Patent Application
20230236188
Lupus is a group of conditions with similar underlying mechanisms involving autoimmunity. In these conditions, antibodies created by the body to attack antigens (e.g., viruses, bacteria) become unable to differentiate between antigens and healthy tissue. Thus, these antibodies begin to attack the body's own healthy tissues. Lupus is generally a chronic disease in which the signs and symptoms tend to come and go. Lupus also increases the risk of developing various other diseases such as heart disease, osteoporosis, and kidney disease. Types of lupus include, for example, systemic lupus erythematosus (SLE), cutaneous lupus erythematosus (CLE) (CLE includes, e.g., acute cutaneous lupus erythematosus (ACLE), subacute cutaneous lupus erythematosus (SCLE), intermittent cutaneous lupus erythematosus, and chronic cutaneous lupus), drug-induced lupus, and neonatal lupus. About 70% of all cases of lupus are SLE.
Diagnosing and monitoring of lupus remain problematic. Thus, the need exists for novel ways of identifying, assessing, and treating individuals affected by the disease.
In certain embodiments, the present invention provides a method of treating or preventing lupus in a subject, comprising: (a) identifying the subject as having at least one differentially regulated biomarker selected from CD40, CD40L, CD86, CD80, and PD1; and (b) administering an agent that inhibits the CD40 or CD28 signaling pathway, thereby treating or preventing lupus in the subject. For example, the lupus is systemic lupus erythematosus (SLE).
In certain specific embodiments, the method of the present invention comprises identifying the subject as having at least two, at least three, or at least four, differentially regulated biomarker selected from CD40, CD40L, CD86, CD80, and PD1. To illustrate, the differentially regulated biomarker comprises down-regulated expression of CD40, up-regulated expression of CD40L, up-regulated expression of CD86, up-regulated expression of CD80, and/or up-regulated expression of PD1.
In certain specific embodiments, the method of the present invention administering an agent that specifically binds to CD40 (e.g., an anti-CD40 antibody). Optionally, the agent is an anti-CD40 domain antibody (e.g., BMS-986090). In certain specific embodiments, the method of the present invention administering an agent that specifically binds to CD40L (e.g., an anti-CD40L antibody). Optionally, the agent is an anti-CD40L domain antibody (e.g., BMS-986004). In certain specific embodiments, the method of the present invention administering an agent that specifically binds to CD28 (e.g., an anti-CD28 antibody). Optionally, the agent is an anti-CD28 domain antibody (e.g., BMS-931699).
In certain specific embodiments, the differentially regulated biomarker is detected in a whole blood sample of the subject. For example, the expression level (mRNA or protein) of the differentially regulated biomarker is detected. To illustrate, the differentially regulated biomarker is detected by a method comprising contacting a sample from the subject with an antibody which binds to the biomarker. In a specific embodiment, the subject is an African American.
In other embodiments, the present invention provides a method of treating or preventing lupus in a subject, comprising: (a) administering an agent that inhibits the CD40 or CD28 signaling pathway; (b) determining whether the agent neutralizes at least one differentially regulated biomarker selected from CD40, CD40L, CD86, CD80, and PD1; and (c) adjusting the dosing of the agent in the subject, thereby treating or preventing lupus in the subject. For example, the lupus is systemic lupus erythematosus (SLE).
In certain specific embodiments, the method of the present invention comprises determining whether the agent neutralizes at least two, at least three, or at least four, differentially regulated biomarker selected from CD40, CD40L, CD86, CD80, and PD1. To illustrate, the differentially regulated biomarker comprises down-regulated expression of CD40, up-regulated expression of CD40L, up-regulated expression of CD86, up-regulated expression of CD80, and/or up-regulated expression of PD1. For example, the agent neutralizes the differentially regulated biomarker by at least 10%, at least 20%, at least 30%, at least 40% or at least 50%.
In certain specific embodiments, the method of the present invention administering an agent that specifically binds to CD40 (e.g., an anti-CD40 antibody). Optionally, the agent is an anti-CD40 domain antibody (e.g., BMS-986090). In certain specific embodiments, the method of the present invention administering an agent that specifically binds to CD40L (e.g., an anti-CD40L antibody). Optionally, the agent is an anti-CD40L domain antibody (e.g., BMS-986004). In certain specific embodiments, the method of the present invention administering an agent that specifically binds to CD28 (e.g., an anti-CD28 antibody). Optionally, the agent is an anti-CD28 domain antibody (e.g., BMS-931699).
In certain specific embodiments, the differentially regulated biomarker is detected in a whole blood sample of the subject. For example, the expression level (mRNA or protein) of the differentially regulated biomarker is detected. To illustrate, the differentially regulated biomarker is detected by a method comprising contacting a sample from the subject with an antibody which binds to the biomarker. In a specific embodiment, the subject is an African American.
In other embodiments, the present invention provides a kit comprising: (1) an antibody which specifically binds to at least one differentially regulated biomarker selected from CD40, CD40L, CD86, CD80, and PD1; and (2) instructions for use of said kit. For example, the kit comprise at least two antibodies which specifically bind to at least two differentially regulated biomarker selected from CD40, CD40L, CD86, CD80, and PD1.
European American SLE patients Summary of frequencies of CD40L+ CD4+ CD45RO− naïve T cells (
Lupus is an autoimmune disease that results in multi-organ involvement. This anti-self response in SLE patients is characterized by autoantibodies directed against a variety of nuclear and cytoplasmic cellular components. These autoantibodies bind to their respective antigens, forming immune complexes that circulate and eventually deposit in tissues. This immune complex deposition causes chronic inflammation and tissue damage.
Diagnosing and monitoring disease activity are problematic in patients with lupus. Diagnosis is problematic because the spectrum of disease is broad and ranges from subtle or vague symptoms to life-threatening multi-organ failure. There also are other diseases with multi-system involvement that can be mistaken for lupus, and vice versa. Monitoring disease activity also is problematic in caring for patients with lupus. Lupus progresses in a series of flares, or periods of acute illness, followed by remissions. The symptoms of a flare, which vary considerably between patients and even within the same patient, include malaise, fever, symmetric joint pain, and photosensitivity (development of rashes after brief sun exposure). Other symptoms of lupus include hair loss, ulcers of mucous membranes and inflammation of the lining of the heart and lungs, which leads to chest pain. Red blood cells, platelets and white blood cells can be targeted in lupus, resulting in anemia and bleeding problems. More seriously, immune complex deposition and chronic inflammation in the blood vessels can lead to kidney involvement and occasionally kidney failure, requiring dialysis or kidney transplantation. Since the blood vessel is a major target of the autoimmune response in lupus, premature strokes and heart disease are not uncommon. Over time, however, these flares can lead to irreversible organ damage.
Systemic Lupus Erythematosus (SLE) is a complex systemic autoimmune disease driven by both innate and adaptive immune cells. African Americans tend to present with more severe disease at an earlier age compared to patients of European ancestry. In order to better understand the immunological differences between African American and European American patients, Applicants analyzed the frequencies of B cell subsets and the expression of B cell activation markers from a total of 72 SLE patients and 69 normal healthy volunteers. Applicants found that B cells expressing the activation markers CD86, CD80, PD1 and CD40L, as well as CD19+CD27−IgD− double negative B cells, were enriched in African American patients vs. patients of European ancestry. In addition to increased expression of CD40L, surface levels of CD40 on B cells were lower, suggesting the engagement of the CD40 pathway. In vitro experiments confirmed that CD40L expressed by B cells could lead to CD40 activation and internalization on adjacent B cells. Thus, Applicants' findings help the development of novel diagnostics and therapies for lupus.
In certain embodiments, the present invention provides a method of treating or preventing lupus (e.g., SLE) in a subject, comprising: (a) identifying the subject as having at least one differentially regulated biomarker selected from CD40, CD40L, CD86, CD80, and PD1; and (b) administering an agent that inhibits the CD40 or CD28 signaling pathway, thereby treating or preventing lupus in the subject. In certain specific embodiments, the method of the present invention comprises identifying the subject as having at least two, at least three, or at least four, differentially regulated biomarker selected from CD40, CD40L, CD86, CD80, and PD1. To illustrate, the differentially regulated biomarker comprises down-regulated expression of CD40, up-regulated expression of CD40L, up-regulated expression of CD86, up-regulated expression of CD80, and/or up-regulated expression of PD1. In certain specific embodiments, the method of the present invention administering an agent that specifically binds to CD40 (e.g., an anti-CD40 antibody). Optionally, the agent is an anti-CD40 domain antibody (e.g., BMS-986090). In certain specific embodiments, the method of the present invention administering an agent that specifically binds to CD40L (e.g., an anti-CD40L antibody). Optionally, the agent is an anti-CD40L domain antibody (e.g., BMS-986004). In certain specific embodiments, the method of the present invention administering an agent that specifically binds to CD28 (e.g., an anti-CD28 antibody). Optionally, the agent is an anti-CD28 domain antibody (e.g., BMS-931699). In certain specific embodiments, the differentially regulated biomarker is detected in a whole blood sample of the subject. For example, the expression level (mRNA or protein) of the differentially regulated biomarker is detected. To illustrate, the differentially regulated biomarker is detected by a method comprising contacting a sample from the subject with an antibody which binds to the biomarker. In a specific embodiment, the subject is an African American.
In other embodiments, the present invention provides a method of treating or preventing lupus in a subject, comprising: (a) administering an agent that inhibits the CD40 or CD28 signaling pathway; (b) determining whether the agent neutralizes at least one differentially regulated biomarker selected from CD40, CD40L, CD86, CD80, and PD1; and (c) adjusting the dosing of the agent in the subject, thereby treating or preventing lupus in the subject. In certain specific embodiments, the method of the present invention comprises determining whether the agent neutralizes at least two, at least three, or at least four, differentially regulated biomarker selected from CD40, CD40L, CD86, CD80, and PD1. To illustrate, the differentially regulated biomarker comprises down-regulated expression of CD40, up-regulated expression of CD40L, up-regulated expression of CD86, up-regulated expression of CD80, and/or up-regulated expression of PD1. For example, the agent neutralizes the differentially regulated biomarker by at least 10%, at least 20%, at least 30%, at least 40% or at least 50%. In certain specific embodiments, the method of the present invention administering an agent that specifically binds to CD40 (e.g., an anti-CD40 antibody). Optionally, the agent is an anti-CD40 domain antibody (e.g., BMS-986090). In certain specific embodiments, the method of the present invention administering an agent that specifically binds to CD40L (e.g., an anti-CD40L antibody). Optionally, the agent is an anti-CD40L domain antibody (e.g., BMS-986004). In certain specific embodiments, the method of the present invention administering an agent that specifically binds to CD28 (e.g., an anti-CD28 antibody). Optionally, the agent is an anti-CD28 domain antibody (e.g., BMS-931699). In certain specific embodiments, the differentially regulated biomarker is detected in a whole blood sample of the subject. For example, the expression level (mRNA or protein) of the differentially regulated biomarker is detected. To illustrate, the differentially regulated biomarker is detected by a method comprising contacting a sample from the subject with an antibody which binds to the biomarker. In a specific embodiment, the subject is an African American.
In other embodiments, the present invention provides a kit comprising: (1) an antibody which specifically binds to at least one differentially regulated biomarker selected from CD40, CD40L, CD86, CD80, and PD1; and (2) instructions for use of said kit. For example, the kit comprise at least two antibodies which specifically bind to at least two differentially regulated biomarker selected from CD40, CD40L, CD86, CD80, and PD1.
As used herein, each of the following terms has the meaning associated with it in this section.
As used herein, the articles “a” and “an” refer to one or to more than one (e.g., to at least one) of the grammatical object of the article.
The term “or” is used herein to mean, and is used interchangeably with, the term “and/or”, unless context clearly indicates otherwise.
The term “differentially regulated biomarker”, “differentially expressed biomarker” as described herein (e.g., CD40, CD40L, CD86, CD80, and PD1) refers to an increase or decrease in the expression level of a biomarker in a test sample, such as a sample derived from a patient suffering from lupus that is greater or less than the standard error of the assay employed to assess expression. For example, the alteration can be at least twice or more times greater than or less than the expression level of the biomarkers in a control sample (e.g., a sample from a healthy subject not having the associated disease), or the average expression level in several control samples. The altered expression of a biomarker can be determined at the protein or nucleic acid (e.g., mRNA) level.
A “biomarker” or “marker” is a gene, mRNA, or protein that undergoes alterations in expression that are associated with progression of lupus or responsiveness to treatment. The alteration can be in amount and/or activity in a biological sample (e.g., a blood, plasma, urine or a serum sample) obtained from a subject having lupus, as compared to its amount and/or activity, in a biological sample obtained from a baseline or prior value for the subject, the subject at a different time interval, an average or median value for a lupus patient population, a healthy control, or a healthy subject population (e.g., a control); such alterations in expression and/or activity are associated with progression of a disease state, such as lupus. For example, a marker of the invention which is associated with progression of lupus or predictive of responsiveness to therapeutics can have an altered expression level, protein level, or protein activity, in a biological sample obtained from a subject having, or suspected of having, lupus as compared to a biological sample obtained from a control subject.
A “nucleic acid” “marker” or “biomarker” is a nucleic acid (e.g., DNA, mRNA, cDNA) encoded by or corresponding to a marker as described herein. For example, such marker nucleic acid molecules include DNA (e.g. , genomic DNA and cDNA) comprising the entire or a partial sequence of any of the nucleic acid sequences set forth, or the complement or hybridizing fragment of such a sequence. The marker nucleic acid molecules also include RNA comprising the entire or a partial sequence of any of the nucleic acid sequences set forth herein, or the complement of such a sequence, wherein all thymidine residues are replaced with uridine residues. A “marker protein” is a protein encoded by or corresponding to a marker of the invention. A marker protein comprises the entire or a partial sequence of a protein encoded by any of the sequences set forth herein, or a fragment thereof. The terms “protein” and “polypeptide” are used interchangeably herein.
As used herein, a “disease progression” includes a measure (e.g., one or more measures) of a worsening, stability, or improvement of one or more symptoms and/or disability in a subject. In certain embodiments, disease progression is evaluated as a steady worsening, stability, or improvement of one or more symptoms and/or disability over time, as opposed to a relapse, which is relatively short in duration. In certain embodiments, the disease progression value is acquired in a subject with lupus (e.g., a subject with SLE, CLE, ACLE, SCLE, intermittent cutaneous lupus erythematosus, chronic cutaneous lupus, drug-induced lupus, or neonatal lupus).
Lupus is “treated,” “inhibited, “reduced,” or “prevented” if at least one symptom of the disease is reduced, alleviated, terminated, slowed, or prevented. As used herein, lupus is also “treated,” “inhibited,” or “reduced,” or “prevented,” if recurrence or relapse of the disease is reduced, slowed, delayed, or prevented. Exemplary clinical symptoms of lupus that can be used to aid in determining the disease status in a subject can include e.g., painful joints/arthralgia, fever of more than 100° F./38° C., arthritis/swollen joints, prolonged or extreme fatigue, skin rashes, anemia, kidney involvement, pain in the chest on deep breathing/pleurisy, butterfly-shaped rash across the cheeks and nose, sun or light sensitivity/photosensitivity, hair loss, blood clotting problems, Raynaud's phenomenon/fingers turning white and/or blue in the cold, seizures, mouth or nose ulcers, and any combination thereof. Clinical signs of lupus are routinely classified and standardized, e.g., using an SLEDAI rating system.
As used herein, the “Systemic Lupus Erythematosus Disease Activity Index” or “SLEDAI” is intended to have its customary meaning in the medical practice. EDSS is a rating system that is frequently used for classifying and standardizing MS. The accepted scores range from 0 (normal) to 105 (death due to lupus). A SLEDAI score of between 1-5 is indicative of mild disease activity in the subject; a SLEDAI score of between 6-10 is indicative of moderate disease activity in the subject; a SLEDAI score of between 11-19 is indicative of high disease activity in the subject; a SLEDAI score of 20-105 is indicative of very high disease activity in the subject.
“Responsiveness,” to “respond” to treatment, and other forms of this verb, as used herein, refer to the reaction of a subject to treatment with a lupus therapy. As an example, a subject responds to an lupus therapy if at least one symptom of lupus (e.g., disease progression) in the subject is reduced or retarded by about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or more. In another example, a subject responds to a lupus therapy, if at least one symptom of lupus in the subject is reduced by about 5%, 10%, 20%, 30%, 40%, 50% or more as determined by any appropriate measure, e.g., one or more of: a value of disease progression, a change in symptoms, and/or a modified SLEDAI value. In another example, a subject responds to treatment with a lupus therapy, if the subject has an increased time to progression. Several methods can be used to determine if a patient responds to a treatment including the assessments described herein, as set forth above.
An “overexpression,” “significantly higher level of expression,” or “upregulation” of the gene products refers to an expression level in a test sample that is greater than the standard error of the assay employed to assess the level of expression. In embodiments, the overexpression can be at least two, at least three, at least four, at least five, or at least ten or more times more than the expression level of the gene in a control sample or the average expression level of gene products in several control samples.
An “underexpression,” “significantly lower level of expression,” or “down-regulation” of the gene products refers to an expression level in a test sample that is lower than the standard error of the assay employed to assess the level of expression. In embodiments, the underexpression can be at least two, at least three, at least four, at least five, or at least ten or more times less than the expression level of the gene in a control sample or the average expression level of gene products in several control samples.
The term “antibody” as referred to herein includes whole antibodies and any antigen binding fragment (i.e., “antigen-binding portion”) or single chains thereof. An “antibody” refers to a glycoprotein comprising at least two heavy (H) chains and two light (L) chains inter-connected by disulfide bonds, or an antigen binding portion thereof.
Each heavy chain is comprised of a heavy chain variable region (abbreviated herein as VH) and a heavy chain constant region. The heavy chain constant region is comprised of three domains, CH1, CH2 and CH3. Each light chain is comprised of a light chain variable region (abbreviated herein as VL) and a light chain constant region. The light chain constant region is comprised of one domain, CL. The VH and VL regions can be further subdivided into regions of hypervariability, termed complementarity determining regions (CDR), interspersed with regions that are more conserved, termed framework regions (FR). Each VH and VL is composed of three CDRs and four FRs, arranged from amino-terminus to carboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4. The variable regions of the heavy and light chains contain a binding domain that interacts with an antigen. The constant regions of the antibodies may mediate the binding of the immunoglobulin to host tissues or factors, including various cells of the immune system (e.g., effector cells) and the first component (C1q) of the classical complement system.
The term “antigen-binding portion” of an antibody (or simply “antibody portion”), as used herein, refers to one or more fragments of an antibody that retain the ability to specifically bind to an antigen. It has been shown that the antigen-binding function of an antibody can be performed by fragments of a full-length antibody. Examples of binding fragments encompassed within the term “antigen-binding portion” of an antibody include (i) a Fab fragment, a monovalent fragment consisting of the VH, VL, CL and CH1 domains; (ii) a F(ab′)2 fragment, a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region; (iii) a Fd fragment consisting of the VH and CH1 domains; (iv) a Fv fragment consisting of the VL and VH domains of a single arm of an antibody, (v) a dAb fragment (Ward et al., Nature, 341:544-546 (1989)), which consists of a VH domain; and (vi) an isolated complementarity determining region (CDR). Furthermore, although the two domains of the Fv fragment, VL and VH, are coded for by separate genes, they can be joined, using recombinant methods, by a synthetic linker that enables them to be made as a single protein chain in which the VL and VH regions pair to form monovalent molecules (known as single chain Fv (scFv); see e.g., Bird et al., Science, 242:423-426 (1988); and Huston et al., Proc. Natl. Acad. Sci. USA, 85:5879-5883 (1988)). Such single chain antibodies are also intended to be encompassed within the term “antigen-binding portion” of an antibody. These antibody fragments are obtained using conventional techniques known to those with skill in the art, and the fragments are screened for utility in the same manner as are intact antibodies.
An “isolated antibody”, as used herein, is intended to refer to an antibody that is substantially free of other antibodies having different antigenic specificities. Moreover, an isolated antibody may be substantially free of other cellular material and/or chemicals.
The terms “monoclonal antibody” or “monoclonal antibody composition” as used herein refer to a preparation of antibody molecules of single molecular composition. A monoclonal antibody composition displays a single binding specificity and affinity for a particular epitope.
The term “probe” refers to any molecule which is capable of selectively binding to a specifically intended target molecule, for example a marker of the invention. Probes can be either synthesized by one skilled in the art, or derived from appropriate biological preparations. For purposes of detection of the target molecule, probes can be specifically designed to be labeled, as described herein. Examples of molecules that can be utilized as probes include, but are not limited to, RNA, DNA, proteins, antibodies, and organic monomers.
“Sample,” “tissue sample,” “patient sample,” “patient cell or tissue sample” or “specimen” each refers to a biological sample obtained from a tissue or bodily fluid of a subject or patient. The source of the tissue sample can be solid tissue as from a fresh, frozen and/or preserved organ, tissue sample, biopsy, or aspirate; blood or any blood constituents (e.g., serum, plasma); bodily fluids such as urine, cerebral spinal fluid, whole blood, plasma and serum. The sample can include a non-cellular fraction (e.g., urine, plasma, serum, or other non-cellular body fluid). In one embodiment, the sample is a urine sample. In other embodiments, the body fluid from which the sample is obtained from an individual comprises blood (e.g., whole blood). In certain embodiments, the blood can be further processed to obtain plasma or serum. In another embodiment, the sample contains a tissue, cells (e.g., peripheral blood mononuclear cells (PBMC)). In one embodiment, the sample is a urine sample. For example, the sample can be a fine needle biopsy sample, an archival sample (e.g., an archived sample with a known diagnosis and/or treatment history), a histological section (e.g., a frozen or formalin-fixed section, e.g., after long term storage), among others. The term sample includes any material obtained and/or derived from a biological sample, including a polypeptide, and nucleic acid (e.g., genomic DNA, cDNA, RNA) purified or processed from the sample. Purification and/or processing of the sample can involve one or more of extraction, concentration, antibody isolation, sorting, concentration, fixation, addition of reagents and the like. The sample can contain compounds that are not naturally intermixed with the tissue in nature such as preservatives, anticoagulants, buffers, fixatives, nutrients, antibiotics or the like.
The amount of a biomarker, e.g., expression of gene products (e.g., one or more the biomarkers described herein), in a subject is “significantly” higher or lower than the normal amount of a marker, if the amount of the marker is greater or less, respectively, than the normal level by an amount greater than the standard error of the assay employed to assess amount, or at least two, three, four, five, ten or more times that amount. Alternatively, the amount of the marker in the subject can be considered “significantly” higher or lower than the normal amount if the amount is at least about 1.5, two, at least about three, at least about four, or at least about five times, higher or lower, respectively, than the normal amount of the marker.
In certain embodiments, an antibody or antigen binding portion thereof can be used in a method for the detection of a differentially regulated biomarker protein (e.g., CD40, CD40L, CD86, CD80 or PD1) in a subject. For example, a body fluid (e.g., blood, serum or plasma) or tissue sample from the subject is contacted with an antibody or antigen binding portion thereof under conditions suitable for the formation of antibody-antigen complexes. The presence or amount of such complexes can then be determined by methods described herein and otherwise known in the art (see, e.g., O'Connor et al., Cancer Res., 48:1361-1366 (1988)), in which the presence or amount of complexes found in the test sample is compared to the presence or amount of complexes found in a series of standards or control samples containing a known amount of antigen. To illustrate, the method can employ an immunoassay, e.g., an enzyme immunoassay (EIA), enzyme-linked immunosorbent assay (ELISA), immunofluorescent assays, Western blotting, immunoelectrophoresis, fluid or gel precipitin reactions, immunodiffusion (single or double), radioimmunoassay (RIA), indirect competitive immunoassay, direct competitive immunoassay, non-competitive immunoassay, sandwich immunoassay, agglutination assay or other immunoassay describe herein and known in the art (see, e.g., Zola, Monoclonal Antibodies: A Manual of Techniques, pp. 147-158, CRC Press, Inc. (1987)). Immunoassays may be constructed in heterogeneous or homogeneous formats. Heterogeneous immunoassays are distinguished by incorporating a solid phase separation of bound analyte from free analyte or bound label from free label. Solid phases can take a variety of forms well known in the art, including but not limited to tubes, plates, beads, and strips. One particular form is the microtiter plate. The solid phase material may be comprised of a variety of glasses, polymers, plastics, papers, or membranes. Particularly desirable are plastics such as polystyrene. Heterogeneous immunoassays may be competitive or non-competitive (i.e., sandwich formats) (see, e.g., U.S. Pat. No. 7,195,882).
The antibody used for detecting the biomarker may be labeled. The label may be any detectable functionality that does not interfere with the binding of the antigen biomarker. Examples of suitable labels are those numerous labels known for use in immunoassay, including moieties that may be detected directly, such as fluorochrome, chemiluminscent, and radioactive labels, as well as moieties, such as enzymes, that must be reacted or derivatized to be detected. Examples of such labels include the radioisotopes 32P, 14C, 125I, 3H, and 131I, fluorophores such as rare-earth chelates or fluorescein and its derivatives, rhodamine and its derivatives, dansyl, umbelliferone, luceriferases, e.g., firefly luciferase and bacterial luciferase (see, e.g., U.S. Pat. No. 4,737,456), luciferin, 2,3-dihydrophthalazinediones, HRP, alkaline phosphatase, β-galactosidase, glucoamylase, lysozyme, saccharide oxidases, e.g., glucose oxidase, galactose oxidase, and glucose-6-phosphate dehydrogenase, heterocyclic oxidases such as uricase and xanthine oxidase, coupled with an enzyme that employs hydrogen peroxide to oxidize a dye precursor such as HRP, lactoperoxidase, or microperoxidase, biotin (detectable by, e.g., avidin, streptavidin, streptavidin-HRP, and streptavidin-β-galactosidase with MUG), spin labels, bacteriophage labels, stable free radicals, and the like.
In certain embodiments, nucleic acids molecules which encode one or more differentially regulated biomarker nucleic acid (e.g., CD40, CD40L, CD86, CD80 or PD1) may be detected. As used herein, the term “nucleic acid molecule” is intended to include DNA molecules (e.g., cDNA or genomic DNA) and RNA molecules (e.g., mRNA) and analogs of the DNA or RNA generated using nucleotide analogs. The nucleic acid molecule can be single-stranded or double-stranded; in certain embodiments the nucleic acid molecule is double-stranded DNA. Nucleic acid probes are sufficient for use as hybridization probes to identify nucleic acid molecules that correspond to a biomarker of the invention, e.g., those suitable for use as PCR primers for the amplification or mutation of nucleic acid molecules.
If so desired, a differentially regulated biomarker nucleic acid molecule can be isolated using standard molecular biology techniques and the sequence information in the database records described herein. Using all or a portion of such nucleic acid sequences, nucleic acid molecules can be isolated using standard hybridization and cloning techniques (e.g., as described in Sambrook et al., ed., Molecular Cloning: A Laboratory Manual, 2nd ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989). A biomarker nucleic acid molecule can be amplified using cDNA, mRNA, or genomic DNA as a template and appropriate oligonucleotide primers according to standard PCR amplification techniques. The biomarker nucleic acid molecule so amplified can be cloned into an appropriate vector and characterized by DNA sequence analysis.
Furthermore, oligonucleotides (e.g., probes) corresponding to all or a portion of a nucleic acid molecule can be prepared by standard synthetic techniques, e.g., using an automated DNA synthesizer. Probes based on the sequence of a biomarker nucleic acid molecule can be used to detect transcripts (e.g., mRNA) or genomic sequences corresponding to one or more biomarkers of the invention. The probe comprises a label group attached thereto, e.g., a radioisotope, a fluorescent compound, an enzyme, or an enzyme co-factor. Such probes can be used as part of a diagnostic test kit for identifying cells or tissues which overexpress or underexpress the protein, such as by measuring levels of a nucleic acid molecule encoding the protein in a sample of cells from a subject.
In certain embodiments, the present invention provides kits for detecting a biomarker in a biological sample (e.g., tissue, whole blood, serum, plasma, buccal scrape, saliva, cerebrospinal fluid, urine, stool, and bone marrow). For example, the kits comprise one or more antibodies (monoclonal or polyclonal) against one or more biomarkers (e.g., CD40, CD40L, CD86, CD80 or PD1), instructions for use of the kits, and optionally reagents necessary for facilitating an antibody-antigen complex formation and/or detection. The antibody may be labeled or unlabeled. Where the label is an enzyme, the kit will ordinarily include substrates and cofactors required by the enzyme, where the label is a fluorophore, a dye precursor that provides the detectable chromophore, and where the label is biotin, an avidin such as avidin, streptavidin, or streptavidin conjugated to HRP or β-galactosidase with MUG.
Such kits can be used to determine if a subject is suffering from or is at increased risk of developing lupus. Such kits can also be used for assessing the disease progression of a subject having lupus. Such kits can further be used for assessing a subject's response to a lupus therapy. Such kits can also be used for selecting or adjusting a dosing of a lupus therapy.
In certain aspects, methods of the present invention can be used for selecting a subject suitable for a lupus therapy, for assessing the disease progression of a subject having lupus, for assessing a subject's response to a lupus therapy, and/or for selecting or adjusting a dosing of a lupus therapy.
In one specific embodiment, the invention provides novel and effective methods of treating lupus in a subject. In one specific embodiment, the method comprises: (a) identifying the subject as having at least one differentially regulated biomarker selected from CD40, CD40L, CD86, CD80, and PD1; and (b) administering an agent that inhibits the CD40 or CD28 signaling pathway, thereby treating or preventing lupus in the subject. In another specific embodiment, the method comprises: (a) administering an agent that inhibits the CD40 or CD28 signaling pathway; (b) determining whether the agent neutralizes at least one differentially regulated biomarker selected from CD40, CD40L, CD86, CD80, and PD1; and (c) adjusting the dosing of the agent in the subject, thereby treating or preventing lupus in the subject. In the methods of the invention, one or more of the biomarkers in a sample can be detected by any of assays as described above.
The term “treating” includes the administration of an agent to prevent or delay the onset of the symptoms, complications, or biochemical indicia of lupus, alleviating the symptoms or arresting or inhibiting further development of the disease. Treatment may be prophylactic (to prevent or delay the onset of the disease, or to prevent the manifestation of clinical or subclinical symptoms thereof) or therapeutic suppression or alleviation of symptoms after the manifestation of the disease.
The term “dosage,” “dose,” or “dosing” as used herein interchangeably, refers to an amount of a therapeutic agent which is administered to a subject having lupus.
The term “therapeutically effective dosage/dose/dosing,” as used herein, refers to an amount of a therapeutic agent which preferably results in a decrease in severity of disease symptoms, an increase in frequency and duration of disease symptom-free periods, or a prevention of impairment or disability due to the disease affliction. One of ordinary skill in the art would be able to determine such amounts based on such factors as the subject's size, the severity of the subject's symptoms, and the particular composition or route of administration selected.
There are several therapeutic agents presently used to modify the course of lupus. Such agents include, but are not limited to, nonsteroidal anti-inflammatory drugs (NSAID); antimalarials (e.g., hydroxychloroquine); corticosteroids (e.g., glucocorticoids); immunosuppressants (e.g., azathioprine, mycophenolate mofetil, or methotrexate); intravenous immunoglobulins; and a monoclonal antibody such as belimumab.
In certain embodiments, the methods of the invention provide the use of alternative therapies for the treatment of lupus. Such agents include, but are not limited to, an anti-CD40L antibody, an anti-CD40 antibody, and an anti-CD28 antibody. For example, an anti-CD40L antibody is a domain antibody which binds to and antagonize the CD40L activity, such as BMS-986004. BMS-986004 and uses thereof are disclosed in, e.g., WO 2013/056068, WO 2015/143209, and PCT/US2015/049338 (referred to therein as BMS2h-572-633-Fc fusion having the sequence of SEQ ID NO: 1355), the content of which is expressly incorporated by reference. For example, an anti-CD40 antibody is a domain antibody which binds to and antagonize the CD40 activity, such as BMS-986090. BMS-986090 and uses thereof are disclosed in, e.g., WO 2012/145673 and WO 2015/134988 (referred to therein as BMS3h-56-269-Fc fusion having the sequence of SEQ ID NO: 1287), the content of which is expressly incorporated by reference. For example, an anti-CD28 antibody is a domain antibody which binds to and antagonize the CD28 activity, such as BMS-931699. BMS-931699 and uses thereof are disclosed in, e.g., WO 2010/009391 and PCT/US2015/053233 (referred to therein as pegylated Bms1h-239-891 (D70C) having the sequence of SEQ ID NO: 543), the content of which is expressly incorporated by reference.
The present disclosure is further illustrated by the following examples, which should not be construed as further limiting. The contents of all figures and all references, patents and published patent applications cited throughout this application are expressly incorporated herein by reference in their entireties.
Systemic Lupus Erythematosus (SLE) is a complex systemic disease that can affect multiple organs. Both innate and adaptive immune cells are involved in driving the disease [1]. In particular B cells and autoantibody production are believed to participate in the pathogenesis of SLE. Indeed, SLE is characterized by the presence of anti-nuclear antibodies (ANA), anti-dsDNA, anti-Smith antigen (Sm) or anti-ribonucleoprotein (RNP) antibodies and disease activity and flares have been associated with the expansion of antibody-secreting cells [2].
SLE presentation varies greatly depending on the ancestral background. Compared to European Americans, African Americans are at higher risk of developing SLE and tend to be diagnosed earlier and suffer from a more severe disease with a higher rate of flares and progression to lupus nephritis (LN) and increased risk of death due to LN-related end-stage-renal disease. Although these disparities can be explained by the genetic background at disease onset, other factors such as poor socio-economic status, lack of social support or lower access to healthcare are major contributors to the accelerated and more severe course of disease [3-6]. Little is known about the immunological mechanisms of SLE that could account for the variations in susceptibility and severity in different ethnic groups. African American and Hispanics with moderate-to-severe active SLE showed a better response to rituximab in a phase II/III trial [7]. Also, a trend to better response with rituximab was seen in African American patients with LN [8]. These data suggest a B-cell-driven disease in these ethnic groups and imply that patients of different ancestries may respond differentially to treatments. In order to better understand mechanisms of disease and how they could be impacted by ancestral backgrounds, Applicants analyzed the B cell compartment of African American and European American SLE patients and healthy volunteer controls. Applicants discovered a distinct activated B cell signature in African American SLE patients with expansion of CD19+IgD−CD27− double negative (DN) B cells, higher expression of CD86 and CD40 ligand (CD40L) and lower CD40 surface expression in B cells, suggestive of a constitutively active CD40 pathway in these patients.
Activated Phenotype of B cells from African American SLE Patients
Applicants analyzed the expression of activation markers on B cells on 69 normal healthy volunteers (NHV) and 68 SLE patients, self-reported as of either African or European ancestry. Disease activity, which was low to moderate, medications, except for glucocorticoid use (which was more prevalent in the African American group), and co-morbidities were similar in the 2 ancestry groups (Table 1). Increased expression of the co-stimulatory molecule CD86 by SLE B cells has been previously described [9]. Applicants found an increased frequency of CD86 expressing B cells, both in the CD27− and CD27+ compartments in African American patients (average percentages of CD86+ cells: 11% of CD27− B cells and 16% of CD27+ B cells), compared to NHV of either ancestry (average percentages of CD86+ cells: 1.5% of CD27− B cells and 6-9% of CD27+ B cells) or SLE patients of European ancestry (average percentages of CD86+ cells: 2.7% of CD27− B cells and 9% of CD27+ B cells) (
Applicants also analyzed the expression of CD80 and programmed cell death protein 1 (PD1), which are upregulated on B cells upon activation [10] (
Increased CD40 Ligand (CD40L) and Decreased CD40 Surface Expressions on B Cells from African American SLE Patients
CD40L was shown to be increased in SLE T and B cells [11-13]. Applicants found increased expression of CD40L by CD27− B cells, not by CD27+ B cells, in our SLE cohort compared to NHV (
CD40, the receptor for CD40L, is constitutively expressed on B cells. Applicants observed that in some patients, a subset of B cells expressed lower levels of surface CD40 (‘CD40lo’ B cells) (
Applicants then determined if the same patients harbored both CD40lo B cells and CD40L+ B cells. There was a good correlation between the frequencies of CD40lo B cells and CD40L+ B cells in African American patients (Spearman r=0.6987, p<0.0005) (
Engagement of CD40 on murine B cells by sCD40L leads to rapid loss of surface CD40 expression by receptor internalization [16-18]. To test whether CD40L expressed by B cells could engage CD40 on B cells and explain the phenotype observed in SLE African American patients, Applicants cultured purified B cells from NHV with soluble CD40L-isoleucine zipper (CD40L-IZ) or anti-IgM F(ab′)2. Within 3 h, Applicants observed the appearance of ‘CD40lo’ B cells in wells cultured with CD40L-IZ, but not with anti-IgM F(ab′)2 stimulation. Expression of CD86 was upregulated by CD40L-IZ at 24 h, similar to what was seen with anti-IgM F(ab′)2 (
In order to visualize internalization of CD40, Applicants used an Amnis® ImageStream that combines fluorescence microscopy with the throughput and power of quantification of a flow cytometer. Freshly isolated NHV B cells display a regular ring-shaped pattern of CD40 staining on the surface (
CD40 engagement leads to activation of multiple pathways, including the NF-κB pathway. Applicants therefore quantified the nuclear translocation of the NF-κB p50 sub-unit following CD40 activation using the Similarity feature, which measures the similarity of p50 NF-κB fluorescence to 7-Aminoactinomycin D (7-AAD) nuclear staining [20]. Applicants used a cut-off of similarity>0 for NF-κB nuclear translocation. 29% of unstimulated cells had some degree of nuclear translocation (
Applicants then sought to induce CD40L expression on B cells. Stimulation for 3 days of purified B cells with CD40L-IZ lead to upregulation of CD40L, concomitant to CD86 upregulation (
Applicants then explored if CD40L upregulated on B cells could induce CD40 internalization and NF-κB translocation. Applicants cultured purified NHV B cells with CD40L-IZ or CpG for 3 days and confirmed CD40L upregulation in the cells cultured with CD40L-IZ. The CpG− and CD40L-IZ-stimulated B cells were the washed and co-cultured with freshly isolated B cells from the same donors at a 1:1 ratio. The fresh B cells were labeled with anti-CD40-PE (to follow CD40 internalization) and with anti-CD45 APC-Cy7, which allowed Applicants to distinguish them from the CpG− or CD40L-IZ-stimulated B cells. After one hour of co-culture, Applicants analyzed CD40 internalization and p50 NF-κB translocation on the CD45-APC-Cy7 labeled B cells. B cells that had been cultured with CD40L-IZ and had upregulated CD40L were able to induce CD40 internalization on freshly isolated autologous B cells (average internalization score of 1.26 vs. 0.41 in unstimulated cells, p<0.05, 19.5% of cells with internalized CD40 vs. 2.1% in unstimulated cells, p<0.05) (
In order to determine if the activated phenotype of B cells from African American SLE patients could potentially result in dysregulated B cell subsets and B-cell driven autoimmunity, Applicants analyzed the frequencies of B cell populations in a subgroup of our cohort that contained 21 African American patients and 21 European American patients. Patients characteristics (disease scores, medications, co-morbidities) were similar in this subgroup and the original cohort (Table 2).
This analysis of cell subset frequencies was performed on whole blood. Applicants found that, in addition to being increased in all SLE patients compared to NHV, as previously reported [21-23], double negative (DN) CD19+CD27−IgD− B cells were greatly enriched in African American patients (
CD27− B cells contain both naïve IgD+ and DN IgD− B cells. IgD+ represent on average 88% and 67% of CD27− B cells in SLE patients of European and African ancestries respectively. To rule out that the increased frequencies of DN B cells in African American patients could explain the increased frequencies of CD86+ CD27− B cells described in
African Ancestry is the Strongest Factor Associated with the Increased Activated B Cell Phenotype Observed in SLE Patients
To independently confirm that self-reported African American ancestry was the main factor associated with the differences in B cell phenotypes, rather than other confounding factors such as medication, Applicants performed multiple linear regression analyses over a total of 15 demographic and clinical factors, including sex, age, duration of disease, disease scores, co-morbidities, clinical treatment, etc. (detailed in Methods section). For all six B cell phenotypic endpoints tested as response variables (% of DN, CD86+CD27−, CD86+CD27+, CD40L+CD27−, CD40loCD27−, CD40loCD27+ B cells), the African American ancestry was the strongest variable associated (Table 4). Other variables more weakly associated with these parameters include the total count of ACR criteria associated with the percentage of DN B cells, and glucocorticoid use associated with increased percentages of CD86+ CD27− and CD86+ CD27+ B cells. This suggests that glucocorticoid use is linked to the frequencies of CD86+ CD27− and CD86+CD27+ B cells to a lesser extent than African American ancestry. Although glucocorticoids have been previously shown to increase CD40L expression by lymphocytes [24], Applicants could not identify an effect of glucocorticoid use on the frequencies of CD40L+ CD27− B cells in our cohort (
Although SLEDAI-2k was not identified as a confounding factor for the activated B cell phenotype, Applicants observed a moderate correlation between SLEDAI-2k and the percentage of CD86+ CD27− B cells in African American SLE patients (
Patients with Higher CD40lo CD27− B Cell Frequencies have also Increased Anti-Sm, Anti-Sm/RNP and Anti-dsDNA Autoantibody Titers
The secretion of autoantibodies is a hallmark of SLE. By forming immune complexes with autoantigens, autoantibodies have a direct pathogenic role on tissues and organs, and activate innate and adaptive immune cells. In fact, the presence of autoantibodies, such as anti-dsDNA antibodies, has been associated with flares [6, 25]. Therefore, Applicants analyzed antibody titers in African American patients vs. patients of European descent. There was an increase of anti-Sm/RNP and anti-RNP70 titers in African Americans SLE patients compared to European American patients (
Applicants obtained peripheral blood in 2014 and 2015 from 68 SLE patients (29 patients self-identified as ‘Black or African American’ and 39 patients of European ancestry self-identified as ‘Caucasian’) who were visiting their physician at Northwell Health, Great Neck, N.Y. Most patients were on standard of care treatment for general SLE. Details of medication and associated co-morbidities are summarized in Table 1. Healthy subjects were analyzed in parallel (Table 5). Blood was shipped overnight. Immediately upon reception, plasma was collected and frozen for further use and peripheral blood mononuclear cells (PBMC) were purified.
80 μl of heparin anticoagulated blood or 1 million freshly isolated PBMC were incubated with pre-mixed cocktails of conjugated antibodies. Antibodies used for whole blood were: CD3-eFluor®450 or CD3-Alexa Fluor(AF)700 (both OKT3), CD45RA-fluorescein isothiocyanate (FITC) (JS-83), CD27− allophycocyanin (APC) (O323), IgD-FITC (IA6-2), CD24− phycoerythrin (PE) (SN3 A5-2H10), CD38-peridinin-Chlorophyll-protein(PerCP)-eFluor710(HB7) (all eBiosciences), CD4-PE-cyanine(Cy)7(OKT4), CXCR3-AF647(G025H7), CCR6-Brilliant violet(BV)785(G034E3), PD1-BV605(EH12.2H7), CD19-BV421 (HIB19) (all Biolegend), CD8a-APC-H7(SK1), CCR7-PE-CF594(150503), CXCR5-BV510(RF8B2), CD20-APC-H7 (2H7) (all BD Biosciences); for PBMC: CD3-APC-eFLuor®780(UCHT1), CD4-PerCPCy5.5(RPA-T4), CD8a-PECy7(RPA-T8), PD1-PerCPCy5.5(EH12.2H7), (all eBiosciences), CD19-APC-Cy7(HIB19), CD40-PE(5C3), CD40L-PE(24-31), CD80-FITC(2D10), CD86-APC(IT2.2), CD45RO-Pacific Blue (UCHL1) (all Biolegend), CD27-BV605(L128) (BD Biosciences). Whole blood samples were lysed for red blood cells and fixed with FACS lysing buffer. Stained PBMC samples were fixed in 1.5% paraformaldehyde. Samples were run on LSR-Fortessa or LSRII (BD Biosciences) and analyzed with FlowJo V10.0.7. Exclusion of doublets was systematically applied in the gating strategy (
Upregulation of Surface Markers During in vitro B Cell Activation
Total B cells were purified from freshly isolated PBMC by magnetic negative selection as described by manufacturer (Stemcell tech.). 250,000 cells/well were cultured in RPMI supplemented with antibiotics and 10% FBS without or with 1 μg/ml of human CD40L isoleucine zipper (CD40L-IZ) [26], 20 μg/ml of goat anti-human IgM F(ab′)2 (Jackson Immunoresearch), 1 μg/ml of CpG ODN2006-B (Invivogen) or co-cultured with 25,000 Chinese hamster ovary (CHO) cells stably transfected with human CD40LG (hCD40L-CHO cells) at Bristol-Myers Squibb. Parental CHO DG44 cells were obtained from Dr. Lawrence Chasin (Columbia University, New York, N.Y.). At indicated timepoints, cells were collected, washed and stained with CD19-APC-Cy7(HIB19, Biolegend), CD27-BV605(L128, BD Biosciences), CD80-FITC(2D10, Biolegend), CD86-APC(IT2.2, Biolegend), CD40-PE, (5C3, Biolegend), CD40L-PE(24-31 Biolegend), PD1-PerCPCy5.5 (EH12.2H7, eBiosciences), fixed in 1% paraformaldehyde and run on LSRII (BD Biosciences). Samples were analyzed with FlowJo V10.0.7.
To compare the response to CD40L stimulation by B cells from different ancestral backgrounds, CD40L-driven upregulation was tested in a whole blood assay. Ninety μl of heparin anticoagulated blood (SLE and NHV) was rested for one hour before addition of 10 μg/ml of CD40L-IZ. After an overnight incubation, samples were stained with CD20-APC and CD86-PE (eBiosciences) and run on Canto II (BD Biosciences).
Total B cells were isolated from frozen PBMCs by magnetic negative selection as described by manufacturer (StemCell Technologies, Inc.). Freshly isolated B cells were stained for 30 min on ice with anti-CD40-PE (clone 5C3, BioLegend) and with anti-CD45-APC/Cy7 (clone H130, BioLegend) in Stain Buffer (BSA) (BD Biosciences) containing Hu FcR Binding Inhibitor (eBioscience). After staining, B cells (3.0×106 cells/well in 12 well plate) were incubated for 1 h at 37° C. (5% CO2) in RPMI 1640 supplemented with heat-inactivated 10% FBS, 1% penicillin-streptomycin and 1% L-glutamine in the presence or absence of 1 μg/ml CD40L-IZ, hCD40L-CHO cells (1:10 hCD40L-CHO: B cell ratio), or autologous B cells previously activated for 72 hrs at 37° C. (5% CO2) in RPMI with 1 μg/ml CD40L-IZ or 1 μg/ml CpG ODN2006-B (Invivogen) (1:1 ratio). B cell stimulation was stopped by incubating cells on ice for 10 minutes. Cells were washed and stained on ice in BD Stain Buffer with CD19-BV510 (clone H1B19, BioLegend). After fixation in 4% paraformaldehyde (PFA) (Alfa Aesar), cells were permeabilized for 20 min at 4° C. in 1X BD Perm/Wash buffer (BD Biosciences). Permeabilized cells were then stained on ice in Perm/Wash buffer with anti-NF-κB p50-AF488 (clone 4D1, BioLegend), washed in Perm/Wash buffer, and then fixed again. A nuclear staining dye, 7-AAD Viability Staining Solution (BioLegend) was added to all samples ten minutes prior to data acquisition.
ImageStream data acquisition and analysis were performed as previously described [19, 20]. Data acquisition was done using Amnis® ImageStreamX Mark II imaging flow cytometer (EMD Millipore) and INSIRE acquisition software. Collected images were analyzed using IDEAS V.6.2 image-analysis software (Amnis/EMD Millipore). In each sample, sixty thousand events were collected and imaged in the Extended Depth of Field mode (EDF). Digital spectral compensation was performed on a pixel-by-pixel basis using single-stained controls. Acquired cellular imagery was analyzed for the degree of CD40 and CD45 internalization using the Internalization feature [19], and for the degree of NF-κB p50 nuclear translocation using the Similarity feature [20], as described in IDEAS V.6.2 documentation.
Levels of sCD40L and BAFF in plasma were detected with human CD40L and human BAFF ELISA kits respectively (both R&D Systems) following manufacturer instructions. For autoantibody titers, plasma samples were diluted 100 fold into sample dilution buffer and incubated on a pre-coated plate with dsDNA (ALPCO), Sm (ALPCO), Sm/RNP (ALPCO) or RNP70 (Genway). ELISA was developed with horseradish peroxidase conjugated anti-human IgG followed by TMB substrate. The reaction was stopped with 1M Hydrochloric acid and read on dual wavelength spectrophotometer. Values were calculated based on the standard curve and were reported as IU/ml.
Descriptive and single factor statistical analyses were performed with GraphPad Prism 5. Mann-Whitney non parametric T test was used to compare groups. P values were adjusted to correct for multiple comparisons and repeated measures. The following formula was used: adjusted p=1−(1−α)k, where α is the non-adjusted p value, and k is the number of comparisons. k was set at 30. Correlations were analyzed with Spearman correlation. P value of 0.05 or lower was considered significant.
Multiple linear regression analysis was performed in R statistical package. To ensure normality, log transformation was used for all six tested endpoints as response variables (% of CD86+ in CD27− and CD27+ B cells, % of CD40lo CD27− and CD27+ B cells, % of CD40L+ CD27− B cells, % of DNB cells). The co-variates tested as predictor variables were: age, sex, self-reported African American ancestry, duration of disease, SLEDAI-2k, total count of ACR criteria and some of its components (renal disorder, discoid rash, malar rash and arthritis), the presence of nephritis and low complement and treatment with hydroxychloroquine, mycophenolate mofetil and glucocorticoids. The presence of the co-morbidities ITP, Sjogren's syndrome, antiphospholipid syndrome and the effect of belimumab were not tested because of the paucity of samples being positive for these variables. A variable selection procedure based on Akaike's information criterion was used to select informative predictor variables.
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This application is a continuation of 371 PCT application Ser. No. 16/085,007 filed Mar. 15, 2017, which is the national phase filing in the U.S. of PCT/US2017/022496 filed Mar. 15, 2017, which claims benefit to U.S. Provisional Application No. 62/309,290 filed Mar. 16, 2016, which is hereby incorporated in its entirety for all purposes.
| Number | Date | Country | |
|---|---|---|---|
| 62309290 | Mar 2016 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 16085007 | Sep 2018 | US |
| Child | 18152056 | US |
