US20120142544A1 - Diagnostic transcriptomic biomarkers in inflammatory cardiomyopathies - Google Patents

Diagnostic transcriptomic biomarkers in inflammatory cardiomyopathies Download PDF

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US20120142544A1
US20120142544A1 US13/376,046 US201013376046A US2012142544A1 US 20120142544 A1 US20120142544 A1 US 20120142544A1 US 201013376046 A US201013376046 A US 201013376046A US 2012142544 A1 US2012142544 A1 US 2012142544A1
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myocarditis
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Joshua M. Hare
Bettina Heidecker
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University of Miami
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
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    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
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    • C12Q2600/112—Disease subtyping, staging or classification
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    • C12Q2600/00—Oligonucleotides characterized by their use
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers

Definitions

  • This invention relates to biomarkers of heart disease, myocarditis, novel drug therapeutic targets, compositions and methods of predicting, diagnosing and treating heart diseases and related disorders thereof. More specifically, the invention concerns methods and compositions based on unique molecular signatures associated with various aspects of cardiac diseases and disorders.
  • the myocardites are inflammatory diseases of the heart that have variable clinical presentations and are caused by a range of underlying inflammatory variants. Of new onset heart failure, 10-30% may be caused by cardiac inflammation, and viral infection systemic or local inflammatory diseases, or genetic predisposition represent inciting factors. Myocarditis can be difficult to diagnose requiring multiple endomyocardial biopsies (EMBs). Even with multiple biopsies, consensus among pathologists has been difficult to attain. Inaccurate or uncertain diagnosis is of major concern, since emerging therapies specifically targeting inflammatory or viral heart disease, have the potential to reverse the disease process. In a previous decision analysis investigating the value of EMBs to improve clinical outcome with specific therapy, histological inaccuracy was a major limiting factor for efficacy of treatment.
  • EMBs endomyocardial biopsies
  • biomarkers that function as very sensitive diagnostic biomarker for myocarditis, cardiovascular diseases and disorders, heart disease and disorders thereof, were identified.
  • the biomarkers also distinguish between various cardiac diseases and disorders allowing for accurate diagnosis.
  • the biomarkers provide for the identification of individuals at risk of developing cardiac diseases and disorders.
  • the transcriptomic biomarkers provide for the early diagnosis of cardiovascular diseases or disorders.
  • Transcriptomic biomarkers were identified to distinguish or differentially diagnose between giant cell myocarditis and cardiac sarcoidosis; peripartum cardiomyopathy and lymphocytic cardiomyopathy; myocarditis and idiopathic dilated cardiomyopathy; cardiac sarcoidosis, giant cell myocarditis, peripartum cardiomyopathy, and systemic lupus erythematosus with cardiac involvement.
  • the biomarkers or marker signatures comprised molecules some of which were up-regulated, down-regulated, no change, absent, etc (i.e., differentially expressed) as compared to normal healthy controls. The signatures not only allow for the early diagnosis and diagnostic differentiation between various diseases and disorders hut also for identifying individuals at risk for one or more cardiovascular diseases or disorders.
  • PAM Prediction Analysis of Microarrays
  • FIG. 3 Distinction of patients with idiopathic dilated cardiomyopathy vs lymphocytic myocarditis based on results from quantitative realtime RT-PCR: This heatmap was created with an unsupervised clustering approach based on Euclidean distance in R, using the detected gene expression levels from quantitative realtime RT-PCR as confirmatory test. Columns represent samples and rows represent genes labeled with their corresponding gene symbol. Application of the developed 13 genes molecular signature through realtime RT-PCR correctly identified all samples.
  • PCA Principal Components Analysis
  • genes, gene names, and gene products disclosed herein are intended to correspond to homologs from any species for which the compositions and methods disclosed herein are applicable. Thus, the terms include, but are not limited to genes and gene products from humans and mice. It is understood that when a gene or gene product from a particular species is disclosed, this disclosure is intended to be exemplary only, and is not to be interpreted as a limitation unless the context in which it appears clearly indicates.
  • the genes disclosed herein which in some embodiments relate to mammalian nucleic acid and amino acid sequences are intended to encompass homologous and/or orthologous genes and gene products from other animals including, but not limited to other mammals, fish, amphibians, reptiles, and birds, in preferred embodiments, the genes or nucleic acid sequences are human.
  • a “molecular signature” or “signature” or “biomarker” or “transcriptomic based biomarker” are used interchangeably herein and refers to the biomolecules identified in Tables 1 to 19.
  • Table 1 comprising the biomolecules listed therein, represents one biomarker or molecular signature
  • Table 2 comprising the biomolecules listed therein, represents another one biomarker or molecular signature; and so forth.
  • each newly identified biomolecules can be assigned to any one or more biomarker or molecular signature.
  • Each biomolecule can also be removed, reassigned or reallocated to a molecular signature.
  • the molecular signature comprises at least ten biomolecules.
  • the ten biomolecules are selected from the genes identified herein, or from newly identified biomolecules. Any one of the signatures can be used in the diagnosis of a disease or disorder, for example, myocarditis and idiopathic cardiomyopathy or differentiate between myocarditis and idiopathic cardiomyopathy. Mammalian sequences are preferred, with human sequences the most preferred.
  • biomolecule refers to DNA, RNA (including mRNA, rRNA, tRNA and tmRNA), nucleotides, nucleosides, analogs, polynucleotides, peptides and any combinations thereof.
  • a base “position” as used herein refers to the location of a given base or nucleotide residue within a nucleic acid.
  • array refers to an ordered spatial arrangement, particularly an arrangement of immobilized biomolecules.
  • addressable array refers to an array wherein the individual elements have precisely defined x and y coordinates, so that a given element at a particular position in the array can be identified.
  • probe and “biomolecular probe” refer to a biomolecule used to detect a complementary biomolecule. Examples include antigens that detect antibodies, oligonucleotides that detect complimentary oligonucleotides, and ligands that detect receptors. Such probes are preferably immobilized on a microelectrode comprising a substrate.
  • bioarray As used herein, the terms “bioarray,” “biochip” and “biochip array” refer to an ordered spatial arrangement of immobilized biomolecules on a microelectrode arrayed on a solid supporting substrate.
  • Preferred probe molecules include aptamers, nucleic acids, oligonucleotides, peptides, ligands, antibodies and antigens; peptides and proteins are the most preferred probe species.
  • Biochips encompass substrates containing arrays or microarrays, preferably ordered arrays and most preferably ordered, addressable arrays, of biological molecules that comprise one member of a biological binding pair.
  • such arrays are oligonucleotide arrays comprising a nucleotide sequence that is complementary to at least one sequence that may be or is expected to be present in a biological sample.
  • proteins, peptides or other small molecules can be arrayed in such biochips for performing, inter alia, immunological analyses (wherein the arrayed molecules are antigens) or assaying biological receptors (wherein the arrayed molecules are ligands, agonists or antagonists of said receptors).
  • Expression/amount of a gene, biomolecule, or biomarker in a first sample is at a level “greater than” the level in a second sample if the expression level/amount of the gene or biomarker in the first sample is at least about 1 time, 1.2 times, 1.5 times, 1.75 times, 2 times, 3 times 4 times, 5 times, 6 times, 7 times, 8 times, 9 times, 10 times, 20 times, 30 times, the expression level/amount of the gene or biomarker in the second sample or a normal sample.
  • Expression levels/amounts can be determined based on any suitable criterion known in the art, including but not limited to mRNA, cDNA, proteins, protein fragments and/or gene copy. Expression levels/amounts can be determined qualitatively and/or quantitatively.
  • modulate it is meant that any of the mentioned activities, are, e.g., increased, enhanced, increased, agonized (acts as an agonist), promoted, decreased, reduced, suppressed blocked, or antagonized (acts as an agonist). Modulation can increase activity more than 1-fold, 2-fold, 3-fold, 5-fold, 10-fold, 100-fold, etc., over baseline values. Modulation can also decrease its activity below baseline values.
  • variants are an alternative form of a gene. Variants may result from at least one mutation in the nucleic acid sequence and may result in altered mRNAs or in polypeptides whose structure or function may or may not be altered. Any given natural or recombinant gene may have none, one, or many allelic forms. Common mutational changes that give rise to variants are generally ascribed to natural deletions, additions, or substitutions of nucleotides. Each of these types of changes may occur alone, or in combination with the others, one or more times in a given sequence.
  • complementary means that two sequences are complementary when the sequence of one can bind to the sequence of the other in an anti-parallel sense wherein the 3′-end of each sequence binds to the 5′-end of the other sequence and each A, T(U), G, and C of one sequence is then aligned with a T(U), A, C, and G, respectively, of the other sequence.
  • the complementary sequence of the oligonucleotide has at least 80% or 90%, preferably 95%, most preferably 100%, complementarity to a defined sequence.
  • alleles or variants thereof can be identified.
  • a BLAST program also can be employed to assess such sequence identity.
  • complementary sequence as it refers to a polynucleotide sequence, relates to the base sequence in another nucleic acid molecule by the base-pairing rules. More particularly, the term or like term refers to the hybridization or base pairing between nucleotides or nucleic acids, such as, for instance, between the two strands of a double stranded DNA molecule or between an oligonucleotide primer and a primer binding site on a single stranded nucleic acid to be sequenced or amplified.
  • Complementary nucleotides are, generally, A and T (or A and U), or C and G.
  • Two single stranded RNA or DNA molecules are said to be substantially complementary when the nucleotides of one strand, optimally aligned and compared and with appropriate nucleotide insertions or deletions, pair with at least about 95% of the nucleotides of the other strand, usually at least about 98%, and more preferably from about 99% to about 100%.
  • Complementary polynucleotide sequences can be identified by a variety of approaches including use of well-known computer algorithms and software, for example the BLAST program.
  • aptamer or “selected nucleic acid binding species” shall include non-modified or chemically modified RNA or DNA.
  • the method of selection may be by, but is not limited to, affinity chromatography and the method of amplification by reverse transcription (RT) or polymerase chain reaction (PCR).
  • the term “signaling aptamer” shall include aptamers with reporter molecules, preferably a fluorescent dye, appended to a nucleotide in such a way that upon conformational changes resulting from the aptamer's interaction with a ligand, the reporter molecules yields a differential signal, preferably a change in fluorescence intensity.
  • fragment or segment as applied to a nucleic acid sequence, gene or polypeptide, will ordinarily be at least about 5 contiguous nucleic acid bases (for nucleic acid sequence or gene) or amino acids (for polypeptides), typically at least about 10 contiguous nucleic acid bases or amino acids, more typically at least about 20 contiguous nucleic acid bases or amino acids, usually at least about 30 contiguous nucleic acid bases or amino acids, preferably at least about 40 contiguous nucleic acid bases or amino acids; more preferably at least about 50 contiguous nucleic acid bases or amino acids, and even more preferably at least about 60 to 80 or more contiguous nucleic acid bases or amino acids in length, “Overlapping fragments” as used herein, refer to contiguous nucleic acid or peptide fragments which begin at the amino terminal end of a nucleic acid or protein and end at the carboxy terminal end of the nucleic acid or protein.
  • Each nucleic acid or peptide fragment has at least about one contiguous nucleic acid or amino acid position in common with the next nucleic acid or peptide fragment, more preferably at least about three contiguous nucleic acid bases or amino acid positions in common, most preferably at least about ten contiguous nucleic acid bases amino acid positions in common.
  • Bio samples include solid and body fluid samples. Preferably, the sample is obtained from heart. However, the biological samples used in the present invention can include cells, protein or membrane extracts of cells, blood or biological fluids such as ascites fluid or brain fluid (e.g., cerebrospinal fluid).
  • biological fluids such as ascites fluid or brain fluid (e.g., cerebrospinal fluid).
  • solid biological samples include, but are not limited to, samples taken from tissues of the central nervous system, bone, breast, kidney, cervix, endometrium, head/neck, gallbladder, parotid gland, prostate, pituitary gland, muscle, esophagus, stomach, small intestine, colon, liver, spleen, pancreas, thyroid, heart, lung, bladder, adipose, lymph node, uterus, ovary, adrenal gland, testes, tonsils and thymus.
  • body fluid samples include, but are not limited to blood, serum, semen, prostate fluid, seminal fluid, urine, saliva, sputum, mucus, bone marrow, lymph, and tears.
  • sample is used herein in its broadest sense.
  • a sample comprising polynucleotides, polypeptides, peptides, antibodies and the like may comprise a bodily fluid; a soluble fraction of a cell preparation, or media in which cells were grown; a chromosome, an organelle, or membrane isolated or extracted from a cell; genomic DNA, RNA, or cDNA, polypeptides, or peptides in solution or bound to a substrate; a cell; a tissue; a tissue print; a fingerprint, skin or hair; and the like.
  • Diagnostic means identifying the presence or nature of a pathologic condition. Diagnostic methods differ in their sensitivity and specificity.
  • the “sensitivity” of a diagnostic assay is the percentage of diseased individuals who test positive (percent of “true positives”). Diseased individuals not detected by the assay are “false negatives.” Subjects who are not diseased and who test negative in the assay, are termed “true negatives.”
  • the “specificity” of a diagnostic assay is 1 minus the false positive rate, where the “false positive” rate is defined as the proportion of those without the disease who test positive. While a particular diagnostic method may not provide a definitive diagnosis of a condition, it suffices if the method provides a positive indication that aids in diagnosis.
  • the invention comprises molecular signatures that function as very sensitive diagnostic biomarkers for heart failure, heart diseases, myocarditis, and other heart disorders. These biomarkers also identify individuals at risk of developing cardiovascular diseases or disorders.
  • Myocarditis is a common disease that is estimated to cause up to 30% of dilated, cardiomyopathy, even in patients initially asymptomatic. Myocarditis can also present as sudden cardiac death and affects individuals of all ages. In childhood, myocarditis causes a greater percentage of heart failure than in adulthood.
  • standard diagnostic tools which are currently available, e.g. ECG, cardiac enzymes and immunohistochemistry.
  • TLBs biomarkers
  • 9,878 genes were identified and which were differentially expressed in lymphocytic myocarditis vs. IDCM (FC>1.2, FDR ⁇ 5%), from which a transcriptomic biomarker containing 62 genes was identified, which distinguished myocarditis with 100% sensitivity (95% CI: 46-100%) and 100% specificity (95% CI: 66-100%).
  • Multiple classification algorithms and quantitative realtime RT-PCR analysis further reduced this subset to a highly robust molecular signature of 13 genes, which still performed with 100% accuracy.
  • TBBs were also obtained to distinguish between giant cell myocarditis and cardiac sarcoidosis, and peripartum cardiomyopathy vs lymphocytic cardiomyopathy.
  • Transcriptomic biomarkers can improve the clinical detection of patients with inflammatory diseases of the heart. This approach advances the clinical management and treatment of cardiac disorders with highly variable outcome.
  • diagnosis to distinguish between giant cell myocarditis and cardiac sarcoidosis; peripartum cardiomyopathy vs lymphocytic cardiomyopathy; myocarditis and idiopathic dilated cardiomyopathy; cardiac sarcoidosis, giant cell myocarditis, peripartum cardiomyopathy, and systemic lupus erythematosus with cardiac involvement comprises identifying a marker signature set forth in any one of Tables 1 to 19, complementary sequences, fragments, alleles, variants and gene products thereof.
  • a transcriptomic biomarker comprises a molecular signature such as for example: marker signature I: (1552302_at) FLJ77644.TMEM106, (1552553_a_at) NLRC4, (1552584_at) IL12RB1, (1554899_s_at) FCER1G, (1555349_a_at) ITGB2, (1559584_a_at) C16orf54, hCG — 1644884, (1563245_at) MGST1, (1565162_s_at) ANXA2, (1568126_at) SPP1, (1568574_x_at) IFI30, (201442_at) CTSC, (201487_at) LAPTM5, (201721_s_at) CD14, (201743_at) CAPG, (201850_at) PLTP, (202075_s_at) VAMP8, (202546_at) LYN, (202625_at) ITGB2, (202803_s_at) PCK
  • a transcriptomic biomarker for the diagnosis between giant cell myocarditis and idiopathic dilated cardiomyopathy comprising a marker signature set forth as: (210667_at) AQP4, (221212_x_at) PBRM1, (227145_at) LOXL4, (228329_at) DAB1, (231577_s_at) GBP1, (231906_at) HOXD8, (235334_at) ST6GALNAC3, (237783_at) PLAC8L1, complementary sequences, fragments, alleles, variants and gene products thereof.
  • a transcriptomic biomarker for the diagnosis between sarcoidosis and idiopathic dilated cardiomyopathy comprising a marker signature set forth as: (1552974_at) NA, (1553781_at) ZC3HAV1L, (1554478_a_at) HEATR3, (1556760_a_at) NA, (1556883_a_at) LOC440896, (1557717_at) LOC338862, (1560144-at) NA, (1560683_at) BCL8, (1560684_x_at) BCL8, (1561543_at) NA, (1562035_at) NA, (1563054_at) NA, (1563452_at) K1AA0241, (1564107_at) NA, (1564733_at) NA, (1565788_at) (1566550_at) NA, (1568589_at) NA, (201291_s_at) TOP2A, (204666_s_at) RP5-1000E
  • a transcriptomic biomarker for the diagnosis between peripartum cardiomyopathy and idiopathic dilated cardiomyopathy comprising a marker signature set forth as: (1553972_a_at) CBS, (1557833_at) NA, (1560395_at) NA; (201909_at) LOC100133662, RPS4Y1; (204409_s_at, 204410_at) EIF1AY, (205000_at, 205001_s_at) DDX3Y; (205033_s_at) DEFA1, DEFA3, LOC728358, (205048_s_at) PSPH, (205609_at) ANGPT1, (206624_at) LOC100130216, USP9Y; (206700_s_at) JARID1D, (207063_at) CYorf14, (208067_x_at) LOC100130224, UTY; (209771_x_at) CD24, (211018_at) LSS, (211
  • a transcriptomic biomarker for the diagnosis between systemic lupus erythematosus and idiopathic dilated cardiomyopathy comprising a marker signature set forth as: (1552946_at) ZNF114, (1553607_at) C21orf109, (1555485_s_at) FAM153B, (1558882_at) LOC401233, (1561012_at) NA, (156618_at) NA, (1569539_at) NA, (1569794_at) NA, (207781_s_at) ZNF711, (222375_at) NA, (229288_at) NA, (229523_at) TTMA, (235803_at) NA, (238553_at) EPHA7, (238755_at) NA, (240783_at) NA, (240903_at) NA, (242641_at) NA, (243012_at) NA, (2446260_at) NA, (244636_
  • a transcriptomic biomarker for the diagnosis between giant cell myocarditis and lymphocytic myocarditis comprising the marker signature set forth as: (156328_at) NA, (204477_at) RABIF, (205275_at) GTPBP1, (214313_s_at) EIF5B, complementary sequences, fragments, alleles, variants and gene products thereof.
  • a transcriptomic biomarker for the diagnosis between sarcoidosis and lymphocytic myocarditis comprising a marker signature set forth as: (20447_at) RABIF, (205275_at) GIPBP1, (214313_s_at) EIF5B, (224500_s_at) MON1A, (236093_at) NA, (243564_at) PDE1C, complementary sequences, fragments, alleles, variants and gene products thereof.
  • a transcriptomic biomarker for the diagnosis between peripartum cardiomyopathy and lymphocytic myocarditis comprising a marker signature set forth as: (156328_at) NA, (205275_at) GTPBP1, (207300_s_at) F7, (214313_s_at) EIF5B, (214473_x_at) PMS2L3, (227509_x_at) NA, (228232_s_at) VSIG2, (230731_x_at) ZDHHC8, (232586_x_at) LOC100133315, (236093_at) NA, (237867_s_at) PID1, (243564_at) PDE1C, complementary sequences, fragments, alleles, variants and gene products thereof.
  • a transcriptomic biomarker thr the diagnosis between systemic lupus erythematosus and lymphocytic myocarditis comprising a marker signature set forth as: (1556205_at) NA, (202179_at) BLMH, (203134_at) PICALM, (203540_at) GFAP, (205554_s_at) DNASE1L3, (205673_s_at) ASB9, (205794_s_at) NOVA1, (209220_at) GPC3, (209304_x_at) GADD45B, (209540_at) IGF1, (209923_s_at) BRAP, (212173_at) AK2, (213469_at) LPPR4 (214338_at) DNAJB12, (216269_s_at) ELN, (217950_at) NOSIP, (218180_s_at) EPS8L2, (220117_at) ZNF385D, (220941_s_
  • a transcriptomic biomarker for the differential diagnosis between giant cell myocarditis and sarcoidosis comprising a marker signature set forth as: (1553894_at) CCDC122, (1557311_at) LOC100131354, (1557996_at) POLR2J4, (1558430_at) NA, (1559227_s_at) VHL, (1561789_at) NA, (1569312_at) NA, (205238_at) CXorf34, (211734_s_at) FCER1A, (218699_at) RAP2C, (225207_at) PDK4, (231114_at) SPATA22, (231418_at) NA, (231819_at) NA, (231956_at) KIAA1618, (233927_at) NA, (239151_at) CTGLF6, (241788_x_at) NA, (242691_at) NA, complementary sequences, fragments, alleles, variants
  • a transcriptomic biomarker for the diagnosis of myocarditis comprising a marker signature set forth as: (1552302_at) FLJ77644, TMEM106A; (1552310_at) C15orf40, (1553212_at) KRT78, (1555349_a_at) ITGB2, (1555878_at) RPS24, (1556033_at) NA, (1556507_at) NA, (1558605_at) NA (1559224_at) LCE1E, (1562785_at) HERC6, (1565662_at) NA, (1565830_at) NA, (202375_at) SEC24D, (202445_s_at) NOTCH2, (203741_s_at) ADCY7, (204222_s_at) GLIPR1, (206052_s_at) SLBP, (206333_at) MSI1, (206770_s_at) SLC35A3, (209307_at) SWAP70, (211089_
  • a transcriptomic biomarker for the diagnosis of myocarditis versus idiopathic dilated cardiomyopathy comprising a marker signature set forth as: MSI1 (1556507_at), KRT78, KRT78 (1556507_at), KRT78 (1556507_at), 1556507_at, complementary sequences, fragments, alleles, variants and gene products thereof.
  • a transcriptomic biomarker for the diagnosis and differential diagnosis between myocarditis and idiopathic dilated cardiomyopathy comprising the marker signatures set forth in Tables 1, 2, 3, or 15, complementary sequences, fragments, alleles, variants and gene products thereof.
  • a transcriptomic biomarker for the diagnosis between giant cell myocarditis and idiopathic dilated cardiomyopathy comprising the marker signatures set forth in Table 4, complementary sequences, fragments, alleles, variants and gene products thereof.
  • a transcriptomic biomarker for the diagnosis between sarcoidosis and idiopathic dilated cardiomyopathy comprising the marker signature set forth in Table 5, complementary sequences, fragments, alleles, variants and gene products thereof.
  • a transcriptomic biomarker for the diagnosis between peripartum cardiomyopathy and idiopathic dilated cardiomyopathy comprising the marker signature set forth in Table 6, complementary sequences, fragments, alleles, variants and acne products thereof.
  • a transcriptomic biomarker for the diagnosis between systemic lupus erythematosus and idiopathic dilated cardiomyopathy comprising the marker signature set forth in Table 7, complementary sequences, fragments, alleles, variants and gene products thereof.
  • a transcriptomic biomarker for the diagnosis between giant cell myocarditis and lymphocytic myocarditis comprising the marker signature set forth in Table 8, complementary sequences, fragments, alleles, variants and gene products thereof.
  • a transcriptomic biomarker for the diagnosis between sarcoidosis and lymphocytic myocarditis comprising the marker signature set forth in Table 9, complementary sequences, fragments, alleles, variants and gene products thereof.
  • a transcriptomic biomarker for the diagnosis between peripartum cardiomyopathy and lymphocytic myocarditis comprising the marker signature set forth in Table 10, complementary sequences, fragments, alleles, variants and acne products thereof.
  • a transcriptomic biomarker for the diagnosis between systemic lupus erythematosus and lymphocytic myocarditis comprising the marker signature set forth in Table 11, complementary sequences, fragments, alleles, variants and gene products thereof.
  • a transcriptomic biomarker for the diagnosis between giant cell myocarditis and sarcoidosis comprising the marker signature set forth in Table 12, complementary sequences, fragments, alleles, variants and acne products thereof.
  • a transcriptomic biomarker for the diagnosis of myocarditis comprising the marker signature set forth in Table 14, complementary sequences, fragments, alleles, variants and gene products thereof.
  • a transcriptomic biomarker for the diagnosis of subtypes of inflammatory cardiomyopathy vs idiopathic dilated cardiomyopathy comprising the marker signatures set forth in Table 18, complementary sequences, fragments, alleles, variants and gene products thereof.
  • a transcriptomic biomarker for the diagnosis of rare types of inflammatory cardiomyopathy lymphocytic myocarditis comprising the marker signatures set forth in Table 19, complementary sequences, fragments, alleles, variants and gene products thereof.
  • each gene sequence set froth in Tables 1 to 19 comprises an antibody or aptamer specific for each gene sequence set froth in Tables 1 to 19, complementary sequences, fragments, alleles, variants and gene products thereof, complementary sequences, fragments, alleles, variants and gene products thereof.
  • a biochip comprising nucleic acid sequences set forth in Tables 1 to 19, complementary sequences, fragments, alleles, variants and gene products thereof.
  • a method of diagnosing myocarditis and other cardiac disorders comprising: identifying in a biological sample from a patient a molecular signature set forth in Tables 1 to 19, complementary sequences, fragments, alleles, variants and gene products thereof; assessing the probability of identification of each component gene in each sample; assigning each to a class; and, diagnosing myocarditis and other cardiac disorders.
  • a method of diagnosing heart disease or myocarditis comprising: identifying in a biological sample from a patient a molecular signature set forth in Tables 1 to 19, complementary sequences, fragments, alleles, variants and gene products thereof; assessing the probability of identification of each component gene in each sample; assigning each to a class; and, diagnosing heart disease or myocarditis.
  • kits comprising a transcriptomic biomarker of any one or more molecular signatures set forth in Tables 1 to 19.
  • a vector encoding any one or more biomolecules selected from Tables 1 to 19.
  • the detection in a cell or patient of the biomolecules, complementary sequences, fragments, alleles, variants and gene products thereof is diagnostic of myocarditis, idiopathic cardiomyopathy, heart, diseases and disorders thereof.
  • the biomolecule sequences, complementary sequences, fragments, alleles, variants and gene products thereof are modulated at levels by at least between 1%, 2%, 5%, 10% in a cell or patient as compared to levels in a normal cell or normal subject; more preferably, the gene biomarker sequences, complementary sequences, fragments, alleles, variants and gene products thereof, are modulated by about 50% in a cell or a patient as compared to levels in a normal cell or normal subject; more preferably, the gene biomarker sequences, complementary sequences, fragments, alleles, variants and gene products thereof, are modulated by about 75% in a cell or a patient as compared to levels in a normal cell or normal subject.
  • modulated refers to an increase or decrease in level, concentration, amount etc, as compared to a normal cell or normal healthy subject.
  • the term can also be applied as “differential expression” wherein one or more markers are increased, decreased or remain at baseline levels relative to each other and baseline normal controls.
  • each biomarker is detected on chip based methods such as those described in detail in the examples which follow.
  • cardiac disorders and diseases for example, heart failure, myocarditis, idiopathic cardiomyopathy and the like.
  • Other methods are also known in the art and one or more methods can be utilized.
  • transcriptomic biomarkers are directed to the examination of expression of transcriptomic biomarkers in a mammalian tissue or cell sample, wherein the determination of that expression of one or more such transcriptomic biomarkers is predictive of prognostic outcome or diagnostic of cardiac and cardiovascular diseases and disorders, such as for example, myocarditis, Coronary Heart Disease, angina, Acute Coronary Syndrome, Aortic Aneurysm and Dissection, arrhythmias, Cardiomyopathy, Congenital Heart Disease, congestive heart failure or chronic heart failure, pericarditis, and the like.
  • the Molecular signatures or Transcriptomic biomarker comprise the biomolecules identified in Tables 1 to 19.
  • Microarrays In general, using nucleic acid microarrays, test and control mRNA samples from test and control tissue samples are reverse transcribed and labeled to generate cDNA probes. The probes are then hybridized to an array of nucleic acids immobilized on a solid support. The array is configured such that the sequence and position of each member of the array is known. For example, a selection of genes that have potential to be expressed in certain disease states may be arrayed on a solid support. Hybridization of a labeled probe with a particular array member indicates that the sample from which the probe was derived expresses that gene. Differential gene expression analysis of disease tissue can provide valuable information.
  • Microarray technology utilizes nucleic acid hybridization techniques and computing technology to evaluate the mRNA expression profile of thousands of genes within a single experiment.
  • WO 01/75166 published Oct. 11, 2001;
  • DNA microarrays are miniature arrays containing gene fragments that are either synthesized directly onto or spotted onto glass or other substrates.
  • a typical microarray experiment involves the following steps: 1) preparation of fluorescently labeled target from RNA isolated from the sample, 2) hybridization of the labeled target to the microarray, 3) washing, staining, and scanning of the array, 4) analysis of the scanned image and 5) generation of gene expression profiles.
  • DNA microarrays Two main types of DNA microarrays are being used: oligonucleotide (usually 25 to 70 mers) arrays and gene expression arrays containing PCR products prepared from cDNAs.
  • oligonucleotides can be either prefabricated and spotted to the surface or directly synthesized on to the surface (in situ).
  • the Affymetrix GENECHIPTM system is a commercially available microarray system which comprises arrays fabricated by direct synthesis of oligonucleotides on a glass surface.
  • Probe/Gene Arrays Oligonucleotides, usually 25 mers, are directly synthesized onto a glass wafer by a combination of semiconductor-based photolithography and solid phase chemical synthesis technologies. Each array contains up to 400,000 different oligonucleotides and each oligonucleotide is present in millions of copies. Since oligonucleotide probes are synthesized in known locations on the array, the hybridization patterns and signal intensities can be interpreted in terms of gene identity and relative expression levels by the Affymetrix Microarray Suite software. Each gene is represented on the array by a series of different oligonucleotide probes.
  • Each probe pair consists of a perfect match oligonucleotide and a mismatch oligonucleotide.
  • the perfect match probe has a sequence exactly complimentary to the particular gene and thus measures the expression of the gene.
  • the mismatch probe differs from the perfect match probe by a single base substitution at the center base position, disturbing the binding of the target gene transcript. This helps to determine the background and nonspecific hybridization that contributes to the signal measured for the perfect match oligonucleotide.
  • the Microarray Suite software subtracts the hybridization intensities of the mismatch probes from those of the perfect match probes to determine the absolute or specific intensity value for each probe set. Probes are chosen based on current information from GenBank and other nucleotide repositories.
  • a GeneChip Hybridization Oven (“rotisserie” oven) is used to carry out the hybridization of up to 64 arrays at one time.
  • the fluidics station performs washing and staining of the probe arrays. It is completely automated and contains four modules, with each module holding one probe array. Each module is controlled independently through Microarray Suite software using preprogrammed fluidics protocols.
  • the scanner is a confocal laser fluorescence scanner which measures fluorescence intensity emitted by the labeled cRNA bound to the probe arrays.
  • the computer workstation with Microarray Suite software controls the fluidics station and the scanner.
  • Microarray Suite software can control up to eight fluidics stations using preprogrammed hybridization, wash, and stain protocols for the probe array.
  • the software also acquires and converts hybridization intensity data into a presence/absence call for each gene using appropriate algorithms.
  • the software detects changes in gene expression between experiments by comparison analysis and formats the output into .txt files, which can be used with other software programs for further data analysis.
  • the expression of a selected biomarker may also be assessed by examining gene deletion or gene amplification.
  • Gene deletion or amplification may be measured by any one of a wide variety of protocols known in the art, for example, by conventional Southern blotting, Northern blotting to quantitate the transcription of mRNA (Thomas, Proc. Natl. Acad. Sci . USA, 77:5201-5205 (1980)), dot blotting (DNA analysis), or in situ hybridization (e.g., FISH), using an appropriately labeled probe, cytogenetic methods or comparative genomic hybridization (CGH) using an appropriately labeled probe.
  • FISH in situ hybridization
  • a polypeptide corresponding to a marker is detected.
  • a preferred agent for detecting a polypeptide of the invention is an antibody or aptamer capable of binding to a polypeptide corresponding to a marker of the invention, preferably an antibody with a detectable label.
  • Antibodies can be polyclonal, or more preferably, monoclonal. An intact antibody, or a fragment thereof e.g., Fab or F(ab′) 2 can be used.
  • labeled with regard to the probe or antibody, is intended to encompass direct-labeling of the probe or antibody by coupling, i.e., physically linking, a detectable substance to the probe or antibody, as well as indirect-labeling of the probe or antibody by reactivity with another reagent that is directly-labeled.
  • indirect labeling include detection of a primary antibody using a fluorescently-labeled secondary antibody and end-labeling of a DNA probe with biotin such that it can be detected with fluorescently-labeled streptavidin.
  • Proteins from individuals can be isolated using techniques that are well-known to those of skill in the art.
  • the protein isolation methods employed can, e.g., be such as those described in Harlow & Lane (1988), supra.
  • a variety of formats can be employed to determine whether a sample contains a protein that binds to a given antibody.
  • Biomarkers in a sample can be analyzed by a number of methodologies, many of which are known in the art and understood by the skilled artisan, including but not limited to, immunohistochemical and/or Western analysis, quantitative blood based assays (as for example Serum ELISA) (to examine, for example, levels of protein expression), biochemical enzymatic activity assays, in situ hybridization, Northern analysis and/or PCR analysis of mRNAs, as well as any one of the wide variety of assays that can be performed by gene and/or tissue array analysis. Typical protocols for evaluating the status of genes and gene products are found, for example in Ausubel et al.
  • a sample may be contacted with an antibody specific for said biomarker under conditions sufficient for an antibody-biomarker complex to form, and then detecting said complex.
  • the presence of the biomarker may be detected in a number of ways, such as by Western blotting and ELISA procedures for assaying a wide variety of tissues and samples, including plasma or serum.
  • a wide range of immunoassay techniques using such an assay format are available, see, e.g., U.S. Pat. Nos. 4,016,043, 4,424,279 and 4,018,653. These include both single-site and two-site or “sandwich” assays of the non-competitive types, as well as in the traditional competitive binding assays. These assays also include direct binding of a labeled antibody to a target biomarker.
  • Sandwich assays are among the most useful and commonly used assays. A number of variations of the sandwich assay technique exist, and all are intended to be encompassed by the present invention. Briefly, in a typical forward assay, an unlabelled antibody is immobilized on a solid substrate, and the sample to be tested brought into contact with the bound molecule. After a suitable period of incubation, for a period of time sufficient to allow formation of an antibody-antigen complex, a second antibody specific to the antigen, labeled with a reporter molecule capable of producing a detectable signal is then added and incubated, allowing time sufficient for the formation of another complex of antibody-antigen-labeled antibody.
  • any unreacted material is washed away, and the presence of the antigen is determined by observation of a signal produced by the reporter molecule.
  • the results may either be qualitative, by simple observation of the visible signal, or may be quantitated by comparing with a control sample containing known amounts of biomarker.
  • a simultaneous assay in which both sample and labeled antibody are added simultaneously to the bound antibody.
  • a first antibody having specificity for the biomarker is either covalently or passively bound to a solid surface.
  • the solid surface is typically glass or a polymer, the most commonly used polymers being cellulose, polyacrylamide, nylon, polystyrene, polyvinyl chloride or polypropylene.
  • the solid supports may be in the form of tubes, beads, discs of microplates, or any other surface suitable for conducting an immunoassay.
  • the binding processes are well-known in the art and generally consist of cross-linking covalently binding or physically adsorbing, the polymer-antibody complex is washed in preparation for the test sample. An aliquot of the sample to be tested is then added to the solid phase complex and incubated for a period of time sufficient (e.g. 2-40 minutes or overnight if more convenient) and under suitable conditions (e.g. from room temperature to 40° C. such as between 25° C. and 32° C. inclusive) to allow binding of any subunit present in the antibody. Following the incubation period, the antibody subunit solid phase is washed and dried and incubated with a second antibody specific for a portion of the biomarker. The second antibody is linked to a reporter molecule which is used to indicate the binding of the second antibody to the molecular marker.
  • An alternative method involves immobilizing the target biomarkers in the sample and then exposing the immobilized target to specific antibody which may or may not be labeled with a reporter molecule. Depending on the amount of target and the strength of the reporter molecule signal, a bound target may be detectable by direct labeling with the antibody. Alternatively, a second labeled antibody, specific to the first antibody is exposed to the target-first antibody complex to form a target-first antibody-second antibody tertiary complex. The complex is detected by the signal emitted by the reporter molecule.
  • reporter molecule is meant a molecule which, by its chemical nature, provides an analytically identifiable signal which allows the detection of antigen-bound antibody. The most commonly used reporter molecules in this type of assay are either enzymes, fluorophores or radionuclide containing molecules (i.e. radioisotopes) and chemiluminescent molecules.
  • an enzyme is conjugated to the second antibody, generally by means of glutaraldehyde or periodate.
  • glutaraldehyde or periodate As will be readily recognized, however, a wide variety of different conjugation techniques exist, which are readily available to the skilled artisan.
  • Commonly used enzymes include horseradish peroxidase, glucose oxidase, -galactosidase and alkaline phosphatase, amongst others.
  • the substrates to be used with the specific enzymes are generally chosen for the production, upon hydrolysis by the corresponding enzyme, of a detectable color change. Examples of suitable enzymes include alkaline phosphatase and peroxidase.
  • fluorogenic substrates which yield a fluorescent product rather than the chromogenic substrates noted above.
  • the enzyme-labeled antibody is added to the first antibody-molecular marker complex, allowed to bind, and then the excess reagent is washed away. A solution containing the appropriate substrate is then added to the complex of antibody-antigen-antibody. The substrate will react with the enzyme linked to the second antibody, giving a qualitative visual signal which may be further quantitated. Usually spectrophotometrically, to give an indication of the amount of biomarker which was present in the sample.
  • fluorescent compounds such as fluorescein and rhodamine, may be chemically coupled to antibodies without altering their binding capacity.
  • the fluorochrome-labeled antibody When activated by illumination with light of a particular wavelength, the fluorochrome-labeled antibody adsorbs the light energy, inducing a state to excitability in the molecule, followed by emission of the light at a characteristic color visually detectable with a light microscope. As in the ETA, the fluorescent labeled antibody is allowed to bind to the first antibody-molecular marker complex. After washing off the unbound reagent, the remaining tertiary complex is then exposed to the light of the appropriate wavelength, the fluorescence observed indicates the presence of the molecular marker of interest. Immunofluorescence and EIA techniques are both very well established in the art. However, other reporter molecules, such as radioisotope, chemiluminescent or bioluminescent molecules, may also be employed.
  • Methods of the invention further include protocols which examine the presence and/or expression of mRNAs, in a tissue or cell sample.
  • Methods for the evaluation of mRNAs in cells are well known and include, for example, hybridization assays using complementary DNA probes (such as in situ hybridization using labeled riboprobes, Northern blot and related techniques) and various nucleic acid amplification assays (such as RT-PCR and other amplification type detection methods, such as, for example, branched DNA, SISBA, TMA and the like).
  • the level of mRNA corresponding to the marker can be determined both by in situ and by in vitro formats in a biological sample using methods known in the art.
  • Many expression detection methods use isolated RNA.
  • any RNA isolation technique that does not select against the isolation of mRNA can be utilized for the purification of RNA from cells. See, e.g., Asubel et al., Ed., Curr. Prot. Mol. Biol., John Wiley & Sons, NY (1987-1999).
  • large numbers of tissue samples can readily be processed using techniques well-known to those of skill in the art, such as, e.g., the single-step RNA isolation process of U.S. Pat. No. 4,843,155.
  • the isolated mRNA can be used in hybridization or amplification assays that include, but are not limited to, Southern or Northern analyses, PCR analyses and probe arrays.
  • One preferred diagnostic method for the detection of mRNA levels involves contacting the isolated mRNA with a nucleic acid molecule (probe) that can hybridize to the mRNA encoded by the gene being detected.
  • the nucleic acid probe can be, e.g., a full-length cDNA, or a portion thereof, such as an oligonucleotide of at least 7, 15, 30, 50, 100, 250 or 500 nucleotides in length and sufficient to specifically hybridize under stringent conditions to a mRNA or genomic DNA encoding a marker of the present invention.
  • Other suitable probes for use in the diagnostic assays of the invention are described herein. Hybridization of an mRNA with the probe indicates that the marker in question is being expressed.
  • the mRNA is immobilized on a solid surface and contacted with a probe, for example, by running the isolated mRNA on an agarose gel and transferring the mRNA from the gel to a membrane, such as nitrocellulose.
  • the probe(s) are immobilized on a solid surface and the mRNA is contacted with the probe(s), for example, in an Affymetrix gene chip array.
  • a skilled artisan can readily adapt known mRNA detection methods for use in detecting the level of mRNA encoded by the markers of the present invention.
  • amplification of molecules is not required in the present invention as discussed in the examples section, one of skill in the art could use amplification methods.
  • One alternative method for determining the level of mRNA corresponding to a marker of the present invention in a sample involves the process of nucleic acid amplification, e.g., by RT-PCR (the experimental embodiment set forth in Mullis, U.S. Pat. No. 4,683,202 (1987); ligase chain reaction, self-sustained sequence replication, Guatelli et al., Proc. Natl. Acad. Sci . USA, Vol. 87, pp. 1874-1878 (1990); transcriptional amplification system, Kwoh al, Proc. Natl. Acad. Sci . USA, Vol.
  • amplification primers are defined as being a pair of nucleic acid molecules that can anneal to 5′ or 3′ regions of a gene (plus and minus strands, respectively, or vice-versa) and contain a short region in between.
  • amplification primers are from about 10-30 nucleotides in length and flank a region from about 50-200 nucleotides in length. Under appropriate conditions and with appropriate reagents, such primers permit the amplification of a nucleic acid molecule comprising the nucleotide sequence flanked by the primers.
  • mRNA does not need to be isolated form the cells prior to detection.
  • a cell or tissue sample is prepared/processed using known histological methods. The sample is then immobilized on a support, typically a glass slide, and then contacted with a probe that can hybridize to mRNA that encodes the marker.
  • determinations may be based on the normalized expression level of the marker.
  • Expression levels are normalized by correcting the absolute expression level of a marker by comparing its expression to the expression of a gene that is not a marker, e.g., a housekeeping gene that is constitutively expressed.
  • Suitable genes for normalization include housekeeping genes, such as the actin gene or epithelial cell-specific genes. This normalization allows the comparison of the expression level in one sample, e.g., a patient sample, to another sample or between samples from different sources.
  • the expression level can be provided as a relative expression level.
  • the level of expression of the marker is determined for 10 or more samples of normal versus disease biological samples, preferably 50 or more samples, prior to the determination of the expression level for the sample in question.
  • the mean expression level of each of the genes assayed in the larger number of samples is determined and this is used as a baseline expression level for the marker.
  • the expression level of the marker determined for the test sample (absolute level of expression) is then divided by the mean expression value obtained for that marker. This provides a relative expression level.
  • the samples used in the baseline determination will be from patients who do not have the polymorphism.
  • the choice of the cell source is dependent on the use of the relative expression level. Using expression found in normal tissues as a mean expression score aids in validating whether the marker assayed is specific (versus normal cells). In addition, as more data is accumulated, the mean expression value can be revised, providing improved relative expression values based on accumulated data.
  • the antibodies and aptamers specifically bind each component of the biomarkers described herein.
  • the components include the nucleic acid sequences, complementary sequences, fragments, alleles, variants and gene products thereof of each component in each biomarker.
  • Aptamer polynucleotides are typically single-stranded standard phosphodiester DNA (ssDNA). Close DNA analogs can also be incorporated into the aptamer as described below.
  • a typical aptamer discovery procedure is described below: A polynucleotide comprising a randomized sequence between “arms” having constant sequence is synthesized.
  • the arms can include restriction sites for convenient cloning and can also function as priming sites for PCR primers. The synthesis can easily be performed on commercial instruments.
  • the target protein is treated with the randomized polynucleotide.
  • the target protein can be in solution and then the complexes immobilized and separated from unbound nucleic acids by use of an antibody affinity column.
  • the target protein might be immobilized before treatment with the randomized polynucleotide.
  • the target protein-polynucleotide complexes are separated from the uncomplexed material and then the bound polynucleotides are separated from the target protein.
  • the bound nucleic acid can then be characterized, but is more commonly amplified, e.g. by PCR and the binding, separation and amplification steps are repeated.
  • use of conditions increasingly promoting separation of the nucleic acid from the target protein e.g. higher salt concentration, in the binding buffer used in step 2) in subsequent iterations, results in identification of polynucleotides having increasingly high affinity for the target protein.
  • the nucleic acids showing high affinity for the target proteins are isolated and characterized. This is typically accomplished by cloning the nucleic acids using restriction sites incorporated into the arms, and then sequencing the cloned nucleic acid.
  • the affinity of aptamers for their target proteins is typically in the nanomolar range, but can be as low as the picomolar range. That is K D is typically 1 pM to 500 nM, more typically from 1 pM to 100 nM. Aptamers having an affinity of K D in the range of 1 pM to 10 nM are also useful.
  • Aptamer polynucleotides can be synthesized on a commercially available nucleic acid synthesizer by methods known in the art.
  • the product can be purified by size selection or chromatographic methods.
  • Aptamer polynucleotides are typically from about 10 to 200 nucleotides long, more typically from about 10 to 100 nucleotides long, still more typically from about 10 to 50 nucleotides long and yet more typically from about 10 to 25 nucleotides long.
  • a preferred range of length is from about 10 to 50 nucleotides.
  • the aptamer sequences can be chosen as a desired sequence, or random or partially random populations of sequences can be made and then selected for specific binding to a desired target protein by assay in vitro. Any of the typical nucleic acid-protein binding assays known in the art can be used, e.g. “Southwestern” blotting using either labeled oligonucleotide or labeled protein as the probe. See also U.S. Pat. No. 5,445,935 for a fluorescence polarization assay of protein-nucleic acid interaction.
  • a desired aptamer-protein complex for example, aptamer-thrombin complex of the invention can be labeled and used as a diagnostic agent in vitro in much the same manner as any specific protein-binding agent, e.g. a monoclonal antibody.
  • an aptamer-protein complex of the invention can be used to detect and quantitate the amount of its target protein in a sample, e.g. a blood sample, to provide diagnosis of a disease state correlated with the amount of the protein in the sample.
  • a desired aptamer-target/bait molecular complex can also be used for diagnostic imaging, in imaging uses, the complexes are labeled no that they can be detected outside the body.
  • Typical labels are radioisotopes, usually ones with short half-lives.
  • the usual imaging radioisotopes such as 123 I, 124 I, 125 I, 131 I, 99m TC, 186 Re, 188 Re, 64 Cu, 67 Cu, 212 Bi, 213 Bi, 67 Ga, 90 Y, 111 In, 18 F, 3 H, 35 S or 32 P can be used.
  • Nuclear magnetic resonance (NMR) imaging enhancers such as gadolinium-153, can also be used to label the complex for detection by NMR. Methods and reagents for performing the labeling, either in the polynucleotide or in the protein moiety, are considered known in the art.
  • an antibody or aptamer is specific for each biomolecule of in Tables 1 to 19.
  • the molecular signatures are useful for the identification of new drugs in the treatment of cardiovascular diseases and disorders.
  • the molecular signatures would verify whether a patient's treatment is progressing.
  • the molecular signature may change during the course of treatment and reflect normal controls.
  • Small molecule test compounds or candidate therapeutic compounds can initially be members of an organic or inorganic chemical library.
  • small molecules refers to small organic or inorganic molecules of molecular weight below about 3,000 Daltons.
  • the small molecules can be natural products or members of a combinatorial chemistry library.
  • a set of diverse molecules should be used to cover a variety of functions such as charge, aromaticity, hydrogen bonding, flexibility, size, length of side chain, hydrophobicity, and rigidity.
  • Combinatorial techniques suitable for synthesizing small molecules are known in the art, e.g., as exemplified by Obrecht and Villalgordo, Solid-Supported Combinatorial and Parallel Synthesis of Small-Molecular-Weight Compound Libraries, Pergamon-Elsevier Science Limited (1998), and include those such as the “split and pool” or “parallel” synthesis techniques, solid-phase and solution-phase techniques, and encoding techniques (see, for example, Czarnik, Curr. Opin. Chem. Bio., 1:60(1997). In addition, a number of small molecule libraries are commercially available.
  • Particular screening applications of this invention relate to the testing of pharmaceutical compounds in drug research.
  • the reader is referred generally to the standard textbook “In vitro Methods in Pharmaceutical Research”, Academic Press, 1997, and U.S. Pat. No. 5,030,015).
  • Assessment of the activity of candidate pharmaceutical compounds generally involves administering a candidate compound, determining any change in the morphology, marker phenotype and expression, or metabolic activity of the cells and function of the cells that is attributable to the compound (compared with untreated cells or cells treated with an inert compound), and then correlating the effect of the compound with the observed change.
  • the screening may be done, for example, either because the compound is designed to have a pharmacological effect on certain cell types, or because a compound designed to have effects elsewhere may have unintended side effects.
  • Two or more drugs can be tested in combination (by combining with the cells either simultaneously or sequentially), to detect possible drug-drug interaction effects.
  • compounds are screened initially for potential toxicity (Castell et al., pp, 375-410 in “In vitro Methods in Pharmaceutical Research.” Academic Press, 1997), Cytotoxicity can be determined in the first instance by the effect on cell viability, survival, morphology, and expression or release of certain markers, receptors or enzymes. Effects of a drug on chromosomal DNA can be determined by measuring DNA synthesis or repair.
  • [ 3 H]thymidine or BrdU incorporation is consistent with a drug effect. Unwanted effects can also include unusual rates of sister chromatid exchange, determined by metaphase spread. The reader is referred to A. Vickers (PP 375-410 in “In vitro Methods in Pharmaceutical Research,” Academic Press, 1997) for further elaboration.
  • a method of identifying a candidate agent comprising: (a) contacting a biological sample from a patient with the candidate agent and determining the level of expression of one or more biomarkers described herein; (b) determining the level of expression of a corresponding biomarker or biomarkers in an aliquot of the biological sample not contacted with the candidate agent; (c) observing the effect of the candidate agent by comparing the level of expression of the biomarker or biomarkers in the aliquot of the biological sample contacted with the candidate agent and the level of expression of the corresponding biomarker or biomarkers in the aliquot of the biological sample not contacted with the candidate agent; and (d) identifying said agent from said observed effect, wherein an at least 1%, 2%, 5%, 10% difference between the level of expression of the biomarker gene or combination of biomarker genes in the aliquot of the biological sample contacted with the candidate agent and the level of expression of the corresponding biomarker gene, or combination of biomarker genes
  • the effects of the drug are correlated with the expression of the molecular signatures associated with a good prognosis as described in detail in the examples which follow.
  • a candidate agent derived by the method according to the invention is provided.
  • a pharmaceutical preparation comprising an agent according to the invention is provided.
  • a method of producing a drug comprising; the steps of the method according to the invention (i) synthesizing the candidate agent identified in step (c) above or an analog or derivative thereof in an amount sufficient to provide said drug in a therapeutically effective amount to a subject; and/or (ii) combining the drug candidate the candidate agent identified in step (c) above or an analog or derivative thereof with a pharmaceutically acceptable carrier.
  • Vectors, Cells In some embodiments it is desirable to express the biomolecules that comprise a biomarker, in a vector and in cells. The applications of such combinations are unlimited.
  • the vectors and cells expressing the one or more biomolecules can be used in assays, kits, drug discovery, diagnostics, prognostics and the like.
  • the cells can be stem cells isolated from the bone marrow as a progenitor cell, or cells obtained from any other source, such as for example, ATCC.
  • BMDC single marrow derived progenitor cell
  • bone marrow derived stem cell refers to a primitive stem cell with the machinery for self-renewal constitutively active. Included in this definition are stem cells that are totipotent, pluripotent and precursors.
  • a “precursor cell” can be any cell in a cell differentiation pathway that is capable of differentiating into a more mature cell.
  • the term “precursor cell population” refers to a group of cells capable of developing into amore mature cell.
  • a precursor cell population can comprise cells that are totipotent, cells that are pluripotent and cells that are stem cell lineage restricted (i.e.
  • the term “totipotent cell” refers to a cell capable of developing into all lineages of cells.
  • the term “totipotent population of cells” refers to a composition of cells capable of developing into all lineages of cells.
  • the term “pluripotent cell” refers to a cell capable of developing into a variety (albeit not all) lineages and are at least able to develop into all hematopoietic lineages (e.g., lymphoid, erythroid, and thrombocytic lineages).
  • Bone marrow derived stem cells contain two well-characterized types of stem cells.
  • Mesenchymal stem cells normally form chondrocytes and osteoblasts.
  • Hematopoietic stem cells are of mesodermal origin that normally gives rise to cells of the blood and immune system (e.g., erythroid, granulocyte/macrophage, magakaryocite and lymphoid lineages).
  • hematopoietic stem cells also have been shown to have the potential to differentiate into the cells of the liver (including hepatocytes, bile duct cells), lung, kidney (e.g., renal tubular epithelial cells and renal parenchyma), gastrointestinal tract, skeletal muscle fibers, astrocytes of the CNS. Purkinje neurons, cardiac muscle (e.g., cardiomyocytes), endothelium and skin.
  • a method of identifying candidate therapeutic compounds comprises culturing cells expressing at least one biomolecule selected from biomarker signatures in Tables 1 to 19.
  • Such compounds are useful, e.g., as candidate therapeutic compounds for the treatment of heart disease, heart disorders and conditions thereof.
  • methods for screening for candidate therapeutic compounds for the treatment of for example, myocarditis, Coronary Heart Disease, angina, Acute Coronary Syndrome, Aortic Aneurysm and Dissection, arrhythmias, Cardiomyopathy, Congenital Heart Disease, congestive heart failure or chronic heart failure, pericarditis, and the like.
  • the methods include administering the compound to a model of the condition, e.g., contacting a cell (in vitro) model with the compound, or administering the compound to an animal model of the condition, e.g., an animal model of a condition associated with heart disease.
  • the model is then evaluated for an effect of the candidate compound on the clinical outcome in the model and can be considered a candidate therapeutic compound for the treatment of the condition.
  • effects can include clinically relevant effects, decreased pain; increased life span; and so on.
  • effects can be determined on a macroscopic or microscopic scale.
  • Candidate therapeutic compounds identified by these methods can be further verified, e.g., by administration to human subjects in a clinical trial.
  • the biomolecules can be expressed from one or more vectors.
  • a “vector” (sometimes referred to as gene delivery or gene transfer “vehicle”) refers to a macromolecule or complex of molecules comprising a polynucleotide to be delivered to a host cell, either in vitro or in vivo.
  • the polynucleotide to be delivered may comprise a coding sequence of interest in gene therapy.
  • Vectors include, for example, viral vectors (such as adenoviruses (“Ad”), adeno-associated viruses (AAV), and retroviruses), liposomes and other lipid-containing complexes, and other macromolecular complexes capable of mediating delivery of a polynucleotide to a host cell.
  • Vectors can also comprise other components or functionalities that further modulate gene delivery and/or gene expression, or that otherwise provide beneficial properties to the targeted cells.
  • such other components include, for example, components that influence binding or targeting to cells (including components that mediate cell-type or tissue-specific binding); components that influence uptake of the vector nucleic acid by the cell; components that influence localization of the polynucleotide within the cell after uptake (such as agents mediating nuclear localization); and components that influence expression of the polynucleotide.
  • Such components also might include markers, such as detectable and/or selectable markers that can be used to detect or select for cells that have taken up and are expressing the nucleic acid delivered by the vector.
  • Such components can be provided as a natural feature of the vector (such as the use of certain viral vectors which have components or functionalities mediating binding and uptake), or vectors can be modified to provide such functionalities.
  • Other vectors include those described by Chen et al; BioTechniques, 34: 167-171 (2003). Large varieties of such vectors are known in the art and are generally available.
  • a vector expresses one or more biomolecules identified in any one or more of Tables 1 to 19.
  • kits comprising any one or more of the biomarkers or molecular signatures comprising Tables 1 to 19.
  • kits or articles of manufacture are also provided by the invention.
  • Such kits may comprise a carrier means being compartmentalized to receive in close confinement one or more container means such as vials, tubes, and the like, each of the container means comprising one of the separate elements to be used in the method.
  • container means such as vials, tubes, and the like
  • each of the container means comprising one of the separate elements to be used in the method.
  • one of the container means may comprise a probe that is or can be detectably labeled.
  • the kit may also have containers containing nucleotide(s) for amplification of the target nucleic acid sequence and/or a container comprising a reporter-means, such as a biotin-binding protein, such as avidin or streptavidin, bound to a reporter molecule, such as an enzymatic, florescent, or radioisotope label.
  • a reporter-means such as a biotin-binding protein, such as avidin or streptavidin
  • the kit of the invention will typically comprise the container described above and one or more other containers comprising materials desirable from a commercial and user standpoint, including buffers, diluents, filters, needles, syringes, and package inserts with instructions for use.
  • a label may be present on the container to indicate that the composition is used for a specific therapy or non-therapeutic application, and may also indicate directions for either in vivo or in vitro use, such as those described above.
  • kits of the invention have a number of embodiments.
  • a typical embodiment is a kit comprising a container, a label on said container, and a composition contained within said container; wherein the composition includes a primary antibody that binds to the biomolecules of each molecular signature and instructions for using the antibody for evaluating the presence of biomolecules in at least one type of mammalian cell
  • the kit can further comprise a set of instructions and materials for preparing a tissue sample and applying antibody and probe to the same section of a tissue sample.
  • the kit may include both a primary and secondary antibody, wherein the secondary antibody is conjugated to a label, e.g., an enzymatic label.
  • kits comprising a container, a label on said container, and a composition contained within said container; wherein the composition includes a polynucleotide that hybridizes to a complement of the polynucleotides under stringent conditions, the label on said container indicates that the composition can be used to evaluate the presence of a molecular signature in at least one type of mammalian cell, and instructions for using the polynucleotide for evaluating the presence of biomolecule RNA or DNA in at least one type of mammalian cell.
  • kits include, microarrays, one or more buffers (e.g., block buffer, wash buffer, substrate buffer, etc), other reagents such as substrate (e.g., chromogen) which is chemically altered by an enzymatic label, epitope retrieval solution, control samples (positive and/or negative controls), control slide(s) etc.
  • buffers e.g., block buffer, wash buffer, substrate buffer, etc
  • substrate e.g., chromogen
  • control samples positive and/or negative controls
  • Embodiments of the invention may be practiced without the theoretical aspects presented. Moreover, the theoretical aspects are presented with the understanding that Applicants do not seek to be bound by the theory presented.
  • IDC idiopathic dilated cardiomyopathy
  • RNA extraction and microarray hybridization Total RNA was extracted from biopsies as previously described. Quality control of integrity of RNA was performed with the 2100 Bioanalyzer (Agilent). MIAME guidelines were followed for all steps of the procedure. The extracted RNA (average 568 ⁇ 88 ng; Standard Error of the Mean (SEM)) was preprocessed with the Ovation Biotin RNA Amplification and Labeling System (NuGen, Cat. No. 2300-12) for subsequent hybridization with the Human Genome U133 Plus 2.0 Array from Affymetrix without additional amplification step.
  • SEM Standard Error of the Mean
  • This formula provides a value that represents the probability for a particular mapping of an experiment to a map (or network/process) to arise by chance, considering the numbers of genes in the experiment vs the number of genes in the map within the “full set” of all genes on maps.
  • a z-score was calculated for each network, which reflects the saturation with genes from the experiment.
  • a high z-score indicates a network that contains a large amount of genes from the experiment.
  • MiPP misclassification-penalized posteriors classification
  • the MiPP package is an application in the R environment, which employs the libraries MASS for lda/qda (linear/quadratic discriminant analysis and e1071 for SVM (support vector machine).
  • This software sequentially adds genes to a classification model based upon the Misclassication-Penalized Posteriors principle, which takes into account the likelihood that a sample belongs to a given class by using posterior probability of correct classification.
  • First MiPP was used to test several different classification rules, to further reduce the novel molecular signature, consisting of 62 genes.
  • Support vector machine was subsequently applied with radial basis function (SVM-rbf) and lineal function (SVM-lin), quadratic discriminant analysis (qda), linear discriminant analysis (lda) and a combination of lda, qda and svm-rbf.
  • SVM-rbf radial basis function
  • SVM-lin lineal function
  • qda quadratic discriminant analysis
  • lda linear discriminant analysis
  • a combination of lda, qda and svm-rbf a combination of lda, qda and svm-rbf.
  • Linear discriminant analysis uses a linear combination of features, which best separate two or more classes.
  • Quadratic discriminant analysis is closely related to lda, however there is no assumption that the covariance of each of the classes is identical. Models were developed based upon 5-fold cross validation in a train set (2 ⁇ 3 of data) and subsequent validation in an independent test set (1 ⁇ 3 of data).
  • PCA principal components analysis
  • First-strand cDNA was synthesized with a High-Capacity cDNA Reverse-Transcription Kit (Applied Biosystems Inc., CA, USA) from 100 ng total RNA, which was amplified with MessageAmp II Amplification Kit (Applied Biosystems Inc., CA, USA).
  • Table 13 depicts the baseline clinical variables of patients included in the initial case-control population with idiopathic dilated cardiomyopathy (IDCM) and Dallas criteria defined lymphocytic myocarditis. By design, there were no differences in gender, age, functional parameters or medication between the two groups.
  • IDCM idiopathic dilated cardiomyopathy
  • oligonucleotide microarrays were used to analyze RNA obtained from endomyocardial biopsies (EMBs) from affected patients at first presentation with new onset heart failure. 9,878 differentially expressed genes (q ⁇ 5%, fold change (FC)>1.2) were identified in patients with IDCM compared to myocarditis ( FIG. 1 ). Transcripts with FC>2 (141 over-expressed and 16 down-regulated transcripts) are provided as in Tables 13 and 14. Pathway analysis with GeneGo Metacore revealed overexpression of a total of 8 networks in myocarditis vs IDCM (Table 3). No specific networks were revealed within the small amount of down-regulated transcripts with FC>2 (16 genes).
  • the molecular signature still had a high degree of diagnostic accuracy and identified 83% of patients with myocarditis correctly (sensitivity: 91%, 95 CI: 57-100%; specificity: 100%, 95 CI: 66-100%; PPV: 100%, 95 CI: 66-100%; NPV: 91%, 95 CI: 57-100%).
  • PCA principal components analysis
  • transcriptomic data was validated with quantitative realtime RT-PCR.
  • realtime RT-PCR was performed on a subset of 16 genes (Table 17). Genes were selected from the resulting gene lists of the bioinformatic approach, based on biological plausibility and robustness as classifiers for lymphocytic myocarditis.
  • KRT78 and POU4F1 could not be confirmed with realtime RT-PCR. Since KRT78 appeared highly robust as classifier based on the microarray results, two different primer pairs were used to detect either the 3′ or the 5′ end of the gene sequence. However, none of them were able to detect KRT78 in any of the samples. When total RNA was used from immortalized keratinocytes as a positive control, a signal was received from each primer pair.
  • the 13 gene signature When applied to a subset of myocarditis patients with higher ejection fraction, the 13 gene signature performed with a sensitivity of 75% (95CI: 36-96%), specificity of 100% (95CI: 52-100%), PPV of 100% (95CI: 52-100%) and NPV of 75% (95CI: 36-96%).
  • Inflammatory disorders of the heart have been, prior to this study, notoriously difficult to diagnose due to the patchy nature of the inflammation.
  • a wide variety of underlying inflammatory conditions can affect the heart.
  • the transcriptome obtained from a single endomyocardial biopsy was employed to develop biomarkers that enhanced the diagnostic accuracy for detection of cardiac inflammation as well at the ability to separate between important subtypes of cardiac inflammation.
  • This approach illustrated the value of the transcriptome as a diagnostic biomarker for heart diseases and offers insights into anew clinically useful tool.
  • the data herein evidence the results obtained using the TBBs to distinguish between idiopathic and ischemic cardiomyopathy and to predict long term prognosis in new onset dilated cardiomyopathy.
  • the original dataset was established by the inventors in which the TBB was developed and was matched in a case-control fashion, it was further evaluated if the molecular signature is generalizable, or if it is possibly overfit to this particular study design. It has been shown in the past that confounding factors such as gender, age and therapy can affect gene expression.
  • the TBB was applied in an additional validation set containing samples from patients with an average EF that was twice as high as the average EF of the original data set (65 vs 30%), the biomarker performed with almost perfect accuracy.
  • a transcriptomic diagnostic biomarker was discovered herein, derived from a single EMB, which identified samples with lymphocytic myocarditis with very high accuracy. These findings are highly relevant for a clinical application, since this novel diagnostic tool exceeds sensitivity and specificity of any technology that has been applied previously.
  • the molecular signature was highly robust and replicated multiple times by a broad set of established classification algorithms. Validation in two independent data sets revealed high diagnostic accuracy and genes within the transcriptomic biomarker suggest biological plausibility. Altogether, using this approach dramatically increases the diagnostic accuracy of a single EMB, which may be of critical importance to the development and allocation of emerging specific therapies for inflammatory conditions of the heart.
  • Wnt receptor signaling pathway cell-cell adhesion, positive regulation of activated T cell proliferation 211018_at LSS lnosterol synthase (2,3- steroid biosynthetic process, metabolic process, steroid oxidosqualene-lanotherol metabolic process, lipid biosynthetic process cyclase) 211149_at LOC100130224, hypothetical protein chromatin modification, oxidation reduction UTY LOC100130224, ubiquitously transcribed tetratricopeptide repeat gene, Y-linked 213768_s_at OLFM4 olfactomedin 4 cell adhesion 212816_s_at CBS cystathionine-beta-synthase cysteine metabolic process 212906_at GRAMD1B GRAM domain containing 1B NA 214131_at CYorf15B chromosome Y open reading NA frame 15B 214218_s_at XIST X (inactive)-specific transcript NA (non-
  • DNA catabolic process DNA fragmentation during like 3 apoptosis 205673_s_at ASB9 ankyrin repeat and intracellular signaling escade SOCS box-containing 9 205794_s_at NOVA1 neuro-encological RNA processing, synaptic transmission, locomotory behavior, RNA splicing ventral antigen 1 209220_at GPC3 glypican 3 anatomical structure morphogenesis 209304_s_at GADD45B growth arrest and DNA- activation of MAPKKK activity, negative regulation of protein kinase activity, damage-inducible, beta apoptosis, response to stress, multicellular organismal development cell differentiation 209540_at IGF1 insulin-like growth skeletal development, DNA replication, anti-apoptosis, muscle development, factor 1 (somatomedin positive regulation of cell proliferation, satellite cell maintenance involved in C) skeletal muscle regeneration, muscle hypertrophy, myotube cell development positive regulation of tyrosine phosphorylation of Stat5 protein, myo
  • RNA polymerase II DNA directed transcription polypeptide J4

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