=0.61, p<0.0001). Conclusions: The elevation of all the collagen remodeling biomarkers indicates that there is an upregulation of collagen degradation and deposition in AF which could be contributing to atrial fibrosis. The higher TNFa levels indicate that inflammation could also play a role in the pathogenesis of AF. Fatty acid dysregulation biomarkers, including L-FABP and NEFAs, were elevated in AF patients reinforcing the hypothesis that excess fatty acids could also be contributing to atrial fibrosis and epicardial adipose tissue formation.

AAA+ protease-adaptor structures reveal altered conformations and ring specialization

ClpAP, a two-ring AAA+ protease, degrades N-end-rule proteins bound by the ClpS adaptor. Here we present high-resolution cryo-EM structures of Escherichia coli ClpAPS complexes, showing how ClpA pore loops interact with the ClpS N-terminal extension (NTE), which is normally intrinsically disordered. In two classes, the NTE is bound by a spiral of pore-1 and pore-2 loops in a manner similar to substrate-polypeptide binding by many AAA+ unfoldases. Kinetic studies reveal that pore-2 loops of the ClpA D1 ring catalyze the protein remodeling required for substrate delivery by ClpS. In a third class, D2 pore-1 loops are rotated, tucked away from the channel and do not bind the NTE, demonstrating asymmetry in engagement by the D1 and D2 rings. These studies show additional structures and functions for key AAA+ elements. Pore-loop tucking may be used broadly by AAA+ unfoldases, for example, during enzyme pausing/unloading.

PLK-1 Interacting Checkpoint Helicase, PICH, Mediates Cellular Oxidative Stress Response.

Cells respond to oxidative stress by elevating the levels of antioxidants, signaling, and transcriptional regulation, often implemented by chromatin remodeling proteins. The study presented here shows that the expression of PICH, a Rad54-like helicase belonging to the ATP-dependent chromatin remodeling protein family, is upregulated during oxidative stress in HeLa cells. We also show that PICH regulates the expression of Nrf2, a transcription factor regulating antioxidant response in both the absence and presence of oxidative stress. The overexpression of PICH in PICH-depleted cells restored Nrf2 as well as antioxidant gene expression. In turn, Nrf2 regulated the expression of PICH in the presence of oxidative stress. ChIP experiments showed that PICH is present on the Nrf2 as well as antioxidant gene promoters, suggesting that the protein might be regulating the expression of these genes directly by binding to the DNA sequences. In addition, Nrf2 and histone acetylation (H3K27ac) also played a role in activating transcription in the presence of oxidative stress. Both Nrf2 and H3K27ac were found to be present on PICH and antioxidant promoters. Their occupancy was dependent on the PICH expression as fold enrichment was found to be decreased in PICH-depleted cells. PICH ablation led to the reduced expression of Nrf2 and impaired antioxidant response, leading to increased ROS content and thus showing PICH is essential for the cell to respond to oxidative stress.

Integrative transcriptome analysis reveals TEKT2 and PIAS2 involvement in diabetic nephropathy.

Cell heterogeneity has impeded the accurate interpretation of the bulk transcriptome data from patients with diabetic nephropathy (DN). We performed an analysis by integrating bulk and single-cell transcriptome datasets to uncover novel mechanisms leading to DN, especially in the podocytes. Microdissected glomeruli and tubules transcriptome datasets were selected from Gene Expression Omnibus (GEO). Then the consistency between datasets was evaluated. The analysis of the bulk dataset and single-nucleus RNA dataset was integrated to reveal the cell type-specific responses to DN. The candidate genes were validated in kidney tissues from DN patients and diabetic mice. We compared 4 glomerular and 4 tubular datasets and found considerable discrepancies among datasets regarding the deferentially expressed genes (DEGs), involved signaling pathways, and the hallmark enrichment profiles. Deconvolution of the bulk data revealed that the variations in cell-type proportion contributed greatly to this discrepancy. The integrative analysis uncovered that the dysregulation of spermatogenesis-related genes, including TEKT2 and PIAS2, was involved in the development of DN. Importantly, the mRNA level of TEKT2 was negatively correlated with the mRNA levels of NPHS1 (r= -.66, p <.0001) and NPHS2 (r= -.85, p <.0001) in human diabetic glomeruli. Immunostaining confirmed that the expression of TEKT2 and PIAS2 were up-regulated in podocytes of DN patients and diabetic mice. Knocking down TEKT2 resisted high glucose-induced cytoskeletal remodeling and down-regulation of NPHS1 protein in the cultured podocyte. In conclusion, the integrative strategy can help us efficiently use the publicly available transcriptomics resources. Using this approach and combining it with classical research methods, we identified TEKT2 and PIAS2, two spermatogenesis-related genes involved in the pathogenesis of DN. Furthermore, TEKT2 is involved in this pathogenesis by regulating the podocyte cytoskeleton.

Direct Identification of Proteolytic Cleavages on Living Cells Using a Glycan-Tethered Peptide Ligase.

Proteolytic cleavage of cell surface proteins triggers critical processes including cell–cell interactions, receptor activation, and shedding of signaling proteins. Consequently, dysregulated extracellular proteases contribute to malignant cell phenotypes including most cancers. To understand these effects, methods are needed that identify proteolyzed membrane proteins within diverse cellular contexts. Herein we report a proteomic approach, called cell surface N-terminomics, to broadly identify precise cleavage sites (neo-N-termini) on the surface of living cells. First, we functionalized the engineered peptide ligase, called stabiligase, with an N-terminal nucleophile that enables covalent attachment to naturally occurring glycans. Upon the addition of a biotinylated peptide ester, glycan-tethered stabiligase efficiently tags extracellular neo-N-termini for proteomic analysis. To demonstrate the versatility of this approach, we identified and characterized 1532 extracellular neo-N-termini across a panel of different cell types including primary immune cells. The vast majority of cleavages were not identified by previous proteomic studies. Lastly, we demonstrated that single oncogenes, KRAS(G12V) and HER2, induce extracellular proteolytic remodeling of proteins involved in cancerous cell growth, invasion, and migration. Cell surface N-terminomics is a generalizable platform that can reveal proteolyzed, neoepitopes to target using immunotherapies.

Novel molecular mechanisms in Alzheimer's disease: The potential role of DEK in disease pathogenesis.

Alzheimer’s disease and age-related dementias (AD/ADRD) are debilitating diseases that exact a significant physical, emotional, cognitive, and financial toll on the individual and their social network. While genetic risk factors for early-onset AD have been identified, the molecular and genetic drivers of late-onset AD, the most common subtype, remain a mystery. Current treatment options are limited for the 35 million people in the United States with AD/ADRD. Thus, it is critically important to identify novel molecular mechanisms of dementia-related pathology that may be targets for the development of new interventions. Here, we summarize the overarching concepts regarding AD/ADRD pathogenesis. Then, we highlight one potential molecular driver of AD/ADRD, the chromatin remodeling protein DEK. We discuss in vitro, in vivo, and ex vivo findings, from our group and others, that link DEK loss with the cellular, molecular, and behavioral signatures of AD/ADRD. These include associations between DEK loss and cellular and molecular hallmarks of AD/ADRD, including apoptosis, Tau expression, and Tau hyperphosphorylation. We also briefly discuss work that suggests sex-specific differences in the role of DEK in AD/ADRD pathogenesis. Finally, we discuss future directions for exploiting the DEK protein as a novel player and potential therapeutic target for the treatment of AD/ADRD.

Mechanisms of spontaneous Ca2+ release-mediated arrhythmia in a novel 3D human atrial myocyte model: II. Ca2+ -handling protein variation.

Disruption of the transverse-axial tubule system (TATS) in diseases such as heart failure and atrial fibrillation occurs in combination with changes in the expression and distribution of key Ca2+ -handling proteins. Together this ultrastructural and ionic remodelling is associated with aberrant Ca2+ cycling and electrophysiological instabilities that underlie arrhythmic activity. However, due to the concurrent changes in TATs and Ca2+ -handling protein expression and localization that occur in disease it is difficult to distinguish their individual contributions to the arrhythmogenic state. To investigate this, we applied our novel 3D human atrial myocyte model with spatially detailed Ca2+ diffusion and TATS to investigate the isolated and interactive effects of changes in expression and localization of key Ca2+ -handling proteins and variable TATS density on Ca2+ -handling abnormality driven membrane instabilities. We show that modulating the expression and distribution of the sodium-calcium exchanger, ryanodine receptors and the sarcoplasmic reticulum (SR) Ca2+ buffer calsequestrin have varying pro- and anti-arrhythmic effects depending on the balance of opposing influences on SR Ca2+ leak-load and Ca2+ -voltage relationships. Interestingly, the impact of protein remodelling on Ca2+ -driven proarrhythmic behaviour varied dramatically depending on TATS density, with intermediately tubulated cells being more severely affected compared to detubulated and densely tubulated myocytes. This work provides novel mechanistic insight into the distinct and interactive consequences of TATS and Ca2+ -handling protein remodelling that underlies dysfunctional Ca2+ cycling and electrophysiological instability in disease. KEY POINTS: In our companion paper we developed a 3D human atrial myocyte model, coupling electrophysiology and Ca2+ handling with subcellular spatial details governed by the transverse-axial tubule system (TATS). Here we utilize this model to mechanistically examine the impact of TATS loss and changes in the expression and distribution of key Ca2+ -handling proteins known to be remodelled in disease on Ca2+ homeostasis and electrophysiological stability. We demonstrate that varying the expression and localization of these proteins has variable pro- and anti-arrhythmic effects with outcomes displaying dependence on TATS density. Whereas detubulated myocytes typically appear unaffected and densely tubulated cells seem protected, the arrhythmogenic effects of Ca2+ handling protein remodelling are profound in intermediately tubulated cells. Our work shows the interaction between TATS and Ca2+ -handling protein remodelling that underlies the Ca2+ -driven proarrhythmic behaviour observed in atrial fibrillation and may help to predict the effects of antiarrhythmic strategies at varying stages of ultrastructural remodelling.

Inhibition of MORC2 Mediates HDAC4 to Promote Cellular Senescence through p53/p21 Signaling Axis.

(1) Background: Colorectal cancer (CRC) is a common gastrointestinal malignancy, accounting for the second largest gastrointestinal tumor. MORC2, a newly discovered chromatin remodeling protein, plays an important role in the biological processes of various cancers. However, the potential mechanistic role of MORC2 in promoting proliferation of CRC carcinoma remains unclear. (2) Methods: The Cancer Genome Atlas database was analyzed using bioinformatics to obtain gene expression and clinical prognosis data. The cell proliferation was assessed by CCK8 and EdU assays, as well as xenograft. SA-beta-gal staining, Western blot, and ELISA assay were using to assess the cell senescence and potential mechanism. (3) Results: Our data showed that MORC2 expression was elevated in CRC patients. Depletion of MORC2 inhibited cellular proliferation both in vivo and in vitro. Further studies showed that the depletion of MORC2 enhanced p21 and p53 expression through decreasing HDAC4 and increasing pro-inflammatory factors IL-6 and IL-8, thus, promoting cellular senescence. (4) Conclusions: We concluded that increased MORC2 expression in CRC might play a critical role in tumorigenesis by regulating the cellular senescence, in addition, MORC2 could be a novel biomarker for clinical outcomes and prognosis and a treatment target for CRC.

Regulation of human cortical interneuron development by the chromatin remodeling protein CHD2

Mutations in the chromodomain helicase DNA binding protein 2 (CHD2) gene are associated with neurodevelopmental disorders. However, mechanisms by which CHD2 regulates human brain development remain largely uncharacterized. Here, we used a human embryonic stem cell model of cortical interneuron (hcIN) development to elucidate its roles in this process. We identified genome-wide CHD2 binding profiles during hcIN differentiation, defining direct CHD2 targets related to neurogenesis in hcIN progenitors and to neuronal function in hcINs. CHD2 bound sites were frequently coenriched with histone H3 lysine 27 acetylation (H3K27ac) and associated with high gene expression, indicating roles for CHD2 in promoting gene expression during hcIN development. Binding sites for different classes of transcription factors were enriched at CHD2 bound regions during differentiation, suggesting transcription factors that may cooperatively regulate stage-specific gene expression with CHD2. We also demonstrated that CHD2 haploinsufficiency altered CHD2 and H3K27ac coenrichment on chromatin and expression of associated genes, decreasing acetylation and expression of cell cycle genes while increasing acetylation and expression of neuronal genes, to cause precocious differentiation. Together, these data describe CHD2 direct targets and mechanisms by which CHD2 prevents precocious hcIN differentiation, which are likely to be disrupted by pathogenic CHD2 mutation to cause neurodevelopmental disorders.

Collagen Molecular Damage is a Hallmark of Early Atherosclerosis Development.

Remodeling of extracellular matrix proteins underlies the development of cardiovascular disease. Herein, we utilized a novel molecular probe, collagen hybridizing peptide (CHP), to target collagen molecular damage during atherogenesis. The thoracic aorta was dissected from ApoE-/- mice that had been on a high-fat diet for 0-18weeks. Using an optimized protocol, tissues were stained with Cy3-CHP and digested to quantify CHP with a microplate assay. Results demonstrated collagen molecular damage, inferred from Cy3-CHP fluorescence, was a function of location and time on the high-fat diet. Tissue from the aortic arch showed a significant increase in collagen molecular damage after 18weeks, while no change was observed in tissue from the descending aorta. No spatial differences in fluorescence were observed between the superior and inferior arch tissue. Our results provide insight into the early changes in collagen during atherogenesis and present a new opportunity in the subclinical diagnosis of atherosclerosis.

Activity-Induced Cortical Glutamatergic Neuron Nascent Proteins.

Neuronal activity initiates signaling cascades that culminate in diverse outcomes including structural and functional neuronal plasticity, and metabolic changes. While studies have revealed activity-dependent neuronal cell type-specific transcriptional changes, unbiased quantitative analysis of cell-specific activity-induced dynamics in newly synthesized proteins (NSPs) synthesis in vivo has been complicated by cellular heterogeneity and a relatively low abundance of NSPs within the proteome in the brain. Here we combined targeted expression of mutant MetRS (methionine tRNA synthetase) in genetically defined cortical glutamatergic neurons with tight temporal control of treatment with the noncanonical amino acid, azidonorleucine, to biotinylate NSPs within a short period after pharmacologically induced seizure in male and female mice. By purifying peptides tagged with heavy or light biotin-alkynes and using direct tandem mass spectrometry detection of biotinylated peptides, we quantified activity-induced changes in cortical glutamatergic neuron NSPs. Seizure triggered significant changes in ∼300 NSPs, 33% of which were decreased by seizure. Proteins mediating excitatory and inhibitory synaptic plasticity, including SynGAP1, Pak3, GEPH1, Copine-6, and collybistin, and DNA and chromatin remodeling proteins, including Rad21, Smarca2, and Ddb1, are differentially synthesized in response to activity. Proteins likely to play homeostatic roles in response to activity, such as regulators of proteastasis, intracellular ion control, and cytoskeleton remodeling proteins, are activity induced. Conversely, seizure decreased newly synthetized NCAM, among others, suggesting that seizure induced degradation. Overall, we identified quantitative changes in the activity-induced nascent proteome from genetically defined cortical glutamatergic neurons as a strategy to discover downstream mediators of neuronal plasticity and generate hypotheses regarding their function.SIGNIFICANCE STATEMENT Activity-induced neuronal and synaptic plasticity are mediated by changes in the protein landscape, including changes in the activity-induced newly synthesized proteins; however, identifying neuronal cell type-specific nascent proteome dynamics in the intact brain has been technically challenging. We conducted an unbiased proteomic screen from which we identified significant activity-induced changes in ∼300 newly synthesized proteins in genetically defined cortical glutamatergic neurons within 20 h after pharmacologically induced seizure. Bioinformatic analysis of the dynamic nascent proteome indicates that the newly synthesized proteins play diverse roles in excitatory and inhibitory synaptic plasticity, chromatin remodeling, homeostatic mechanisms, and proteasomal and metabolic functions, extending our understanding of the diversity of plasticity mechanisms.

Identification and characterization of a novel homozygous splice site variant of PATL2 causing female infertility due to oocyte germinal vesicle arrest.

Background: This study aims to describe clinical and diagnostic phenotype and identify pathogenic variants of a female with unknown causes of infertility. Methods: Clinical assessment was performed for the phenotype diagnosis. Whole-exome sequencing (WES) and the followed cDNA-PCR sequencing were applied to identify the pathogenic variant and investigate the potentially aberrant mRNA splicing event. The pathogenicity of the variant was analysed using multiple in silico prediction tools, including the 3D protein remodelling. Quantitative RT-PCR (qRT-PCR) was performed to measure PATL2 mRNA expression in the peripheral blood leukocytes of the proband and controls. Results: The proband was diagnosed with the female infertility due to oocyte germinal vesicle (GV) arrest. A novel homozygous splice site variant of PATL2 (NM_001145112.2, c.871-1G>A), inherited from her asymptomatic heterozygous parents, was detected by WES. Sequencing of cDNA amplification products demonstrated that this variant resulted in the exon 10 skipping and in-frame loss of 54 nucleotides in the PATL2 transcript. Quantitative RT-PCR suggested that the mutant transcript escape the mRNA degradation. Conclusion: We identified a novel pathogenic homozygous splice site of PATL2 (c.871-1G>A) underlying the oocyte GV arrest phenotype and elucidated its molecular mechanism. This study expands the variant spectrum of PATL2 and benefits our understanding of its genotype-phenotype correlations.

Human repair-related Schwann cells adopt functions of antigen-presenting cells in vitro.

The plastic potential of Schwann cells (SCs) is increasingly recognized to play a role after nerve injury and in diseases of the peripheral nervous system. Reports on the interaction between immune cells and SCs indicate their involvement in inflammatory processes. However, the immunocompetence of human SCs has been primarily deduced from neuropathies, but whether after nerve injury SCs directly regulate an adaptive immune response is unknown. Here, we performed comprehensive analysis of immunomodulatory capacities of human repair-related SCs (hrSCs), which recapitulate SC response to nerve injury in vitro. We used our well-established culture model of primary hrSCs from human peripheral nerves and analyzed the transcriptome, secretome, and cell surface proteins for pathways and markers relevant in innate and adaptive immunity, performed phagocytosis assays, and monitored T-cell subset activation in allogeneic co-cultures. Our findings show that hrSCs are phagocytic, which is in line with high MHCII expression. Furthermore, hrSCs express co-regulatory proteins, such as CD40, CD80, B7H3, CD58, CD86, and HVEM, release a plethora of chemoattractants, matrix remodeling proteins and pro- as well as anti-inflammatory cytokines, and upregulate the T-cell inhibiting PD-L1 molecule upon pro-inflammatory stimulation with IFNγ. In contrast to monocytes, hrSC alone are not sufficient to trigger allogenic CD4+ and CD8+ T-cells, but limit number and activation status of exogenously activated T-cells. This study demonstrates that hrSCs possess features and functions typical for professional antigen-presenting cells in vitro, and suggest a new role of these cells as negative regulators of T-cell immunity during nerve regeneration.