Patent Application
20180289709
The contents of the text file named “39564-503001WO_ST25.txt”, which was created on Nov. 21, 2011 and is 817 bytes in size, are hereby incorporated by reference in their entirety.
The present invention relates to the treating and/or preventing inflammation associated with an innate immune response to a pathogen.
Cells process environmental signals via signaling and transcriptional networks that culminate with appropriate regulation of output genes. Subtle changes in these networks underlie human diseases, making the elucidation of pathway components and architecture one of the major goals in the post-genome era. For example, innate immune dendritic cells (DCs) rely on multiple sensors, including Toll-like receptors (TLRs), to detect infectious and danger signals before mounting specific immune responses by instructing lymphocytes (Takeuchi & Akira, Pattern recognition receptors and inflammation, Cell, 2010). Defects at the level of input, signal processing, or output of these pathogen-sensing pathways are the underlying causes of many diseases due to their central role in regulating inflammatory processes (Medzhitov, Inflammation 2010: new adventures of an old flame, Cell, 2010). Filling the gaps in our knowledge of these pathways is a critical pre-requisite to future, successful manipulations of the immune system.
Upon activation, signaling networks such as the TLR system not only induce expression of effector genes (e.g., interferons against viral infections), but also induce genes whose products are required for signal propagation and extinction. One example of the latter form of inducible gene in the TLR system is Tnfaip3 (A20), which is known to terminate NF-κB-mediated signals and therefore limit inflammation (Lee et al., Failure to regulate TNF-induced NF-κB and cell death responses in A20-deficient mice, Science, 2000). Moreover, mutations in the human Tnfaip3 locus has been linked to multiple disorders ranging from cancer to lupus, or diabetes. These types of feedback from induced transcripts can also occur by direct optimization of cytoplasmic signaling components. Given this property of signaling networks to optimize the activity and expression of its very own components, we hypothesized that signaling regulators of a network can be extracted from its transcriptional output. Here we verify our hypothesis in the TLR system of DCs and validate a systematic strategy for the identification of signaling regulators. First, both known and candidate signaling regulators of the TLR network were extracted from genome-wide expression profiles from DCs stimulated with pathogen mimics. Second, the expression of TLR signature output genes was measured upon perturbation of selected signaling regulators (Amit et al., Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses, Science, 2009). Using this approach, we correctly assigned functions to six known TLR signaling components and highlight a level of cross talks between these components higher than previously thought. In addition, we identified and functionally validated seventeen new signaling regulators of the TLR network. Among these new regulators, Polo-like kinase (PLK) family member 2 and 4 are cell cycle regulators that are co-opted by anti-viral pathways of innate immune DCs. Lastly, chemical perturbations of PLKs demonstrate the potential of our approach in drug target discovery.
The invention provides methods of decreasing inflammation associated with an innate immune response to a pathogen or pathogen derived molecule by administering to a subject in need thereof a polo-like kinase (Plk) inhibitor. The pathogen is a virus or a component thereof. In some aspects the pathogen binds to a toll-like receptor on the surface or in endomes of a dendritic cell or a cytosolic RIG-1 like receptor of a dentritic cell.
In another aspect the invention provides a method of treating inflammation by administering to a subject in need thereof a polo-like kinase (Plk) inhibitor. The inflammation is a symptom of a disease selected from the group consisting of viral infection, bacteria infection, autoimmune disease, or mucositis.
The invention further provides method of decreasing anti-viral cytokine expression by a dendritic cell by contacting the cell with a polo-like kinase (Plk) inhibitor. In yet another aspect the invention provides a method of decreasing anti-viral cytokine expression in a subject by administering to a subject in need thereof a polo-like kinase (Plk) inhibitor. The cytokine is interferon-β or CXCL-10.
The Plk inhibitor is specific for at least two Plks. For example, the Plk inhibitor is specific for at least Plk2 and Plk4. Alternatively, the Plk the inhibitor is a pan-specific Plk inhibitor. Preferably, the Plk inhibitor is BI 2536, poloxipan, or GW843682X.
In a further aspect the invention provides a method of identifying genes or genetic elements associated with a pathogen specific response by contacting a dendritic cell with a toll-like receptor agonist; and identifying a gene or genetic element whose expression is modulated by the toll-like receptor agonist. Optionally the method further comprises perturbing expression of the gene or genetic element identified and determining a gene whose expression is modulated the perturbation. The toll-like receptor agonist is Pam3CSK4, lipopolysaccharide, polyinosinic: polycytidylic acid, gardiquimod, or CpG. The pathogen is a virus, a bacterium, a fungus or a parasite.
Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention pertains. Although methods and materials similar or equivalent to those described herein can be used in the practice of the present invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are expressly incorporated by reference in their entirety. In cases of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples described herein are illustrative only and are not intended to be limiting.
Other features and advantages of the invention will be apparent from and encompassed by the following detailed description and claims.
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The invention is based upon the discovery that the polo-like kinase (PLK) family of proteins are signaling components of innate immune pathways. In particular, it was discovered that PLKs are co-opted by anti-viral pathways of dendritic cells and inhibition of PLKs impairs anti-viral gene induction in dendritic cells.
A perturbation strategy for reconstruction of regulatory networks was used to identify signaling components of the Toll-Like Receptor (TLR) that are transcriptionally regulated in dendritic cells. Regulatory networks controlling gene expression serve as decision-making circuits within cells. For example, when immune dendritic cells are exposed to viruses, bacteria, or fungi they responds with transcriptional programs that are specific to each pathogen and are essential for establishing appropriate immunological outcomes. However, altered functions of dendritic cells are also known to play a role in diseases such as allergy and autoimmune disease. Thus, identification of regulators in the innate immune pathway will allow therapeutic targeting of specific pathways to control disease.
Two hundred and eighty one (281) genes were found to be differentially regulated in TLR stimulated dendritic cells. Of these 281 genes, it was determined that the cell-cycle regulators polo-like kinase 2 and 4 (PLK) are anti-viral regulators. Inhibition of PLK using commercially available pan-specific PLK small molecule inhibitors resulted in a decrease in anti-viral gene expression in dendritic cells. Specifically, a decrease in IFN-b and CXCL10 mRNA expression in dendritic cells upon LPS stimulation. Accordingly, the invention provides methods of decreasing and/or treating inflammation associated with an innate immune response to a pathogen, e.g., virus, buy administering to a subject a polo-like kinase inhibitor. The invention also provides methods of decreasing anti-viral cytokine expression by contacting a dendritic cell with a PLK inhibitor.
Disease” or “disorder” refers to an impairment of the normal function of an organism. As used herein, a disease may be characterized by, e.g., an immune disorder, an inflammatory response, viral infection, bacterial infection or a combination of any of these conditions.
“Immune-modulating” refers to the ability of a compound of the present invention to alter (modulate) one or more aspects of the immune system. The immune system functions to protect the organism from infection and from foreign antigens by cellular and humoral mechanisms involving lymphocytes, macrophages, and other antigen-presenting cells that regulate each other by means of multiple cell-cell interactions and by elaborating soluble factors, including lymphokines and antibodies, that have autocrine, paracrine, and endocrine effects on immune cells.
“Immune disorder” refers to abnormal functioning of the immune system. Immune disorders can be caused by deficient immune responses (e.g., HIV AIDS) or overactive immune responses (e.g., allergy, auto-immune disorders). Immune disorders can result in the uncontrolled proliferation of immune cells, uncontrolled response to foreign antigens or organisms leading to allergic or inflammatory diseases, aberrant immune responses directed against host cells leading to auto-immune organ damage and dysfunction, or generalized suppression of the immune response leading to severe and recurrent infections.
“Dendritic cells” (DCs) are immune cells that form part of the mammalian immune system. Their main function is to process antigen material and present it on the surface to other cells of the immune system, thus functioning as antigen-presenting cells. They act as messengers between the innate and adaptive immunity.
“Innate immunity” refers to an early system of defense that depends on invariant receptors recognizing common features of pathogens. The innate immune system provides barriers and mechanisms to inhibit foreign substances, in particular through the action of macrophages and neutrophils. The inflammatory response is considered part of innate immunity. The innate immune system is involved in initiating adaptive immune responses and removing pathogens that have been targeted by an adaptive immune response. However, innate immunity can be evaded or overcome by many pathogens, and does not lead to immunological memory.
“Adaptive immunity” refers to the ability to recognize pathogens specifically and to provide enhanced protection against reinfection due to immunological memory based on clonal selection of lymphocytes bearing antigen-specific receptors. A process of random recombination of variable receptor gene segments and the pairing of different variable chains generates a population of lymphocytes, each bearing a distinct receptor, forming a repertoire of receptors that can recognize virtually any antigen. If the receptor on a lymphocyte is specific for a ubiquitous self antigen, the cell is normally eliminated by encountering the antigen early in its development. Adaptive immunity is normally initiated when an innate immune response fails to eliminate a new infection, and antigen and activated antigen-presenting cells are delivered to draining lymphoid tissues. When a recirculating lymphocyte encounters its specific foreign antigen in peripheral lymphoid tissues, it is induced to proliferate and its progeny then differentiate into effector cells that can eliminate the infectious agent. A subset of these proliferating lymphocytes differentiate into memory cells, capable of responding rapidly to the same pathogen if it is encountered again.
Immune disorders can be caused by an impaired or immunocompromised immune system can produce a deficient immune response that leaves the body vulnerable to various viral, bacterial, or fungal opportunistic infections. Causes of immune deficiency can include various illnesses such as viruses, chronic illness, or immune system illnesses. Diseases characterized by an impaired immune system include, but are not limited to, HIV AIDS and severe combined immunodeficiency syndrome (SCIDS).
Immune disorders caused by an excessive response by the immune system. This excessive response can be an excessive response to one or more antigens on a pathogen, or to an antigen that would normally be ignored by the immune system. Diseases characterized by an overactive immune system include, but are not limited to, arthritis, allergy, asthma, pollinosis, atopy, mucositis and auto-immune diseases. Anaphylaxis is a term used to refer an excessive immune system response that can lead to shock.
“Arthritis” refers to inflammation of the joints that can be caused, inter alia, by wear and tear on joints, or auto-immune attack on connective tissues, or exposure to an allergen, e.g., as in adjuvant-induced arthritis. Arthritis is often associated with, or initiated by, deposition of antibody-antigen complexes in joint membranes and activation of an inflammatory response. Sometimes the immune response is initiated by cells rather than antibodies, where the cells can produce a deposit in the joint membrane.
“Allergy” refers to an immune reaction to a normally innocuous environmental antigen (allergen), resulting from the interaction of the antigen with antibodies or primed T cells generated by prior exposure to the same antigen. Allergy is characterized by immune and inflammatory aspects, as the allergic reaction is triggered by binding of the antigen to antigen-specific IgE antibodies bound to a high-affinity IgE receptor on mast cells, which leads to antigen-induced cross-linking of IgE on mast cell surfaces, causing the release of large amounts of inflammatory mediators such as histamine. Later events in the allergic response involve leukotrienes, cytokines, and chemokines, which recruit and activate eosinophils and basophils. The late phase of this response can evolve into chronic inflammation, characterized by the presence of effector T cells and eosinophils, which is most clearly seen in chronic allergic asthma.
“Asthma” refers to a chronic inflammatory disorder affecting the bronchial tubes, usually triggered or aggravated by allergens or contaminants. Asthma is characterized by constriction of the bronchial tubes, producing symptoms including, but not limited to, cough, shortness of breath, wheezing, excess production of mucus, and chest constriction
“Atopy” refers to the tendency to develop so-called “classic” allergic diseases such as atopic dermatitis, allergic rhinitis (hay fever), and asthma, and is associated with a capacity to produce an immunoglobulin E (IgE) response to common allergens. Atopy is often characterized by skin allergies including but not limited to eczema, urticaria, and atopic dermatitis. Atopy can be caused or aggravated by inhaled allergens, food allergens, and skin contact with allergens, but an atopic allergic reaction may occur in areas of the body other than where contact with the allergan occurred. A strong genetic (inherited) component of atopy is suggested by the observation that the majority of atopic dermatitis patients have at least one relative who suffers from eczema, asthma, or hay fever. Atopy is sometimes called a “reagin response.”
“Mucositis” is the painful inflammation and ulceration of the mucous membranes lining the digestive tract, usually as an adverse effect of chemotherapy and radiotherapy treatment for cancer. Mucositis can occur anywhere along the gastrointestinal (GI) tract, but oral mucositis refers to the particular inflammation and ulceration that occurs in the mouth. Oral mucositis is a common and often debilitating complication of cancer treatment.
“Pollinosis,” “hay fever,” or “allergic rhinitis,” are terms that refer to an allergy characterized by sneezing, itchy and watery eyes, a runny nose and a burning sensation of the palate and throat. Often seasonal, pollinosis is usually caused by allergies to airborne substances such as pollen, and the disease can sometimes be aggravated in an individual by exposure to other allergens to which the individual is allergic.
“Auto-immune” refers to an adaptive immune response directed at self antigens. “Auto-immune disease” refers to a condition wherein the immune system reacts to a “self” antigen that it would normally ignore, leading to destruction of normal body tissues. Auto-immune disorders are considered to be caused, at least in part, by a hypersensitivity reaction similar to allergies, because in both cases the immune system reacts to a substance that it normally would ignore. Auto-immune disorders include, but are not limited to, Hashimoto's thyroiditis, pernicious anemia, Addison's disease, type I (insulin dependent) diabetes, rheumatoid arthritis, systemic lupus erythematosus, dermatomyositis, Sjogren's syndrome, lupus erythematosus, multiple sclerosis, myasthenia gravis, Reiter's syndrome, and Grave's disease, alopecia areata, anklosing spondylitis, antiphospholipid syndrome, auto-immune hemolytic anemia, auto-immune hepatitis, auto-immune inner ear disease, auto-immune lymphoproliferative syndrome (ALPS), auto-immune thrombocytopenic purpura (ATP), Behcet's disease, bullous pemphigoid, cardiomyopathy, celiac sprue-dermatitis, chronic fatigue syndrome immune deficiency syndrome (CFIDS), chronic inflammatory demyelinating polyneuropathy, cicatricial pemphigoid, cold agglutinin disease, CREST syndrome, Crohn's disease, Dego's disease, dermatomyositis, dermatomyositis, discoid lupus, essential mixed cryoglobulinemia, fibromyalgia-fibromyositis, Guillain-Barre syndrome, idiopathic pulmonary fibrosis, idiopathic thrombocytopenia purpura (ITP), IgA nephropathy, juvenile arthritis, Meniere's disease, mixed connective tissue disease, pemphigus vulgaris, polyarteritis nodosa, polychondritis, polyglancular syndromes, polymyalgia rheumatica, polymyositis, primary agammaglobulinemia, primary biliary cirrhosis, psoriasis, Raynaud's phenomenon, rheumatic fever, sarcoidosis, scleroderma, stiff-man syndrome, Takayasu arteritis, temporal arteritis/giant cell arteritis, ulcerative colitis, uveitis, vasculitis, vitiligo, and Wegener's granulomatosis.
“Inflammatory response” or “inflammation” is a general term for the local accumulation of fluid, plasma proteins, and white blood cells initiated by physical injury, infection, or a local immune response. Inflammation is an aspect of many diseases and disorders, including but not limited to diseases related to immune disorders, viral infection, arthritis, auto-immune diseases, collagen diseases, allergy, asthma, pollinosis, and atopy. Inflammation is characterized by rubor (redness), dolor (pain), calor (heat) and tumor (swelling), reflecting changes in local blood vessels leading to increased local blood flow which causes heat and redness, migration of leukocytes into surrounding tissues (extravasation), and the exit of fluid and proteins from the blood and their local accumulation in the inflamed tissue, which results in swelling and pain, as well as the accumulation of plasma proteins that aid in host defense. These changes are initiated by cytokines produced by activated macrophages. Inflammation is often accompanied by loss of function due to replacement of parenchymal tissue with damaged tissue (e.g., in damaged myocardium), reflexive disuse due to pain, and mechanical constraints on function, e.g., when a joint swells during acute inflammation, or when scar tissue bridging an inflamed joint contracts as it matures into a chronic inflammatory lesion.
“Anti-inflammatory” refers to the ability of a compound of the present invention to prevent or reduce the inflammatory response, or to soothe inflammation by reducing the symptoms of inflammation such as redness, pain, heat, or swelling.
Inflammatory responses can be triggered by injury, for example injury to skin, muscle, tendons, or nerves. Inflammatory responses can also be triggered as part of an immune response. Inflammatory responses can also be triggered by infection, where pathogen recognition and tissue damage can initiate an inflammatory response at the site of infection. Generally, infectious agents induce inflammatory responses by activating innate immunity. Inflammation combats infection by delivering additional effector molecules and cells to augment the killing of invading microorganisms by the front-line macrophages, by providing a physical barrier preventing the spread of infection, and by promoting repair of injured tissue. “Inflammatory disorder” is sometimes used to refer to chronic inflammation due to any cause.
Diseases characterized by inflammation of the skin, often characterized by skin rashes, include but are not limited to dermatitis, atopic dermatitis (eczema, atopy), contact dermatitis, dermatitis herpetiformis, generalized exfoliative dermatitis, seborrheic dermatitis, drug rashes, erythema multiforme, erythema nodosum, granuloma annulare, poison ivy, poison oak, toxic epidermal necrolysis and roseacae.
Inflammation can result from physical injury to the skin resulting in the “wheal and flare reaction” characterized by a mark at the site of injury due to immediate vasodilatation, followed by an enlarging red halo (the flare) due to spreading vasodilation, and elevation of the skin (swelling, the wheal) produced by loss of fluid and plasma proteins from transiently permeable postcapillary venules at the site of injury.
Inflammation triggered by various kinds of injuries to muscles, tendons or nerves caused by repetitive movement of a part of the body are generally referred to as repetitive strain injury (RSI). Diseases characterized by inflammation triggered by RSI include, but are not limited to, bursitis, carpal tunnel syndrome, Dupuytren's contracture, epicondylitis (e.g. “tennis elbow”), “ganglion” (inflammation in a cyst that has formed in a tendon sheath, usually occurring on the wrist) rotator cuff syndrome, tendinitis (e.g., inflammation of the Achilles tendon), tenosynovitis, and “trigger finger” (inflammation of the tendon sheaths of fingers or thumb accompanied by tendon swelling).
It is understood that the terms “immune disorder” and “inflammatory response” are not exclusive. It is understood that many immune disorders include acute (short term) or chronic (long term) inflammation. It is also understood that inflammation can have immune aspects and non-immune aspects. The role(s) of immune and nonimmune cells in a particular inflammatory response may vary with the type of inflammatory response, and may vary during the course of an inflammatory response. Immune aspects of inflammation and diseases related to inflammation can involve both innate and adaptive immunity. Certain diseases related to inflammation represent an interplay of immune and nonimmune cell interactions, for example intestinal inflammation (Fiocchi et al., 1997, Am J Physiol Gastrointest Liver Physiol 273: G769-G775), pneumonia (lung inflammation), or glomerulonephritis.
It is further understood that many diseases are characterized by both an immune disorder and an inflammatory response, such that the use of discrete terms “immune disorder” or “inflammatory response” is not intended to limit the scope of use or activity of the compounds of the present invention with respect to treating a particular disease. For example, arthritis is considered an immune disorder characterized by inflammation of joints, but arthritis is likewise considered an inflammatory disorder characterized by immune attack on joint tissues. In a disease having both immune and inflammatory aspects, merely measuring the effects of a compound of the present invention on inflammation does not exclude the possibility that the compound may also have immune-modulating activity in the same disease. Likewise, in a disease having both immune and inflammatory aspects, merely measuring the effects of a compound of the present invention on immune responses does not exclude the possibility that the compound may also have anti-inflammatory activity in the same disease.
“Viral infection” as used herein refers to infection of an organism by a virus that is pathogenic to that organism. It is understood that an infection is established after a virus has invaded tissues and then cells of the host organism, after which the virus has used the cellular machinery of the host to carry out functions that may include synthesis of viral enzymes, replication of viral nucleic acid, synthesis of viral packaging, and release of synthesized virus.
“Anti-viral” refers to the ability of a compound of the present invention to prevent, reduce, or eliminate a viral infection For example, an anti-viral compound of the invention may prevent viral attachment to cells, or viral entry, or viral uncoating, or synthesis of viral enzymes, or viral replication, or viral release. In particular, an anti-viral compound of the invention may prevent or otherwise inhibit viral replication in cells infected with the virus. An anti-viral compound of the invention may reduce (interfere with) viral attachment to cells, or viral entry, or viral uncoating, or synthesis of viral enzymes, or viral replication, or viral release, to such a degree that no significant disease (impairment of the normal function of an organism) results from the viral infection. An anti-viral compound of the invention may eliminate the viral infection by killing or weakening the virus so that it does not infect or replicate. An anti-viral compound of the invention may eliminate the viral infection through an immune-modulating effect that stimulates the immune system to kill the virus.
“Viral diseases,” “diseases characterized by viral infection,” and “diseases caused by viral infection” refer to impairment of the normal function of an organism as a result of viral infection. Diseases characterized by viral infection may include other aspects such as immune responses and inflammation. Compounds of the present invention are useful for treating diseases related to viral infection by RNA viruses, including retroviruses, or DNA viruses. A retrovirus includes any virus that expresses reverse transcriptase including, but not limited to, HIV-1, HIV-2, HTLV-I, HTLV-II, FeLV, FIV, SIV, AMV, MMTV, and MoMuLV.
Diseases related to viral infection can be caused by infection with a herpesvirus, arenavirus, coronavirus, enterovirus, bunyavirus, Filovirus, flavivirus, hantavirus, rotavirus, arbovirus, Epstein-Barr virus, cytomegalovirus, infant cytomegalic virus, astrovirus, adenovirus and lentivirus, in particular HIV. Diseases related to viral infection (viral diseases) include, but are not limited to, molluscum contagiosum, HTLV, HTLV-1, HIV/AIDS, human papillomavirus, herpesvirus, herpes, genital herpes, viral dysentery, common cold, flu, measles, rubella, chicken pox, mumps, polio, rabies, mononucleosis, Ebola, respiratory syncytial virus (RSV), Dengue fever, yellow fever, Lassa fever, viral meningitis, West Nile fever, parainfluenza, chickenpox, smallpox, Dengue hemorrhagic fever, progressive multifocal leukoencephalopathy, viral gastroenteritis, acute Appendicitis, hepatitis A, hepatitis B, chronic hepatitis B, hepatitis C, chronic hepatitis C, hepatitis D, hepatitis E, hepatitis X, cold sores, ocular herpes, meningitis, encephalitis, shingles, pneumonia, encephalitis, California serogroup viral, St. Louis encephalitis, Rift Valley Fever, hand, foot, & mouth Disease, Hendra virus, Japanese encephalitis, lymphocytic choriomeningitis, roseola infantum, sandfly fever, SARS, warts, cat scratch disease, slap-cheek syndrome, orf, and pityriasis rosea.
It is understood that the terms “inflammatory response” and “viral infection” and “immune disorder” are not exclusive. Many diseases related to viral infection include inflammatory responses, where the inflammatory responses are usually part of the innate immune system triggered by the invading virus. Inflammation can also be triggered by physical (mechanical) injury to cells and tissues resulting from viral infection. Examples of viral infections characterized by inflammation include, but are not limited to: encephalitis, which is inflammation of the brain following viral infection with, e.g., arbovirus, herpesvirus, and measles (before vaccines were common); meningitis, which is inflammation of the meninges (the membranes that surround the brain and spinal cord) following infection; meningoencephalitis, which is infection and inflammation of both the brain and meninges; encephalomyelitis which is infection and inflammation of the brain and spinal cord; viral gastroenteritis, which is an inflammation of the stomach and intestines caused by a viral infection; viral hepatitis, which is an inflammation of the liver caused by viral infection.
A polo like kinase (PLK) inhibitor is a compound that decreases expression or activity of one or more PLKs. A decrease in PLK expression or activity is defined by a reduction of a biological function of the PLK protein. PLKs include PLK1, PLK2, PLK3 and PLK4. PLKs are serine theronine protein kinases that are involved in the regulation of the cell cycle.
PLK expression is measured by detecting a PLK transcript or protein. PLK inhibitors are known in the art or are identified using methods described herein. For example, a PLK inhibitor is identified by detecting a decrease in cell proliferation by mitotic arrest. Mitotic arrest is measure by methods known in the art such as staining α-tubulin and DNA to identify mitotic statges.
The PLK inhibitor can be a small molecule. A “small molecule” as used herein, is meant to refer to a composition that has a molecular weight in the range of less than about 5 kD to 50 daltons, for example less than about 4 kD, less than about 3.5 kD, less than about 3 kD, less than about 2.5 kD, less than about 2 kD, less than about 1.5 kD, less than about 1 kD, less than 750 daltons, less than 500 daltons, less than about 450 daltons, less than about 400 daltons, less than about 350 daltons, less than 300 daltons, less than 250 daltons, less than about 200 daltons, less than about 150 daltons, less than about 100 daltons. Small molecules can be, e.g., nucleic acids, peptides, polypeptides, peptidomimetics, carbohydrates, lipids or other organic or inorganic molecules. Libraries of chemical and/or biological mixtures, such as fungal, bacterial, or algal extracts, are known in the art and can be screened with any of the assays of the invention.
Suitable, PLK inhibitors useful in the methods of the invention includes those described in WO2006/018185, WO2007/095188, WO2008/076392, US2010/0075973, US 2010/004250 and U.S. Pat. No. 6,673,801. Preferably, the PLK inhibitor is BI-2536 (Current Biology, Volume 17, Issue 4, 316-322, 20 Feb. 2007; CAS#755038-02-9); poloxipan (CAS #1239513-63-3); poloxin (Chemistry & Biology, Volume 15, Issue 5, 415-416, 19 May 2008; CAS#321688-88-4); Thymoquinone, or GW843682X (5-(5,6-Dimethoxy-1H-benzimidazol-1-yl)-3-[[2-(trifluoromethyl)phenyl]methoxy]-2-thiophenecarboxamide; CAS#2977; Lansing et al (2007) In vitro biological activity of a novel small-molecule inhibitor of polo-like kinase 1. Mol. Cancer Ther. 6 450.) The contents of each are hereby incorporated by reference in there entirety.
The PLK inhibitor is BI-2536, which is represented by Formula I below:
The PLK inhibitor is poloxipan, which is represented by Formula II below:
The PLK inhibitor is GW843682X, which is represented by Formula III below:
The PLK inhibitor is poloxin, which is represented by Formula IV below:
The PLK inhibitor is thymoquinone, which is represented by Formula V below:
Other suitable PLK inhibitors useful in the methods of the invention include for example, cyclapolin, DAP-81, ZK-thiazolidinone, Compound 36, and LFM-A13.
Alternatively, the PLK inhibitor is for example an antisense PLK nucleic acid, a PLK-specific short-interfering RNA, or a PLK-specific ribozyme. By the term “siRNA” is meant a double stranded RNA molecule which prevents translation of a target mRNA. Standard techniques of introducing siRNA into a cell are used, including those in which DNA is a template from which an siRNA RNA is transcribed. The siRNA includes a sense PLK nucleic acid sequence, an anti-sense PLK nucleic acid sequence or both. Optionally, the siRNA is constructed such that a single transcript has both the sense and complementary antisense sequences from the target gene, e.g., a hairpin.
Binding of the siRNA to a PLK transcript in the target cell results in a reduction in PLK production by the cell. The length of the oligonucleotide is at least 10 nucleotides and may be as long as the naturally-occurring PLK transcript. Preferably, the oligonucleotide is 19-25 nucleotides in length. Most preferably, the oligonucleotide is less than 75, 50, 25 nucleotides in length.
The PLK inhibitor is specific for at least two PLKs (i.e., PLK1, PLK2, PLK3, PLK4). Preferably, the PLK inhibitor is a pan-specific PLK inhibitor. Most preferably, the PLK inhibitor is specific for at least PLK2 and PLK4.
The invention further provides a method of decreasing and or treating inflammation subject by administering the subject a PLK inhibitor. The inflammation is associated with an innate immune response to a pathogen or a pathogen derived molecule. The pathogen binds a toll-like receptor on the surface of a dendritic cell, or in endosomes. Alternatively, the pathogen bins cytosolic RIG-1-like receptors such as for example RIG-1, MDA-5 of a dentritic cell. The pathogen is preferably a virus. Also provided are methods of decreasing anti-viral cytokine expression in a subject by administering to a subject in need thereof a Plk inhibitor. The cytokine is for example interferon-β or CXCL-10.
Efficaciousness of treatment is determined in association with any known method for diagnosing or treating the particular inflammatory disorder. Alleviation of one or more symptoms of the inflammatory disorder indicates that the compound confers a clinical benefit.
The invention further provides pharmaceutical compositions including a PLK inhibitor that can be administered to achieve a desired effect. The pharmaceutical composition includes at least one PLK inhibitor and a pharmaceutically acceptable carrier or excipient, and may optionally include additional ingredients.
The compounds of the invention can be administered systemically, regionally (e.g., directed towards an organ or tissue), or locally (e.g., intracavity or topically onto the skin), in accordance with any protocol or route that achieves the desired effect. The compounds can be administered as a single or multiple dose each day (e.g., at a low dose), or intermittently (e.g., every other day, once a week, etc. at a higher dose). The compounds and pharmaceutical compositions can be administered via inhalation (e.g., intra-tracheal), oral, intravenous, intraarterial, intravascular, intrathecal, intraperitoneal, intramuscular, subcutaneous, intracavity, transdermal (e.g., topical), or transmucosal (e.g., buccal, vaginal, uterine, rectal, or nasal) delivery. The pharmaceutical compositions can be administered in multiple administrations, by sustained release (e.g., gradual perfusion over time) or in a single bolus.
The term “subject” refers to animals, typically mammalian animals, such as primates (humans, apes, gibbons, chimpanzees, orangutans, macaques), domestic animals (dogs, cats, birds), farm animals (horses, cattle, goats, sheep, pigs) and experimental animals (mouse, rat, rabbit, guinea pig). Subjects include animal disease models. In some embodiments, the subject does not have cancer, has never had cancer, or has not been treated for cancer. For example, in some embodiments the subject has never received a PLK inhibitor to treat cancer.
Amounts administered are typically in an “effective amount” or “sufficient amount” that is an amount sufficient to produce the desired affect. Effective amounts are therefore amounts that induce PLK inhibition and one or more of: inhibiting or reducing susceptibility to inflammation, auto-immune diseases, mucositis, Parkinson's Disease, decreasing one or more symptoms associated with inflammation or viral infection, inhibiting or reducing cytokine expression, preferably interferon-β or CXCL-1-, or decreasing one or more symptoms associated with viral infection.
Effective amounts can objectively or subjectively reduce or decrease the severity or frequency of symptoms associated with inflammation, auto-immune diseases, mucositis, Parkinson's Disease, or an associated disorder or condition. For example, an amount of a compound of the invention that reduces itching, inflammation, pain, discharge or any other symptom or associated condition is an effective amount that produces a satisfactory clinical endpoint. Effective amounts also include a reduction of the amount (e.g., dosage) or frequency of treatment with another medicament to treat inflammation, auto-immune diseases, mucositis, Parkinson's Disease, which is considered a satisfactory clinical endpoint.
Methods of the invention that lead to an improvement in the subject's condition or a therapeutic benefit may be relatively short in duration, e.g., the improvement may last several hours, days or weeks, or extend over a longer period of time, e.g., months or years. An effective amount need not be a complete ablation of any or all symptoms of the condition or disorder. Thus, a satisfactory clinical endpoint for an effective amount is achieved when there is a subjective or objective improvement in the subjects' condition as determined using any of the foregoing criteria or other criteria known in the art appropriate for determining the status of the disorder or condition, over a short or long period of time. An amount effective to provide one or more beneficial effects, as described herein or known in the art, is referred to as an “improvement” of the subject's condition or “therapeutic benefit” to the subject.
An effective amount can be determined based upon animal studies or optionally in human clinical trials. The skilled artisan will appreciate the various factors that may influence the dosage or timing required to treat a particular subject including, for example, the general health, age, or gender of the subject, the severity or stage of the disorder or condition, previous treatments, susceptibility to undesirable side effects, clinical outcome desired or the presence of other disorders or conditions. Such factors may influence the dosage or timing required to provide an amount sufficient for therapeutic benefit.
The invention also provides a method of screening for regulatory and transcriptional networks controlling gene expression. The methods allow the mechanistic basis for pathogen specific responses to be determined. In particular, the invention provides a method for identifying genes or genetic elements associated with a pathogen specific response by contacting a dendritic cell with a toll-like receptor agonist and identifying genes or genetic elements whose expression is induced toll-like receptor agonist. The pathogen is a virus, a bacteria, a fungus or a parasite. Toll like receptor agonists include for example, Pam3CSK4, lipopolysaccharide, polyinosinic: polycytidylic acid, gardiquimod, or CpG. By induced is meant that gene expression is modulated (upregulated or downregulated) due to agonist treatment. Gene expression is measured by methods know in the art. In various embodiments the method further includes perturbing expression of the induced gene or genetic element. This perturbation allows for network reconstruction of the regulatory or transcriptional networks controlling gene expression. For example, RNA expression of the induced genes is inhibited by using anti-sense olignucleotides, siRNA, shRNA, RNAi or any other method known to interfere or inhibit expression of a target gene.
Cells and Mouse Strains
Bone marrow-derived DCs were generated from 6-8 week old female C57BL/6J mice, Crkl mutant mice (Jackson Laboratories), Plk2−/− mice (Elan Pharmaceuticals), or Ifnar1−/− mice (gift from K. Fitzgerald). Primary mouse lung fibroblasts (MLFs) were from C57BL/6J mice.
Viruses
Sendai virus (SeV) strain Cantell and Encephalomyocarditis virus (EMCV) strain EMC (ATCC), Newcastle disease virus (NDV) strain Hitchner B1 (gift from A. Garcia-Sastre), and vesicular stomatitis virus (VSV) strain Indiana (U. von Andrian), were used for infections. Influenza A virus strain A/PR/8/34 and ΔNS1 were grown in Vero cells, and virus titers from MLF supernatants was quantified using 293T cells transfected with a vRNA luciferase reporter plasmid.
mRNA Isolation, qPCR, and Microarrays
Total or polyA+ RNA was extracted and reverse transcribed prior to qPCR analysis with SYBR Green (Roche) in triplicate with GAPDH for normalization. For microarray analysis, Affymetrix Mouse Genome 430A 2.0 Array were used.
Preparation of Dendritic Cells
Bone marrow-derived dendritic cells (BMDCs) were generated from 6-8 week old female C57BL/6J mice (Jackson Laboratories). Bone marrow cells were collected from femora and tibiae and plated at 106 cells/mL on non-tissue culture treated petri dishes in RPMI-1640 medium (Gibco), supplemented with 10% FBS, L-glutamine, penicillin/streptomycin, MEM non-essential amino acids, HEPES, sodium pyruvate, β-mercaptoethanol, and murine GM-CSF (15 ng/mL; Peprotech) or human Flt3L (100 ng/mL; Peprotech). GM-CSF-derived BMDCs were used directly for all RNAi experiments. For all other experiments, floating cells from GM-CSF cultures were sorted at day 5 by MACS using the CD11c (N418) MicroBeads kit (Miltenyi Biotec). Sorted CD11c+ cells were used as GM-CSF-derived BMDCs, and plated at 106 cells/mL and stimulated at 16 h post sorting. For Flt3L culture, floating cells were harvested at day 6-8 and used as Flt3L-derived BMDCs by plating them at 106 cells/mL and stimulating 16 h later. For SILAC experiments, GM-CSF-derived BMDCs were grown in media containing either normal L-arginine (Arg-0) and L-lysine (Lys-0) (Sigma) or L-arginine 13C6-15N4 (Arg-10) and L-lysine 13C6-15N2 (Lys-8) (Sigma Isotec). Concentrations for L-arginine and L-lysine were 42 mg/L and 40 mg/L, respectively. The cell culture media, RPMI-1640 deficient in L-arginine and L-lysine, was a custom media preparation from Caisson Laboratories (North Logan, Utah) and dialyzed serum was obtained from SAFC-Sigma. We followed all standard SILAC media preparation and labeling steps as previously described (Ong and Mann, 2006).
Preparation of Primary Lung Fibroblasts
Mouse lung fibroblasts (MLFs) were derived from lung tissue from 6-8 week old female C57BL/6J mice (Jackson Laboratories). MLFs were isolated as previously described (Tager et al., 2004). Briefly, lungs were digested for 45 min at 37° C. in collagenase and DNase I, filtered, washed, and cultured in DMEM supplemented with 15% FBS. Cells were used for experiments between passages 2 and 5.
Genetically Modified Mice
Bone marrow from Plk2−/− mice and their wild-type littermates were obtained from Elan Pharmaceuticals (Inglis et al., 2009). Ifnar1−/− mice on a C57BL/6J background were a gift from Kate Fitzgerald (originally from Jonathan Sprent based on Muller et al., 1994). Heterozygous Crkl+/− mice on a C57BL/6J background were obtained from the Jackson Laboratory. Crkl+/− C57BL/6J mice were crossed to wild-type Black Swiss mice from Taconic, as Crkl−/− mice on a pure C57BL/6J genetic background have been reported to be embryonic lethal (Guris et al., 2001; Hemmeryckx et al., 2002). Heterozygous Crkl+/− offspring were backcrossed to Crkl+/− C57BL/6J mice to obtain Crkl−/− mice. Mice were kept in a specific pathogen-free facility at MIT. Animal procedures were in accordance with National Institutes of Health Guidelines on animal care and use, and were approved by the MIT Committee on Animal Care (Protocol #0609-058-12).
Viruses
Viruses Sendai virus (SeV), strain Cantell, and Encephalomyocarditis virus (EMCV), strain EMC, were from ATCC. Newcastle disease virus (NDV), strain Hitchner B1 was from Aldolfo Garcia-Sastre (Mount Sinai School of Medicine), and vesicular stomatitis virus (VSV), strain Indiana was from Ulrich von Andrian (Harvard Medical School). Influenza A virus strain A/PR/8/34 and ΔNS1 were grown in Vero cells (which allow efficient growth of the ΔNS1 virus) in serum-free DMEM supplemented with 10% BSA and 1 mg/ml TPCK trypsin. Viral titers were determined by standard MDCK plaque assay. To measure the amount of VSV RNA present in infected tissues, we used previously reported qPCR primers: VSV Forward 5′-TGATACAGTACAATTATTTTGGGAC-3′ (SEQ ID NO: 1), and VSV Reverse 5′-GAGACTTTCTGTTACGGGATCTGG-3′ (SEQ ID NO: 2) (Hole et al., 2006). Viruses were handled according to CDC and NIH guidelines with protocols approved by the Broad Institutional Biosafety Committee.
Reagents
TLR ligands were from Invivogen (Pam3CSK4, ultra-pure E. coli K12 LPS, ODN 1585 CpG type A, and ODN 1668 CpG type B) and Enzo Life Sciences (poly(I:C)), and were used at the following concentrations: Pam3CSK4 (250 ng/mL), poly(I:C) (10 μg/mL), LPS (100 ng/mL), CpG-A (10 μg/mL), CpG-B (10 μg/mL). Heat-killed Listeria monocytogenes (HKLM) was from Invivogen. Polo-like kinase inhibitors were from Selleck (BI 2536; Steegmaier et al., 2007), Sigma (GW843682X, also known as compound 1 and GSK461364; Lansing et al., 2007), and Chembridge (Poloxipan; Reindl et al., 2009). SP 600125 (Jnk inhibitor) was from Enzo Life Sciences. Image-iT FX Signal Enhancer, DAPI, and Alexa Fluor Labeled Secondary Antibodies were obtained from Invitrogen. For immunofluorescence, antibodies against IRF3 (4302S) and NF-κB P65 (4764S) were obtained from Cell Signaling Technology. For cell viability assays, Alamar Blue was from Invitrogen and CellTiter-Glo from Promega.
Virus Titering of MLF Supernatant
293T cells were seeded and transfected with a vRNA luciferase reporter plasmid as previously described (Shapira et al., 2009). Briefly, at 24 h post-transfection, 104 transfected reporter cells were re-seeded in white Costar plates. Supernatants from influenza-infected MLFs were added to reporter cells and incubated for 24 h. Reporter activity was measured with firefly luciferase substrate (Steady-Glo, Promega). Luminescence activity was quantified with the Envision Multilabel Reader (Perkin Elmer).
Cell Cycle Analysis
Cells were fixed in ethanol, washed, and stained for 30 min at room temperature (RT) with propidium iodide (100 μg/mL) prepared in PBS (calcium- and magnesium-free) supplemented with RNAse A (2 mg/mL; Novagen) and triton X-100 (0.1%). Samples were analyzed for DNA content using an Accuri C6 flow cytometer (Accuri) and data was processed using the FlowJo software (Treestar).
ELISA
Cell culture supernatants were assayed using a sandwich ELISA kit for mouse IFN-β (PBL Biomedical Laboratories).
mRNA Isolation
Total RNA was extracted with QIAzol reagent following the miRNeasy kit's procedure (Qiagen), and sample quality was tested on a 2100 Bioanalyzer (Agilent). RNA was reverse transcribed with the High Capacity cDNA Reverse Transcription kit (Applied Biosystems). For experiments with more than 12 samples, we harvested PolyA+RNA in 96- or 384-well plates with the Turbocapture mRNA kit (Qiagen) and reverse transcribed with the Sensiscript RT kit (Qiagen).
qPCR Measurements
Real time quantitative PCR reactions were performed on the LightCycler 480 system (Roche) with FastStart Universal SYBR Green Master Mix (Roche). Every reaction was run in triplicate and GAPDH levels were used as an endogenous control for normalization.
shRNA Knockdowns
High titer lentiviruses encoding shRNAs targeting genes of interest were obtained from The RNAi Consortium (TRC; Broad Institute, Cambridge, Mass., USA) (Moffat et al., 2006). Bone marrow cells were infected with lentiviruses as described (Amit et al., 2009). For each gene of interest, we tested five shRNAs for knock down efficiency using qPCR of the target gene. We selected shRNAs with >75% knockdown efficacy. For combinatorial knockdown, two independent mixtures of two lentiviruses encoding validated shRNAs against Plk2 and 4, respectively, were used to infect bone marrow cells (two Plk2- and two Plk4-specific shRNAs were used to generate these mixtures). Lentivirus-infected cells were composed of 90% CD11c+ cells, which was comparable to sorted BMDCs and to our previous observations (Amit et al., 2009).
mRNA Measurements on nCounter
Details on the nCounter system are presented in full in (Geiss et al., 2008). We used a custom CodeSet constructed to detect a total of 128 genes (including 10 control genes whose expression remain unaffected by TLR stimulation) selected by the GeneSelector algorithm (Amit et al., 2009) as described below. 5×104 bone marrow-derived DCs were lysed in RLT buffer (Qiagen) supplemented with 1% β-mercaptoethanol. 10% of the lysate was hybridized for 16 hours with the CodeSet and loaded into the nCounter prep station followed by quantification using the nCounter Digital Analyzer following the manufacturer's instructions. To score target genes whose expression is significantly affected by shRNA perturbations, we used a fold threshold corresponding to a false discovery rate (FDR) of 2%. Heatmaps and distance matrix analyses were generated using the Gene-E software (broadinstitute.org/cancer/software/GENE-E/).
Custom Nanostring CodeSet Construction Using the GeneSelector Algorithm
We used the CodeSet that we previously used and described in Amit et al., 2009. Briefly, to choose a set of genes that will capture as much as possible of the information on the expression of all genes, we used an information-theoretic approach. We modeled the expression levels X given the experimental condition C with a naive Bayes model where the expression of gene i under condition c follows a normal distribution Xi|C=c˜N(μic,σi2). In this model, the expression levels of all genes depend on the experimental condition C, and we selected genes that are highly informative about C. Formally, for a set of genes Y we used the conditional entropy H(C|Y)=−Σcp(C=c)Σyp(Y=y|C=c)log p(C=c|Y=y) as a measure of the remaining uncertainty in C once the expression levels Y are known. We then used this measure and a greedy procedure to select multiple disjoint gene sets, Y1, . . . , Yk such that for each set Yi, H(C|Yi)<η (we set η=0.5). In the greedy procedure, we select genes one at a time, and with each selected gene re-compute the entropy given the genes already selected in the current set. Once a set is complete (the remaining conditional entropy is below the threshold η), we add all the genes to the selected set, and repeat the procedure (excluding all the selected genes from consideration). We stop when the number of selected genes has reached a user-defined threshold, set by the number of genes feasible for the experimental assay. To select a time point, we used the same approach. Here, we measured entropy under all time points for multiple randomly selected gene sets of several sizes and plotted the average entropy for each timepoint (see Amit et al., 2009). We chose the time point with the minimal entropy (i.e., 6 h post-simulation).
nCounter Data Analysis
After normalization by internal Nanostring controls (spike-normalization following manufacturer's instructions), we normalized the data relying on three control genes (Ndufa7, Tbca, Tomm7) that are the least affected by shRNAs and LPS stimulation. Next, we log-transformed the expression values (Bengtsson and Hossjer, 2006). Five signature genes (Cxcl5, Fos, Fst, Ereg, and Egr2) that were highly variable across control shRNA samples were removed from subsequent analysis. To score target genes whose expression is significantly affected by perturbations, we used a fold threshold corresponding to a false discovery rate (FDR) of 2%. For a given shRNA perturbation, a target gene was called as significantly affected when the ratio of the log-expression of this gene upon shRNA knockdown to the average log-expression of this gene in control shRNA samples was below (or above) a threshold (1/threshold), chosen such that, on average, no more than 2 hits (out of 128 genes in the Nanostring codeset) per control shRNA sample were called. Heatmaps and distance matrix analyses were generated using the software Gene-E (broadinstitute.org/cancer/software/GENE-E/).
Microarray Hybridization and Processing
For oligonucleotide microarray hybridization, 1 μg of RNA were labeled, fragmented, and hybridized to an Affymetrix Mouse Genome 430A 2.0 Array. After scanning, the expression value for each gene was calculated with RMA (Robust Multi-Array) normalization. The average intensity difference values were normalized across the sample set. Probe sets that were absent in all samples according to Affymetrix flags were removed. All values below 50 were floored to 50.
Detection of Regulated Signaling Genes
To identify differentially regulated signaling components (i.e., kinases, phosphatases, and signaling adaptors or scaffolds), we defined regulated probesets for each condition (TLR agonist) as probesets displaying at least 1.7-fold up- or down-regulation in both duplicates of at least one time point, compared to unstimulated controls, using our previously published microarray dataset available in the NCBI Gene Expression Omnibus under the accession number GSE17721 (Amit et al., 2009). Differentially regulated probesets were intersected with lists of kinases, phosphatases, and signaling adaptors and scaffolds. These gene sets were generated combining data from publicly available databases: Panther (pantherdb.org), Gene Ontology (geneontology.org), and DAVID (david.abcc.ncifcrf.gov). Regulated signaling genes were hierarchically clustered using the Cluster software (Eisen et al., 1998).
Antiviral Versus Inflammatory Gene Enrichment
Genes whose expression changed upon BI 2536 treatment in microarrays were evaluated for their enrichment with genes involved in the antiviral and inflammatory programs. When multiple probesets were available for a given gene on the microarray, only the probeset with maximum value was kept for analysis. Thus, the complete microarray consisted of 14088 genes, among which 804 and 550 genes were identified as part of antiviral and inflammatory programs, respectively (Amit et al., 2009). We performed a hypergeometric test on genes whose expression changed at least 3-fold upon BI 2536 treatment compared to vehicle control (DMSO), in either LPS or poly(I:C) samples. In addition, genes whose expression changed upon BI 2536 treatment in microarrays in response to LPS and/or poly(I:C) stimulation were analysed for enrichment of Gene Ontology (GO) processes and canonical pathways from curated databases using the Molecular Signature Database (MSigDB; broadinstitute.org/gsea/msigdb/index.jsp).
Nanowire-Mediated Drug Delivery and Microscopy
BMDCs were plated on top of etched silicon nanowires (Si NWs) coated with small molecules (Shalek et al., 2010). After 24 hours, cells were stimulated with LPS or poly(I:C), and then fixed in 4% formaldehyde in PBS (RT, 10 min). After fixation, each sample was permeabilized with 0.25% Triton-X 100 in PBS (RT, 10 min), incubated with Image-iT FX Signal Enhancer (RT, 30 min), and then blocked with 10% goat serum and 0.25% Triton-X 100 in PBS (RT, 1 hour). After washing, the samples were placed in 3% IgG-Free BSA & 0.25% Triton-X 100 in PBS that contained primary antibodies against either IRF3 or NF-κB P65 (1:175 dilution) and then rocked overnight at 4° C. The following day, the samples were washed with PBS and then incubated with an Alexa Fluor labeled secondary antibody (1:250 dilution) in 3% IgG-Free BSA & 0.25% Triton-X 100 in PBS (RT, 60 min). After washing with PBS, the samples were counterstained with 300 ng/mL of DAPI in PBS (RT, 30 min). For each experiment, every stimulus-molecule combination was prepared in triplicate. Once fixed, samples were imaged using an upright confocal microscope (Olympus). For each captured image, the nuclear fraction of the fluorescent protein was calculated after identifying nuclear boundaries using DAPI. Finally, distributions for this quantity across different conditions were compared using a one-way ANOVA analysis.
In Vivo BI 2536 Experiments in a VSV Infection Model
8-week old C57BL/6 male mice (from Charles River Laboratories) received 500 μg of BI 2536 (or vehicle) intravenously, and 50 μg into the footpad 3 hours before and 2 hours after infection with 106 pfu of VSV, as previously described (Iannacone et al., 2010), into the footpad. Mice were sacrificed 6 hours post-infection and the draining popliteal lymph nodes were harvested in RNAlater solution (Ambion) before subsequent RNA analysis. All experimental animal procedures were approved by the Institutional Animal Committees of Harvard Medical School and IDI. All infectious work was performed in designated BL2+ workspaces, in accordance with institutional guidelines, and approved by the Harvard Committee on Microbiological Safety.
MicroWestern Arrays
The MicroWestern Array (MWA) method previously described (Ciaccio et al., 2010) was modified to accommodate a larger number of lysates. The lysates were printed in a ‘double-block’ format with each MWA being 18 mm wide by 9 mm long. Twelve samples plus protein marker (Li-cor 928-40000) were printed with a non-contact piezoelectric arrayer (GeSiM NP2) along the top edge of the block, each block printed forty-eight times on the acrylamide gel. The deck layout is included in
Phosphotyrosine Peptide Analysis
Tyrosine-phosphorylated peptides were prepared using a PhosphoScan Kit (Cell Signaling Technology) as previously described (Rush et al., 2005). Briefly, 100 million cells were lysed in lysis buffer (20 mM HEPES, 25 mM sodium pyrophosphate, 10 mM beta-glycerophosphate, 9 M urea, 1 mM ortho-vanadate, 1 Roche Ser/Thr phosphatase inhibitor tablet) assisted by sonication on ice using Misonix S-4000 sonicator with five 30-second bursts at 4 watts. Lysates were pre-cleared by centrifugation for 15 min at 20,000 g. ˜10 mg of total proteins from each SILAC label were mixed, reduced with 10 mM dithiothreitol and alkylated with 25 mM iodoacetamide. After 4-fold dilution 200 μg sequencing grade modified trypsin (Promega, V5113) was added in an enzyme to substrate ratio of 1:100. The total peptide mixtures were then desalted using a tC18 SepPak cartridge (Waters, 500 mg, W AT036790) and resuspended in IAP buffer (50 mM MOPS/NaOH pH 7.2, 10 mM Na2HPO4, 50 mM NaCl). Peptide immunoprecipitation was performed with protein-G agarose bead-bound anti-phosphotyrosine antibodies pY100. Peptides captured by phosphotyrosine antibodies were eluted under acidic conditions (0.15% trifluoroacetic acid). The IP eluate was analyzed by data-dependent LC-MS/MS using a Thermo LTQ-Orbitrap instrument.
Global Serine, Threonine, and Tyrosine Phosphorylation Analysis
Quantitative analysis of serine, threonine and tyrosine phosphorylated peptides was performed essentially as described (Villen and Gygi, 2008) with some modifications. After stimulation, cells were lysed for 20 min in ice-cold lysis buffer (8 M Urea, 75 mM NaCl, 50 mM Tris pH 8.0, 1 mM EDTA, 2 μg/ml Aprotinin (Sigma, A6103), 10 μg/ml Leupeptin (Roche, #11017101001), 1 mM PMSF, 10 mM NaF, 2 mM Na3VO4, 50 ng/ml Calyculin A (Calbiochem, #208851), Phosphatase inhibitor cocktail 1 (1/100, Sigma, P2850) and Phosphatase inhibitor cocktail 2 (1/100, Sigma, P5726). Lysates were precleared by centrifugation at 16,500 g for 10 min and protein concentrations were determined by BCA assay (Pierce). We obtained 3 mg total protein per label out of 30 million cells. Cell lysates were mixed in equal amounts per label and proteins were reduced with 5 mM dithiothreitol and alkylated with 10 mM iodoacetamide. Samples were diluted 1:4 with HPLC water (Baker) and sequencing-grade modified trypsin (Promega, V5113) was added in an enzyme to substrate ratio of 1:150. After 16 h digest, samples were acidified with 0.5% trifluoroacetic acid (final concentration). Tryptic peptides were desalted on reverse phase tC18 SepPak columns (Waters, 500 mg, WAT036790) and lyophilized to dryness. Peptides were reconstituted in 500 μl strong cation exchange buffer A (7 mM KH2PO4, pH 2.65, 30% MeCN) and separated on a Polysulfoethyl A column from PolyLC (250×9.4 mm, 5 μm particle size, 200 A pore size) using an Akta Purifier 10 system (GE Healthcare). We used an 80 min gradient with a 20 min equilibration phase with buffer A, a linear increase to 30% buffer B (7 mM KH2PO4, pH 2.65, 350 mM KCL, 30% MeCN) within 33 min, 100% B for 7 min and a final equilibration with Buffer A for 20 min. The flow rate was 3 ml/min and the sample was injected after the initial 20 min equilibration phase. Upon injection, 3 ml fractions were collected with a P950 fraction collector throughout the run. 60 fractions were collected of which 3-4 adjacent fractions were combined to obtain 12 samples. Pooling of SCX fractions was guided by the UV214-trace and fractions were combined starting where the first peptide peak appeared. The 12 samples were desalted with reverse phase tC18 SepPak columns (Waters, 100 mg, WAT036820) and lyophilized to dryness. SCX-separated peptides were subjected to IMAC (immobilized metal affinity chromatography) as described (Villen and Gygi, 2008). Briefly, peptides were reconstituted in 200 μl IMAC binding buffer (40% MeCN, 0.1% FA) and incubated for 1 h with 5 μl of packed Phos-Select beads (Sigma, P9740) in batch mode. After incubation, samples were loaded on C18 StageTips (Rappsilber et al., 2007), washed twice with 50 μl IMAC binding buffer and washed once with 50 μl 1% formic acid. Phosphorylated peptides were eluted from the Phos-Select resin to the C18 material by loading 3 times 70 μl of 500 mM K2HPO4 (pH 7.0). StageTips were washed with 50 μl of 1% formic acid to remove phosphate salts and eluted with 80 μl of 50% MeCN/0.1% formic acid. Samples were dried down by vacuum centrifugation and reconstituted in 8 μl 3% MeCN/0.1% formic acid.
NanoLC-MS/MS Analysis
All peptide samples were separated on an online nanoflow HPLC system (Agilent 1200) and analyzed on a LTQ Orbitrap Velos (Thermo Fisher Scientific) mass spectrometer. 4 μl of peptide sample were autosampled onto a 14 cm reverse phase fused-silica capillary column (New Objective, PicoFrit PF360-75-10-N-5 with 10 μm tip opening and 75 μm inner diameter) packed in-house with 3 μm ReproSil-Pur C18-AQ media (Dr. Maisch GmbH). The HPLC setup was connected via a custom-made electrospray ion source to the mass spectrometer. After sample injection, peptides were separated at an analytical flowrate of 200 nL/min with an 70 min linear gradient (˜0.29% B/min) from 10% solvent A (0.1% formic acid in water) to 30% solvent B (0.1% formic acid/90% acetonitrile). The run time was 130 min for a single sample, including sample loading and column reconditioning. Data-dependent acquisition was performed using the Xcalibur 2.1 software in positive ion mode. The instrument was recalibrated in real-time by co-injection of an internal standard from ambient air (“lock mass option”) (Olsen et al., 2005). Survey spectra were acquired in the orbitrap with a resolution of 60,000 and a mass range from 350 to 1750 m/z. In parallel, up to 16 of the most intense ions per cycle were isolated, fragmented and analyzed in the LTQ part of the instrument. Ions selected for MS/MS were dynamically excluded for 20 s after fragmentation. For the second biological replicate analysis peptides observed to be regulated in the first analysis were loaded into a global parent mass inclusion list and 4 MS/MS scans were reserved for precursors from the inclusion list whereas 12 were performed on the most intense ions per duty cycle.
Identification and Quantification of Peptides and Proteins
Mass spectra were processed using the Spectrum Mill software package (Agilent Technologies) v4.0 b that includes in-house developed features for SILAC-based quantitation and phoshosite localization and also with the MaxQuant software package (version 1.0.13.13) (Cox and Mann, 2008), which was used in combination with a Mascot search engine (version 2.2.0, Matrix Science). For peptide identification in Spectrum Mill an International Protein Index protein sequence database (IPI version 3.60, mouse) was used which was reversed on-the-fly at search time. In MaxQuant a concatenated forward and reversed IPI protein sequence database (version 3.60, mouse) was queried. The mass tolerance for precursor ions and for fragment ions was set to 7 ppm and 0.5 Da, respectively. Cysteine carbamidomethylation was searched as a fixed modification, whereas oxidation on methionine, N-acetylation (Protein) and phosphorylation on serine, threonine or tyrosine residues were considered as variable modifications. The enzyme specificity was set to trypsin and cleavage N-terminal of proline was allowed. The maximum of missed cleavages was set to 3. For peptide identification the maximum peptide FDR was set to 1%. The minimum identification score was to 5 in Spectrum Mill and to 10 in MaxQuant. SILAC ratios were obtained from the peptide export table in Spectrum Mill and the evidence table in MaxQuant. Arginine to Proline conversion was determined to be 3.42% and 5.55% for both biological replicates, respectively. The conversion was calculated by defining Arg-10 as a fixed modification and by quantifying the ratio between peptides containing normal L-proline (Pro-0) and 13C5-15N1-labeled proline (Pro-6) with MaxQuant. Each peptide SILAC ratio was corrected for arginine to proline conversion by the formula r[c]=r[o]/((1−p)̂n), where r[c] is the corrected ratio, r[o] the observed ratio, p the conversion rate and n the number of proline residues per peptide. The median ratios of all non-phosphorylated peptides were used to normalize the M/L, and H/L ratios of all phosphorylated peptides. To allow better peptide grouping, phosphosite localization information obtained from SpectrumMill and MaxQuant were further simplified. Probability scores greater or equal 0.75 were called fully localized and designated with (1.0), scores smaller 0.75 and greater or equal to 0.5 were called ambiguously localized and designated with (0.5), whereas scores smaller than 0.5 were called non-localized and the total number of phosphorylation sites per peptide was designated with an underscore after the peptide sequence. Median SILAC ratios of phosphopeptides for each experiment were calculated over all versions of the same peptide including different charge states and methionine oxidation states. The highest scoring versions of each distinct peptide were reported per experiment. Overlapping data between SpectrumMill and MaxQuant as well as between different biological replicates was analyzed for discrepancies by calculating the mean and standard deviation over all residuals for different ratios of the same phosphopeptide. Residuals were calculated by subtracting the two values for each phosphopeptide derived by SpectrumMill or MaxQuant as well as by two different biological replicates. All peptides were filtered from the data set that had residuals greater than 3 standard deviations distant from the mean as they were not reproducible between two biological replicates or between SpectrumMill and MaxQuant. Data derived from both software packages was combined and MaxQuant data was reported when the same phosphopeptide was identified and quantified by both programs. Log 2 phosphopeptide ratios of BI-2536 treated vs untreated dendritic cells followed a normal distribution that was fitted using least squares regression. Mean and standard deviation values derived from the Gaussian fit were used to calculate p-values. An FDR-based measure was used to assess significance of the findings (Storey and Tibshirani, 2003).
To discover new components of pathogen-sensing pathways, we used genome-wide mRNA profiles, previously measured at 10 time points along 24 hours following stimulation of primary bone marrow-derived DCs (BMDCs) with lipopolysaccharide (LPS; TLR4 agonist), polyinosinic:polycytidylic acid (poly(I:C); recognized by TLR3 and the cytosolic viral sensor MDA-5), or Pam3CSK4 (PAM; TLR2 agonist) (Amit et al., 2009). These three TLRs activate transcriptional programs referred to here as “inflammatory” (TLR2), “antiviral” (TLR3), or both (TLR4) (
Our analysis uncovered 280 genes annotated as known or putative signaling molecules that were differentially expressed following stimulation: 115 kinases, 69 phosphatases, and 96 other regulators, such as adaptors and scaffolds (
We perturbed our 6 positive controls and 17 of the 23 candidates in BMDCs using shRNA-encoding lentiviruses (six candidates showed poor knockdown efficiency). We stimulated the cells with LPS, and measured the effect of gene silencing on the mRNA levels of 118 TLR response signature genes, representing the inflammatory and antiviral programs, using a multiplex mRNA counting method (
Perturbing 5 of the 6 positive control signaling molecules strongly affected the expression of TLR signature genes, consistent with their known roles (
All of the 17 candidate signaling molecules tested, except Plk2 (discussed below), affected at least 6 of the 118 genes (on average, 16.6 targets±10.4SD), and 12 affected more than 10% of the genes (
We identified both primary (e.g., Myd88) and secondary (e.g., Stat1) mediators of TLR responses. While secondary mediators are not part of the initial intracellular signaling cascade, they are important physiological components of the TLR response and their pertubation can lead to similar phenotypic outcomes as that of primary components. For example, the receptor tyrosine kinase Mertk acted as both a positive and negative regulator of some inflammatory and antiviral genes (e.g., Ifnb1) respectively (
Among the 17 candidate signaling proteins, perturbation of the tyrosine kinase adaptor Crkl decreased expression of 13% of the signature genes, especially antiviral ones (
To test whether Crkl is a primary component of the TLR pathway, we measured if Crkl phosphorylation is rapidly modified after TLR signaling initiation. Using SILAC-based (Ong et al., 2002) quantitative phosphoproteomics, we identified and quantified 62 phospho-tyrosine (pTyr)-containing peptides from BMDCs stimulated with LPS for 30 minutes (
Several lines of evidence suggest that Crkl acts through Jnk2 (Mapk9) signaling. First, the MAP kinase Jnk2 (Mapk9) is co-regulated at the phosphorylation level with Crkl upon LPS stimulation (
To discover potential drug targets among our 17 candidates, we next focused on Polo-like kinase (Plk) 2, a well-known cell cycle regulator and drug target (Strebhardt, 2010). The roles of Plks in non-dividing, differentiated cells are poorly defined (Archambault and Glover, 2009; Strebhardt, 2010). We have previously shown that transcriptional regulators of cell cycle processes (e.g., Rb11, Rb, Myc, Jun, E2fs) are co-opted to function in the antiviral responses in DCs (Amit et al., 2009). However, neither knockdown (
To test our hypothesis, we simultaneously perturbed Plk2 and 4 in BMDCs using two independent mixes of different pairs of shPlk2/shPlk4 (
We next targeted Plks in BMDCs using BI 2536, a commercial pan-specific Plk small molecule inhibitor (Steegmaier et al., 2007). We compared genome-wide mRNA profiles from BMDCs treated with either BI 2536 or DMSO vehicle before stimulation with LPS or poly(I:C) (Experimental Procedures). BI 2536 treatment repressed mostly antiviral gene expression compared to DMSO (99/193 genes in response to poly(I:C), P<1×10−71, hypergeometric test; 67/194 in response to LPS). The 311 unique LPS- and/or poly(I:C)-induced genes that are repressed by BI 2536, are significantly enriched for genes related to cytokine signaling (e.g., IL-10, type I IFNs, IL-1), TLR signaling, and DC signaling, and for GO processes related to defense and immune responses (
BI 2536 reduced the mRNA levels of Cxcl10 and Ifnb1 (by qPCR) and of secreted IFN-β in a dose-dependent manner, while Cxcl1 expression was not significantly affected (
We next used confocal microscopy to monitor the effect of BI 2536 on the subcellular localization of IRF3, a key antiviral transcription factor. To more effectively deliver the drug, we plated BMDCs on vertical silicon nanowires (Shalek et al., 2010) pre-coated with BI 2536 pre-stimulation. Nanowires alone had no effect on the TLR response (
DCs can be broadly categorized into two major subtypes—conventional and plasmacytoid DCs—each relying on distinct mechanisms to induce type I IFNs and antiviral gene expression (Blasius and Beutler, 2010). In conventional DCs (cDCs), antiviral responses are activated through TLR4/3 signaling (via TRIF), or through the cytosolic sensors RIG-I or MDA-5 (via MAVS) (
To assess the impact of Plk inhibition on the outcome of viral infection, we infected primary mouse lung fibroblasts (MLFs) with influenza virus. BI 2536-treated MLFs infected with influenza failed to produce interferon (
Next, we tested the effects of Plk inhibition in virally infected mice. BI 2536 exhibits good tolerability in mice (Steegmaier et al., 2007) and humans (Mross et al., 2008), and is currently in Phase II clinical trials as an anti-tumor agent in several cancers (Strebhardt, 2010). Given its efficacy and safety in vivo, we tested whether BI 2536 would also affect the response to viral infection in animals. In mice infected with VSV, BI 2536 strongly suppressed 13D). Concomitantly, VSV replication in the lymph node rapidly increased as reflected by elevated VSV RNA levels (
We next sought to discover the signaling pathways between Plks and antiviral gene transcription. We used MicroWestern Arrays (MWAs) (Ciaccio et al., 2010) to measure changes in the phosphorylation and protein levels of 20 and 6 TLR pathway proteins, respectively, in BMDCs at each of 12 combinations of four time points (0, 20, 40, 80 min after LPS stimulation) and three perturbations (vehicle control, BI 2536, and negative control JNK inhibitor SP 600125). While LPS stimulation alone led to the expected changes (e.g., early peak of phosphorylation for ERK1/2, p38, and Mapkapk2, and rapid degradation of IκBα;
Next, we used SILAC-based unbiased phosphoproteomics (
The Plk-dependent phosphoproteins include several known regulators of antiviral pathways (e.g., Prdm1, Fos, Unc13d) (Crozat et al., 2007; Keller and Maniatis, 1991; Takayanagi et al., 2002), as well as many additional protein candidates with no previously known function in viral sensing (
We perturbed 25 Plk-dependent phosphoproteins, using shRNA perturbation in BMDCs followed by qPCR and TLR gene signature measurements. These candidates satisfied three criteria: (1) there was no prior knowledge of their function in viral sensing pathways; (2) their phosphoprotein levels were consistently up- or down-regulated upon BI 2536 treatment (in two independent experiments); and (3) they had detectable mRNA expression and/or differential expression upon stimulation.
Of the 18 phosphoproteins showing efficient knockdown, 11 caused a significant decrease in Ifnb1 mRNA levels with a single shRNA (Sash1, Dock8, Nek6, Nek7, Nfatc2, and Ankrd17;
9 of the 11 Plk-dependent phosphoproteins affected the TLR signature comparably to major antiviral regulators (
This application is a continuation of U.S. application Ser. No. 13/878,386 filed Sep. 25, 2013, which is a national stage application, filed under 35 U.S.C. § 371, of PCT Application No. PCT/US2011/055437, filed Oct. 7, 2011, which claims the benefit of provisional applications U.S. Ser. No. 61/391,490, filed Oct. 8, 2010 and U.S. Ser. No. 61/497,251 filed Jun. 15, 2011, the contents which are each herein incorporated by reference in their entirety.
This invention was made with government support under AI057159 awarded by the National Institutes of Health. The government has certain rights in the invention.
| Number | Date | Country | |
|---|---|---|---|
| 61391490 | Oct 2010 | US | |
| 61497251 | Jun 2011 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 13878386 | Sep 2013 | US |
| Child | 15782674 | US |
