https://www.seas.upenn.edu/%7Edischer/pdfs/Cell_on_Gel-CELLpaper.pdf

Matrix elasticity directs stem cell lineage specification.

Labeling deoxyribonucleic acid to high specific activity in vitro by nick translation with DNA polymerase I

New M13 vectors for cloning.

The reverse transcription polymerase chain reaction (RT-PCR) is the most sensitive method for the detection of low-abundance mRNA, often obtained from limited tissue samples. However, it is a complex technique, there are substantial problems associated with its true sensitivity, reproducibility and specificity and, as a quantitative method, it suffers from the problems inherent in PCR. The recent introduction of fluorescence-based kinetic RT-PCR procedures significantly simplifies the process of producing reproducible quantification of mRNAs and promises to overcome these limitations. Nevertheless, their successful application depends on a clear understanding of the practical problems, and careful experimental design, application and validation remain essential for accurate quantitative measurements of transcription. This review discusses the technical aspects involved, contrasts conventional and kinetic RT-PCR methods for quantitating gene expression and compares the different kinetic RT-PCR systems. It illustrates the usefulness of these assays by demonstrating the significantly different levels of transcription between individuals of the housekeeping gene family, glyceraldehyde-3-phosphate-dehydrogenase (GAPDH).

/pdf/absolute-quantification-of-mrna-using-real-time-reverse-2kyvkvy0jn.pdf

Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays.

▪ Abstract The matrix metalloproteinases (MMPs) constitute a multigene family of over 25 secreted and cell surface enzymes that process or degrade numerous pericellular substrates. Their targets include other proteinases, proteinase inhibitors, clotting factors, chemotactic molecules, latent growth factors, growth factor–binding proteins, cell surface receptors, cell-cell adhesion molecules, and virtually all structural extracellular matrix proteins. Thus MMPs are able to regulate many biologic processes and are closely regulated themselves. We review recent advances that help to explain how MMPs work, how they are controlled, and how they influence biologic behavior. These advances shed light on how the structure and function of the MMPs are related and on how their transcription, secretion, activation, inhibition, localization, and clearance are controlled. MMPs participate in numerous normal and abnormal processes, and there are new insights into the key substrates and mechanisms responsible for regula...

/pdf/how-matrix-metalloproteinases-regulate-cell-behavior-1ljn27ub20.pdf

How Matrix Metalloproteinases Regulate Cell Behavior

A membrane-filter technique for the detection of complementary DNA

Cell-mediated (type-1) immunity is necessary for immune protection against most intracellular pathogens and, when excessive, can mediate organ-specific autoimmune destruction. Mice deficient in Eta-1 (also called osteopontin) gene expression have severely impaired type-1 immunity to viral infection [herpes simplex virus–type 1 (KOS strain)] and bacterial infection ( Listeria monocytogenes ) and do not develop sarcoid-type granulomas. Interleukin-12 (IL-12) and interferon-γ production is diminished, and IL-10 production is increased. A phosphorylation-dependent interaction between the amino-terminal portion of Eta-1 and its integrin receptor stimulated IL-12 expression, whereas a phosphorylation-independent interaction with CD44 inhibited IL-10 expression. These findings identify Eta-1 as a key cytokine that sets the stage for efficient type-1 immune responses through differential regulation of macrophage IL-12 and IL-10 cytokine expression.

https://science.sciencemag.org/content/sci/287/5454/860.full.pdf

Eta-1 (Osteopontin): An Early Component of Type-1 (Cell-Mediated) Immunity

In this review most of the various known, suspected, or postulated functions of osteopontin, a secreted highly acidic phosphoprotein, are discussed in terms of what we currently know about the protein. These include 1) binding of OPN both to cells via a GRGDS cell adhesion sequence that recognizes the alpha v beta 3 integrin and to extracellular matrix components via poorly characterized motifs, 2) regulation of the formation and remodeling of mineralized tissue, 3) recruiting and stimulating macrophages and lymphocytes as part of a nonspecific response to microbial infections, 4) multiple interactions with Ca2+ that likely influence OPN protein conformation and may be important in Ca(2+)-mediated or Ca(2+)-dependent processes, 5) inhibiting the growth of calcium oxalate crystals by disruption of the growing crystal lattice, 6) effects on gene expression, Ca2+ regulation, and nitric oxide production, and 7) involvement in cell migration. OPN production is frequently augmented when cell signaling pathways are activated by any of a variety of stimuli, for example in cancer cells.

Osteopontin: a protein with diverse functions.

OPN is a multifunctional cytokine and adhesion protein that contains an integrin-binding RGD sequence and additional sequences that interact with CD44v6/7 or other adhesive receptors. Its expression is increased in response to early proinflammatory cytokines and to mechanical strain in bone. The function of the secreted protein may be altered by extracellular enzymes, including thrombin and kinases. The study of OPN-null mice has revealed roles for OPN in a broad range of homeostatic (bone remodeling, tissue debridement) and pathologic (cellular immunity, wound healing, cancer metastasis) processes. While these processes seem disparate, they are linked by several common themes, including enhanced expression of OPN in response to stress or tissue injury, and stimulation of cell motility and cell survival pathways via interactions of OPN with adhesive receptors.

OPN is chemotactic for various cell types, notably monocytes/macrophages, which are attracted to sites of infection and inflammation. It is essential for cell-mediated immunity and a normal Th1 cytokine response during granuloma formation. OPN serves both to attach bone cells to bone matrix and to generate intracellular signals essential for normal osteoclast motility on bone; it may mediate osteocyte recognition of bone strain. OPN activates intracellular signaling pathways and regulates gene expression as a consequence of its interactions with its various receptors. The best-characterized is the integrin-stimulated FAK-Src-Rho pathway, which alters gelsolin function and podosome formation in osteoclasts. Identification and dissection of the signal transduction pathways and their targets are complicated by the fact that OPN can engage more than one type of receptor on the cell. For this reason, it is important to ascertain which receptors are in play in any given experimental system.

There is compelling evidence that soluble OPN can in a variety of situations help cells survive an otherwise lethal insult. Remarkably, this survival signaling is mediated by receptors that are generally considered to be receptors for ECM components. We suggest that OPN delivers an antiapoptotic “ECM-like” signal via multiple ligand-receptor interactions to cells, both adherent and nonadherent.

/pdf/osteopontin-as-a-means-to-cope-with-environmental-insults-48y8pvvhw1.pdf

Osteopontin as a means to cope with environmental insults: regulation of inflammation, tissue remodeling, and cell survival

Multiple sclerosis is a demyelinating disease, characterized by inflammation in the brain and spinal cord, possibly due to autoimmunity. Large-scale sequencing of cDNA libraries, derived from plaques dissected from brains of patients with multiple sclerosis (MS), indicated an abundance of transcripts for osteopontin (OPN). Microarray analysis of spinal cords from rats paralyzed by experimental autoimmune encephalomyelitis (EAE), a model of MS, also revealed increased OPN transcripts. Osteopontin-deficient mice were resistant to progressive EAE and had frequent remissions, and myelin-reactive T cells in OPN-/- mice produced more interleukin 10 and less interferon-gamma than in OPN+/+ mice. Osteopontin thus appears to regulate T helper cell-1 (TH1)-mediated demyelinating disease, and it may offer a potential target in blocking development of progressive MS.

https://science.sciencemag.org/content/sci/294/5547/1731.full.pdf

David T. Denhardt

Papers

A membrane-filter technique for the detection of complementary DNA

Eta-1 (Osteopontin): An Early Component of Type-1 (Cell-Mediated) Immunity

Osteopontin: a protein with diverse functions.

Osteopontin as a means to cope with environmental insults: regulation of inflammation, tissue remodeling, and cell survival

The influence of the proinflammatory cytokine, osteopontin, on autoimmune demyelinating disease.