The Caenorhabditis elegans aristaless Orthologue, alr-1, Is Required for Maintaining the Functional and Structural Integrity of the Amphid Sensory Organs

The homeobox-containing aristaless-related protein ARX has been directly linked to the development of a number of human disorders involving mental retardation and epilepsy and clearly plays a critical role in development of the vertebrate central nervous system. In this work, we investigate the role of ALR-1, the Caenorhabditis elegans aristaless orthologue, in amphid sensory function. Our studies indicate that ALR-1 is required for maintenance of the amphid organ structure throughout larval development. Mutant analysis indicates a progressive loss in the amphid neurons' ability to fill with lipophilic dyes as well as a declining chemotactic response. The degeneration in amphid function corresponds with a failure of the glial-like amphid socket cell to maintain its specific cell shape and cell–cell contacts. Consistent with ALR-1 expression within the amphid socket cell, our results indicate a cell autonomous role for ALR-1 in maintaining cell shape. Furthermore, we demonstrate a role for ALR-1 in the proper morphogenesis of the anterior hypodermis. Genetic interaction tests also suggest that ALR-1 may function cooperatively with the cell adhesion processes in maintaining the amphid sensory organs.

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Annexin A2 in Fibrinolysis, Inflammation and Fibrosis

International Journal of Molecular Sciences ◽

10.3390/ijms22136836 ◽

2021 ◽

Vol 22 (13) ◽

pp. 6836

Author(s):

Hana I. Lim ◽

Katherine A. Hajjar

Keyword(s):

Cell Surface ◽

Tissue Injury ◽

Critical Role ◽

Annexin A2 ◽

Hemorrhagic Disease ◽

Membrane Repair ◽

Endothelial Cell Surface ◽

Human Disorders ◽

A Cell ◽

Organ Fibrosis

As a cell surface tissue plasminogen activator (tPA)-plasminogen receptor, the annexin A2 (A2) complex facilitates plasmin generation on the endothelial cell surface, and is an established regulator of hemostasis. Whereas A2 is overexpressed in hemorrhagic disease such as acute promyelocytic leukemia, its underexpression or impairment may result in thrombosis, as in antiphospholipid syndrome, venous thromboembolism, or atherosclerosis. Within immune response cells, A2 orchestrates membrane repair, vesicle fusion, and cytoskeletal organization, thus playing a critical role in inflammatory response and tissue injury. Dysregulation of A2 is evident in multiple human disorders, and may contribute to the pathogenesis of various inflammatory disorders. The fibrinolytic system, moreover, is central to wound healing through its ability to remodel the provisional matrix and promote angiogenesis. A2 dysfunction may also promote tissue fibrogenesis and end-organ fibrosis.

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Combinatorial specification of blastomere identity by glp-1-dependent cellular interactions in the nematode Caenorhabditis elegans

Development ◽

10.1242/dev.120.11.3325 ◽

1994 ◽

Vol 120 (11) ◽

pp. 3325-3338 ◽

Cited By ~ 11

Author(s):

I.P. Moskowitz ◽

S.B. Gendreau ◽

J.H. Rothman

Keyword(s):

Caenorhabditis Elegans ◽

Cell Lineage ◽

New Combination ◽

Cellular Interaction ◽

Specific Cell ◽

Cellular Interactions ◽

Nematode Caenorhabditis Elegans ◽

Cell Embryo ◽

Extensive Cell ◽

A Cell

Most somatic cells in the nematode Caenorhabditis elegans arise from AB, the anterior blastomere of the 2-cell embryo. While the daughters of AB, ABa and ABp, are equivalent in potential at birth, they adopt different fates as a result of their unique positions. One such difference is that the distribution of epidermal precursors arising from ABp is reversed along the anterior-posterior axis relative to those arising from ABa. We have found that a strong mutation in the glp-1 gene eliminates this ABa/ABp difference. Furthermore, extensive cell lineage analyses showed that ABp adopts an ABa-like fate in this mutant. This suggests that glp-1 acts in a cellular interaction that makes ABp distinct from ABa. One ABp-specific cell type was previously shown to be induced by an interaction with a neighboring cell, P2. By removing P2 from early embryos, we have found that the widespread differences between ABa and ABp arise from induction of the entire ABp fate by P2. Lineage analyses of genetically and physically manipulated embryos further suggest that the identifies of the AB great-granddaughters (AB8 cells) are controlled by three regulatory inputs that act in various combinations. These inputs are: (1) induction of the ABp-specific fate by P2, (2) a previously described induction of particular AB8 cells by a cell called MS, and (3) a process that controls whether an AB8 cell is an epidermal precursor in the absence of either induction. When an AB8 cell is caused to receive a new combination of these regulatory inputs, its lineage pattern is transformed to resemble the lineage of the wild-type AB8 cell normally receiving that combination of inputs. These lineage patterns are faithfully reproduced irrespective of position in the embryo, suggesting that each combination of regulatory inputs directs a unique lineage program that is intrinsic to each AB8 cell.

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scPred: Cell type prediction at single-cell resolution

10.1101/369538 ◽

2018 ◽

Cited By ~ 13

Author(s):

José Alquicira-Hernández ◽

Anuja Sathe ◽

Hanlee P Ji ◽

Quan Nguyen ◽

Joseph E Powell

Keyword(s):

Feature Selection ◽

Single Cell ◽

Critical Role ◽

Pancreatic Tissue ◽

Molecular Techniques ◽

Computational Genomics ◽

Specific Cell ◽

Cell Type ◽

Machine Learning Classification ◽

A Cell

AbstractSingle-cell RNA sequencing has enabled the characterization of highly specific cell types in many human tissues, as well as both primary and stem cell-derived cell lines. An important facet of these studies is the ability to identify the transcriptional signatures that define a cell type or state. In theory, this information can be used to classify an unknown cell based on its transcriptional profile; and clearly, the ability to accurately predict a cell type and any pathologic-related state will play a critical role in the early diagnosis of disease and decisions around the personalized treatment for patients. Here we present a new generalizable method (scPred) for prediction of cell type(s), using a combination of unbiased feature selection from a reduced-dimension space, and machine-learning classification. scPred solves several problems associated with the identification of individual gene feature selection, and is able to capture subtle effects of many genes, increasing the overall variance explained by the model, and correspondingly improving the prediction accuracy. We validate the performance of scPred by performing experiments to classify tumor versus non-tumor epithelial cells in gastric cancer, then using independent molecular techniques (cyclic immunohistochemistry) to confirm our prediction, achieving an accuracy of classifying the disease state of individual cells of 99%. Moreover, we apply scPred to scRNA-seq data from pancreatic tissue, colorectal tumor biopsies, and circulating dendritic cells, and show that scPred is able to classify cell subtypes with an accuracy of 96.1-99.2%. Collectively, our results demonstrate the utility of scPred as a single cell prediction method that can be used for a wide variety of applications. The generalized method is implemented in software available here: https://github.com/IMB-Computational-Genomics-Lab/scPred/

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Metabolic Regulation and Related Molecular Mechanisms in Various Stem Cell Functions

Current Stem Cell Research & Therapy ◽

10.2174/1574888x15666200512105347 ◽

2020 ◽

Vol 15 (6) ◽

pp. 531-546 ◽

Cited By ~ 1

Author(s):

Hwa-Yong Lee ◽

In-Sun Hong

Keyword(s):

Stem Cells ◽

Stem Cell ◽

Oxidative Phosphorylation ◽

Metabolic Pathways ◽

Critical Role ◽

The Self ◽

Specific Cell ◽

Differentiation Potential ◽

Self Renewal ◽

Cell Functions

Recent studies on the mechanisms that link metabolic changes with stem cell fate have deepened our understanding of how specific metabolic pathways can regulate various stem cell functions during the development of an organism. Although it was originally thought to be merely a consequence of the specific cell state, metabolism is currently known to play a critical role in regulating the self-renewal capacity, differentiation potential, and quiescence of stem cells. Many studies in recent years have revealed that metabolic pathways regulate various stem cell behaviors (e.g., selfrenewal, migration, and differentiation) by modulating energy production through glycolysis or oxidative phosphorylation and by regulating the generation of metabolites, which can modulate multiple signaling pathways. Therefore, a more comprehensive understanding of stem cell metabolism could allow us to establish optimal culture conditions and differentiation methods that would increase stem cell expansion and function for cell-based therapies. However, little is known about how metabolic pathways regulate various stem cell functions. In this context, we review the current advances in metabolic research that have revealed functional roles for mitochondrial oxidative phosphorylation, anaerobic glycolysis, and oxidative stress during the self-renewal, differentiation and aging of various adult stem cell types. These approaches could provide novel strategies for the development of metabolic or pharmacological therapies to promote the regenerative potential of stem cells and subsequently promote their therapeutic utility.

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par-4, a gene required for cytoplasmic localization and determination of specific cell types in Caenorhabditis elegans embryogenesis.

Genetics ◽

10.1093/genetics/130.4.771 ◽

1992 ◽

Vol 130 (4) ◽

pp. 771-790 ◽

Cited By ~ 5

Author(s):

D G Morton ◽

J M Roos ◽

K J Kemphues

Keyword(s):

Caenorhabditis Elegans ◽

Cell Types ◽

Intestinal Cells ◽

Specific Cell ◽

Cytoplasmic Localization ◽

Loss Of Function ◽

Embryo Viability ◽

Cell Stage ◽

Maternal Genome

Abstract Specification of some cell fates in the early Caenorhabditis elegans embryo is mediated by cytoplasmic localization under control of the maternal genome. Using nine newly isolated mutations, and two existing mutations, we have analyzed the role of the maternally expressed gene par-4 in cytoplasmic localization. We recovered seven new par-4 alleles in screens for maternal effect lethal mutations that result in failure to differentiate intestinal cells. Two additional par-4 mutations were identified in noncomplementation screens using strains with a high frequency of transposon mobility. All 11 mutations cause defects early in development of embryos produced by homozygous mutant mothers. Analysis with a deficiency in the region indicates that it33 is a strong loss-of-function mutation. par-4(it33) terminal stage embryos contain many cells, but show no morphogenesis, and are lacking intestinal cells. Temperature shifts with the it57ts allele suggest that the critical period for both intestinal differentiation and embryo viability begins during oogenesis, about 1.5 hr before fertilization, and ends before the four-cell stage. We propose that the primary function of the par-4 gene is to act as part of a maternally encoded system for cytoplasmic localization in the first cell cycle, with par-4 playing a particularly important role in the determination of intestine. Analysis of a par-4; par-2 double mutant suggests that par-4 and par-2 gene products interact in this system.

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A Region of the Myosin Rod Important for Interaction With Paramyosin in Caenorhabditis elegans Striated Muscle

Genetics ◽

10.1093/genetics/156.2.631 ◽

2000 ◽

Vol 156 (2) ◽

pp. 631-643

Author(s):

Pamela E Hoppe ◽

Robert H Waterston

Keyword(s):

Caenorhabditis Elegans ◽

Heavy Chain ◽

Molecular Interaction ◽

Striated Muscle ◽

Genetic Interaction ◽

Specific Interaction ◽

Thick Filament ◽

Parallel Arrangement ◽

Myosin Rod

Abstract The precise arrangement of molecules within the thick filament, as well as the mechanisms by which this arrangement is specified, remains unclear. In this article, we have exploited a unique genetic interaction between one isoform of myosin heavy chain (MHC) and paramyosin in Caenorhabditis elegans to probe the molecular interaction between MHC and paramyosin in vivo. Using chimeric myosin constructs, we have defined a 322-residue region of the MHC A rod critical for suppression of the structural and motility defects associated with the unc-15(e73) allele. Chimeric constructs lacking this region of MHC A either fail to suppress, or act as dominant enhancers of, the e73 phenotype. Although the 322-residue region is required for suppression activity, our data suggest that sequences along the length of the rod also play a role in the isoform-specific interaction between MHC A and paramyosin. Our genetic and cell biological analyses of construct behavior suggest that the 322-residue region of MHC A is important for thick filament stability. We present a model in which this region mediates an avid interaction between MHC A and paramyosin in parallel arrangement in formation of the filament arms.

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Superior Alignment of Human iPSC-Osteoblasts Associated with Focal Adhesion Formation Stimulated by Oriented Collagen Scaffold

International Journal of Molecular Sciences ◽

10.3390/ijms22126232 ◽

2021 ◽

Vol 22 (12) ◽

pp. 6232

Author(s):

Ryosuke Ozasa ◽

Aira Matsugaki ◽

Tadaaki Matsuzaka ◽

Takuya Ishimoto ◽

Hui-Suk Yun ◽

...

Keyword(s):

Bone Tissue ◽

Structural Organization ◽

Critical Role ◽

Bone Matrix ◽

Adhesion Formation ◽

Focal Adhesions ◽

Collagen Scaffold ◽

Patient Specific ◽

Specific Cell ◽

Adhesion Behavior

Human-induced pluripotent stem cells (hiPSCs) can be applied in patient-specific cell therapy to regenerate lost tissue or organ function. Anisotropic control of the structural organization in the newly generated bone matrix is pivotal for functional reconstruction during bone tissue regeneration. Recently, we revealed that hiPSC-derived osteoblasts (hiPSC-Obs) exhibit preferential alignment and organize in highly ordered bone matrices along a bone-mimetic collagen scaffold, indicating their critical role in regulating the unidirectional cellular arrangement, as well as the structural organization of regenerated bone tissue. However, it remains unclear how hiPSCs exhibit the cell properties required for oriented tissue construction. The present study aimed to characterize the properties of hiPSCs-Obs and those of their focal adhesions (FAs), which mediate the structural relationship between cells and the matrix. Our in vitro anisotropic cell culture system revealed the superior adhesion behavior of hiPSC-Obs, which exhibited accelerated cell proliferation and better cell alignment along the collagen axis compared to normal human osteoblasts. Notably, the oriented collagen scaffold stimulated FA formation along the scaffold collagen orientation. This is the first report of the superior cell adhesion behavior of hiPSC-Obs associated with the promotion of FA assembly along an anisotropic scaffold. These findings suggest a promising role for hiPSCs in enabling anisotropic bone microstructural regeneration.

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Computational-Driven Epitope Verification and Affinity Maturation of TLR4-Targeting Antibodies

International Journal of Molecular Sciences ◽

10.3390/ijms22115989 ◽

2021 ◽

Vol 22 (11) ◽

pp. 5989

Author(s):

Bilal Ahmad ◽

Maria Batool ◽

Moon Suk Kim ◽

Sangdun Choi

Keyword(s):

Rational Design ◽

Structural Integrity ◽

Critical Role ◽

Autoimmune Encephalitis ◽

Affinity Maturation ◽

Antibody Binding ◽

Computational Techniques ◽

Multiple Strategies ◽

Binding Epitope

Toll-like receptor (TLR) signaling plays a critical role in the induction and progression of autoimmune diseases such as rheumatoid arthritis, systemic lupus erythematous, experimental autoimmune encephalitis, type 1 diabetes mellitus and neurodegenerative diseases. Deciphering antigen recognition by antibodies provides insights and defines the mechanism of action into the progression of immune responses. Multiple strategies, including phage display and hybridoma technologies, have been used to enhance the affinity of antibodies for their respective epitopes. Here, we investigate the TLR4 antibody-binding epitope by computational-driven approach. We demonstrate that three important residues, i.e., Y328, N329, and K349 of TLR4 antibody binding epitope identified upon in silico mutagenesis, affect not only the interaction and binding affinity of antibody but also influence the structural integrity of TLR4. Furthermore, we predict a novel epitope at the TLR4-MD2 interface which can be targeted and explored for therapeutic antibodies and small molecules. This technique provides an in-depth insight into antibody–antigen interactions at the resolution and will be beneficial for the development of new monoclonal antibodies. Computational techniques, if coupled with experimental methods, will shorten the duration of rational design and development of antibody therapeutics.

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The AF-6 Homolog Canoe Acts as a Rap1 Effector During Dorsal Closure of the Drosophila Embryo

Genetics ◽

10.1093/genetics/165.1.159 ◽

2003 ◽

Vol 165 (1) ◽

pp. 159-169

Author(s):

Benjamin Boettner ◽

Phoebe Harjes ◽

Satoshi Ishimaru ◽

Michael Heke ◽

Hong Qing Fan ◽

...

Keyword(s):

Molecular Mechanisms ◽

Genetic Interaction ◽

Critical Role ◽

Adherens Junction ◽

Small Gtpases ◽

Drosophila Embryo ◽

Dorsal Closure ◽

Cell Sheets ◽

Jnk Pathway

Abstract Rap1 belongs to the highly conserved Ras subfamily of small GTPases. In Drosophila, Rap1 plays a critical role in many different morphogenetic processes, but the molecular mechanisms executing its function are unknown. Here, we demonstrate that Canoe (Cno), the Drosophila homolog of mammalian junctional protein AF-6, acts as an effector of Rap1 in vivo. Cno binds to the activated form of Rap1 in a yeast two-hybrid assay, the two molecules colocalize to the adherens junction, and they display very similar phenotypes in embryonic dorsal closure (DC), a process that relies on the elongation and migration of epithelial cell sheets. Genetic interaction experiments show that Rap1 and Cno act in the same molecular pathway during DC and that the function of both molecules in DC depends on their ability to interact. We further show that Rap1 acts upstream of Cno, but that Rap1, unlike Cno, is not involved in the stimulation of JNK pathway activity, indicating that Cno has both a Rap1-dependent and a Rap1-independent function in the DC process.

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Self-Assembling Polypeptide Hydrogels as a Platform to Recapitulate the Tumor Microenvironment

Cancers ◽

10.3390/cancers13133286 ◽

2021 ◽

Vol 13 (13) ◽

pp. 3286

Author(s):

Dariusz Lachowski ◽

Carlos Matellan ◽

Ernesto Cortes ◽

Alberto Saiani ◽

Aline F. Miller ◽

...

Keyword(s):

Cell Culture ◽

Tumor Microenvironment ◽

Cancer Cell ◽

Critical Role ◽

Hypoxia Inducible Factor ◽

Pancreatic Cancer Cell Line ◽

Cancer Cell Line ◽

Culture Systems ◽

A Cell

The tumor microenvironment plays a critical role in modulating cancer cell migration, metabolism, and malignancy, thus, highlighting the need to develop in vitro culture systems that can recapitulate its abnormal properties. While a variety of stiffness-tunable biomaterials, reviewed here, have been developed to mimic the rigidity of the tumor extracellular matrix, culture systems that can recapitulate the broader extracellular context of the tumor microenvironment (including pH and temperature) remain comparably unexplored, partially due to the difficulty in independently tuning these parameters. Here, we investigate a self-assembled polypeptide network hydrogel as a cell culture platform and demonstrate that the culture parameters, including the substrate stiffness, extracellular pH and temperature, can be independently controlled. We then use this biomaterial as a cell culture substrate to assess the effect of stiffness, pH and temperature on Suit2 cells, a pancreatic cancer cell line, and demonstrate that these microenvironmental factors can regulate two critical transcription factors in cancer: yes-associated protein 1 (YAP) and hypoxia inducible factor (HIF-1A).

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