US20200171024A1 - Biomarkers for the diagnosis and treatment of fibrotic lung disease - Google Patents

Biomarkers for the diagnosis and treatment of fibrotic lung disease Download PDF

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US20200171024A1
US20200171024A1 US16/624,500 US201816624500A US2020171024A1 US 20200171024 A1 US20200171024 A1 US 20200171024A1 US 201816624500 A US201816624500 A US 201816624500A US 2020171024 A1 US2020171024 A1 US 2020171024A1
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subject
lung disease
polymorphism
fibrotic lung
sequence encoding
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David A. Schwartz
Ivana V. Yang
Joyce S. Lee
Christopher M. Evans
Marvin I. SCHWARZ
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University of Colorado
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The Regents Of The University Of Colorado, A Body Corporate
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
    • A61K31/496—Non-condensed piperazines containing further heterocyclic rings, e.g. rifampin, thiothixene or sparfloxacin
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/185—Acids; Anhydrides, halides or salts thereof, e.g. sulfur acids, imidic, hydrazonic or hydroximic acids
    • A61K31/19—Carboxylic acids, e.g. valproic acid
    • A61K31/195—Carboxylic acids, e.g. valproic acid having an amino group
    • A61K31/197—Carboxylic acids, e.g. valproic acid having an amino group the amino and the carboxyl groups being attached to the same acyclic carbon chain, e.g. gamma-aminobutyric acid [GABA], beta-alanine, epsilon-aminocaproic acid or pantothenic acid
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
    • A61K31/44—Non condensed pyridines; Hydrogenated derivatives thereof
    • A61K31/4412—Non condensed pyridines; Hydrogenated derivatives thereof having oxo groups directly attached to the heterocyclic ring
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K9/00—Medicinal preparations characterised by special physical form
    • A61K9/0012—Galenical forms characterised by the site of application
    • A61K9/0053—Mouth and digestive tract, i.e. intraoral and peroral administration
    • A61K9/0056—Mouth soluble or dispersible forms; Suckable, eatable, chewable coherent forms; Forms rapidly disintegrating in the mouth; Lozenges; Lollipops; Bite capsules; Baked products; Baits or other oral forms for animals
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P11/00—Drugs for disorders of the respiratory system
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • 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
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/185—Acids; Anhydrides, halides or salts thereof, e.g. sulfur acids, imidic, hydrazonic or hydroximic acids
    • A61K31/19—Carboxylic acids, e.g. valproic acid
    • A61K31/195—Carboxylic acids, e.g. valproic acid having an amino group
    • A61K31/197—Carboxylic acids, e.g. valproic acid having an amino group the amino and the carboxyl groups being attached to the same acyclic carbon chain, e.g. gamma-aminobutyric acid [GABA], beta-alanine, epsilon-aminocaproic acid or pantothenic acid
    • A61K31/198—Alpha-amino acids, e.g. alanine or edetic acid [EDTA]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
    • A61K31/44—Non condensed pyridines; Hydrogenated derivatives thereof
    • A61K31/4418—Non condensed pyridines; Hydrogenated derivatives thereof having a carbocyclic group directly attached to the heterocyclic ring, e.g. cyproheptadine
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers

Definitions

  • the disclosure is directed to molecular biology, genetics, and therapeutics for fibrotic lung disease.
  • Fibrotic pulmonary diseases are progressive and irreversible. Standard therapies are mere palliative as they cannot address the underlying disease mechanism once the subject has progressed to a point at which symptoms are present.
  • Standard therapies are mere palliative as they cannot address the underlying disease mechanism once the subject has progressed to a point at which symptoms are present.
  • the methods of the disclosure provide a preventative or efficacious treatment, as opposed to a merely palliative treatment, for asymptomatic subjects as well as those subjects at risk of developing the disease.
  • the disclosure provides a method of treating a fibrotic lung disease in a subject comprising administering to the subject an effective amount of a therapeutic agent, wherein the subject is asymptomatic and wherein the subject is at risk of developing the fibrotic lung disease.
  • the subject presents radiographic Usual Interstitial Pneumonia (UIP).
  • the subject has fibrotic interstitial lung disease (FILD).
  • FILD fibrotic interstitial lung disease
  • the subject has a blood relative with familial interstitial pneumonia (FIP).
  • the blood relative is a sibling.
  • the subject has a mutation in a sequence encoding Mucin 5B (MUC5B), Telomerase RNA Component (TERC), Family with sequence similarity 13 member A (FAM13A), Telomerase Reverse Transcriptase (TERT), Desmoplakin (DSP), Zinc-alpha 2-Glycoprotein 1 (AZGP1), Oligonucleotide/oligosaccharide-binding Fold Containing 1 (OBFC1), ATPase Phospholipid Transporting 11A (ATP11A), Isovaleryl-CoA dehydrogenase (IVD)/Dispatched RND Transporter Family Member 2 (DISP2), Dipeptidyl Peptidase 9 (DPP9), Sialic Acid Binding Ig-Like Lectin 14 (SIGLEC14), Adrenomedullin 2 (ADM2), Tetraspanin 5 (TSPAN5), Calcium/Calmodulin-Dependent Protein Kin
  • the subject has a mutation in a sequence encoding MUC5B, TERC, FAM13A, TERT, DSP, AZGP1, OBFC1, ATP11A, IVD/DISP2, DPP9, SIGLEC14, ADM2, TSPAN5, CAMKK1 or MMP-7.
  • the subject has a mutation in a nucleic acid or amino acid sequence encoding a gene or gene product that is upregulated in a subject having a fibrotic pulmonary disease of the disclosure.
  • the subject has a mutation in a nucleic acid or amino acid sequence encoding Leukotriene A4 Hydrolase (LTA4H), Surfactant Protein B (SFTPB), Breast Cancer Anti-Estrogen Resistance 3 (BCAR3), C-X-C motif Chemokine Ligand 13 (CXCL13), EPH Receptor A2 (EPHA2), Serum Amyloid A1 (SAA1), Phospholipase A2 Group IIA (PLA2G2A), Insulin-Like Growth Factor Binding Protein 3 (IGFBP3), C-C Motif Chemokine Ligand 28 (CCL28), S100 Calcium Binding Protein A12 (S100A12), Thromboxane A Synthase 1 (LTA4H), Surfactant Protein B (SFTPB), Breast Cancer Anti-
  • the subject has a mutation in a nucleic acid or amino acid sequence encoding a gene or gene product that is downregulated in a subject having a fibrotic pulmonary disease of the disclosure.
  • the subject has a mutation in a nucleic acid or amino acid sequence encoding Surfactant Protein D (SFTPD), Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH), Histone Cluster 1 H1 Family Member C (HIST1H1C), YTH Domain Containing 1 (YTHDC1), Plexin A1 (PLXNA1), Serine Peptidase Inhibitor Kazal Type 6 (SPINK6), LDL Receptor Related Protein Associated Protein 1 (LRPAP1), Secretoglobin Family 3A Member 1 (SCGB3A1), H2A Histone Family Member Z (H2AFZ) or Chromosome 1 Open Reading Frame 162 (Clorf162).
  • SFTPD Surfactant Protein D
  • GPDH Glyceraldeh
  • the subject has a mutation in a sequence encoding MUC5B.
  • the mutation is a polymorphism in a sequence encoding a MUC5B promoter.
  • the polymorphism is rs35705950 comprising (SEQ ID NO: 7).
  • the human subject has a mutation in a sequence encoding TERC.
  • the mutation is a polymorphism in a sequence encoding TERC or a regulatory sequence thereof.
  • the polymorphism is rs6793295 comprising (SEQ ID NO: 1).
  • the human subject has a mutation in a sequence encoding intronic FAM13A.
  • the mutation is a polymorphism in a sequence encoding intronic FAM13A or a regulatory sequence thereof.
  • the polymorphism is rs2609260.
  • the human subject has a mutation in a sequence encoding intronic TERT.
  • the mutation is a polymorphism in a sequence encoding intronic TERT or a regulatory sequence thereof.
  • the polymorphism is rs4449583.
  • the human subject has a mutation in a sequence encoding intronic DSP.
  • the mutation is a polymorphism in a sequence encoding intronic DSP or a regulatory sequence thereof.
  • the polymorphism is rs2076295.
  • the human subject has a mutation in a sequence encoding intronic ZKSCAN1.
  • the mutation is a polymorphism in a sequence encoding intronic ZKSCAN1 or a regulatory sequence thereof.
  • the polymorphism is rs6963345.
  • the human subject has a mutation in a sequence encoding intronic OBFC1.
  • the mutation is a polymorphism in a sequence encoding intronic OBFC1 or a regulatory sequence thereof.
  • the polymorphism is rs2488000.
  • the human subject has a mutation in a sequence encoding an AK025511 3′ UTR.
  • the mutation is a polymorphism in a sequence encoding an AK025511 3′ UTR or a regulatory sequence thereof.
  • the polymorphism is rs1278769.
  • the human subject has a mutation in a sequence encoding IVD.
  • the mutation is a polymorphism in a sequence encoding intronic IVD or a regulatory sequence thereof.
  • the polymorphism is rs35700143.
  • the human subject has a mutation in a sequence encoding intronic DPP9.
  • the mutation is a polymorphism in a sequence encoding intronic DPP9 or a regulatory sequence thereof.
  • the polymorphism is rs12610495.
  • the subject has a mutation in a sequence encoding FAM13A.
  • the mutation is a polymorphism in a sequence encoding FAM13A or a regulatory sequence thereof.
  • the polymorphism is rs2609255 comprising (SEQ ID NO: 2).
  • the subject has a mutation in a sequence encoding TERT.
  • the mutation is a polymorphism in a sequence encoding TERT or a regulatory sequence thereof.
  • the polymorphism is rs2736100 comprising (SEQ ID NO: 3).
  • the subject has a mutation in a sequence encoding DSP.
  • the mutation is a polymorphism in a sequence encoding DSP or a regulatory sequence thereof.
  • the polymorphism is rs2076295 comprising (SEQ ID NO: 4).
  • the subject has a mutation in a sequence encoding AZGP1.
  • the mutation is a polymorphism in a sequence encoding AZGP1 or a regulatory sequence thereof.
  • the polymorphism is rs4727443 comprising (SEQ ID NO: 5).
  • the subject has a mutation in a sequence encoding OBFC1.
  • the mutation is a polymorphism in a sequence encoding OBFC1 or a regulatory sequence thereof.
  • the polymorphism is rs11191865 comprising (SEQ ID NO: 6).
  • the subject has a mutation in a sequence encoding ATP11A.
  • the mutation is a polymorphism in a sequence encoding ATP11A or a regulatory sequence thereof.
  • the polymorphism is rs12787690 comprising (SEQ ID NO: 8).
  • the subject has a mutation in a sequence encoding IVD/DISP2.
  • the mutation is a polymorphism in a sequence encoding IVD/DISP2 or a regulatory sequence thereof.
  • the polymorphism is rs2034650 comprising (SEQ ID NO: 9).
  • the subject has a mutation in a sequence encoding DPP9.
  • the mutation is a polymorphism in a sequence encoding DPP9 or a regulatory sequence thereof.
  • the polymorphism is rs12610495 comprising (SEQ ID NO: 10).
  • the fibrotic lung disease is pulmonary fibrosis, idiopathic pulmonary fibrosis (IPF), an interstitial lung abnormality (ILA), or an asymptomatic ILA.
  • the fibrotic lung disease is pulmonary fibrosis or IPF.
  • the fibrotic lung disease is IPF.
  • the therapeutic agent comprises a N-acetylcysteine, pirfenidone, and nintedanib.
  • the therapeutic agent comprises pirfenidone.
  • the effective dosage is administered orally as a capsule or a tablet. In some embodiments, including those embodiments wherein the therapeutic agent comprises pirfenidone, the effective dosage is about 2400 mg/day. In some embodiments, the effective dosage is administered according to an escalating dosage regimen.
  • the escalating dosage regimen comprises (a) administering to the subject about 800 mg of pirfenidone per day for a first week; (b) administering to the subject about 1600 mg of pirfenidone per day for a second week; and (c) administering to the subject about 2400 mg of pirfenidone per day for the remainder of the treatment.
  • the escalating dosage regimen comprises (a) administering to the subject a capsule or tablet comprising about 250 mg of pirfenidone three times a day for a first week; (b) administering to the subject two capsules or tablets comprising about 250 mg of pirfenidone three times a day for a second week; and (c) administering to the subject three capsules or tablets comprising about 250 mg of pirfenidone three times a day for the remainder of the treatment.
  • the capsule or tablet comprises 267 mg of pirfenidone.
  • the therapeutic agent comprises nintedanib.
  • the effective dosage is administered orally as a capsule or a tablet. In some embodiments, including those embodiments wherein the therapeutic agent comprises nintedanib, the effective dosage is about 300 mg/day. In some embodiments, the effective dosage is about 150 mg administered twice per day, wherein the daily doses are administered about 12 hours apart from one another. In some embodiments, including those embodiments wherein the therapeutic agent comprises nintedanib, the effective dosage is about 200 mg/day. In some embodiments, the effective dosage is about 100 mg administered twice per day, wherein the daily doses are administered about 12 hours apart from one another.
  • the effective dosage is administered according to a modified or interrupted dosage regimen.
  • the modified or interrupted dosage regimen comprises (a) administering to the subject about 300 mg of nintedanib per day until the subject presents an elevated level of liver enzymes compared to a control level of liver enzymes; (b) administering to the subject about 200 mg of nintedanib per day until the subject presents the control level of liver enzymes; and (c) administering to the subject about 300 mg of nintedanib per day for the remainder of the treatment; wherein the control level of liver enzymes is a level detected in the subject prior to an initiation of the treatment.
  • the modified or interrupted regimen comprises (a) administering to the subject a capsule or tablet comprising about 150 mg of nintedanib twice per day until the subject presents an elevated level of liver enzymes compared to a control level of liver enzymes; (b) administering to the subject two capsules or tablets comprising about 100 mg twice per day until the subject presents an elevated level of liver enzymes compared to a control level of liver enzymes; and (c) administering to the subject a capsule or tablet comprising about 150 mg of nintedanib twice per day for the remainder of the treatment; wherein the control level of liver enzymes is a level detected in the subject prior to an initiation of the treatment.
  • the therapeutic agent prevents the onset or development of a sign or symptom of the fibrotic lung disease.
  • the therapeutic agent delays the onset or development of a sign or symptom of the fibrotic lung disease when compared to the expected onset of the sign or symptom in the absence of treatment with the therapeutic agent.
  • the therapeutic agent reduces the severity of a sign or symptom of the fibrotic lung disease when compared to the expected severity of the sign or symptom in the absence of treatment with the therapeutic agent.
  • the therapeutic agent reduces the severity of a sign or symptom of the fibrotic lung disease when compared to the expected severity of the sign or symptom in the absence of treatment with the therapeutic agent.
  • the at least one sign of the fibrotic lung disease is detectable before the subject presents a symptom of the fibrotic lung disease.
  • the at least one sign comprises gradual or unintended weight loss, clubbing of the fingers or toes, rapid and shallow breathing, fibrotic lesions in one or both lungs detectable by radiography, or a cough.
  • the symptom comprises shortness of breath during exercise, shortness of breath at rest, a dry and hacking cough, repeated bouts of coughing, and uncontrollable bouts of coughing.
  • the method prevents the onset of a secondary condition associated with a severe form of the fibrotic lung disease.
  • a secondary condition comprises a collapsed lung, an infected lung, a blood clot in a lung, lung cancer, respiratory failure, pulmonary hypertension, heart failure or death.
  • the disclosure provides a method of identifying a therapeutic agent or target thereof for the treatment of a fibrotic lung disease, comprising administering to a non-human subject a dose of a composition that modifies transcription or translation of a sequence encoding Mucin 5B (MUC5B), Telomerase RNA Component (TERC), Family with sequence similarity 13 member A (FAM13A), Telomerase Reverse Transcriptase (TERT), Desmoplakin (DSP), Zinc-alpha 2-Glycoprotein 1 (AZGP1), Oligonucleotide/oligosaccharide-binding Fold Containing 1 (OBFC1), ATPase Phospholipid Transporting 11A (ATP11A), Isovaleryl-CoA dehydrogenase (IVD)/Dispatched RND Transporter Family Member 2 (DISP2), Dipeptidyl Peptidase 9 (DPP9), Sialic Acid Binding Ig-Like Lectin 14 (SIGLEC14), Ad
  • the method of identifying a therapeutic agent or target thereof for the treatment of a fibrotic lung disease comprising administering to a non-human subject a composition that modifies an activity of a product of a sequence encoding MUC5B, TERC, FAM13A, TERT, DSP, AZGP1, OBFC1, ATP11A, IVD/DISP2, DPP9, SIGLEC14, ADM2, TSPAN5, CAMKK1 or MMP-7, wherein the dose of the composition is tolerable to the non-human subject and wherein the dose of the composition is therapeutically effective.
  • the composition that modifies transcription or translation decreases or inhibits transcription or translation.
  • the composition decreases or inhibits transcription or translation of a sequence encoding a gene selected from the group consisting of Leukotriene A4 Hydrolase (LTA4H), Surfactant Protein B (SFTPB), Breast Cancer Anti-Estrogen Resistance 3 (BCAR3), C—X—C motif Chemokine Ligand 13 (CXCL13), EPH Receptor A2 (EPHA2), Serum Amyloid A1 (SAA1), Phospholipase A2 Group IIA (PLA2G2A), Insulin-Like Growth Factor Binding Protein 3 (IGFBP3), C-C Motif Chemokine Ligand 28 (CCL28), S100 Calcium Binding Protein A12 (S100A12), Thromboxane A Synthase 1 (TBXAS1), Leukocyte Cell Derived Chemotaxin 1 (LECT1), Complement C3 (C3),
  • LTA4H Leukotriene A4 Hydrolase
  • SFTPB Surfactant Protein B
  • BCAR3 Breast
  • the composition that modifies transcription or translation increases or activates transcription or translation.
  • the composition increases or activates transcription or translation of a sequence encoding a gene selected from the group consisting of Surfactant Protein D (SFTPD), Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH), Histone Cluster 1 H1 Family Member C (HIST1H1C), YTH Domain Containing 1 (YTHDC1), Plexin A1 (PLXNA1), Serine Peptidase Inhibitor Kazal Type 6 (SPINK6), LDL Receptor Related Protein Associated Protein 1 (LRPAP1), Secretoglobin Family 3A Member 1 (SCGB3A1), H2A Histone Family Member Z (H2AFZ) or Chromosome 1 Open Reading Frame 162 (Clorf162).
  • SFTPD Surfactant Protein D
  • GPDH Glyceraldehyde-3-Phosphate Dehydrogenase
  • HIST1H1C Histone Cluster 1 H1 Family Member C
  • YTHDC1 YTH Domain
  • the composition that modifies an activity decreases or inhibits the activity.
  • the composition decreases or inhibits the activity of a sequence encoding a gene selected from Leukotriene A4 Hydrolase (LTA4H), Surfactant Protein B (SFTPB), Breast Cancer Anti-Estrogen Resistance 3 (BCAR3), C—X—C motif Chemokine Ligand 13 (CXCL13), EPH Receptor A2 (EPHA2), Serum Amyloid A1 (SAA1), Phospholipase A2 Group IIA (PLA2G2A), Insulin-Like Growth Factor Binding Protein 3 (IGFBP3), C-C Motif Chemokine Ligand 28 (CCL28), S100 Calcium Binding Protein A12 (S100A12), Thromboxane A Synthase 1 (TBXAS1), Leukocyte Cell Derived Chemotaxin 1 (LECT1), Complement C3 (C3), Gastrin Releasing
  • LTA4H Leukotriene A4 Hydrolase
  • SFTPB Surfactant Protein B
  • BCAR3 Breast
  • the composition that modifies an activity increases or activates the activity.
  • the composition increases or activates the activity of a sequence encoding Surfactant Protein D (SFTPD), Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH), Histone Cluster 1 H1 Family Member C (HIST1H1C), YTH Domain Containing 1 (YTHDC1), Plexin A1 (PLXNA1), Serine Peptidase Inhibitor Kazal Type 6 (SPINK6), LDL Receptor Related Protein Associated Protein 1 (LRPAP1), Secretoglobin Family 3A Member 1 (SCGB3A1), H2A Histone Family Member Z (H2AFZ) or Chromosome 1 Open Reading Frame 162 (C1 orf162).
  • SFTPD Surfactant Protein D
  • GPDH Glyceraldehyde-3-Phosphate Dehydrogenase
  • HIST1H1C Histone Cluster 1 H1 Family Member C
  • YTHDC1 YTH Domain Containing 1
  • the non-human subject is a mammal.
  • the mammal is genetically-modified.
  • the genetically-modified mammal is a model organism for the fibrotic lung disease.
  • the fibrotic lung disease is pulmonary fibrosis, idiopathic pulmonary fibrosis (IPF), an interstitial lung abnormality (ILA), or an asymptomatic ILA.
  • the fibrotic lung disease is pulmonary fibrosis or IPF.
  • the fibrotic lung disease is IPF.
  • the non-human subject carries a mutation in a sequence encoding MUC5B.
  • the mutation comprises a polymorphism in a sequence encoding a MUC5B promoter.
  • the polymorphism is rs35705950.
  • the non-human subject carries a mutation in a sequence encoding TERC, FAM13A, TERT, DSP, ZKSCAN1, AZGP1, OBFC1, MUC5B, AK025511, ATP11A, IVD/DISP2, DPP9, SIGLEC14, ADM2, TSPAN5, CAMKK1 or MMP-7.
  • the composition prevents the onset or development of a sign or symptom of the fibrotic lung disease.
  • the composition delays the onset or development of a sign or symptom of the fibrotic lung disease when compared to the expected onset of the a sign or symptom in the absence of treatment with the composition.
  • the composition delays the onset or development of a sign or symptom of the fibrotic lung disease when compared to the expected onset of the sign or symptom when treated using a standard therapeutic intervention.
  • the composition reduces the severity of a sign or symptom of the fibrotic lung disease when compared to the expected severity of the sign or symptom in the absence of treatment with the composition.
  • the composition reduces the severity of a sign or symptom of the fibrotic lung disease when compared to the expected severity of the sign or symptom when treated using a standard therapeutic intervention.
  • the standard therapeutic intervention comprises a N-acetylcysteine, pirfenidone, and nintedanib.
  • the standard therapeutic intervention comprises pirfenidone.
  • an effective dosage of pirfenidone is about 2400 mg/day.
  • the effective dosage is administered orally as a capsule or a tablet.
  • the effective dosage is administered three times per day.
  • the effective dosage is administered according to an escalating dosage regimen.
  • the escalating dosage regimen comprises, administering to the non-human subject about 800 mg of pirfenidone per day for a first week; administering to the non-human subject about 1600 mg of pirfenidone per day for a second week; and administering to the non-human subject about 2400 mg of pirfenidone per day for the remainder of the treatment.
  • the escalating dosage regimen comprises, administering to the non-human subject a capsule or tablet comprising about 250 mg of pirfenidone three times a day for a first week; administering to the non-human subject two capsules or tablets comprising about 250 mg of pirfenidone three times a day for a second week; and administering to the non-human subject three capsules or tablets comprising about 250 mg of pirfenidone three times a day for the remainder of the treatment.
  • the capsule or tablet comprises 267 mg of pirfenidone.
  • the standard therapeutic intervention comprises nintedanib.
  • an effective dosage of nintedanib is administered orally as a capsule or a tablet.
  • the effective dosage is about 300 mg/day.
  • the effective dosage is about 150 mg administered twice per day, wherein the daily doses are administered about 12 hours apart from one another.
  • the effective dosage is about 200 mg/day.
  • the effective dosage is about 100 mg administered twice per day, wherein the daily doses are administered about 12 hours apart from one another.
  • the non-human subject presents at least one sign of the fibrotic lung disease.
  • the at least one sign comprises gradual or unintended weight loss, clubbing of the fingers or toes, rapid and shallow breathing, fibrotic lesions in one or both lungs detectable by radiography, or a cough.
  • the compound prevents the onset of a secondary condition associated with a severe form of the fibrotic lung disease.
  • the compound prevents the onset for at 1 year, 2 years, 3 years, 4 years, 5 years or any whole or fractional number of years in between.
  • secondary condition comprises a collapsed lung, an infected lung, a blood clot in a lung, lung cancer, respiratory failure, pulmonary hypertension, heart failure or death.
  • the disclosure provides a composition for the treatment of a fibrotic lung disease identified by a method of the disclosure, including, a method of identifying a therapeutic agent or target thereof for the treatment of a fibrotic lung disease of the disclosure.
  • the disclosure provides a method of treating fibrotic lung disease in a human subject of the disclosure comprising administering a therapeutically effective amount of a composition identified by a method of the disclosure, wherein the subject is asymptomatic and wherein the subject is at risk of developing the fibrotic lung disease.
  • the subject is wild type (e.g. does not comprises a mutation or a sequence variation) with respect to a nucleic acid or amino acid sequence encoding one or more of TERC, FAM13A, TERT, DSP, ZKSCAN1, AZGP1, OBFC1, MUC5B, AK025511, ATP11A, IVD/DISP2, DPP9, SIGLEC14, ADM2, TSPAN5, CAMKK1 or MMP-7.
  • the human subject presents radiographic Usual Interstitial Pneumonia (UIP).
  • UIP radiographic Usual Interstitial Pneumonia
  • fibrotic interstitial lung disease FILD
  • FIP familial interstitial pneumonia
  • a composition identified by a method of the disclosure wherein the human subject has a mutation or a sequence variation in a nucleic acid or an amino acid sequence encoding TERC, FAM13A, TERT, DSP, ZKSCAN1, AZGP1, OBFC1, MUC5B, AK025511, ATP11A, IVD/DISP2, DPP9, SIGLEC14, ADM2, TSPAN5, CAMKK1 or MMP-7.
  • the mutation comprises a polymorphism in a sequence encoding a MUC5B promoter.
  • the polymorphism is rs35705950.
  • the fibrotic lung disease is pulmonary fibrosis, idiopathic pulmonary fibrosis (IPF), an interstitial lung abnormality (ILA), or an asymptomatic ILA.
  • IPF idiopathic pulmonary fibrosis
  • ILA interstitial lung abnormality
  • the fibrotic lung disease is pulmonary fibrosis or IPF.
  • the fibrotic lung disease is IPF.
  • the method prevents the onset of a secondary condition associated with a severe form of the fibrotic lung disease.
  • a secondary condition comprises a collapsed lung, an infected lung, a blood clot in a lung, lung cancer, respiratory failure, pulmonary hypertension, heart failure or death.
  • FIG. 1 is a map depicting an exemplary hierarchical clustering of differentially expressed genes for pre-pulmonary fibrosis subjects and normal subjects.
  • FIG. 2A-B is a pair of volcano plots showing serum sample quality control using Principal component analysis (PCA).
  • PCA Principal component analysis
  • FIG. 3 is a volcano plot of 3315 plasma proteins, comparing results from 70 patients with established IPF and 70 controls. Solid red symbols represent 57 proteins that were significantly up-regulated and solid blue symbols 12 proteins that were significantly down-regulated in patients with IPF after controlling for multiple comparisons and age/gender/smoking.
  • FIG. 4 is a survival plot showing receiver operator curves of predictive model for PrePF in asymptomatic relatives from FIP families.
  • AUC Area Under Curve
  • FIG. 6A is a microscopic image demonstrating that MUC5B is produced in bronchoalveolar epithelia of patients with IPF (brown staining in photomicrographs). Staining is increased in the airways of patients positive for rs35705950 (TT) compared to WT (GG).
  • FIG. 6B is a graph showing the percentage of MUC5B positive area of bronchiolar epithelium. Unbiased stereological assessment of staining demonstrates that the volume fraction of stained airways (% positive area) is significantly greater in both the GT heterozygotes and the TT homozygotes.
  • FIG. 7A-B is series of bar graphs showing that Scgb1a1- and SFPTC promoter show significant worsening of fibrosis (hydroxyproline) after bleomycin while Muc5b ⁇ / ⁇ mice are protected.
  • FIG. 7A is a series of graphs and
  • FIG. 7B is a series of confocal images showing that the concentration of Muc5b is directly related to the fibroproliferative response to bleomycin.
  • Representative images from second harmonic generation (SHG) demonstrate increased lung collagen (red) in transgenic mice following bleomycin injury.
  • FIG. 8 is bar graph showing that the baseline expression of ER stress genes in lung tissue from WT and Scgb1a1 Muc5bTg mice.
  • Muc5bTg mice have greater ER stress gene expression than their WT littermates (all genes in the ER stress pathway, with p ⁇ 0.05).
  • Bleomycin also induces ER stress (data not shown).
  • FIG. 9 is a pair of microscopic images showing enhanced CHOP (Ddit3) protein in wild type (WT, top photograph) and Scgb1a1-Muc5bTg mice (bottom photograph) after repeat bleomycin.
  • FIG. 10 is a pair of microscopic images and corresponding graphs showing the expanded mucus layer and decreased mucociliary transport in SFTPC-Muc5bTg mice compared to littermate wild-type mice. Statistical differences were assessed by Mann-Whitney U Test.
  • FIG. 11 is a series of schematic diagram showing that the MUC5B variant and other biomarkers can identify an at-risk population or those with PrePF, establishing the opportunity for primary and secondary prevention of IPF.
  • the ‘at-risk’ population and the population with PrePF is large (19% with the MUC5B promoter variant and 1.8% of individuals ⁇ 50 years of age respectively), IPF is diagnosed in a small population with established, end-stage disease and PrePF can be identified using the MUC5B variant rs35705950. Results indicate that PrePF (detected via chest CT scan) is associated with a poor prognosis suggesting that PrePF may be a harbinger of IPF.
  • FIG. 12 is a schematic diagram showing a method of screening at-risk populations (family members of patients with IPF) to identify individuals with PrePF. Focus is placed on identifying the genetic variants and biomarkers that increase the yield of PrePF on HRCT scan, in addition to gender, age, and physiology scores.
  • FIG. 13 is a table describing the baseline characteristics of patients with rheumatoid arthritis.
  • FIG. 14 is a table describing the genotypic association of MUC5B rs35705950 single nucleotide polymorphism in patients with RA, with and without interstitial lung disease
  • FIG. 15 is a table describing the dominant genotypic association of MUC5B rs35705950 single nucleotide polymorphism in patients with RA-ILD and a usual interstitial pneumonia or possible usual interstitial pneumonia pattern (RA-UIP) and in patients with RA-ILD and a pattern inconsistent with usual interstitial pneumonia (RA non-UIP).
  • RA-UIP usual interstitial pneumonia or possible usual interstitial pneumonia pattern
  • RA non-UIP a pattern inconsistent with usual interstitial pneumonia
  • FIG. 16A is a forest plot of odds ratios ⁇ OR) and 95% confidence intervals ⁇ C1) depicting the lack of association of the MUC5B rs35705950 promoter variant with RA without 1LD ⁇ RA-nolLD).
  • the boxes indicate OR, and the horizontal lines indicate 95% C1 for the best-fitting genetic model for each association test.
  • the black dotted line represents a mean OR value of 1.
  • the red boxes and red lines indicate the overall OR and 95% C1, respectively.
  • the associations were adjusted for the country of origin and sex.
  • the associations were adjusted for the country of origin, sex, age at inclusion and smoking.
  • FIG. 16B is a forest plot of odds ratios (OR) and 95% confidence intervals ⁇ C1) depicting the additive genotypic association of the MUC5B rs 35705950 promoter variant with RA-ILD.
  • the red dotted line represent the mean value of overall OR value.
  • the boxes indicate OR, and the horizontal lines indicate 95% C1 for the best-fitting genetic model for each association test.
  • the black dotted line represents a mean OR value of 1.
  • the red boxes and red lines indicate the overall OR and 95% C1, respectively.
  • the associations were adjusted for the country of origin and sex.
  • the associations were adjusted for the country of origin, sex, age at inclusion and smoking.
  • FIG. 16C is a forest plot of odds ratios ⁇ OR) and 95% confidence intervals ⁇ C1) depicting dominant genotypic association of the MUC5B re35705950 promoter variant with ILD among patients with RA and those with the usual interstitial pneumonia or possible usual interstitial pneumonia (UIP) pattern.
  • the boxes indicate OR, and the horizontal lines indicate 95% C1 for the best-fitting genetic model for each association test.
  • the red dotted line represent the mean value of overall OR value.
  • the black dotted line represents a mean OR value of 1.
  • the red boxes and red lines indicate the overall OR and 95% C1, respectively.
  • the associations were adjusted for the country of origin and sex.
  • the associations were adjusted for the country of origin, sex, age at inclusion and smoking.
  • FIG. 17 is a series of photographs depicting MUC5B expression in explanted lung issue from rheumatoid arthritis associates interstitial lung disease.
  • Representative lung tissue images from unaffected control GG genotype, Panel A
  • RA-ILD case #1 GG genotype, Panel B
  • RA-ILD case #2 GT genotype, Panel C.
  • Panel B and C low power view of the usual interstitial pneumonia pattern in explanted lung tissue of RA-ILD; top inset with high power view of bronchiole with MUC5B staining; middle and bottom insets with high power view of MUC5B staining in metaplastic epithelia lining honeycomb cysts and MUC5B staining of mucous in honeycomb cysts.
  • FIG. 18 is a flow chart depicting the screening and enrollment process for study subjects.
  • FIG. 19A-D is a series of photographs depicting High-resolution CT (HRCT) images of: 19 A) chest from a study subject whose scan was read as normal, without signs of interstitial lung disease or fibrosis.
  • IPF Idiopathic Pulmonary Fibrosis
  • FIG. 20 is a table depicting a summary of characteristics of study subjects used in quantitative CT Analyses.
  • FIG. 23 is a table depicting patterns of CT abnormalities in scans with probable or definite fibrotic ILD. * Because a confident single diagnosis was relatively uncommon, most cases included consideration of several patterns. For this reason, the percentages add up to more than 100%.
  • FIG. 24 is a box plot depicting fibrosis score by visual diagnosis. Boxplots of fibrosis scores based on quantitative HRCT assessment for each visual diagnosis category. Fibrosis score means were significantly different (ANOVA, p ⁇ 0.0001) across groups defined by visual diagnosis. Comparison of fibrosis score between groups showed significant differences for all comparisons (p ⁇ 0.01 for all).
  • FIG. 25A-C is a series of graphs depicting Receiver Operating Characteristic (ROC) curves for quantitative imaging measures of Fibrosis and PrePF.
  • FIG. 5A depicts ROC curves for visual diagnosis compared to log HAA scores.
  • FIG. 5B depicts ROC Curves for visual diagnosis compared to fibrosis scores.
  • ROC analysis showed that fibrosis score discriminates subjects with visual diagnosis of PrePF.
  • Average area under the curve (AUC) in fivefold cross validation was 0.85 (range 0.83-0.87) and average accuracy, sensitivity, and specificity in the test partitions were 0.83 (range 0.74-0.86), 0.74 (range 0.56-0.92) and 0.84 (range 0.76-0.89) respectively.
  • Optimal threshold for fibrosis score ranged from 1.40-1.42.
  • FIG. 5C depicts Density plots of fibrosis scores for visually diagnosed PrePF (pink) and No Fibrosis (blue) scans—the fibrosis score optimal threshold is indicated with the red line (1.40).
  • FIG. 26 is a series of tables depicting Dyspnea questionnaire data.
  • FIG. 26A depicts breathlessness responses for the cohort.
  • FIG. 26B depicts breathlessness responses by Visual CT diagnosis.
  • FIG. 27 is a graph that depicts the prevalence of PrePF in FIP Siblings Cohort by Age and MUC5B Genotype.
  • PrePF prevalence in this FIP siblings cohort increases by age, as shown in this graph.
  • Subjects with the variant are depicted by the red line, while those without it are depicted with the blue line.
  • FIG. 28 is a table depicting subject characteristics based on Quantitative Fibrosis Score. Clinical characteristics and genotype breakdown of subjects with quantitative HRCT analyses. The cutoff of 1.4 for the logarithm of fibrosis score is based on analyses presented in the text. * p-value compares characteristic between groups. Linear regression values regress fibrosis score on age, male sex, smoking history, and MUC5B promoter variant. **In the reported model, rs35705950 coded as a dominant allele given small number of TT subjects.
  • FIG. 29 is a table depicting an exploratory genetic association study of 13 pulmonary fibrosis susceptibility variants in RA-ILD.
  • the present disclosure provides a method of treating a fibrotic lung disease in a subject comprising administering to the subject an effective amount of a therapeutic agent, wherein the subject is asymptomatic and wherein the subject is at risk of developing the fibrotic lung disease.
  • the disclosure provides a method of identifying a therapeutic agent or target thereof for the treatment of a fibrotic lung disease, comprising administering to a non-human subject a dose of a composition that modifies transcription or translation of a sequence encoding Mucin 5B (MUC5B), Telomerase RNA Component (TERC), Family with sequence similarity 13 member A (FAM13A), Telomerase Reverse Transcriptase (TERT), Desmoplakin (DSP), Zinc-alpha 2-Glycoprotein 1 (AZGP1), Oligonucleotide/oligosaccharide-binding Fold Containing 1 (OBFC1), ATPase Phospholipid Transporting 11A (ATP11A), Isovaleryl-CoA dehydrogenase (IVD)/Dispatched RND Transporter Family Member 2 (DISP2), Dipeptidyl Peptidase 9 (DPP9), Sialic Acid Binding Ig-Like Lectin 14 (SIGLEC14), Ad
  • the disclosure provides method of identifying a therapeutic agent or target thereof for the treatment of a fibrotic lung disease, comprising administering to a non-human subject a composition that modifies an activity of a product of a sequence encoding MUC5B, TERC, FAM13A, TERT, DSP, AZGP1, OBFC1, ATP11A, IVD/DISP2, DPP9, SIGLEC14, ADM2, TSPAN5, CAMKK1 or MMP-7, wherein the dose of the composition is tolerable to the non-human subject and wherein the dose of the composition is therapeutically effective.
  • the composition that modifies transcription or translation decreases or inhibits transcription or translation.
  • the composition decreases or inhibits transcription or translation of a sequence encoding a gene selected from the group consisting of Leukotriene A4 Hydrolase (LTA4H), Surfactant Protein B (SFTPB), Breast Cancer Anti-Estrogen Resistance 3 (BCAR3), C—X—C motif Chemokine Ligand 13 (CXCL13), EPH Receptor A2 (EPHA2), Serum Amyloid A1 (SAA1), Phospholipase A2 Group IIA (PLA2G2A), Insulin-Like Growth Factor Binding Protein 3 (IGFBP3), C-C Motif Chemokine Ligand 28 (CCL28), S100 Calcium Binding Protein A12 (S100A12), Thromboxane A Synthase 1 (TBXAS1), Leukocyte Cell Derived Chemotaxin 1 (LECT1), Complement C3 (C3)
  • LTA4H Leukotriene A4
  • the composition that modifies transcription or translation increases or activates transcription or translation.
  • the composition increases or activates transcription or translation of a sequence encoding a gene selected from the group consisting of Surfactant Protein D (SFTPD), Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH), Histone Cluster 1 H1 Family Member C (HIST1H1C), YTH Domain Containing 1 (YTHDC1), Plexin A1 (PLXNA1), Serine Peptidase Inhibitor Kazal Type 6 (SPINK6), LDL Receptor Related Protein Associated Protein 1 (LRPAP1), Secretoglobin Family 3A Member 1 (SCGB3A1), H2A Histone Family Member Z (H2AFZ) or Chromosome 1 Open Reading Frame 162 (C1 orf162).
  • SFTPD Surfactant Protein D
  • GPDH Glyceraldehyde-3-Phosphate Dehydrogenase
  • HIST1H1C Hi
  • the composition that modifies an activity decreases or inhibits the activity.
  • the composition decreases or inhibits the activity of a sequence encoding a gene selected from Leukotriene A4 Hydrolase (LTA4H), Surfactant Protein B (SFTPB), Breast Cancer Anti-Estrogen Resistance 3 (BCAR3), C-X-C motif Chemokine Ligand 13 (CXCL13), EPH Receptor A2 (EPHA2), Serum Amyloid A1 (SAA1), Phospholipase A2 Group IIA (PLA2G2A), Insulin-Like Growth Factor Binding Protein 3 (IGFBP3), C-C Motif Chemokine Ligand 28 (CCL28), 5100 Calcium Binding Protein A12 (S100A12), Thromboxane A Synthase 1 (TBXAS1), Leukocyte Cell Derived Chemotaxin 1 (LECT1), Complement C3 (C3), Gastrin Releasing P
  • LTA4H Leukotriene A4
  • the composition that modifies an activity increases or activates the activity.
  • the composition increases or activates the activity of a sequence encoding Surfactant Protein D (SFTPD), Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH), Histone Cluster 1 H1 Family Member C (HIST1H1C), YTH Domain Containing 1 (YTHDC1), Plexin A1 (PLXNA1), Serine Peptidase Inhibitor Kazal Type 6 (SPINK6), LDL Receptor Related Protein Associated Protein 1 (LRPAP1), Secretoglobin Family 3A Member 1 (SCGB3A1), H2A Histone Family Member Z (H2AFZ) or Chromosome 1 Open Reading Frame 162 (C1 orf162).
  • SFTPD Surfactant Protein D
  • GPDH Glyceraldehyde-3-Phosphate Dehydrogenase
  • HIST1H1C Histone Cluster 1 H1 Family Member C
  • the non-human subject is a mammal.
  • mammal is genetically-modified.
  • the genetically-modified mammal is a model organism for the fibrotic lung disease.
  • the fibrotic lung disease is pulmonary fibrosis, idiopathic pulmonary fibrosis (IPF), an interstitial lung abnormality (ILA), or an asymptomatic ILA.
  • the fibrotic lung disease is pulmonary fibrosis or IPF.
  • the fibrotic lung disease is IPF.
  • the non-human subject carries a mutation in a sequence encoding MUC5B.
  • the mutation comprises a polymorphism in a sequence encoding a MUC5B promoter.
  • the polymorphism is rs35705950.
  • the non-human subject carries a mutation in a sequence encoding TERC, FAM13A, TERT, DSP, AZGP1, OBFC1, ATP11A, IVD/DISP2, DPP9, SIGLEC14, ADM2, TSPAN5, CAMKK1 or MMP-7.
  • the composition prevents the onset or development of a sign or symptom of the fibrotic lung disease.
  • the composition delays the onset or development of a sign or symptom of the fibrotic lung disease when compared to the expected onset of the sign or symptom in the absence of treatment with the composition. In some embodiments, the composition delays the onset or development of a sign or symptom of the fibrotic lung disease when compared to the expected onset of the sign or symptom when treated using a standard therapeutic intervention.
  • the composition reduces the severity of a sign or symptom of the fibrotic lung disease when compared to the expected severity of the sign or symptom in the absence of treatment with the composition. In some embodiments, the composition reduces the severity of a sign or symptom of the fibrotic lung disease when compared to the expected severity of the sign or symptom when treated using a standard therapeutic intervention.
  • the standard therapeutic intervention comprises a N-acetylcysteine, pirfenidone, and nintedanib.
  • the standard therapeutic intervention comprises pirfenidone.
  • an effective dosage of pirfenidone is about 2400 mg/day.
  • the effective dosage is administered orally as a capsule or a tablet.
  • the effective dosage is administered three times per day.
  • the effective dosage is administered according to an escalating dosage regimen.
  • the escalating dosage regimen comprises (a) administering to the non-human subject about 800 mg of pirfenidone per day for a first week; (b) administering to the non-human subject about 1600 mg of pirfenidone per day for a second week; and (c) administering to the non-human subject about 2400 mg of pirfenidone per day for the remainder of the treatment.
  • the escalating dosage regimen comprises (a) administering to the non-human subject a capsule or tablet comprising about 250 mg of pirfenidone three times a day for a first week; (b) administering to the non-human subject two capsules or tablets comprising about 250 mg of pirfenidone three times a day for a second week; and (c) administering to the non-human subject three capsules or tablets comprising about 250 mg of pirfenidone three times a day for the remainder of the treatment.
  • the capsule or tablet comprises 267 mg of pirfenidone.
  • the standard therapeutic intervention comprises nintedanib.
  • an effective dosage of nintedanib is administered orally as a capsule or a tablet.
  • the effective dosage is about 300 mg/day.
  • the effective dosage is about 150 mg administered twice per day, wherein the daily doses are administered about 12 hours apart from one another.
  • the effective dosage is about 200 mg/day.
  • the effective dosage is about 100 mg administered twice per day, wherein the daily doses are administered about 12 hours apart from one another.
  • the non-human subject presents at least one sign of the fibrotic lung disease.
  • the at least one sign comprises gradual or unintended weight loss, clubbing of the fingers or toes, rapid and shallow breathing, fibrotic lesions in one or both lungs detectable by radiography, or a cough.
  • the compound prevents the onset of a secondary condition associated with a severe form of the fibrotic lung disease. In some embodiments, the compound prevents the onset for at 1 year, 2 years, 3 years, 4 years, 5 years or any whole or fractional number of years in between.
  • the secondary condition comprises a collapsed lung, an infected lung, a blood clot in a lung, lung cancer, respiratory failure, pulmonary hypertension, heart failure or death.
  • the disclosure provides a composition for the treatment of a fibrotic lung disease identified by a method of the disclosure for identifying a therapeutic agent or target thereof for the treatment of a fibrotic lung disease.
  • the disclosure provides a method of treating a fibrotic lung disease in a human subject comprising administering to the subject the composition for the treatment of a fibrotic lung disease identified by a method of the disclosure for identifying a therapeutic agent or target thereof for the treatment of a fibrotic lung disease, wherein the subject is asymptomatic and wherein the subject is at risk of developing the fibrotic lung disease.
  • the human subject presents radiographic Usual Interstitial Pneumonia (UIP).
  • UIP radiographic Usual Interstitial Pneumonia
  • the human subject has fibrotic interstitial lung disease (FILD).
  • the human subject has a blood relative with familial interstitial pneumonia (FIP).
  • the blood relative is a sibling.
  • the human subject has a mutation in a sequence encoding MUC5B, TERC, FAM13A, TERT, DSP, AZGP1, OBFC1, ATP11A, IVD/DISP2, DPP9, SIGLEC14, ADM2, TSPAN5, CAMKK1 or MMP-7.
  • the mutation comprises a polymorphism in a sequence encoding a MUC5B promoter.
  • the polymorphism is rs35705950.
  • the fibrotic lung disease is pulmonary fibrosis, idiopathic pulmonary fibrosis (IPF), an interstitial lung abnormality (ILA), or an asymptomatic ILA.
  • the fibrotic lung disease is pulmonary fibrosis or IPF.
  • the fibrotic lung disease is IPF.
  • the method prevents the onset of a secondary condition associated with a severe form of the fibrotic lung disease.
  • the secondary condition comprises a collapsed lung, an infected lung, a blood clot in a lung, lung cancer, respiratory failure, pulmonary hypertension, heart failure or death.
  • IPF Idiopathic Pulmonary Fibrosis
  • IPF idiopathic pulmonary fibrosis
  • PrePF idiopathic pulmonary fibrosis
  • MUC5B promoter variant is critical to early disease recognition and 4) identification of PrePF represents an opportunity to prevent extensive lung fibrosis.
  • a common gain-of-function MUC5B promoter variant rs35705950 is a strong risk factor (genetic and otherwise), accounting for at least 30% of the total risk of developing IPF.
  • the MUC5B promoter variant rs35705950 may be used to identify individuals with PrePF.
  • MUC5B promoter variant rs35705950 is also predictive of radiographic progression of PrePF and is present in over 50% of non-Hispanic white patients with IPF and is also associated with unique clinical and biological IPF phenotypes.
  • PrePF can be predicted using a combination of clinical risk factors, the MUC5B promoter variant rs35705950, and a panel of biomarkers.
  • This disclosure provides methods of treating subjects with Preclinical Pulmonary Fibrosis (PrePF) and who may also be at risk for developing IPF. The methods of the disclosure fundmentally change the clinical approach to treating subjects with IPF, shifting the focus from a merely palliative to a proactive and preventive therapy.
  • RA-ILD Arthritis-Associated Interstitial Lung Disease
  • RA Rheumatoid arthritis
  • HRCT high-resolution computed-tomography
  • RA-ILD shares several characteristics with idiopathic pulmonary fibrosis (IPF), including common environmental risk factors, the high prevalence of the usual interstitial pneumonia (UIP) pattern, the progressive nature of the disease, and poor survival.
  • IPF idiopathic pulmonary fibrosis
  • UPF interstitial pneumonia
  • WES whole-exome sequencing
  • the common gain-of-function promoter variant rs3570595013 of the gene encoding mucin5B is the strongest genetic risk factor for IPF, observed in at least 50% of the cases of IPF and accounting for 30% of the risk of developing this disease.
  • the MUC5B promoter variant is associated with increased expression of MUC5B in lung parenchyma of unaffected controls and cases of IPF. Consequently, it is hypothesized that the MUC5B promoter variant rs35705950 would also contribute to the occurrence of RA-ILD. To test this hypothesis, a multi-ethnic association study of the MUC5B promoter variantand RA-ILD in seven distinct case series was performed.
  • the MUC5B promoter variant rs35705950 is also a strong risk factor for RA-ILD, especially among those with radiographic evidence of UIP.
  • the effect of the MUC5B promoter variant on the development of ILD associated with RA was similar in magnitude and direction to that observed in IPF.
  • the relationship between the MUC5B promoter variant and RA-ILD may be specific to UIP and may not generalizable to other autoimmune conditions of the lung.
  • the MUC5B promoter variant has not been found to be associated with risk of ILDs linked to systemic sclerosis or autoimmune myositis.
  • RA-ILD shares more characteristics with IPF, notably the increased frequency of the UIP pattern (both radiologic and histologic), an increased prevalence of male sex and older age, and genetic susceptibility as assessed by an excess of mutations in genes linked to FIP in a cohort of RA-ILD, and now the MUC5B promoter variant rs35705950.
  • the disclosure demonstrates that the MUC5B promoter variant is a risk factor for UIP, and not simply limited to IPF and RA-ILD.
  • the MUC5B promoter variant is a risk factor for chronic hypersensitivity pneumonitis, another condition known to have a sub-phenotype of UIP.
  • HRCT underestimates the presence of ILD and the UIP pattern of fibrosis, our point estimates for association with the MUC5B variant are likely conservative. Similar to IPF, early forms of RA-ILD can be identified using the MUC5B promoter variant as biomarker.
  • the disclosure demonstrates that Muc5b is overexpressed by the bronchoalveolar epithelia and MUC5B mRNA is co-expressed by cells expressing surfactant protein C, as has been shown in IPF.
  • These findings suggest either type 2 alveolar epithelial cells can express MUC5B or that in patients with RA-ILD, the cells in the distal airspace de-differentiate.
  • the disclosure demonstrates for the first time that cells that overexpress MUC5B are undergoing ER stress, a recognized mechanism of cell injury and repair.
  • these findings indicate that the gain-of-function MUC5B promoter variant rs35705950 injures alveolar epithelia by inducing ER stress.
  • RA-ILD is a complex genetic phenotype with the minor allele of the MUC5B promoter variant rs35705950 identified as a risk factor for the disease.
  • the odds ratios for the association of MUC5B promoter variant with RA-ILD is equivalent to that observed with IPF and substantively higher than those for the most other common risk variants for RA-ILD, including cigarette smoking and the human leukocyte antigen locus for RA.
  • the MUC5B promoter variant is a risk factor for UIP in general and may prove relevant beyond RA-ILD and IPF.
  • MUC5B in the bronchoalveolar epithelia co-incident with markers of ER stress suggest that the MUC5B promoter variant may be causing pulmonary fibrosis by initiating microscopic foci of injury and repair.
  • the MUC5B promoter variant appears to predict ILD in the RA population, identifying potential opportunities for early ILD detection in patients with RA.
  • FIP Familial Interstitial Pneumonia
  • HRCT provides visualization of the lung parenchyma and plays a key role in the diagnosis of the Idiopathic Interstitial Pneumonias (IIPs), including IPF.
  • IIPs Idiopathic Interstitial Pneumonias
  • qHRCT Quantitative HRCT evaluation provides measures of fibrosis extent that, in subjects diagnosed with IPF, correlate with degree of physiologic impairment at baseline, and may be more sensitive to subtle changes in disease status than routinely used physiological metrics.
  • the design and utility of quantitative methods in the context of early forms of fibrotic ILD requires further study. Deep learning methods have been increasingly used in imaging to identify and classify CT patterns, and may be particularly valuable in detection of early lung fibrosis.
  • PrePF is prevalent among FIP relatives, and a texture-based quantitative method of HRCT analyses is useful in identifying these abnormalities in this population, and key risk factors, including the MUC5B promoter variant, predict those at risk of this disease.
  • PrePF subjects are older, more likely to be male, and more likely to have smoked than the unaffected subjects; additionally, the gain-of-function MUC5B promoter variant rs35705950, which has been shown in prior studies to be associated with pulmonary fibrosis, is more common in PrePF subjects when compared to their unaffected family members. Given the subtlety of the fibrotic change in many of these cases of PrePF, the high prevalence of potential UIP pattern on HRCT scan suggests that PrePF subjects may progress to IPF over time.
  • the present disclosure also provides methods of detecting the biomarkers of the present disclosure. Methods of detecting a genetic variant are further described in US Application US 2016-0060701A1(the contents of which are incorporated herein by reference in their entirety).
  • the practice of the present disclosure employs, unless otherwise indicated, conventional methods of analytical biochemistry, microbiology, molecular biology and recombinant DNA techniques within the skill of the art. Such techniques are explained fully in the literature. (See, e.g., Sambrook, J. et al. Molecular Cloning: A Laboratory Manual. 3rd, ed., Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N. Y., 2000; DNA Cloning: A Practical Approach, Vol. I & II (D.
  • the methods of the invention are not limited to any particular way of detecting the presence or absence of a genetic variant (e.g. SNP) and can employ any suitable method to detect the presence or absence of a variant(s), of which numerous detection methods are known in the art.
  • Dynamic allele-specific hybridization can be used to detect a genetic variant. DASH genotyping takes advantage of the differences in the melting temperature in DNA that results from the instability of mismatched base pairs. The process can be vastly automated and encompasses a few simple principles.
  • the aspects and embodiments described herein provide methods for assessing the presence or absence of SNPs in a sample (e.g. biological sample) from a subject suspected of having or developing an interstitial lung disease (e.g., because of family history).
  • one or more SNPs are screened in one or more samples from a subject.
  • the SNPs can be associated with one or more genes, e.g., one or more genes or other genes associated with mucous secretions as disclosed herein.
  • the target genomic segment is amplified and separated from non-target sequence, e.g., through use of a biotinylated primer and chromatography.
  • a probe that is specific for the particular allele is added to the amplification product.
  • the probe can be designed to hybridize specifically to a variant sequence or to the dominant allelic sequence.
  • the probe can be either labeled with or added in the presence of a molecule that fluoresces when bound to double-stranded DNA.
  • the signal intensity is then measured as temperature is increased until the Tm can be determined.
  • a non-matching sequence either genetic variant or dominant allelic sequence, depending on probe design, will result in a lower than expected Tm.
  • DASH genotyping relies on a quantifiable change in Tm, and is thus capable of measuring many types of mutations, not just SNPs.
  • Other benefits of DASH include its ability to work with label free probes and its simple design and performance conditions.
  • Molecular beacons can also be used to detect a genetic variant.
  • This method makes use of a specifically engineered single-stranded oligonucleotide probe.
  • the oligonucleotide is designed such that there are complementary regions at each end and a probe sequence located in between. This design allows the probe to take on a hairpin, or stem-loop, structure in its natural, isolated state. Attached to one end of the probe is a fluorophore and to the other end a fluorescence quencher. Because of the stem-loop structure of the probe, the fluorophore is in close proximity to the quencher, thus preventing the molecule from emitting any fluorescence.
  • the molecule is also engineered such that only the probe sequence is complementary to the targeted genomic DNA sequence.
  • the probe sequence of the molecular beacon encounters its target genomic DNA sequence during the assay, it will anneal and hybridize. Because of the length of the probe sequence, the hairpin segment of the probe will be denatured in favor of forming a longer, more stable probe-target hybrid. This conformational change permits the fluorophore and quencher to be free of their tight proximity due to the hairpin association, allowing the molecule to fluoresce.
  • the molecular beacon will preferentially stay in its natural hairpin state and no fluorescence will be observed, as the fluorophore remains quenched.
  • the unique design of these molecular beacons allows for a simple diagnostic assay to identify SNPs at a given location. If a molecular beacon is designed to match a wild-type allele and another to match a mutant of the allele, the two can be used to identify the genotype of an individual. If only the first probe's fluorophore wavelength is detected during the assay then the individual is homozygous to the wild type.
  • a microarray can also be used to detect genetic variants. Hundreds of thousands of probes can be arrayed on a small chip, allowing for many genetic variants or SNPs to be interrogated simultaneously. Because SNP alleles only differ in one nucleotide and because it is difficult to achieve optimal hybridization conditions for all probes on the array, the target DNA has the potential to hybridize to mismatched probes. This can be addressed by using several redundant probes to interrogate each SNP. Probes can be designed to have the SNP site in several different locations as well as containing mismatches to the SNP allele. By comparing the differential amount of hybridization of the target DNA to each of these redundant probes, it is possible to determine specific homozygous and heterozygous alleles.
  • Restriction fragment length polymorphism can be used to detect genetic variants and SNPs.
  • RFLP makes use of the many different restriction endonucleases and their high affinity to unique and specific restriction sites. By performing a digestion on a genomic sample and determining fragment lengths through a gel assay it is possible to ascertain whether or not the enzymes cut the expected restriction sites. A failure to cut the genomic sample results in an identifiably larger than expected fragment implying that there is a mutation at the point of the restriction site which is rendering it protected from nuclease activity.
  • PCR- and amplification-based methods can be used to detect genetic variants.
  • tetra-primer PCR employs two pairs of primers to amplify two alleles in one PCR reaction.
  • the primers are designed such that the two primer pairs overlap at a SNP location but each matches perfectly to only one of the possible alleles.
  • the two primer pairs can be designed such that their PCR products are of a significantly different length allowing for easily distinguishable bands by gel electrophoresis, or such that they are differently labeled.
  • Primer extension can also be used to detect genetic variants.
  • Primer extension first involves the hybridization of a probe to the bases immediately upstream of the SNP nucleotide followed by a ‘mini-sequencing’ reaction, in which DNA polymerase extends the hybridized primer by adding a base that is complementary to the SNP nucleotide. The incorporated base that is detected determines the presence or absence of the SNP allele. Because primer extension is based on the highly accurate DNA polymerase enzyme, the method is generally very reliable. Primer extension is able to genotype most SNPs under very similar reaction conditions making it also highly flexible. The primer extension method is used in a number of assay formats, and can be detected using e.g., fluorescent labels or mass spectrometry.
  • Primer extension can involve incorporation of either fluorescently labeled ddNTP or fluorescently labeled deoxynucleotides (dNTP).
  • ddNTPs probes hybridize to the target DNA immediately upstream of SNP nucleotide, and a single, ddNTP complementary to the SNP allele is added to the 3′ end of the probe (the missing 3′-hydroxyl in didioxynucleotide prevents further nucleotides from being added).
  • Each ddNTP is labeled with a different fluorescent signal allowing for the detection of all four alleles in the same reaction.
  • allele-specific probes have 3′ bases which are complementary to each of the SNP alleles being interrogated.
  • the target DNA contains an allele complementary to the 3′ base of the probe, the target DNA will completely hybridize to the probe, allowing DNA polymerase to extend from the 3′ end of the probe. This is detected by the incorporation of the fluorescently labeled dNTPs onto the end of the probe. If the target DNA does not contain an allele complementary to the probe's 3′ base, the target DNA will produce a mismatch at the 3′ end of the probe and DNA polymerase will not be able to extend from the 3′ end of the probe.
  • the iPLEX® SNP genotyping method takes a slightly different approach, and relies on detection by mass spectrometer. Extension probes are designed in such a way that many different SNP assays can be amplified and analyzed in a PCR cocktail.
  • the extension reaction uses ddNTPs as above, but the detection of the SNP allele is dependent on the actual mass of the extension product and not on a fluorescent molecule. This method is for low to medium high throughput, and is not intended for whole genome scanning.
  • Primer extension methods are, however, amenable to high throughput analysis. Primer extension probes can be arrayed on slides allowing for many SNPs to be genotyped at once. Broadly referred to as arrayed primer extension (APEX), this technology has several benefits over methods based on differential hybridization of probes. Comparatively, APEX methods have greater discriminating power than methods using differential hybridization, as it is often impossible to obtain the optimal hybridization conditions for the thousands of probes on DNA microarrays (usually this is addressed by having highly redundant probes).
  • Oligonucleotide ligation assays can also be used to detect genetic variants.
  • DNA ligase catalyzes the ligation of the 3′ end of a DNA fragment to the 5′ end of a directly adjacent DNA fragment. This mechanism can be used to interrogate a SNP by hybridizing two probes directly over the SNP polymorphic site, whereby ligation can occur if the probes are identical to the target DNA.
  • two probes can be designed; an allele-specific probe which hybridizes to the target DNA so that its 3′ base is situated directly over the SNP nucleotide and a second probe that hybridizes the template upstream (downstream in the complementary strand) of the SNP polymorphic site providing a 5′ end for the ligation reaction. If the allele-specific probe matches the target DNA, it will fully hybridize to the target DNA and ligation can occur. Ligation does not generally occur in the presence of a mismatched 3′ base. Ligated or unligated products can be detected by gel electrophoresis, MALDI-TOF mass spectrometry or by capillary electrophoresis.
  • the 5′-nuclease activity of Taq DNA polymerase can be used for detecting genetic variants.
  • the assay is performed concurrently with a PCR reaction and the results can be read in real-time.
  • the assay requires forward and reverse PCR primers that will amplify a region that includes the SNP polymorphic site. Allele discrimination is achieved using FRET, and one or two allele-specific probes that hybridize to the SNP polymorphic site.
  • the probes have a fluorophore linked to their 5′ end and a quencher molecule linked to their 3′ end. While the probe is intact, the quencher will remain in close proximity to the fluorophore, eliminating the fluorophore's signal.
  • the allele-specific probe if the allele-specific probe is perfectly complementary to the SNP allele, it will bind to the target DNA strand and then get degraded by 5′-nuclease activity of the Taq polymerase as it extends the DNA from the PCR primers. The degradation of the probe results in the separation of the fluorophore from the quencher molecule, generating a detectable signal. If the allele-specific probe is not perfectly complementary, it will have lower melting temperature and not bind as efficiently. This prevents the nuclease from acting on the probe.
  • FRET detection can be used for detection in primer extension and ligation reactions where the two labels are brought into close proximity to each other. It can also be used in the 5′-nuclease reaction, the molecular beacon reaction, and the invasive cleavage reactions where the neighboring donor/acceptor pair is separated by cleavage or disruption of the stem-loop structure that holds them together. FRET occurs when two conditions are met. First, the emission spectrum of the fluorescent donor dye must overlap with the excitation wavelength of the acceptor dye. Second, the two dyes must be in close proximity to each other because energy transfer drops off quickly with distance. The proximity requirement is what makes FRET a good detection method for a number of allelic discrimination mechanisms.
  • a variety of dyes can be used for FRET, and are known in the art. The most common ones are fluorescein, cyanine dyes (Cy3 to Cy7), rhodamine dyes (e.g. rhodamine 6G), the Alexa series of dyes (Alexa 405 to Alexa 730). Some of these dyes have been used in FRET networks (with multiple donors and acceptors). Optics for imaging all of these require detection from UV to near IR (e.g. Alex 405 to Cy7), and the Atto series of dyes (Atto-Tec GmbH). The Alexa series of dyes from Invitrogen cover the whole spectral range. They are very bright and photostable.
  • Example dye pairs for FRET labeling include Alexa-405/Alex-488, Alexa-488/Alexa-546, Alexa-532/Alexa-594, Alexa-594/Alexa-680, Alexa-594/Alexa-700, Alexa-700/Alexa-790, Cy3/Cy5, Cy3.5/Cy5.5, and Rhodamine-Green/Rhodamine-Red, etc.
  • Fluorescent metal nanoparticles such as silver and gold nanoclusters can also be used (Richards et al. (2008) J Am Chem Soc 130:5038-39; Vosch et al. (2007) Proc Natl Acad Sci USA 104:12616-21; Petty and Dickson (2003) J Am Chem Soc 125:7780-81 Available filters, dichroics, multichroic mirrors and lasers can affect the choice of dye.
  • nucleic acid complexes e.g., formed in in vitro assays to indicate the presence of a genetic variant sequence.
  • a nucleic acid complex can also be formed to detect the presence of a dominant allelic sequence, depending on the design of the probe or primer, e.g., in assays to distinguish homozygous and heterozygous subjects.
  • the complex comprises a first nucleic acid hybridized to a genetic variant nucleic acid, wherein the genetic variant nucleic acid is a genetic variant in a gene selected from MUC5B, TERC, FAM13A, TERT, DSP, AZGP1, OBFC1, ATP11A, IVD/DISP2, DPP9, SIGLEC14, ADM2, TSPAN5, CAMKK1 or MMP-7.
  • the genetic variant nucleic acid is an amplification product.
  • the genetic variant nucleic acid is on genomic DNA, e.g., from a subject that has or is suspected of having an interstitial lung disease.
  • the first nucleic acid is an amplification product or a primer extension product. In some embodiments, the first nucleic acid is labeled. In some embodiments, the nucleic acid complex further comprises a second nucleic acid hybridized to the genetic variant nucleic acid. In some embodiments, the second nucleic acid is labeled e.g., with a FRET or other fluorescent label. In some embodiments, the first and second nucleic acids form a FRET pair when hybridized to a genetic variant sequence.
  • the nucleic acid complex further comprises an enzyme, such as a DNA polymerase (e.g., standard DNA polymerase or thermostable polymerase such as Taq) or ligase.
  • an enzyme such as a DNA polymerase (e.g., standard DNA polymerase or thermostable polymerase such as Taq) or ligase.
  • a method for determining if an individual is predicted to develop and/or progress rapidly with an interstitial pneumonia comprising: detecting in a biological sample from the individual, at least one of: a) the presence of a marker polymorphism selected from the group consisting of: rs35705950; and/or, b) a level of gene expression of a marker gene or plurality of marker genes selected from the group consisting of: a marker gene having at least 95% sequence identity with at least one sequence selected from the group consisting of MUC5B, TERC, FAM13A, TERT, DSP, AZGP1, OBFC1, ATP11A, IVD/DISP2, DPP9, SIGLEC14, ADM2, TSPAN5, CAMKK1 or MMP-7, or homologs or variants thereof c) polypeptides encoded by the marker genes of b) d) fragments of polypeptides of c); and e) a polynucleotide which is fully complementary to at least a portion of
  • the genes detected share 100% sequence identity with the corresponding marker gene in b).
  • the presence or level of at least one of the plurality of markers is determined and compared to a standard level or reference set.
  • the standard level or reference set is determined according to a statistical procedure for risk prediction.
  • the statistical procedure for risk prediction comprises using the sum of the gene expression of the marker or markers or the presence or absence of a set of markers, weighted by a Proportional Hazards coefficient.
  • the presence of the at least one marker is determined by detecting the presence or absence or expression level of a polypeptide.
  • the method further comprises detecting the presence of the polypeptide using a reagent that specifically binds to the polypeptide or a fragment thereof.
  • the reagent is selected from the group consisting of an antibody, an antibody derivative, and an antibody fragment.
  • the presence of the marker is determined by obtaining the sequence of genomic DNA at the locus of the polymorphism.
  • the presence of the marker is determined by obtaining RNA from the biological sample; generating cDNA from the RNA; amplifying the cDNA with probes or primers for marker genes; obtaining from the amplified cDNA the expression levels of the genes or gene expression products in the sample.
  • the individual is a human.
  • the method further comprises: a) comparing the expression level of the marker gene or plurality of marker genes in the biological sample to a control level of the marker gene(s) selected from the group consisting of: a control level of the marker gene that has been correlated with interstitial lung disease, the risk of developing interstitial lung disease, or having a interstitial lung disease; and a control level of the marker that has been correlated with slow or no progression of interstitial lung disease, or low risk of developing an interstitial lung disease; and b) selecting the individual as being predicted to progress rapidly in the development of interstitial pneumonia, if the expression level of the marker gene in the individual's biological sample is statistically similar to, or greater than, the control level of expression of the marker gene that has been correlated with interstitial lung disease, or c) selecting the individual as being predicted to not develop interstitial lung disease, or to progress slowly, if the level of the marker gene in the individual's biological sample is statistically less than the control level of the marker gene that has been correlated with
  • the method further comparing the presence of a polymorphism, in the biological sample to a set of genetic variants or polymorphic markers from an individual or control group having developed interstitial lung disease, and, selecting the individual as being predicted to develop or to progress with interstitial pneumonia if the polymorphic markers present in the biological sample are identical to or statistically similar to a set of polymorphic markers from the individual or control group or, selecting the individual as being predicted to develop or rapidly progress with interstitial pneumonia, if the polymorphic markers present in the biological sample are not identical to or statistically similar to the set of genetic variants or polymorphic markers from the individual or control group.
  • a method for monitoring the progression of interstitial lung disease in a subject comprising: i) measuring expression levels of a plurality of gene markers in a first biological sample obtained from the subject, wherein the plurality of markers comprise a plurality of markers selected from the group consisting of: a marker gene having at least 95% sequence identity with a sequence selected from the group consisting of a) MUC5B, TERC, FAM13A, TERT, DSP, AZGP1, OBFC1, ATP11A, IVD/DISP2, DPP9, SIGLEC14, ADM2, TSPAN5, CAMKK1 or MMP-7, or homologs or variants thereof; b) polypeptides encoded by the marker genes of a), c) fragments of polypeptides of d); and e) a polynucleotide which is fully complementary to at least a portion of a marker gene of b); ii) measuring expression levels of the plurality of markers in a second biological sample obtained from the subject; and i
  • the marker genes detected share 100% sequence identity with the corresponding marker gene in a).
  • the method further comprises performing a follow-up step selected from the group consisting of CT scan of the chest and pathological examination of lung tissues from the subject.
  • the first biological sample from the subject is obtained at a time to, and the second biological sample from the subject is obtained at a later time t 1 .
  • the first biological sample and the second biological sample are obtained from the subject are obtained more than once over a range of times.
  • a method of assessing the efficacy of a treatment for interstitial lung disease or interstitial pneumonia in a subject comprising comparing: i) the expression level of a marker measured in a first sample obtained from the subject at a time to, wherein the marker is selected from the group consisting of a) a marker gene having at least 95% sequence identity with a sequence selected from the group consisting of MUC5B, TERC, FAM13A, TERT, DSP, AZGP1, OBFC1, ATP11A, IVD/DISP2, DPP9, SIGLEC14, ADM2, TSPAN5, CAMKK1 or MMP-7, or homologs or variants thereof; b) polypeptides encoded by the marker genes of a)
  • the genes detected share 100% sequence identity with the corresponding marker gene in a).
  • the time t0 is before the treatment has been administered to the subject, and the time t1 is after the treatment has been administered to the subject.
  • the comparing is repeated over a range of times.
  • An assay system for predicting individual prognosis therapy for interstitial pneumonia comprising a means to detect at least one of: a) the presence of a marker polymorphism selected from the group consisting of: rs35705950; and/or, b) a level of gene expression of a marker gene or plurality of marker genes selected from the group consisting of: a marker gene having at least 95% sequence identity with a sequence selected from the group consisting of MUC5B, TERC, FAM13A, TERT, DSP, AZGP1, OBFC1, ATP11A, IVD/DISP2, DPP9, SIGLEC14, ADM2, TSPAN5, CAMKK1 or MMP-7, or homologs or variants thereof c) polypeptides encoded by the marker genes of b) d) fragments of polypeptides of c); and e) a polynucleotide which is fully complementary to at least a portion of a marker gene of b).
  • the means to detect comprises nucleic acid probes comprising at least 10 to 50 contiguous nucleic acids of the marker polymorphisms or gene(s), or complementary nucleic acid sequences thereof.
  • the means to detect comprises binding ligands that specifically detect polypeptides encoded by the marker genes.
  • the genes detected share 100% sequence identity with the corresponding marker gene in b).
  • the means to detect comprises at least one of nucleic acid probe and binding ligands disposed on an assay surface.
  • the assay surface comprises a chip, array, or fluidity card.
  • the probes comprise complementary nucleic acid sequences to at least 10 to 50 nucleic acid sequences of the marker genes.
  • the binding ligands comprise antibodies or binding fragments thereof.
  • the assay system further comprises: a control selected from information containing a predetermined control level or set of genetic variants or polymorphic markers that has been correlated with diagnosis, development, progression, or life expectancy in interstitial lung disease patients.
  • a method of detecting a level of gene expression of one or more marker genes in a human subject with interstitial pneumonia comprising, optionally, obtaining a biological sample from a human individual with interstitial pneumonia; detecting the level of expression of a gene selected from MUC5B, TERC, FAM13A, TERT, DSP, AZGP1, OBFC1, ATP11A, IVD/DISP2, DPP9, SIGLEC14, ADM2, TSPAN5, CAMKK1 or MMP-7, or homologs or variants thereof, in one or more cells from the biological sample from the individual.
  • the method further comprises detecting the level of expression of a gene selected from MUC5B, TERC, FAM13A, TERT, DSP, AZGP1, OBFC1, ATP11A, IVD/DISP2, DPP9, SIGLEC14, ADM2, TSPAN5, CAMKK1 or MMP-7, or homologs or variants thereof, in one or more cells from the biological sample from the individual.
  • a gene selected from MUC5B, TERC, FAM13A, TERT, DSP, AZGP1, OBFC1, ATP11A, IVD/DISP2, DPP9, SIGLEC14, ADM2, TSPAN5, CAMKK1 or MMP-7, or homologs or variants thereof, in one or more cells from the biological sample from the individual.
  • the method further comprises detecting the level of expression of a gene selected from MUC5B, TERC, FAM13A, TERT, DSP, AZGP1, OBFC1, ATP11A, IVD/DISP2, DPP9, SIGLEC14, ADM2, TSPAN5, CAMKK1 or MMP-7, or homologs or variants thereof in one or more cells from the biological sample from the individual.
  • a gene selected from MUC5B, TERC, FAM13A, TERT, DSP, AZGP1, OBFC1, ATP11A, IVD/DISP2, DPP9, SIGLEC14, ADM2, TSPAN5, CAMKK1 or MMP-7, or homologs or variants thereof in one or more cells from the biological sample from the individual.
  • a method of treating an interstitial lung disease in a subject in need of such treatment comprising: detecting a level of one or more marker genes selected from MUC5B, TERC, FAM13A, TERT, DSP, AZGP1, OBFC1, ATP11A, IVD/DISP2, DPP9, SIGLEC14, ADM2, TSPAN5, CAMKK1 or MMP-7, or homologs or variants thereof in a biological sample obtained from the human subject; and, administering an effective amount of an effective treatment.
  • the method further comprises detecting the level of expression of a gene selected from MUC5B, TERC, FAM13A, TERT, DSP, AZGP1, OBFC1, ATP11A, IVD/DISP2, DPP9, SIGLEC14, ADM2, TSPAN5, CAMKK1 or MMP-7, or homologs or variants thereof, in one or more cells from the biological sample from the individual.
  • a gene selected from MUC5B, TERC, FAM13A, TERT, DSP, AZGP1, OBFC1, ATP11A, IVD/DISP2, DPP9, SIGLEC14, ADM2, TSPAN5, CAMKK1 or MMP-7, or homologs or variants thereof, in one or more cells from the biological sample from the individual.
  • the method further comprises detecting the level of expression of a gene selected from MUC5B, TERC, FAM13A, TERT, DSP, AZGP1, OBFC1, ATP11A, IVD/DISP2, DPP9, SIGLEC14, ADM2, TSPAN5, CAMKK1 or MMP-7, or homologs or variants thereof, in one or more cells from the biological sample from the individual.
  • a gene selected from MUC5B, TERC, FAM13A, TERT, DSP, AZGP1, OBFC1, ATP11A, IVD/DISP2, DPP9, SIGLEC14, ADM2, TSPAN5, CAMKK1 or MMP-7, or homologs or variants thereof, in one or more cells from the biological sample from the individual.
  • Methods of detecting a genetic variant are further described, for example, in U.S. Pat. No. 8,673,565 (the contents of which are herein incorporated by reference in their entirety).
  • Genetic variations in the mucin genes are associated with pulmonary diseases. These genetic variations can be found in any part of the gene, e.g., in the regulatory regions, introns, or exons. Relevant genetic variations may also be found the intergene regions, e.g., in sequences between mucin genes. Insertions, substitutions, and deletions are included in genetic variants. Single nucleotide polymorphisms (SNPs) are exemplary genetic variants.
  • SNPs are associated with pulmonary disorders (e.g. FIP or IPF).
  • pulmonary disorders e.g. FIP or IPF.
  • the studies disclosed herein demonstrate that presence of one or more of these SNPs associated with MUC5B can lead to predisposition to a pulmonary disorder.
  • some of these SNPs are related to a transcription factor binding site.
  • the transcription factor binding site can effect modulation of MUC5B expression, for example E2F3 loss, and HOXA9 and PAX-2 generation.
  • the disclosure thus provides methods for assessing the presence or absence of SNPs in a sample from a subject suspected of having or developing a pulmonary disorder (e.g., because of family history).
  • one or more SNPs are screened in one or more samples from a subject.
  • the SNPs can be associated with one or more genes, e.g., one or more MUC genes or other genes associated with mucous secretion.
  • a MUC gene associated SNP is associated with MUC5B and/or another MUC gene, such as MUC5AC or MUC1.
  • SNPs contemplated for diagnostic, treatment, or prognosis can include SNPs found within a MUC gene and/or within a regulatory or promoter region associated with a MUC gene.
  • one or more SNPs can include, but are not limited to, detection of the SNPs of MUC5B alone or in combination with other genetic variations or SNPs and/or other diagnostic or prognostic methods.
  • Various degrees of stringency of hybridization may be employed in the assay. As the conditions for hybridization become more stringent, there must be a greater degree of complementarity between the probe and the target for duplex formation to occur. Thus, high stringency conditions are typically used for detecting a SNP.
  • a genetic variant MUC5B gene in a subject is detected by contacting a nucleic acid in a sample from the subject with a probe having substantial identity to a subsequence of the MUC5B gene, and determining whether the nucleic acid indicates that the subject has a genetic variant MUC5B gene.
  • the sample can be processed prior to amplification, e.g., to separate genomic DNA from other sample components.
  • the probe has at least 90, 92, 94, 95, 96, 98, 99, or 100% identity to the MUC5B gene subsequence.
  • the probe is between 10-500 nucleotides in length, e.g., 10-100, 10-40, 10-20, 20-100, 100-400, etc. In the case of detecting a SNP, the probe can be even shorter, e.g., 8-20 nucleotides in length.
  • the MUC5B gene sequence to be detected includes at least 8 contiguous nucleotides, e.g., at least 10, 15, 20, 25, 30, 35 or more contiguous nucleotides. In some embodiments, the sequence to be detected includes 8 contiguous nucleotides, e.g., at least 10, 15, 20, 25, 30, 35 or more contiguous nucleotides.
  • the degree of stringency can be controlled by temperature, ionic strength, pH and/or the presence of a partially denaturing solvent such as formamide.
  • the stringency of hybridization is conveniently varied by changing the concentration of formamide within the range up to and about 50%.
  • the degree of complementarity (sequence identity) required for detectable binding will vary in accordance with the stringency of the hybridization medium and/or wash medium. In certain embodiments, in particular for detection of a particular SNP, the degree of complementarity is about 100 percent. In other embodiments, sequence variations can result in ⁇ 100% complementarity, ⁇ 90% complimentarity probes, ⁇ 80% complimentarity probes, etc., in particular, in a sequence that does not involve a SNP. In some examples, e.g., detection of species homologs, primers may be compensated for by reducing the stringency of the hybridization and/or wash medium.
  • High stringency conditions for nucleic acid hybridization are well known in the art.
  • conditions may comprise low salt and/or high temperature conditions, such as provided by about 0.02 M to about 0.15 M NaCl at temperatures of about 50° C. to about 70° C.
  • Other exemplary conditions are disclosed in the following Examples. It is understood that the temperature and ionic strength of a desired stringency are determined in part by the length of the particular nucleic acid(s), the length and nucleotide content of the target sequence(s), the charge composition of the nucleic acid(s), and by the presence or concentration of formamide, tetramethylammonium chloride or other solvent(s) in a hybridization mixture.
  • Nucleic acids can be completely complementary to a target sequence or exhibit one or more mismatches.
  • Nucleic acids of interest can also be amplified using a variety of known amplification techniques. For instance, polymerase chain reaction (PCR) technology may be used to amplify target sequences (e.g., genetic variants) directly from DNA, RNA, or cDNA.
  • PCR polymerase chain reaction
  • a stretch of nucleic acids is amplified using primers on either side of a targeted genetic variation, and the amplification product is then sequenced to detect the targeted genetic variation (using, e.g., Sanger sequencing, Pyrosequencing, Nextgen® sequencing technologies).
  • the primers can be designed to hybridize to either side of the upstream regulatory region of the MUC5B gene, and the intervening sequence determined to detect a SNP in the promoter region.
  • one of the primers can be designed to hybridize to the targeted genetic variant.
  • a genetic variant nucleotide can be identified using RT-PCR, e.g., using labeled nucleotide monomers. In this way, the identity of the nucleotide at a given position can be detected as it is added to the polymerizing nucleic acid.
  • the ScorpionTM system is a commercially available example of this technology.
  • a genetic variant MUC5B gene in a subject is detected by amplifying a nucleic acid in a sample from the subject to form an amplification product, and determining whether the amplification product indicates a genetic variant MUC5B gene.
  • the sample can be processed prior to amplification, e.g., to separate genomic DNA from other sample components.
  • amplifying comprises contacting the sample with amplification primers having substantial identity to MUC5B genomic subsequences, e.g., at least 90, 92, 94, 95, 96, 98, 99, or 100% identity.
  • the sequence to be amplified is between 30-1000 nucleotides in length, e.g., 50-500, 50-400, 100-400, 50-200, 100-300, etc.
  • the sequence to be amplified or detected includes at least 8 contiguous nucleotides, e.g., at least 10, 15, 20, 25, 30, 35 or more contiguous nucleotides.
  • the sequence to be amplified or detected includes 8 contiguous nucleotides, e.g., at least 10, 15, 20, 25, 30, 35 or more contiguous nucleotides.
  • the contiguous nucleotides include nucleotide 28.
  • Amplification techniques can also be useful for cloning nucleic acid sequences, to make nucleic acids to use as probes for detecting the presence of a target nucleic acid in samples, for nucleic acid sequencing, for control samples, or for other purposes.
  • Probes and primers are also readily available from commercial sources, e.g., from Invitrogen, Clonetech, etc.
  • RNA e.g., mRNA
  • Sample levels can be compared to a control level.
  • RNA to be detected can include mRNA.
  • a reverse transcriptase reaction is carried out and the targeted sequence is then amplified using standard PCR.
  • Quantitative PCR qPCR
  • RT-PCR real time PCR
  • Nucleic acid arrays are also useful for detecting nucleic acid expression. Customizable arrays are available from, e.g., Affimatrix.
  • An exemplary human MUC5B mRNA sequence, e.g., for probe and primer design, can be found at GenBank Accession No. AF086604.1.
  • Protein levels can be detected using antibodies or antibody fragments specific for that protein, natural ligands, small molecules, aptamers, etc.
  • An exemplary human MUC5B sequence e.g., for screening a targeting agent, can be found at UniProt Accession No. 000446.
  • Antibody based techniques are known in the art, and described, e.g., in Harlow & Lane (1988) Antibodies: A Laboratory Manual and Harlow (1998) Using Antibodies: A Laboratory Manual; Wild, The Immunoassay Handbook, 3d edition (2005) and Law, Immunoassay: A Practical Guide (1996).
  • the assay can be directed to detection of a molecular target (e.g., protein or antigen), or a cell, tissue, biological sample, liquid sample or surface suspected of carrying an antibody or antibody target.
  • a molecular target e.g., protein or antigen
  • immunoassays includes: competitive and non-competitive formats, enzyme linked immunosorption assays (ELISA), microspot assays, Western blots, gel filtration and chromatography, immunochromatography, immunohistochemistry, flow cytometry or fluorescence activated cell sorting (FACS), microarrays, and more.
  • ELISA enzyme linked immunosorption assays
  • microspot assays Western blots
  • gel filtration and chromatography immunochromatography
  • immunohistochemistry flow cytometry or fluorescence activated cell sorting (FACS)
  • FACS fluorescence activated cell sorting
  • Aptamers are nucleic acids that are designed to bind to a wide variety of targets in a non-Watson Crick manner. An aptamer can thus be used to detect or otherwise target nearly any molecule of interest, including a pulmonary disease associated protein. Methods of constructing and determining the binding characteristics of aptamers are well known in the art. For example, such techniques are described in U.S. Pat. Nos. 5,582,981, 5,595,877 and 5,637,459. Aptamers are typically at least 5 nucleotides, 10, 20, 30 or 40 nucleotides in length, and can be composed of modified nucleic acids to improve stability. Flanking sequences can be added for structural stability, e.g., to form 3-dimensional structures in the aptamer.
  • Protein detection agents described herein can also be used as a treatment and/or diagnosis of pulmonary disease or predictor of disease progression, e.g., propensity for survival, in a subject having or suspected of developing a pulmonary disorder.
  • MUC5B antibodies can be used to assess MUC5B protein levels in a subject having or suspected of developing a pulmonary disorder. It is contemplated herein that antibodies or antibody fragments may be used to modulate MUC5B production in a subject having or suspected of developing a pulmonary disease. In certain embodiments, one or more agents capable of modulating MUC5B may be used to treat a subject having or suspected of developing a pulmonary disorder. One or more antibodies or antibody fragments may be generated to detect one or more of the SNPs disclosed herein by any method known in the art.
  • MUC5B diagnostic tests may include, but are not limited to, alone or in combination, analysis of rs35705950 SNP in MUC5B gene, MUC5B mRNA levels, and/or MUC5B protein levels.
  • the above methods of detection can be applied to additional pulmonary disease markers. That is, the expression level or presence of genetic variants of at least one additional pulmonary disease marker gene can be determined, or the activity of the marker protein can be determined, and compared to a standard control for the pulmonary disease marker.
  • the examination of additional pulmonary disease markers can be used to confirm a diagnosis of pulmonary disease, monitor disease progression, or determine the efficacy of a course of treatment in a subject.
  • pulmonary disease is indicated by an increased number of lymphocytes, e.g., CD4+CD28 ⁇ cells.
  • the invention further includes methods of determining whether the genome of a subject comprises a genetic variant of at least one gene selected from these genes. The presence of a genetic variant indicates that the subject has or is at risk of developing pulmonary disease. Said determining can optionally be combined with determining whether the genome of the subject comprises a genetic variant MUC5B gene, or determining whether the subject has an elevated level of MUC5B RNA or protein to confirm or strengthen the diagnosis or prognosis.
  • Abnormal expression in the following genes can also be indicative of pulmonary disease: Surfactant Protein A, Surfactant Protein D, KL-6/MUC1, CC16, CK-19, Ca 19-9, SLX, MCP-1, MIP-1a, ITAC, glutathione, type III procollagen peptide, sIL-2R, ACE, neopterin, beta-glucuronidase, LDH, CCL-18, CCL-2, CXCL12, MMPI, and osteopontin.
  • Said determining can optionally be combined with determining whether the genome of the subject comprises a genetic variant MUC5B gene, or determining whether the subject has an elevated level of MUC5B RNA or protein to confirm or strengthen the diagnosis or prognosis.
  • the present disclosure provides a peripheral blood biomarker profile for IPF to demonstrate the use of a predictive biomarker profile in cases of preclinical pulmonary fibrosis (PrePF) derived from families with familial IPF.
  • PrePF preclinical pulmonary fibrosis
  • the present disclosure also provides biomarker identification for association between each genetic, epigenetic or protein (gene product) biomarker with PrePF and the predictive value of the combination of biomarkers associated with PrePF.
  • Pirfenidone and nintedanib are effective in patients with mild disease, suggesting that patients with PrePF may be targeted for early intervention, before most of the lung has been irreversibly remodeled.
  • Table 1 below shows additional gene expression changes present in subjects with IPF compared to controls. Specifically, the expression of the genes listed in Table 1 are upregulated in IPF compared to the expression of these same genes in control subjects. Accordingly, the discovery of elevated expression levels of one or more genes listed in Table 1 compared to a control in an asymptomatic subject may indicate that the subject has PrePF and/or that the subject is at risk for developing IPF.
  • the subject has a mutation in a nucleic acid or amino acid sequence encoding a gene or gene product that is upregulated in a subject having a fibrotic pulmonary disease of the disclosure.
  • the subject has a mutation in a nucleic acid or amino acid sequence encoding Leukotriene A4 Hydrolase (LTA4H), Surfactant Protein B (SFTPB), Breast Cancer Anti-Estrogen Resistance 3 (BCAR3), C-X-C motif Chemokine Ligand 13 (CXCL13), EPH Receptor A2 (EPHA2), Serum Amyloid A1 (SAA1), Phospholipase A2 Group IIA (PLA2G2A), Insulin-Like Growth Factor Binding Protein 3 (IGFBP3), C-C Motif Chemokine Ligand 28 (CCL28), 5100 Calcium Binding Protein A12 (S100A12), Thromboxane A Synthase 1 (LTA4H), Surfactant Protein B (SFTPB), Breast Cancer Anti-
  • Table 2 below shows additional gene expression changes present in subjects with IPF compared to controls. Specifically, the expression of the genes listed in Table 2 are downregulated in IPF compared to the expression of these same genes in control subjects. Accordingly, the discovery of decreased expression levels of one or more genes listed in Table 2 compared to a control in an asymptomatic subject may indicate that the subject has PrePF and/or that the subject is at risk for developing IPF.
  • the subject has a mutation in a nucleic acid or amino acid sequence encoding a gene or gene product that is downregulated in a subject having a fibrotic pulmonary disease of the disclosure.
  • the subject has a mutation in a nucleic acid or amino acid sequence encoding Surfactant Protein D (SFTPD), Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH), Histone Cluster 1 H1 Family Member C (HIST1H1C), YTH Domain Containing 1 (YTHDC1), Plexin A1 (PLXNA1), Serine Peptidase Inhibitor Kazal Type 6 (SPINK6), LDL Receptor Related Protein Associated Protein 1 (LRPAP1), Secretoglobin Family 3A Member 1 (SCGB3A1), H2A Histone Family Member Z (H2AFZ) or Chromosome 1 Open Reading Frame 162 (Clorf162).
  • SFTPD Surfactant Protein D
  • GPDH Glyceraldeh
  • the subject having PrePF or at risk of developing IPF has a mutation in a sequence encoding MUC5B, TERC, FAM13A, TERT, DSP, AZGP1, OBFC1, ATP11A, IVD/DISP2, DPP9, SIGLEC14, ADM2, TSPAN5, CAMKK1 or MMP-7.
  • the subject having PrePF or at risk of developing IPF has a mutation in a sequence encoding Telomerase RNA Component (TERC).
  • TRC Telomerase RNA Component
  • the polymorphism is rs6793295 comprising (SEQ ID NO: 1).
  • the subject having PrePF or at risk of developing IPF has a mutation in a sequence encoding Family with sequence similarity 13 member A (FAM13A).
  • the polymorphism is rs2609255 comprising (SEQ ID NO: 2).
  • the subject having PrePF or at risk of developing IPF has a mutation in a sequence encoding Telomerase Reverse Transcriptase (TERT).
  • TERT Telomerase Reverse Transcriptase
  • the polymorphism is rs2736100 comprising (SEQ ID NO: 3).
  • the subject having PrePF or at risk of developing IPF has a mutation in a sequence encoding Desmoplakin (DSP).
  • DSP Desmoplakin
  • the polymorphism is rs2076295 comprising (SEQ ID NO: 4).
  • the subject having PrePF or at risk of developing IPF has a mutation in a sequence encoding Zinc-alpha 2-Glycoprotein 1 (AZGP1).
  • the polymorphism is rs4727443 comprising (SEQ ID NO: 5).
  • the subject having PrePF or at risk of developing IPF has a mutation in a sequence encoding Oligonucleotide/oligosaccharide-binding Fold Containing 1 (OBFC1).
  • OBFC1 Oligonucleotide/oligosaccharide-binding Fold Containing 1
  • the polymorphism is rs11191865 comprising (SEQ ID NO: 6).
  • the subject having PrePF or at risk of developing IPF has a mutation in a sequence encoding Mucin 5B (MUC5B).
  • MUC5B Mucin 5B
  • the polymorphism is rs35705950 comprising (SEQ ID NO: 7).
  • the subject having PrePF or at risk of developing IPF has a mutation in a sequence encoding ATPase Phospholipid Transporting 11A (ATP11A).
  • the polymorphism is rs12787690 comprising (SEQ ID NO: 8).
  • the subject having PrePF or at risk of developing IPF has a mutation in a sequence encoding Isovaleryl-CoA dehydrogenase (IVD)/Dispatched RND Transporter Family Member 2 (DISP2).
  • IVD Isovaleryl-CoA dehydrogenase
  • DISP2 Dispatched RND Transporter Family Member 2
  • the polymorphism is rs2034650 comprising (SEQ ID NO: 9).
  • the subject having PrePF or at risk of developing IPF has a mutation in a sequence encoding Dipeptidyl Peptidase 9 (DPP9).
  • DPP9 Dipeptidyl Peptidase 9
  • the polymorphism is rs12610495 comprising (SEQ ID NO: 10).
  • the wild type human MUC5B gene of the disclosure consists of or comprises the nucleic acid sequence (Genbank Accession number: NM_002458.2):
  • the wild type human MUC5B gene of the disclosure consists of or comprises the amino acid sequence (Genbank Accession number: NP_002449.2):
  • the wild type human TERT gene of the disclosure consists of or comprises the nucleic acid sequence (Genbank Accession number: NM_198253.2, transcript variant 1):
  • the wild type human TERT gene of the disclosure consists of or comprises the amino acid sequence (Genbank Accession number: NP_937983.2, transcript variant 1):
  • the wild type human TERT gene of the disclosure consists of or comprises the nucleic acid sequence (Genbank Accession number: NM_001193376.1, transcript variant 2):
  • the wild type human TERT gene of the disclosure consists of or comprises the amino acid sequence (Genbank Accession number: NP_001180305.1, transcript variant 21:
  • the wild type human FAM13A gene of the disclosure consists of or comprises the nucleic acid sequence (Genbank Accession number: NM_014883.3, transcript variant 1):
  • the wild type human FAM13A gene of the disclosure consists of or comprises the amino acid sequence (Genbank Accession number: NP_055698.2, transcript variant 1):
  • the wild type human FAM13A gene of the disclosure consists of or comprises the nucleic acid sequence (Genbank Accession number: NM_001015045.2, transcript variant 2):
  • the wild type human FAM13A gene of the disclosure consists of or comprises the amino acid sequence (Genbank Accession number: NP_001015045.1, transcript variant 2):
  • the wild type human FAM13A gene of the disclosure consists of or comprises the nucleic acid sequence (Genbank Accession number: NM_001265578.1, transcript variant 3):
  • the wild type human FAM13A gene of the disclosure consists of or comprises the amino acid sequence (Genbank Accession number: NP_001252507.1, transcript variant 3):
  • the wild type human FAM13A gene of the disclosure consists of or comprises the nucleic acid sequence (Genbank Accession number: NM_001265579.1, transcript variant 4):
  • the wild type human FAM13A gene of the disclosure consists of or comprises the amino acid sequence (Genbank Accession number: NP_001252508.1, transcript variant 4):
  • the wild type human FAM13A gene of the disclosure consists of or comprises the nucleic acid sequence (Genbank Accession number: NM_001265580.1, transcript variant 5):
  • the wild type human FAM13A gene of the disclosure consists of or comprises the amino acid sequence (Genbank Accession number: NP_001252509.1, transcript variant 5):
  • the wild type human DSP gene of the disclosure consists of or comprises the nucleic acid sequence (Genbank Accession number: NM_004415.3, transcript variant 1):
  • the wild type human DSP gene of the disclosure consists of or comprises the amino acid sequence (Genbank Accession number: NP_004406.2, transcript variant 1):
  • the wild type human DSP gene of the disclosure consists of or comprises the nucleic acid sequence (Genbank Accession number: NM_001008844.2, transcript variant 2):
  • the wild type human DSP gene of the disclosure consists of or comprises the amino acid sequence (Genbank Accession number: NP_001008844.1, transcript variant 2):
  • the wild type human DSP gene of the disclosure consists of or comprises the nucleic acid sequence (Genbank Accession number: NM_001319034.1, transcript variant 3):
  • the wild type human DSP gene of the disclosure consists of or comprises the amino acid sequence (Genbank Accession number: NP_001305963.1, transcript variant 3):
  • the wild type human AZGP1 gene of the disclosure consists of or comprises the nucleic acid sequence (Genbank Accession number: NM_001185.3):
  • the wild type human AZGP1 gene of the disclosure consists of or comprises the nucleic acid sequence (Genbank Accession number: NP_001176.1):
  • the wild type human OBFC1 gene of the disclosure consists of or comprises the nucleic acid sequence (Genbank Accession number: NM_024928):
  • the wild type human OBFC1 gene of the disclosure consists of or comprises the amino acid sequence (Genbank Accession number: NP_079204.2):
  • the wild type human ATP11A gene of the disclosure consists of or comprises the nucleic acid sequence (Genbank Accession number: NM_015205.2, transcript variant 1):
  • the wild type human in some embodiments of the methods of the disclosure, the wild type human
  • ATP11A gene of the disclosure consists of or comprises the nucleic acid sequence (Genbank Accession number: NP_056020.2, transcript variant 1):
  • the wild type human ATP11A gene of the disclosure consists of or comprises the nucleic acid sequence (Genbank Accession number: NM_032189.3, transcript variant 2):
  • the wild type human ATP11A gene of the disclosure consists of or comprises the amino acid sequence (Genbank
  • the wild type human IVD/DISP2 gene of the disclosure consists of or comprises the nucleic acid sequence (Genbank Accession number: NM_002225.3, transcript variant 1):
  • the wild type human IVD/DISP2 gene of the disclosure consists of or comprises the amino acid sequence (Genbank Accession number: transcript variant 1):
  • the wild type human IVD/DISP2 gene of the disclosure consists of or comprises the nucleic acid sequence (Genbank Accession number: NM_001159508.1, transcript variant 2):
  • the wild type human IVD/DISP2 gene of the disclosure consists of or comprises the nucleic acid sequence (Genbank Accession number: NP_001152980.1, transcript variant 2):
  • the wild type human DPP9 gene of the disclosure consists of or comprises the nucleic acid sequence (Genbank Accession number: NM_139159.41:
  • the wild type human in some embodiments of the methods of the disclosure, the wild type human
  • DPP9 gene of the disclosure consists of or comprises the amino acid sequence (Genbank Accession number: NP_631898.3):
  • the wild type human SIGLEC14 gene of the disclosure consists of or comprises the nucleic acid sequence (Genbank Accession number: NM_001098612.1):
  • the wild type human SIGLEC14 gene of the disclosure consists of or comprises the amino acid sequence (Genbank Accession number: NP_001092082.1):
  • the wild type human ADM2 gene of the disclosure consists of or comprises the nucleic acid sequence (Genbank Accession number: NM_001253845.1):
  • the wild type human ADM2 gene of the disclosure consists of or comprises the amino acid sequence (Genbank Accession number: NP_001240774.1):
  • the wild type human TSPAN5 gene of the disclosure consists of or comprises the nucleic acid sequence (Genbank Accession number: NM_005723.3):
  • the wild type human TSPAN5 gene of the disclosure consists of or comprises the amino acid sequence (Genbank Accession number: NP_005714.2):
  • the wild type human CAMKK1 gene of the disclosure consists of or comprises the nucleic acid sequence (Genbank Accession number: NM_032294.2, transcript variant 1):
  • the wild type human CAMKK1 gene of the disclosure consists of or comprises the amino acid sequence (Genbank Accession number: NP_115670.1, transcript variant 1):
  • the wild type human CAMKK1 gene of the disclosure consists of or comprises the nucleic acid sequence (Genbank Accession number: NM_172206.1, transcript variant 2):
  • the wild type human CAMKK1 gene of the disclosure consists of or comprises the amino acid sequence (Genbank Accession number: NP_757343.2, transcript variant 2):
  • the wild type human CAMKK1 gene of the disclosure consists of or comprises the nucleic acid sequence (Genbank Accession number: NM_172207.2, transcript variant 3):
  • the wild type human CAMKK1 gene of the disclosure consists of or comprises the amino acid sequence (Genbank Accession number: NP_757344.2, transcript variant 3):
  • the wild type human MMPI gene of the disclosure consists of or comprises the nucleic acid sequence (Genbank Accession number: NM_002423.4):
  • the wild type human MMPI gene of the disclosure consists of or comprises the amino acid sequence (Genbank Accession number: NP_002414.1):
  • the wild type human TERC gene of the disclosure consists of or comprises the nucleic acid sequence (Genbank Accession number: NR_001566.1):
  • FILD fibrotic interstitial lung disease
  • FEP Familial Interstitial Pneumonia
  • HRCT high-resolution CT
  • IVA refers to asymptomatic interstitial lung abnormalities.
  • IPF idiopathic pulmonary fibrosis
  • PBMC peripheral blood mononuclear cell
  • the term “alleviate” is meant to describe a process by which the severity of a sign or symptom of a disorder is decreased.
  • a sign or symptom can be alleviated without being eliminated.
  • the administration of pharmaceutical compositions disclosed herein leads to the elimination of a sign or symptom, however, elimination is not required.
  • Effective dosages are expected to decrease the severity of a sign or symptom.
  • a sign is an objective indication of a medical condition that is observable or detectable by a medical professional or lay person (e.g. family member) (for example, with respect to fibrotic pulmonary disease, signs include, but are not limited to, changes in body weight, changes in body temperature and the presence of a fibrotic lesion in one or both lungs detectable by radiography).
  • a symptom is an indication of disease that may be a sign but may also be exclusively observable or subjectively experienced by the subject (for example, with respect to fibrotic pulmonary disease, symptoms may include but are not limited to, a dry or hacking cough, a sore throat, a tight chest, shortness of breath, and a feeling of exhaustion or malaise).
  • co-administered and “co-administration” as relating to a subject refer to administering to the subject a compound of the invention or salt thereof along with a compound that may also treat the disorders or diseases contemplated within the invention.
  • the co-administered compounds are administered separately, or in any kind of combination as part of a single therapeutic approach.
  • the co-administered compound may be formulated in any kind of combinations as mixtures of solids and liquids under a variety of solid, gel, and liquid formulations, and as a solution.
  • composition refers to a mixture of at least one compound useful within the disclosure with a pharmaceutically acceptable carrier.
  • the pharmaceutical composition facilitates administration of the compound to a patient or subject. Multiple techniques of administering a compound exist in the art including, but not limited to, intravenous, oral, aerosol, parenteral, ophthalmic, nasal, pulmonary and topical administration.
  • a “disease” as used herein is a state of health of an animal or subject wherein the animal or subject cannot maintain homeostasis, and wherein if the disease is not ameliorated then the animal's or subject's health continues to deteriorate.
  • a “disorder” as used herein in an animal is a state of health in which the animal or subject is able to maintain homeostasis, but in which the animal's or subject's state of health is less favorable than it would be in the absence of the disorder. Left untreated, a disorder does not necessarily cause a further decrease in the animal's or subject's state of health.
  • the terms “effective amount,” “pharmaceutically effective amount” and “therapeutically effective amount” refer to a nontoxic but sufficient amount of an agent to provide the desired biological result. That result may be reduction and/or alleviation of the signs, symptoms, or causes of a disease, or any other desired alteration of a biological system. An appropriate therapeutic amount in any individual case may be determined by one of ordinary skill in the art using routine experimentation.
  • fibrotic lung disease or “fibroid lung disease” or “pulmonary fibrosis” or “scarring of the lung” refers to a group of diseases characterized by the formation or development of excess fibrous connective tissue (fibrosis) in the lungs.
  • fibrosis fibrous connective tissue
  • Symptoms of pulmonary fibrosis are mainly: shortness of breath, particularly with exertion; chronic dry, hacking coughing; fatigue and weakness; chest discomfort; and loss of appetite and rapid weight loss.
  • Pulmonary fibrosis may be a secondary effect of other diseases, most of them being classified as interstitial lung diseases, such as autoimmune disorders, viral infections or other microscopic injuries to the lung. Pulmonary fibrosis can also appear without any known cause (“idiopathic”). Idiopathic pulmonary fibrosis is a diagnosis of exclusion of a characteristic set of histologic/pathologic features known as usual interstitial pneumonia (UIP).
  • UIP interstitial pneumonia
  • pulmonary fibrosis Diseases and conditions that may cause pulmonary fibrosis as a secondary effect include: inhalation of environmental and occupational pollutants (asbestosis, silicosis and gas exposure); hypersensitivity pneumonitis, most often resulting from inhaling dust contaminated with bacterial, fungal, or animal products; cigarette smoking; connective tissue diseases such as rheumatoid arthritis, SLE; scleroderma, sarcoidosis and Wegener's granulomatosis; infections; medications such as amiodarone, bleomycin (pingyangmycin), busulfan, methotrexate, apomorphine and nitrofurantoin; and radiation therapy to the chest.
  • environmental and occupational pollutants asbestosis, silicosis and gas exposure
  • hypersensitivity pneumonitis most often resulting from inhaling dust contaminated with bacterial, fungal, or animal products
  • connective tissue diseases such as rheumatoid arthritis, SLE; scleroderma
  • a “subject in need thereof” is a subject suffering from fibrotic lung disease relative to the population at large.
  • the subject is a patient who is or is about to be administered with comprising administering to the subject an effective amount of a therapeutic agent.
  • the subject is asymptomatic and is at risk of developing the fibrotic lung disease.
  • a “subject” includes a mammal.
  • the mammal can be e.g., any mammal, e.g., a human, primate, bird, mouse, rat, fowl, dog, cat, cow, horse, goat, camel, sheep or pig.
  • the mammal is a human.
  • the term “pharmaceutically acceptable” refers to a material, such as a carrier or diluent, which does not abrogate the biological activity or properties of the compound, and is relatively non-toxic, i.e., the material may be administered to an individual without causing undesirable biological effects or interacting in a deleterious manner with any of the components of the composition in which it is contained.
  • the term “pharmaceutically acceptable carrier” means a pharmaceutically acceptable material, composition or carrier, such as a liquid or solid filler, stabilizer, dispersing agent, suspending agent, diluent, excipient, thickening agent, solvent or encapsulating material, involved in carrying or transporting a compound useful within the invention within or to the patient such that it may perform its intended function.
  • a pharmaceutically acceptable material, composition or carrier such as a liquid or solid filler, stabilizer, dispersing agent, suspending agent, diluent, excipient, thickening agent, solvent or encapsulating material, involved in carrying or transporting a compound useful within the invention within or to the patient such that it may perform its intended function.
  • Such constructs are carried or transported from one organ, or portion of the body, to another organ, or portion of the body.
  • Each carrier must be “acceptable” in the sense of being compatible with the other ingredients of the formulation, including the compound useful within the invention, and not injurious to the patient.
  • materials that may serve as pharmaceutically acceptable carriers include: sugars, such as lactose, glucose and sucrose; starches, such as corn starch and potato starch; cellulose, and its derivatives, such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; powdered tragacanth; malt; gelatin; talc; excipients, such as cocoa butter and suppository waxes; oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; glycols, such as propylene glycol; polyols, such as glycerin, sorbitol, mannitol and polyethylene glycol; esters, such as ethyl oleate and ethyl laurate; agar; buffering agents, such as magnesium hydroxide and aluminum hydroxide; surface active agents; alginic acid; pyrogen-free water; isotonic saline
  • Pharmaceutically acceptable carriers of the disclosure include, but are not limited to, pharmaceutically acceptable materials, compositions or carriers, such as a liquid or solid fillers, stabilizers, dispersing agents, suspending agents, diluents, excipients, thickening agents, solvents or encapsulating materials, involved in carrying or transporting a compound useful within the invention within or to the patient such that it may perform its intended function.
  • pharmaceutically acceptable materials such as a liquid or solid fillers, stabilizers, dispersing agents, suspending agents, diluents, excipients, thickening agents, solvents or encapsulating materials, involved in carrying or transporting a compound useful within the invention within or to the patient such that it may perform its intended function.
  • Such constructs are carried or transported from one organ, or portion of the body, to another organ, or portion of the body.
  • Each carrier must be “acceptable” in the sense of being compatible with the other ingredients of the formulation, including the compound useful within the invention, and not injurious to the patient.
  • materials that may serve as pharmaceutically acceptable carriers include: sugars, such as lactose, glucose and sucrose; starches, such as corn starch and potato starch; cellulose, and its derivatives, such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; powdered tragacanth; malt; gelatin; talc; excipients, such as cocoa butter and suppository waxes; oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; glycols, such as propylene glycol; polyols, such as glycerin, sorbitol, mannitol and polyethylene glycol; esters, such as ethyl oleate and ethyl laurate; agar; buffering agents, such as magnesium hydroxide and aluminum hydroxide; surface active agents; alginic acid; pyrogen-free water; isotonic saline
  • Suitable forms for administration include forms suitable for systemic administration, oral administration, for example by a capsule or tablet. Once formulated, the compositions of the disclosure can be administered directly to the subject.
  • prevent means avoiding or delaying the onset of symptoms associated with a disease or condition in a subject that has not developed such symptoms at the time the administering of an agent or compound commences.
  • compounds known to be useful in treating pulmonary fibrosis are useful within the methods of the invention.
  • Non-limiting examples of such compounds are pirfenidone (5-methyl-1-phenylpyridin-2-one, or a salt or solvate thereof) and nintedanib (methyl (3Z)-3- ⁇ [(4- ⁇ methyl[(4-methylpiperazin-1-yl)acetyl]amino ⁇ phenyl)amino](phenyl)methylidene ⁇ -2-oxo-2,3-dihydro-1 H-indole-6-carboxylate, or a salt or solvate thereof).
  • the subject identified as having MUC5B promoter polymorphism rs35705950 is administered a compound contemplated within the disclosure.
  • the subject is a mammal. In other embodiments, the mammal is a human.
  • the regimen of administration may affect what constitutes an effective amount.
  • the therapeutic formulations may be administered to the subject either prior to or after the onset of a disease or disorder contemplated in the invention. Further, several divided dosages, as well as staggered dosages may be administered daily or sequentially, or the dose may be continuously infused, or may be a bolus injection. Further, the dosages of the therapeutic formulations may be proportionally increased or decreased as indicated by the exigencies of the therapeutic or prophylactic situation.
  • compositions of the present disclosure may be carried out using known procedures, at dosages and for periods of time effective to treat a disease or disorder contemplated in the invention.
  • An effective amount of the therapeutic compound necessary to achieve a therapeutic effect may vary according to factors such as the state of the disease or disorder in the patient; the age, sex, and weight of the patient; and the ability of the therapeutic compound to treat a disease or disorder contemplated in the invention.
  • Dosage regimens may be adjusted to provide the optimum therapeutic response. For example, several divided doses may be administered daily or the dose may be proportionally reduced as indicated by the exigencies of the therapeutic situation.
  • a non-limiting example of an effective dose range for a therapeutic compound of the invention is from about 1 and 5,000 mg/kg of body weight/per day.
  • One of ordinary skill in the art would be able to study the relevant factors and make the determination regarding the effective amount of the therapeutic compound without undue experimentation.
  • Actual dosage levels of the active ingredients in the pharmaceutical compositions of this invention may be varied so as to obtain an amount of the active ingredient that is effective to achieve the desired therapeutic response for a particular patient, composition, and mode of administration, without being toxic to the patient.
  • the precise therapeutically effective amount for a human subject will depend upon the severity of the disease state, the general health of the subject, the age, weight and gender of the subject, diet, time and frequency of administration, drug combination(s), reaction sensitivities and tolerance/response to therapy. This amount can be determined by routine experimentation and is within the judgement of the clinician.
  • a medical doctor e.g., physician or veterinarian, having ordinary skill in the art may readily determine and prescribe the effective amount of the pharmaceutical composition required.
  • physician or veterinarian could start doses of the compounds of the invention employed in the pharmaceutical composition at levels lower than that required in order to achieve the desired therapeutic effect and gradually increase the dosage until the desired effect is achieved.
  • a suitable dose of a compound of the disclosure may be in the range of from about 0.01 mg to about 5,000 mg per day, such as from about 0.1 mg to about 1,000 mg, for example, from about 1 mg to about 500 mg, such as about 5 mg to about 250 mg per day.
  • the dose may be administered in a single dosage or in multiple dosages, for example from 1 to 4 or more times per day. When multiple dosages are used, the amount of each dosage may be the same or different. For example, a dose of 1 mg per day may be administered as two 0.5 mg doses, with about a 12-hour interval between doses.
  • the therapeutic agent comprises pirfenidone.
  • the effective dosage is administered orally as a capsule or a tablet. In some embodiments, including those embodiments wherein the therapeutic agent comprises pirfenidone, the effective dosage is about 2400 mg/day. In some embodiments, the effective dosage is administered according to an escalating dosage regimen.
  • the escalating dosage regimen comprises (a) administering to the subject about 800 mg of pirfenidone per day for a first week; (b) administering to the subject about 1600 mg of pirfenidone per day for a second week; and (c) administering to the subject about 2400 mg of pirfenidone per day for the remainder of the treatment.
  • the escalating dosage regimen comprises (a) administering to the subject a capsule or tablet comprising about 250 mg of pirfenidone three times a day for a first week; (b) administering to the subject two capsules or tablets comprising about 250 mg of pirfenidone three times a day for a second week; and (c) administering to the subject three capsules or tablets comprising about 250 mg of pirfenidone three times a day for the remainder of the treatment.
  • the capsule or tablet comprises 267 mg of pirfenidone.
  • the therapeutic agent comprises nintedanib.
  • the effective dosage is administered orally as a capsule or a tablet. In some embodiments, including those embodiments wherein the therapeutic agent comprises nintedanib, the effective dosage is about 300 mg/day. In some embodiments, the effective dosage is about 150 mg administered twice per day, wherein the daily doses are administered about 12 hours apart from one another. In some embodiments, including those embodiments wherein the therapeutic agent comprises nintedanib, the effective dosage is about 200 mg/day. In some embodiments, the effective dosage is about 100 mg administered twice per day, wherein the daily doses are administered about 12 hours apart from one another.
  • the effective dosage is administered according to a modified or interrupted dosage regimen.
  • the modified or interrupted dosage regimen comprises (a) administering to the subject about 300 mg of nintedanib per day until the subject presents an elevated level of liver enzymes compared to a control level of liver enzymes; (b) administering to the subject about 200 mg of nintedanib per day until the subject presents the control level of liver enzymes; and (c) administering to the subject about 300 mg of nintedanib per day for the remainder of the treatment; wherein the control level of liver enzymes is a level detected in the subject prior to an initiation of the treatment.
  • the modified or interrupted regimen comprises (a) administering to the subject a capsule or tablet comprising about 150 mg of nintedanib twice per day until the subject presents an elevated level of liver enzymes compared to a control level of liver enzymes; (b) administering to the subject two capsules or tablets comprising about 100 mg twice per day until the subject presents an elevated level of liver enzymes compared to a control level of liver enzymes; and (c) administering to the subject a capsule or tablet comprising about 150 mg of nintedanib twice per day for the remainder of the treatment; wherein the control level of liver enzymes is a level detected in the subject prior to an initiation of the treatment.
  • compositions of the invention are formulated using one or more pharmaceutically acceptable excipients or carriers.
  • pharmaceutical compositions of the invention comprise a therapeutically effective amount of a compound of the invention and a pharmaceutically acceptable carrier.
  • the carrier may be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), suitable mixtures thereof, and vegetable oils.
  • the proper fluidity may be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants.
  • Prevention of the action of microorganisms may be achieved by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, ascorbic acid, thimerosal and the like.
  • isotonic agents for example, sugars, sodium chloride, or polyalcohols such as mannitol and sorbitol, in the composition.
  • compositions or combinations are described as having, including, or comprising specific components or steps, it is contemplated that compositions or combinations also consist essentially of, or consist of, the recited components. Similarly, where methods or processes are described as having, including, or comprising specific process steps, the processes also consist essentially of, or consist of, the recited processing steps.
  • Asymptomatic siblings (>50 years old) of patients with established FIP underwent HRCT scan of the chest. HRCT scans were assessed for FILD by blinded thoracic radiologists; when possible, specific radiographic patterns were identified. PBMCs RNA and DNA were isolated. Genotyping for rs35705950 and microarray analysis were performed (SurePrint G3 Human Gene Expression Microarray). Data were analyzed using Partek Genomics Suite and RStudio. Four-hundred eighty-eight FIP siblings from 271 families were evaluated, 25 HRCT scans were excluded due to technically inadequacy, leaving 463 to be interpreted. Of these, 19% (n 88) met criteria for FILD.
  • Microarray analysis on PBMC RNA from 40 subjects with FILD and 105 unaffected siblings revealed 1,272 differentially expressed genes (FDR ⁇ 0.05, fold-change>2); hierarchical clustering performed on the top 194 differentially expressed probes illustrates segregation of FILD subjects from unaffected siblings ( FIG. 1 ).
  • MUC5B promoter variant rs35705950 is present in over 50% of non-Hispanic white (NHW) patients with IPF and is associated with unique biological and clinical IPF phenotypes.
  • PrePF can be predicted using a combination of clinical risk factors, the MUC5B promoter variant rs35705950, and a panel of biomarkers.
  • FIG. 5 shows that MUC5B promoter variant is associated with enhanced MUC5B expression in both unaffected subjects and in patients with IPF and in IPF, MUC5B message and protein are expressed in bronchoalveolar epithelia ( FIG. 6 ) and honeycomb cysts.
  • the concentration of Muc5b is directly related to the fibroproliferative response to bleomycin ( FIG. 7 )
  • Muc5b protein is expressed in the injured lung following bleomycin challenge
  • Preliminary studies also show that mucociliary clearance is decreased in mice that over-express Muc5b (SFTPC-Muc5b Tg ) and in humans with IPF ( FIG. 10 ).
  • Interstitial lung abnormalities on HRCT scans show asymptomatic relatives of patients with familial IPF and in the elderly. Similar to patients with IPF, interstitial lung abnormalities in asymptomatic subjects are associated with advanced age, cigarette smoking, reduced lung volume and decreased exercise tolerance. Moreover, the MUC5B promoter variant rs35705950 is associated with a higher prevalence of interstitial lung abnormalities on HRCT scan and is predictive of radiographic progression. Suggesting that interstitial lung abnormalities on HRCT scan are a precursor of IPF. However, interstitial lung abnormalities are not specific and include non-fibrotic and fibrotic HRCT defects, and consequently, the prevalence of interstitial lung abnormalities (>5% in the general population ⁇ 50 years of age is orders of magnitude higher than IPF.
  • PrePF Preclinical Pulmonary Fibrosis
  • IPF is under-diagnosed; 2) PrePF is prevalent in at-risk populations; 3) approximately 75% of the cases of PrePF are progressive; 4) radiographic progression of PrePF is associated with increased morbidity and mortality; and 5) MUC5B variant rs35705950, peripheral blood biomarkers, clinical/biological, and radiographic screening should be useful in identifying those with PrePF ( FIG. 11 ).
  • IPF takes years to develop, most patients with IPF are diagnosed in the advanced stage when little can be done to influence survival. Once the lung has undergone remodeling, the non-compliant, stiff lung matrix causes additional remodeling through activation of myofibroblasts, resulting in a feed-forward loop of lung remodeling. Earlier diagnosis of IPF detects subjects with a lower burden of fibrotic lung disease.
  • This disclosure provides a strategic approach to screening for early forms of IPF needs to be established ( FIG. 11 ). While the MUC5B promoter variant is predictive of PrePF (defined as chest HRCT consistent with probable or definite fibrosis (e.g., bilateral subpleural reticular changes, honeycombing, or traction bronchiectasis) occurring in asymptomatic subjects ⁇ 40 years of age that emerge from at-risk populations), the MUC5B promoter variant is present in ⁇ 19% of the NHW population and IPF occurs infrequently ( ⁇ 0.1%).
  • PrePF defined as chest HRCT consistent with probable or definite fibrosis (e.g., bilateral subpleural reticular changes, honeycombing, or traction bronchiectasis) occurring in asymptomatic subjects ⁇ 40 years of age that emerge from at-risk populations)
  • the MUC5B promoter variant is present in ⁇ 19% of the NHW population and IPF occurs infrequently ( ⁇ 0.1%).
  • PrePF preclinical pulmonary fibrosis
  • HRCT scans were performed on 496 asymptomatic family members ⁇ 40 years of age previously phenotyped as unaffected from 263 families with familial IPF.
  • PrePF consistent with the operational definition (defined as abnormalities on chest HRCT consistent with probable or definite fibrosis (e.g., bilateral subpleural reticular changes, honeycombing, or traction bronchiectasis) occurring in asymptomatic subjects ⁇ 40 years that emerge from at-risk populations), was present in 77 (15.5%) of 496 asymptomatic individuals from families with familial IPF.
  • Preliminary analysis of PBMC gene expression profiles evaluated by microarrays from 38 cases of PrePF and 187 subjects without fibrosis identified 16 genes significantly differentially expressed between the two groups (p-value ⁇ 0.05 and >1.5 fold change).
  • genes differentially expressed in PrePF are those involved in innate immunity and inflammatory responses (SIGLEC14), antibacterial effects (ADM2), growth and motility (TSPAN5), and protein phosyphorylation (CAMKK1).
  • PBMC gene expression appears to contribute to the ability to predict PrePF in an at-risk population ( FIG. 3 ).
  • RNA-sequencing analysis was performed on 40 PrePF subjects and 80 subjects with a normal HRCT scan. Sequencing of the polyA-enriched libraries was prepared using Illumina TrueSEQ reagents and multiplexing 10 samples on each lane of HiSEQ4000 to obtain on average 35-40 million reads per sample. This high coverage allows for the consideration of a broad dynamic range of mRNA transcripts for biomarker selection. Platform selection of serum and plasma samples from the same subjects are used for proteomic analysis.
  • a multivariable logistic regression model for PrePF with biomarkers and covariates is used for inclusion and a step-wise forward selection procedure is constructed. Variables stay in the model if associated at P ⁇ 0.01 after adjustment for the variables already in the model. Protein biomarkers that are significantly associated with established IPF and the top 20 differentially expressed genes in PrePF are considered for inclusion in a multivariable model. The number of potential biomarkers allowed in the joint model is restricted to approximately 20 given the number cases of PrePF expected. Secondarily, interactions between MUC5B genotype and the other biomarkers are tested for, which allow for the possibility that different biomarker profiles are diagnostic in IPF patients with/without the MUC5B risk allele.
  • the observed expression and other biomarker values from those associated with PrePF in the siblings of FIP patients is used to obtain the probability, for each sibling, having PrePF.
  • ROC receiver operating characteristic
  • Either the raw or standardized values, for a given model, is used to observe biomarker values in the PrePF siblings and non-PrePF siblings to obtain the probability of being in the disease group based on the model parameters developed using the FIP siblings.
  • the thresholds identified among the FIP siblings are used to classify each individual as predicted to have PrePF or not. This categorization allows for the calculation of the sensitivity, specificity, positive predictive value, and negative predictive value of the predictive model among the siblings of independent cases of IPF to that observed in the siblings of FIP cases.
  • Example 7 MUC5B Promoter Variant r35705950is a Risk Factor for Rheumatoid Arthritis—Interstitial Lung Disease
  • the discovery cohort included patients with RA, with and without ILD (RA-noILD) as assessed by chest HRCT, and controls, from the French RA-ILD network.
  • the multi-ethnic replication cohorts were obtained from six countries (China, Greece, Japan, Mexico, the Netherlands and United States). This included patients with RA-ILD and RA-noILD patients, and controls. All cases fulfilled the 2010 European League against Rheumatism-American College of Rheumatology (EULAR-ACR) and/or 1987 ACR revised criteria for RA.
  • EULAR-ACR European League against Rheumatism-American College of Rheumatology
  • the ILD status of patients with RA was established by chest HRCT images that were centrally reviewed by experienced readers for each participating cohort.
  • Genotyping of the MUC5B rs35705950 single nucleotide polymorphism involved use of Taqman Genotyping Assays (Applied Biosystems, Foster City, Calif., USA) as previously reported, by direct Sanger Sequencing or imputation from genome-wide association study data.
  • lung tissue was analyzed from nine patients with RA-ILD undergoing lung transplantation (University of California, San Francisco) compared to six unaffected controls with ILD (NHLBI Lung Tissue Research Consortium; https://ltrcpublic.com) or concordant expression of other relevant markers of pulmonary fibrosis.
  • the tissue was formalin fixed, paraffin embedded and cut in 4 um sections. Tissue sections were deparaffinized in xylene, followed by dehydration in series of ethanol. Following citrate buffer antigen retrieval, slides were incubated overnight with primary antibodies against MUC5B (1:4000, Santa Cruz, Dallas, Tex.). Secondary antibody diluted 1:1000 tagged with HRP (Life Technologies) was visualized using an Aperio CS2 slide scanner (Leica, Buffalo Grove, Ill.).
  • This case-control genetic study included 620 RA-ILD cases, 614 RA-noILD cases and 5448 unaffected controls.
  • the discovery cohort included 118 RA-ILD cases, 105 RAnoILD cases and 1229 unaffected controls.
  • the multi-ethnic replication sample included 502 RA-ILD, 509 RA-noILD cases and 4219 unaffected controls.
  • RA-ILD As compared with RA-noILD, patients with RA-ILD were more frequently male, older and more frequently smoked cigarettes (54.7% versus 36.1%) ( FIG. 13 ). However, after adjusting for sex, the relationship between RA-ILD and cigarette smoking was no longer statistically significant ( FIG. 13 ). After adjustment, RA-ILD and RA-noILD patients did not differ in rheumatoid factor (RF) and/or anti-citrullinated protein antibody (ACPA) positivity, erosive status of RA, exposure to methotrexate or the mean RA duration from diagnosis at inclusion in the cohort. Overall, 41% of patients with RA-ILD had a UIP or possible UIP HRCT pattern.
  • RF rheumatoid factor
  • ACPA anti-citrullinated protein antibody
  • RA-ILD lung tissue explants 5 GG and 4 GT
  • 6 unaffected controls 3 GG and 3 GT
  • RA-ILD lung tissue demonstrated MUC5B in the cytoplasm of the bronchioles and in areas of microscopic honeycombing, including staining of the metaplastic epithelia lining the honeycomb cysts and the mucous within the cyst ( FIG. 17 ).
  • the controls demonstrated MUC5B expression in the bronchioles only. There were no obvious differences in MUC5B expression by genotype.
  • Example 8 MUC5B Promoter Variant is Associated with Visually and Quantitatively Detected Preclinical Pulmonary Fibrosis
  • FIP Familial Interstitial Pneumonia
  • HRCT provides visualization of the lung parenchyma and plays a key role in the diagnosis of the Idiopathic Interstitial Pneumonias (IIPs), including IPF.
  • IIPs Idiopathic Interstitial Pneumonias
  • qHRCT Quantitative HRCT evaluation provides measures of fibrosis extent that, in subjects diagnosed with IPF, correlate with degree of physiologic impairment at baseline, and may be more sensitive to subtle changes in disease status than routinely used physiological metrics.
  • the design and utility of quantitative methods in the context of early forms of fibrotic ILD requires further study. Deep learning methods have been increasingly used in imaging to identify and classify CT patterns, and may be particularly valuable in detection of early lung fibrosis.
  • This study aims to: (1) examine risk factors, including two common fibrosis-associated genetic variants in MUC5B and TERT, for undiagnosed pulmonary fibrosis (PrePF) in FIP first-degree relatives; and (2) determine the utility of a deep learning, texture-based qHRCT method in the detection of early fibrosis in this cohort.
  • risk factors including two common fibrosis-associated genetic variants in MUC5B and TERT, for undiagnosed pulmonary fibrosis (PrePF) in FIP first-degree relatives.
  • non-Hispanic white (NHW) relatives of FIP patients defined as those in families with two or more cases of pulmonary fibrosis, were contacted for enrollment.
  • First-degree relatives without a known prior diagnosis of pulmonary fibrosis and greater than 40 years of age were offered HRCT scans of the chest and asked to undergo peripheral blood draw.
  • Study subjects younger than 40 years of age or older than 40 years of age who reported on pre-study questionnaires to be personally affected by pulmonary fibrosis were excluded ( FIG. 18 ).
  • PrePF was defined as the presence of “probable” or “definite” fibrotic ILD on HRCT in FIP relatives who had no known diagnosis of pulmonary fibrosis at the time of study enrollment ( FIGS. 18, 19 ).
  • 100 inspiratory volumetric HRCT of never-smoking control subjects from the COPDGene cohort were analyzed ( FIG. 20 ). The lungs were segmented in a semi-automatic fashion using open source software followed by manual editing, if necessary, performed by trained analysts.
  • FIG. 21 Examples of the categorization of different parts of CT scans are shown in FIG. 21 . Some studies were acquired with contiguous thin axial sections while others used 1 or 2 cm intervals. Also, reconstruction kernel, a parameter that affects image sharpness and noise, was not standardized.
  • Fibrosis quantification on CT scans was performed using a deep learning technique, with a convolutional neural network (CNN) algorithm trained with image regions of normal and abnormal lung identified by expert radiologists. Training data and an earlier algorithm version were described previously.
  • CNN convolutional neural network
  • Classification categories included normal lung, airways, reticular abnormality, honeycombing and ground glass.
  • pixels in the “not normal” category were split into two subcategories: “not normal” low density and “not normal” high density using the threshold value of ⁇ 650 Hounsfield Units (HU). Subject level scores were computed as the percentage of total lung volume classified in each category.
  • HRCT fibrosis score was defined as the sum of CNN classification scores for reticular abnormality, honeycombing, ground glass, and “not normal high density” ( FIG. 21 ).
  • % HAA Percent high attenuation area
  • fibrosis score Log of qHRCT fibrosis score (hereafter, “fibrosis score”) and log (% HAA) were compared with visual scores using ANOVA and Tukey's honest significant difference (HSD) test.
  • HSD Tukey's honest significant difference
  • ROC receiver-operating characteristic
  • Optimal threshold for discriminating visual diagnosis of fibrotic ILD was determined with Youden's method. Five-fold cross-validation was performed to test detection accuracy, sensitivity and specificity, and consistency of optimal threshold. Linear regression was performed to test association between the MUC5B genotype and qHRCT fibrosis score and log (% HAA).
  • a p-value of ⁇ 0.05 was considered statistically significant for differences between groups as well as for associations between individual variables and outcomes in linear and logistic regression modeling. Statistical analyses were performed using RStudio (Version 0.99.473).
  • the minor allele (T) frequency of the MUC5B promoter polymorphism rs35705950 was 0.22 in this cohort; 45% of the subjects in this cohort had one or two copies of the minor allele ( FIG. 22 ).
  • the minor allele (C) frequency of the TERT variant rs2736100 was 0.47 in the entire cohort; 69% of the subjects in the cohort having one or two copies of the minor allele ( FIG. 22 ).
  • PrePF Preclinical Pulmonary Fibrosis
  • ROC analysis showed that fibrosis score discriminates subjects with visual diagnosis of PrePF ( FIG. 25B ).
  • Average area under the curve (AUC) in five-fold cross validation was 0.85 (range 0.83-0.87) and average accuracy, sensitivity, and specificity in the test partitions were 0.83 (range 0.74-0.86), 0.74 (range 0.56-0.92), and 0.84 (range 0.76-0.89), respectively.
  • Optimal threshold for fibrosis score ranged from 1.40-1.42, corresponding to 4.1% fibrotic area in examined lung.
  • ROC analysis of log % HAA had lower mean AUC 0.80 (range 0.79-0.81) and average accuracy, sensitivity, and specificity of 0.67 (range 0.63-0.70), 0.82 (range 0.75-0.91) and 0.64 (range 0.62-0.70) respectively ( FIG. 25A ).
  • Optimal threshold for log % HAA ranged from 1.49-1.57. Utilizing a cutoff of 1.49 for log % HAA, the sensitivity was 88%, specificity was 55%, and accuracy was 60%; the negative predictive value of this test was 96%, exceeding its positive predictive value (26%).
  • each score component was tested individually for association with the MUC5B variant, controlling for age and sex.

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