SAMHD1 Functions and Human Diseases

Deoxynucleoside triphosphate (dNTP) molecules are essential for the replication and maintenance of genomic information in both cells and a variety of viral pathogens. While the process of dNTP biosynthesis by cellular enzymes, such as ribonucleotide reductase (RNR) and thymidine kinase (TK), has been extensively investigated, a negative regulatory mechanism of dNTP pools was recently found to involve sterile alpha motif (SAM) domain and histidine-aspartate (HD) domain-containing protein 1, SAMHD1. When active, dNTP triphosphohydrolase activity of SAMHD1 degrades dNTPs into their 2′-deoxynucleoside (dN) and triphosphate subparts, steadily depleting intercellular dNTP pools. The differential expression levels and activation states of SAMHD1 in various cell types contributes to unique dNTP pools that either aid (i.e., dividing T cells) or restrict (i.e., nondividing macrophages) viral replication that consumes cellular dNTPs. Genetic mutations in SAMHD1 induce a rare inflammatory encephalopathy called Aicardi–Goutières syndrome (AGS), which phenotypically resembles viral infection. Recent publications have identified diverse roles for SAMHD1 in double-stranded break repair, genome stability, and the replication stress response through interferon signaling. Finally, a series of SAMHD1 mutations were also reported in various cancer cell types while why SAMHD1 is mutated in these cancer cells remains to investigated. Here, we reviewed a series of studies that have begun illuminating the highly diverse roles of SAMHD1 in virology, immunology, and cancer biology.

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Organoids to Dissect Gastrointestinal Virus–Host Interactions: What Have We Learned?

Viruses ◽

10.3390/v13060999 ◽

2021 ◽

Vol 13 (6) ◽

pp. 999

Author(s):

Sue E. Crawford ◽

Sasirekha Ramani ◽

Sarah E. Blutt ◽

Mary K. Estes

Keyword(s):

Cell Types ◽

Human Infection ◽

Viral Pathogens ◽

Host Interactions ◽

Complex Interactions ◽

Microbe Interactions ◽

Host Microbe Interactions ◽

Human Intestinal Epithelium ◽

Human Viruses ◽

Human Infections

Historically, knowledge of human host–enteric pathogen interactions has been elucidated from studies using cancer cells, animal models, clinical data, and occasionally, controlled human infection models. Although much has been learned from these studies, an understanding of the complex interactions between human viruses and the human intestinal epithelium was initially limited by the lack of nontransformed culture systems, which recapitulate the relevant heterogenous cell types that comprise the intestinal villus epithelium. New investigations using multicellular, physiologically active, organotypic cultures produced from intestinal stem cells isolated from biopsies or surgical specimens provide an exciting new avenue for understanding human specific pathogens and revealing previously unknown host–microbe interactions that affect replication and outcomes of human infections. Here, we summarize recent biologic discoveries using human intestinal organoids and human enteric viral pathogens.

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The Ribosomal Gene Loci—The Power behind the Throne

Genes ◽

10.3390/genes12050763 ◽

2021 ◽

Vol 12 (5) ◽

pp. 763

Author(s):

Konstantin I. Panov ◽

Katherine Hannan ◽

Ross D. Hannan ◽

Nadine Hein

Keyword(s):

Genome Stability ◽

Cell Cycle Progression ◽

Global Gene Expression ◽

Cell Types ◽

Ribosomal Gene ◽

Cellular Growth ◽

Rrna Genes ◽

Dynamic Regulation ◽

Pol I ◽

Polymerase I

Nucleoli form around actively transcribed ribosomal RNA (rRNA) genes (rDNA), and the morphology and location of nucleolus-associated genomic domains (NADs) are linked to the RNA Polymerase I (Pol I) transcription status. The number of rDNA repeats (and the proportion of actively transcribed rRNA genes) is variable between cell types, individuals and disease state. Substantial changes in nucleolar morphology and size accompanied by concomitant changes in the Pol I transcription rate have long been documented during normal cell cycle progression, development and malignant transformation. This demonstrates how dynamic the nucleolar structure can be. Here, we will discuss how the structure of the rDNA loci, the nucleolus and the rate of Pol I transcription are important for dynamic regulation of global gene expression and genome stability, e.g., through the modulation of long-range genomic interactions with the suppressive NAD environment. These observations support an emerging paradigm whereby the rDNA repeats and the nucleolus play a key regulatory role in cellular homeostasis during normal development as well as disease, independent of their role in determining ribosome capacity and cellular growth rates.

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Metabolism of 3′-Azido-3′-Deoxythymidine and 3′-Fluoro-3′-Deoxythymidine in Combination in Human Immunodeficiency Virus Infected Lymphoblastoid Cells

Antiviral Chemistry and Chemotherapy ◽

10.1177/095632029200300306 ◽

1992 ◽

Vol 3 (3) ◽

pp. 165-170 ◽

Cited By ~ 5

Author(s):

S. Cox

Keyword(s):

Human Immunodeficiency Virus ◽

Virus Replication ◽

Cell Types ◽

Human Immunodeficiency Virus Replication ◽

Lymphoblastoid Cells ◽

Synergistic Inhibition ◽

Immunodeficiency Virus ◽

Deoxynucleoside Triphosphate ◽

The Individual

A combination of 3′-azido-3′-deoxythymidine (AZT) with 3′-fluoro-3′-deoxythymidine (FLT) has been shown previously to give synergistic inhibition of human immunodeficiency virus replication and greatly reduced cytotoxicity in vitro. The phosphorylation of the compounds, and their effect upon the natural deoxynucleoside triphosphate pools, were compared in CEM, H9, and HIV-infected H9 lymphoblastoid cells, both for the compounds when used alone and when combined together. Higher levels of FLT triphosphate than AZT triphosphate, and higher levels of AZT monophosphate than FLT monosphosphate, were formed in all cell types. Both compounds were phosphorylated most efficiently in CEM cells, whereas they were least efficiently phosphorylated in infected H9 cells. Owing to competition, the phosphorylation of both analogues was reduced when used in combination, compared to the phosphorylation of the separate compounds. The phosphorylation of the separate compounds was therefore at a maximum and was not increased by combining the compounds. The two compounds competed equally with each other for phosphorylation when used at a ratio of AZT: FLT of 5: 1. Both analogues severely reduced the deoxynucleoside triphosphate pools in uninfected and human immunodeficiency virus-infected H9 cells, but not in CEM cells. The effects of the two compounds were similar to those found when the compounds were combined, and thus H9 cells were shown to be much more sensitive to the effects of the analogues upon deoxynucleoside triphosphate pools than CEM cells were. Thus the synergistic combination of 3′-azido-3′-deoxythymidine and 3′-fluoro-3′-deoxythymidine was shown to have a similar metabolism and a similar effect upon cellular deoxynucleoside triphosphate pools to the individual compounds.

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TMOD-29. STANDARDIZED GENERATION OF TUMOR-ORGANOIDS AS NOVEL DRUG SCREENING MODEL IN MENINGIOMA

Neuro-Oncology ◽

10.1093/neuonc/noab196.890 ◽

2021 ◽

Vol 23 (Supplement_6) ◽

pp. vi221-vi222

Author(s):

Gerhard Jungwirth ◽

Tao Yu ◽

Cao Junguo ◽

Catharina Lotsch ◽

Andreas Unterberg ◽

...

Keyword(s):

Drug Screening ◽

Cancer Biology ◽

Drug Testing ◽

Large Scale ◽

Ex Vivo ◽

Cell Types ◽

Cellular Heterogeneity ◽

Drug Responses ◽

Novel Drug ◽

Tumor Organoids

Abstract Tumor-organoids (TOs) are novel, complex three-dimensional ex vivo tissue cultures that under optimal conditions accurately reflect genotype and phenotype of the original tissue with preserved cellular heterogeneity and morphology. They may serve as a new and exciting model for studying cancer biology and directing personalized therapies. The aim of our study was to establish TOs from meningioma (MGM) and to test their usability for large-scale drug screenings. We were capable of forming several hundred TO equal in size by controlled reaggregation of freshly prepared single cell suspension of MGM tissue samples. In total, standardized TOs from 60 patients were formed, including eight grade II and three grade III MGMs. TOs reaggregated within 3 days resulting in a reducted diameter by 50%. Thereafter, TO size remained stable throughout a 14 days observation period. TOs consisted of largely viable cells, whereas dead cells were predominantly found outside of the organoid. H&E stainings confirmed the successful establishment of dense tissue-like structures. Next, we assessed the suitability and reliability of TOs for a robust large-scale drug testing by employing nine highly potent compounds, derived from a drug screening performed on several MGM cell lines. First, we tested if drug responses depend on TO size. Interestingly, drug responses to these drugs remained identical independent of their sizes. Based on a sufficient representation of low abundance cell types such as T-cells and macrophages an overall number of 25.000 cells/TO was selected for further experiments revealing FDA-approved HDAC inhibitors as highly effective drugs in most of the TOs with a mean z-AUC score of -1.33. Taken together, we developed a protocol to generate standardized TO from MGM containing low abundant cell types of the tumor microenvironment in a representative manner. Robust and reliable drug responses suggest patient-derived TOs as a novel drug testing model in meningioma research.

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Facetto: Combining Unsupervised and Supervised Learning for Hierarchical Phenotype Analysis in Multi-Channel Image Data

10.1101/722918 ◽

2019 ◽

Cited By ~ 1

Author(s):

Robert Krueger ◽

Johanna Beyer ◽

Won-Dong Jang ◽

Nam Wook Kim ◽

Artem Sokolov ◽

...

Keyword(s):

Supervised Learning ◽

Visual Analytics ◽

Cancer Biology ◽

Large Scale ◽

Hierarchical Structures ◽

Image Data ◽

Automated Analysis ◽

Cell Types ◽

High Dimensional ◽

Exploration Process

AbstractFacetto is a scalable visual analytics application that is used to discover single-cell phenotypes in high-dimensional multi-channel microscopy images of human tumors and tissues. Such images represent the cutting edge of digital histology and promise to revolutionize how diseases such as cancer are studied, diagnosed, and treated. Highly multiplexed tissue images are complex, comprising 109or more pixels, 60-plus channels, and millions of individual cells. This makes manual analysis challenging and error-prone. Existing automated approaches are also inadequate, in large part, because they are unable to effectively exploit the deep knowledge of human tissue biology available to anatomic pathologists. To overcome these challenges, Facetto enables a semi-automated analysis of cell types and states. It integrates unsupervised and supervised learning into the image and feature exploration process and offers tools for analytical provenance. Experts can cluster the data to discover new types of cancer and immune cells and use clustering results to train a convolutional neural network that classifies new cells accordingly. Likewise, the output of classifiers can be clustered to discover aggregate patterns and phenotype subsets. We also introduce a new hierarchical approach to keep track of analysis steps and data subsets created by users; this assists in the identification of cell types. Users can build phenotype trees and interact with the resulting hierarchical structures of both high-dimensional feature and image spaces. We report on use-cases in which domain scientists explore various large-scale fluorescence imaging datasets. We demonstrate how Facetto assists users in steering the clustering and classification process, inspecting analysis results, and gaining new scientific insights into cancer biology.

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The structural basis for cancer drug interactions with the catalytic and allosteric sites of SAMHD1

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1805593115 ◽

2018 ◽

Vol 115 (43) ◽

pp. E10022-E10031 ◽

Cited By ~ 11

Author(s):

Kirsten M. Knecht ◽

Olga Buzovetsky ◽

Constanze Schneider ◽

Dominique Thomas ◽

Vishok Srikanth ◽

...

Keyword(s):

Genome Stability ◽

Structural Basis ◽

Cancer Drug ◽

Allosteric Site ◽

Nucleotide Analogs ◽

Antiviral Therapies ◽

Allosteric Sites ◽

Catalytically Active ◽

Deoxynucleoside Triphosphate ◽

Patient Responses

SAMHD1 is a deoxynucleoside triphosphate triphosphohydrolase (dNTPase) that depletes cellular dNTPs in noncycling cells to promote genome stability and to inhibit retroviral and herpes viral replication. In addition to being substrates, cellular nucleotides also allosterically regulate SAMHD1 activity. Recently, it was shown that high expression levels of SAMHD1 are also correlated with significantly worse patient responses to nucleotide analog drugs important for treating a variety of cancers, including acute myeloid leukemia (AML). In this study, we used biochemical, structural, and cellular methods to examine the interactions of various cancer drugs with SAMHD1. We found that both the catalytic and the allosteric sites of SAMHD1 are sensitive to sugar modifications of the nucleotide analogs, with the allosteric site being significantly more restrictive. We crystallized cladribine-TP, clofarabine-TP, fludarabine-TP, vidarabine-TP, cytarabine-TP, and gemcitabine-TP in the catalytic pocket of SAMHD1. We found that all of these drugs are substrates of SAMHD1 and that the efficacy of most of these drugs is affected by SAMHD1 activity. Of the nucleotide analogs tested, only cladribine-TP with a deoxyribose sugar efficiently induced the catalytically active SAMHD1 tetramer. Together, these results establish a detailed framework for understanding the substrate specificity and allosteric activation of SAMHD1 with regard to nucleotide analogs, which can be used to improve current cancer and antiviral therapies.

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Exosomal miRNA: Small Molecules, Big Impact in Colorectal Cancer

Journal of Oncology ◽

10.1155/2019/8585276 ◽

2019 ◽

Vol 2019 ◽

pp. 1-18 ◽

Cited By ~ 9

Author(s):

Valentin Vautrot ◽

Gaëtan Chanteloup ◽

Mohammed Elmallah ◽

Marine Cordonnier ◽

François Aubin ◽

...

Keyword(s):

Colorectal Cancer ◽

Cancer Biology ◽

Noncoding Rna ◽

Cell Types ◽

Response To Therapy ◽

Bioactive Molecules ◽

Premetastatic Niche ◽

Rna Molecules ◽

Small Noncoding Rna ◽

Exosomal Mirna

Colorectal cancer (CRC) is one of the major causes of cancer-related deaths worldwide. Tumor microenvironment (TME) contains many cell types including stromal cells, immune cells, and endothelial cells. The TME modulation explains the heterogeneity of response to therapy observed in patients. In this context, exosomes are emerging as major contributors in cancer biology. Indeed, exosomes are implicated in tumor proliferation, angiogenesis, invasion, and premetastatic niche formation. They contain bioactive molecules such as proteins, lipids, and RNAs. More recently, many studies on exosomes have focused on miRNAs, small noncoding RNA molecules able to influence protein expression. In this review, we describe miRNAs transported by exosomes in the context of CRC and discuss their influence on TME and their potential as circulating biomarkers. This overview underlines emerging roles for exosomal miRNAs in cancer research for the near future.

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The Emerging Role of Galectins and O-GlcNAc Homeostasis in Processes of Cellular Differentiation

Cells ◽

10.3390/cells9081792 ◽

2020 ◽

Vol 9 (8) ◽

pp. 1792 ◽

Cited By ~ 1

Author(s):

Rada Tazhitdinova ◽

Alexander V. Timoshenko

Keyword(s):

Cancer Biology ◽

Cellular Differentiation ◽

Current Knowledge ◽

Expression Profiles ◽

Cell Types ◽

Innovative Strategies ◽

Protein Levels ◽

Differentiated Cells ◽

Independent Functions

Galectins are a family of soluble β-galactoside-binding proteins with diverse glycan-dependent and glycan-independent functions outside and inside the cell. Human cells express twelve out of sixteen recognized mammalian galectin genes and their expression profiles are very different between cell types and tissues. In this review, we summarize the current knowledge on the changes in the expression of individual galectins at mRNA and protein levels in different types of differentiating cells and the effects of recombinant galectins on cellular differentiation. A new model of galectin regulation is proposed considering the change in O-GlcNAc homeostasis between progenitor/stem cells and mature differentiated cells. The recognition of galectins as regulatory factors controlling cell differentiation and self-renewal is essential for developmental and cancer biology to develop innovative strategies for prevention and targeted treatment of proliferative diseases, tissue regeneration, and stem-cell therapy.

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The carboxy-terminal transactivation domain of Oct-4 acquires cell specificity through the POU domain.

Molecular and Cellular Biology ◽

10.1128/mcb.17.1.154 ◽

1997 ◽

Vol 17 (1) ◽

pp. 154-162 ◽

Cited By ~ 67

Author(s):

A Brehm ◽

K Ohbo ◽

H Schöler

Keyword(s):

Dna Binding ◽

Cell Lines ◽

Regulatory Mechanism ◽

Cell Types ◽

Binding Domain ◽

Dna Binding Domain ◽

Cell Type ◽

Pou Domain ◽

Cell Type Specific ◽

Carboxy Terminal

The POU transcription factor Oct-4 is expressed in totipotent and pluripotent cells of the early mouse embryo and the germ cell lineage. Transactivation capacities of regions flanking the DNA binding domain of Oct-4 were analyzed in undifferentiated and differentiated cell lines. The amino- and carboxy-terminal regions (N domain and C domain) fused to the Gal4 DNA binding domain both functioned as transactivation domains in all cell lines tested. However, the C domain failed to activate transcription in some cell lines in the context of the native protein. The underlying regulatory mechanism appears to involve the POU domain of Oct-4 and can discriminate between different POU domains, since constructs in which the C domain was instead fused to the POU domain of Pit-1 were again equally active in all cell lines. These results indicate that the C domain is subject to cell-type-specific regulation mediated by the Oct-4 POU domain. Phosphopeptide analysis revealed that the cell-type-specific difference of C-domain activity correlates with a difference in Oct-4 phosphorylation status. Since Oct-4 is expressed in a variety of distinct cell types during murine embryogenesis, these results suggest an additional regulatory mechanism for determining Oct-4 function in rapidly changing cell types during development.

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Commensal bacteria promote type I interferon signaling to maintain immune tolerance

10.1101/2021.10.21.464743 ◽

2021 ◽

Author(s):

Adriana Vasquez Ayala ◽

Kazuhiko Matsuo ◽

Chia-Yun Hsu ◽

Marvic Carrillo Terrazas ◽

Hiutung Chu

Keyword(s):

Immune Tolerance ◽

Type I Interferon ◽

Host Cells ◽

Type I Interferons ◽

Type I ◽

Type I Ifn ◽

Interferon Signaling ◽

Mesenteric Lymph Nodes ◽

Viral Pathogens ◽

Physiological Processes

Type I interferons (IFN) play essential roles in numerous physiological processes, acting as central coordinators in the host response against pathogens. Upon sensing of microbial ligands, host cells rapidly activate the type I IFN response to prime innate and adaptive immune responses. Recent studies suggest tonic IFN are maintained by commensal microbes and critical in mounting an effective immune response to viral pathogens. Further, emerging developments have extended an immunoregulatory role of type I IFN in the maintenance of immune homeostasis. Yet whether immunomodulatory bacteria from the gut microbiota operate through IFN signaling to promote immune tolerance remains largely unanswered. Here we show that commensal microbes are necessary to maintain type I IFN responses in intestinal tissues. Specifically, Bacteroides fragilis induced type I IFN response in dendritic cells (DCs) and this pathway is necessary for the induction of IL-10-producing Foxp3+ regulatory T cells (Tregs). In addition, we show upregulation of type I IFN related genes in Tregs from mesenteric lymph nodes and colonic lamina propria of mice colonized with B. fragilis. Our findings demonstrate type I interferon signaling plays an important role in microbiota-mediated immune tolerance in the gut.

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