WO2023012318A1 - Polypeptides variants bmp9 et leurs utilisations - Google Patents

Polypeptides variants bmp9 et leurs utilisations Download PDF

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Publication number
WO2023012318A1
WO2023012318A1 PCT/EP2022/072038 EP2022072038W WO2023012318A1 WO 2023012318 A1 WO2023012318 A1 WO 2023012318A1 EP 2022072038 W EP2022072038 W EP 2022072038W WO 2023012318 A1 WO2023012318 A1 WO 2023012318A1
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amino acid
bmp9
substitution
isolated
mutant polypeptide
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PCT/EP2022/072038
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English (en)
Inventor
Jinquan Luo
Karl Walter KAVALKOVICH
Tobias Gebhard SCHIPS
Annmarie WINKIS
Julien HÄSLER
Jey Raju Jeyaseelan
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Actelion Pharmaceuticals Ltd
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Publication of WO2023012318A1 publication Critical patent/WO2023012318A1/fr

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/475—Growth factors; Growth regulators
    • C07K14/51—Bone morphogenetic factor; Osteogenins; Osteogenic factor; Bone-inducing factor

Definitions

  • This invention relates to isolated BMP9 and pro-BMP9 mutant polypeptides, nucleic acids and expression vectors encoding the antibodies, recombinant cells containing the vectors, and compositions comprising the isolated BMP9 and pro-BMP9 mutant polypeptides.
  • Methods of making the isolated BMP9 and pro-BMP9 mutant polypeptides, and methods of using the isolated BMP9 and pro-BMP9 mutant polypeptides to treat vascular and/or respiratory diseases in a subject in need thereof, including pulmonary arterial hypertension (PAH) and/or associated complications, are also provided.
  • PAH pulmonary arterial hypertension
  • Bone morphogenetic protein-9 also known as growth differentiation factor 2 (GDF2) or hereditary hemorrhagic telangiectasia 5 (HHT5), is a polypeptide in humans encoded by the BMP9 gene (GDF2 gene).
  • BMP9 belongs to the transforming growth factor beta (TGF- ⁇ ) superfamily, and contains an amino-terminal TGF-0 like propeptide (or prodomain; from residues 23-319) and a carboxy-terminal TGF-0 superfamily domain (or growth factor domain; from residues 320-429). BMP9 also contains a signal peptide at residues 1-22.
  • BMP9 is synthesized as a pre-pro-protein that undergoes successive proteolytic processing to cleave the signal peptide and the propeptide to produce the mature growth factor domain.
  • BMP9 is usually present as a noncovalent complex of the growth factor domain with the prodomain.
  • the noncovalent complex of the prodomain and growth factor domain is termed ‘pro-BMP9’.
  • BMP9 acts selectively on vascular endothelial cells, inhibiting endothelial cell apoptosis, migration, and angiogenesis. Additionally, BMP9 is one of the most potent BMPs for inducing orthotopic bone formation in vivo.
  • BMP signaling can cause endothelial dysfunction, which can play a role in vascular and respiratory diseases (e.g., pulmonary arterial hypertension (PAH)).
  • PHA pulmonary arterial hypertension
  • BMPR2 BMP receptor type II
  • BMP9 BMP9 modulates endothelial cell signaling
  • PAH pulmonary arterial hypertension
  • BMPR2 BMP receptor type II
  • ALK-1 ALK-1
  • type III receptor accessory protein, endoglin have been shown in patients with PAH. It has been shown that rescue of BMPR2 endothelial signaling or enhancement of endothelial BMPR2 with BMP9 can reverse the effects of pulmonary arterial hypertension.
  • SMAD1 is usually expressed at higher levels in endothelial cells relative to SMAD5 or SMAD8, so BMP9 signaling in endothelial cells may be predominantly activated through pSMAD 1.
  • BMP9 can act on Alk-l/ActRIIa and Alk-l/ActRIIb heterotetrameric type I and type II receptor complexes in osteogenic cell types to promote bone formation
  • overexpression of BMP9 to enhance or induce endothelial BMPR2 could lead to unwanted bone formation in vivo.
  • BMP9 polypeptides comprising endothelial cell signaling activity without having osteogenic activity would be useful for the treatment of vascular and/or respiratory diseases resulting from dysregulated BMPR2/ALK-1 /endoglin signaling, as enhanced or increased endothelial cell signaling can treat the disease without any unwanted side effects (e.g., bone formation) from enhanced or increased osteogenic activity.
  • the invention relates to isolated BMP9 and pro-BMP9 mutant polypeptides.
  • the isolated BMP9 mutant polypeptides of the invention refer to a mutant polypeptide comprising the growth factor domain of BMP9.
  • An isolated pro-BMP9 mutant polypeptide of the invention refers to the prodomain-bound form of BMP9, which is a noncovalent complex of a polypeptide of the prodomain of BMP9 with a polypeptide of the growth factor domain.
  • Amino acid residue numbering used throughout this specification corresponds to amino acid positions in the sequence of SEQ ID NO: 1, which is a wild type BMP9 sequence that lacks any mutations.
  • SEQ ID NO: 29 which represents the sequence of the growth factor domain of BMP is therefore composed of the amino acids at positions 320-429 of SEQ ID NO: 1, and thus mutations to SEQ ID NO: 29 are referred to by their position in SEQ ID NO: 1.
  • isolated BMP9 mutant polypeptides wherein the isolated BMP9 mutant polypeptide comprises endothelial cell signaling activity through pSMAD 1/5/8 and reduced or eliminated osteogenic activity, and wherein the isolated BMP9 mutant polypeptide comprises an amino acid sequence having at least 98% sequence identity with the amino acid sequence of SEQ ID NO: 29.
  • isolated BMP9 mutant polypeptides wherein the isolated BMP9 mutant polypeptide comprises endothelial cell signaling activity through pSMAD 1 and reduced or eliminated osteogenic activity, and wherein the isolated BMP9 mutant polypeptide comprises an amino acid sequence having at least 98% sequence identity with the amino acid sequence of SEQ ID NO: 29.
  • the isolated mutant BMP9 polypeptide is in the form of a homodimer.
  • isolated pro-BMP9 mutant polypeptides wherein the isolated pro-BMP9 mutant polypeptide comprises endothelial cell signaling activity through pSMADl/5/8 and reduced or eliminated osteogenic activity, and wherein the isolated pro-BMP9 mutant polypeptide comprises a growth factor domain comprising an amino acid sequence having at least 98% sequence identity with the amino acid sequence of SEQ ID NO: 29.
  • isolated pro-BMP9 mutant polypeptides wherein the isolated pro-BMP9 mutant polypeptide comprises endothelial cell signaling activity through pSMAD 1 and reduced or eliminated osteogenic activity, and wherein the isolated pro-BMP9 mutant polypeptide comprises a growth factor domain comprising an amino acid sequence having at least 98% sequence identity with the amino acid sequence of SEQ ID NO: 29.
  • the isolated mutant pro-BMP9 polypeptide is in the form of a homodimer.
  • a homodimer of pro-BMP9 is composed of four subunits - two prodomains and two growth factor domains.
  • the isolated BMP9 mutant polypeptide comprises at least one amino acid substitution at an amino acid position selected from 333, 346, 347, 401, 402, 408, 412, 416, and 418. In some embodiments the isolated BMP9 mutant polypeptide comprises at least one amino acid substitution at an amino acid position selected from 346 and 347. In one embodiment the isolated BMP9 mutant polypeptide comprises an amino acid substitution at amino acid position 346. In another embodiment the isolated BMP9 mutant polypeptide comprises an amino acid substitution at amino acid position 347. In some instances, the isolated mutant BMP9 polypeptide is in the form of a homodimer.
  • the isolated pro-BMP9 mutant polypeptide comprises at least one amino acid substitution at an amino acid position selected from 333, 346, 347, 401, 402, 408, 412, 416, and 418. In some embodiments the isolated pro-BMP9 mutant polypeptide comprises at least one amino acid substitution at an amino acid position selected from 346 and 347. In one embodiment the isolated pro-BMP9 mutant polypeptide comprises an amino acid substitution at amino acid position 346. In another embodiment the isolated pro-BMP9 mutant polypeptide comprises an amino acid substitution at amino acid position 347. In some instances, the isolated mutant pro-BMP9 polypeptide is in the form of a homodimer.
  • the isolated BMP9 mutant polypeptide comprises at least one amino acid substitution at one of the following amino acid positions: a) amino acid position 333, wherein the amino acid substitution is selected from an R333 A or R333N substitution; b) amino acid position 346, wherein the amino acid substitution is selected from an I346W or I346F substitution; c) amino acid position 347, wherein the amino acid substitution is selected from an A347R, A347M, A347Q, A347K or A347E substitution; d) amino acid position 401, wherein the amino acid substitution is an I401L substitution; e) amino acid position 402, wherein the amino acid substitution is selected from an S402M, S402I or S402H substitution; f) amino acid position 408, wherein the amino acid substitution is a D408I substitution; g) amino acid position 412, wherein the amino acid substitution is selected from a P412Y, P412W, P412L, P412H
  • the isolated mutant BMP9 polypeptide is in the form of a homodimer.
  • the isolated pro-BMP9 mutant polypeptide comprises at least one amino acid substitution at one of the following amino acid positions: a) amino acid position 333, wherein the amino acid substitution is selected from an R333 A or R333N substitution; b) amino acid position 346, wherein the amino acid substitution is selected from an I346W or I346F substitution; c) amino acid position 347, wherein the amino acid substitution is selected from an A347R, A347M, A347Q, A347K or A347E substitution; d) amino acid position 401, wherein the amino acid substitution is an I401L substitution; e) amino acid position 402, wherein the amino acid substitution is selected from an S402M, S402I or S402H substitution; f) amino acid position 408, wherein the amino acid substitution is a D408I substitution; g) amino acid position 412, wherein the amino acid substitution is selected from a P412Y, P412W, P412L, P4
  • the isolated BMP9 mutant polypeptide comprises at least one amino acid substitution at one of the following amino acid positions: a) amino acid position 346, wherein the amino acid substitution is selected from an I346W or I346F substitution; b) amino acid position 347, wherein the amino acid substitution is selected from an A347R, A347M, A347Q, A347K or A347E substitution; c) amino acid position 401, wherein the amino acid substitution is an 140 IL substitution; d) amino acid position 402, wherein the amino acid substitution is selected from an S402M, S402I or S402H substitution; e) amino acid position 408, wherein the amino acid substitution is a D408I substitution; f) amino acid position 412, wherein the amino acid substitution is a P412H substitution; g) amino acid position 416, wherein the amino acid substitution is selected from a Y416R, Y416P or Y416N substitution; and/or
  • the isolated mutant BMP9 polypeptide is in the form of a homodimer.
  • the isolated pro-BMP9 mutant polypeptide comprises at least one amino acid substitution at one of the following amino acid positions: a) amino acid position 346, wherein the amino acid substitution is selected from an I346W or I346F substitution; b) amino acid position 347, wherein the amino acid substitution is selected from an A347R, A347M, A347Q, A347K or A347E substitution; c) amino acid position 401, wherein the amino acid substitution is an I401L substitution; d) amino acid position 402, wherein the amino acid substitution is selected from an S402M, S402I or S402H substitution; e) amino acid position 408, wherein the amino acid substitution is a D408I substitution; f) amino acid position 412, wherein the amino acid substitution is a P412H substitution; g) amino acid position 416, wherein the amino acid substitution is selected from a Y416R, Y416P or Y416N substitution; and/
  • the isolated BMP9 mutant polypeptide comprises at least one amino acid substitution at one of the following amino acid positions: a) amino acid position 346, wherein the amino acid substitution is an I346F or I346W substitution; b) amino acid position 347, wherein the amino acid substitution is selected from an A347Q or A347E substitution; c) amino acid position 401, wherein the amino acid substitution is an I401L substitution; d) amino acid position 402, wherein the amino acid substitution is an S402I substitution; e) amino acid position 408, wherein the amino acid substitution is a D408I substitution; f) amino acid position 416, wherein the amino acid substitution is a Y416N substitution; and/or g) amino acid position 418, wherein the amino acid substitution is a Y418I substitution.
  • the isolated mutant BMP9 polypeptide is in the form of a homodimer.
  • the isolated pro-BMP9 mutant polypeptide comprises at least one amino acid substitution at one of the following amino acid positions: a) amino acid position 346, wherein the amino acid substitution is an I346F or I346W substitution; b) amino acid position 347, wherein the amino acid substitution is selected from an A347Q or A347E substitution; c) amino acid position 401, wherein the amino acid substitution is an 140 IL substitution; d) amino acid position 402, wherein the amino acid substitution is an S402I substitution; e) amino acid position 408, wherein the amino acid substitution is a D408I substitution; f) amino acid position 416, wherein the amino acid substitution is a Y416N substitution; and/or g) amino acid position 418, wherein the amino acid substitution is a Y418I substitution.
  • the isolated BMP9 mutant polypeptide comprises at least one amino acid substitution at one of the following amino acid positions: a) amino acid position 346, wherein the amino acid substitution is an I346W substitution; and/or b) amino acid position 347, wherein the amino acid substitution is selected from an A347Q or A347E substitution.
  • the isolated mutant BMP9 polypeptide is in the form of a homodimer.
  • the isolated BMP9 mutant polypeptide comprises an I346W substitution. In another embodiment, the isolated BMP9 mutant polypeptide comprises an A347Q substitution. In another embodiment, the isolated BMP9 mutant polypeptide comprises an A347E substitution. In some instances, the isolated mutant BMP9 polypeptide is in the form of a homodimer.
  • the isolated pro-BMP9 mutant polypeptide comprises at least one amino acid substitution at one of the following amino acid positions: a) amino acid position 346, wherein the amino acid substitution is an I346W substitution; and/or b) amino acid position 347, wherein the amino acid substitution is selected from an A347Q or A347E substitution.
  • the isolated pro-BMP9 mutant polypeptide comprises an I346W substitution. In another embodiment, the isolated pro-BMP9 mutant polypeptide comprises an A347Q substitution. In another embodiment, the isolated pro-BMP9 mutant polypeptide comprises an A347E substitution. [0020] In certain embodiments, the isolated BMP9 mutant polypeptide amino acid sequence is selected from one of SEQ ID NOs: 30-54. In an embodiment, the amino acid sequence of the isolated BMP9 mutant polypeptide is SEQ ID NO: 32. In an embodiment, the amino acid sequence of the isolated BMP9 mutant polypeptide is SEQ ID NO: 36. In an embodiment, the amino acid sequence of the isolated BMP9 mutant polypeptide is SEQ ID NO: 38. In some instances, the isolated mutant BMP9 polypeptide is in the form of a homodimer.
  • the isolated pro-BMP9 mutant polypeptide is a noncovalent complex of a polypeptide having the amino acid sequence of SEQ ID NO: 55 and a polypeptide having an amino acid sequence selected from one of SEQ ID NOs: 30-54.
  • the isolated pro-BMP9 mutant polypeptide is a noncovalent complex of a polypeptide having the amino acid sequence of SEQ ID NO: 55 and a polypeptide having an amino acid sequence of SEQ ID NO: 32.
  • the isolated pro-BMP9 mutant polypeptide is a noncovalent complex of a polypeptide having the amino acid sequence of SEQ ID NO: 55 and a polypeptide having an amino acid sequence of SEQ ID NO: 36.
  • the isolated pro-BMP9 mutant polypeptide is a noncovalent complex of a polypeptide having the amino acid sequence of SEQ ID NO: 55 and a polypeptide having an amino acid sequence of SEQ ID NO: 38.
  • isolated nucleic acids encoding the isolated BMP9 mutant polypeptides of the invention. Also provided are isolated nucleic acids encoding the isolated pro-BMP9 mutant polypeptides of the invention.
  • vectors comprising the isolated nucleic acids encoding the isolated BMP9 mutant polypeptides of the invention. Also provided are vectors comprising the isolated nucleic acids encoding the isolated pro-BMP9 mutant polypeptides of the invention.
  • host cells comprising the vectors comprising the isolated nucleic acids encoding the isolated BMP9 mutant polypeptides of the invention. Also provided are host cells comprising the vectors comprising the isolated nucleic acids encoding the isolated pro-BMP9 mutant polypeptides of the invention. [0025] In certain embodiments, provided is a pharmaceutical composition comprising an isolated BMP9 mutant polypeptide of the invention and a pharmaceutically acceptable carrier. In certain other embodiments, provided is a pharmaceutical composition comprising an isolated pro-BMP9 mutant polypeptide of the invention and a pharmaceutically acceptable carrier.
  • vascular disease can, for example, be selected from the group consisting of pulmonary hypertension (PH), pulmonary arterial hypertension (PAH), idiopathic pulmonary fibrosis (IPF), pulmonary venous occlusive disease (PVOD), hereditary haemorrhagic telangiectasia, atherosclerosis, and hepatopulmonary syndrome.
  • PH pulmonary hypertension
  • PAH pulmonary arterial hypertension
  • IPF idiopathic pulmonary fibrosis
  • PVOD pulmonary venous occlusive disease
  • hereditary haemorrhagic telangiectasia atherosclerosis
  • atherosclerosis and hepatopulmonary syndrome
  • hepatopulmonary syndrome hereditary haemorrhagic telangiectasia
  • a respiratory disease in a subject in need thereof, the method comprising administering to the subject the pharmaceutical compositions of the invention.
  • the respiratory disease can, for example, be selected from the group consisting of an obstructive lung disease, a pulmonary vascular disease, a respiratory failure or respiratory distress syndrome, an acute respiratory disease syndrome (ARDS), COVID19, and an interstitial lung disease (ILD).
  • ARDS acute respiratory disease syndrome
  • COVID19 COVID19
  • ILD interstitial lung disease
  • Also provided are methods of producing an isolated BMP9 mutant polypeptide of the invention comprising culturing a cell comprising a nucleic acid encoding the BMP9 mutant polypeptide under conditions to produce the BMP9 mutant polypeptide, and recovering the BMP9 mutant polypeptide from the cell or culture. Also provided are methods of producing an isolated pro-BMP9 mutant polypeptide of the invention, comprising culturing a cell comprising a nucleic acid encoding the pro-BMP9 mutant polypeptide under conditions to produce the pro-BMP9 mutant polypeptide, and recovering the pro-BMP9 mutant polypeptide from the cell or culture.
  • FIG. 1 shows a schematic of a structural comparison.
  • (Left) BMPR2 structure (gray) is superimposed on ActRIIb (black) in the ribbons representation.
  • (Right) An expanded view of the ActRIIb and BMP9 binding interface with several interface residues, as well as the corresponding BMPR2 residues, shown in stick models (W60, K56, F83 on ActRIIb side).
  • FIG. 2 shows a schematic of a core BMP9 epitope and deduced epitope regions (view from ActRIIb).
  • the core epitope is shown in black and the gray areas around the “core epitope” indicate likely residues that are involved in differential binding to ActRIIb and BMPR2.
  • FIG. 3 shows a schematic of a BMP9 sequence (SEQ ID NO: 27) with selected positions (gray highlighted) for mutational analysis.
  • the numbers above the sequence indicate positional number starting with the initiation Met in the pre-pro-form.
  • Double underlined residues are core BMP9 epitope residues that interact with both ActRIIb and BMPR2.
  • FIG. 4 shows a graph demonstrating expression and purification of BMP9 mutant polypeptides.
  • FIG. 5 shows a graph demonstrating pSMADl and pSMAD3 activity of BMP9 mutant polypeptides.
  • FIG. 6 shows a chart demonstrating alkaline phosphatase activation by BMP9 mutant polypeptides.
  • FIG. 7 shows a graph demonstrating alkaline phosphatase activity of BMP9 mutant polypeptides.
  • FIG. 8 shows graphs demonstrating pSMADl (left) and pSMAD3 (right) activity of BMP9 mutant polypeptides harboring a reduced alkaline phosphatase activity.
  • FIG. 9 shows a schematic of potentially non-osteogenic BMP9 point mutations.
  • FIGs. 10A-10B show the osteogenic potential of BMP9 mutant polypeptides.
  • FIG. 10A shows a graph demonstrating the osteogenic potential of BMP9 mutant polypeptides R333A, P412F, and P412L.
  • FIG. 10A shows a graph demonstrating the osteogenic potential of BMP9 mutant polypeptides R333A, P412F, and P412L.
  • 10B shows a graph demonstrating the osteogenic potential of BMP9 mutant polypeptides I346F, I346W, A347E, A347Q, I401L, S402I, D408I, Y416N and Y418I.
  • any numerical values such as a concentration or a concentration range described herein, are to be understood as being modified in all instances by the term “about.”
  • a numerical value typically includes ⁇ 10% of the recited value.
  • a concentration of 1 mg/mL includes 0.9 mg/mL to 1.1 mg/mL.
  • a concentration range of 1% to 10% (w/v) includes 0.9% (w/v) to 11% (w/v).
  • the use of a numerical range expressly includes all possible subranges, all individual numerical values within that range, including integers within such ranges and fractions of the values unless the context clearly indicates otherwise.
  • the terms “comprises”, “comprising”, “includes”, “including”, “has”, “having”, “contains” or “containing”, or any other variation thereof, will be understood to imply the inclusion of a stated integer or group of integers but not the exclusion of any other integer or group of integers and are intended to be non-exclusive or open-ended.
  • a composition, a mixture, a process, a method, an article or an apparatus that comprises a list of elements is not necessarily limited to only those elements but can include other elements not expressly listed or inherent to such composition, mixture, process, method, article or apparatus.
  • “or” refers to an inclusive or and not to an exclusive or. For example, a condition A or B is satisfied by any one of the following: A is true (or present) and B is false (or not present), A is false (or not present) and B is true (or present), and both A and B are true (or present).
  • the conjunctive term “and/or” between multiple recited elements is understood as encompassing both individual and combined options. For instance, where two elements are conjoined by “and/or”, a first option refers to the applicability of the first element without the second. A second option refers to the applicability of the second element without the first. A third option refers to the applicability of the first and second elements together. Any one of these options is understood to fall within the meaning, and therefore satisfy the requirement of the term “and/or” as used herein. Concurrent applicability of more than one of the options is also understood to fall within the meaning, and therefore satisfy the requirement of the term “and/or”.
  • subject means any animal, preferably a mammal, most preferably a human.
  • mammal encompasses any mammal. Examples of mammals include, but are not limited to, cows, horses, sheep, pigs, cats, dogs, mice, rats, rabbits, guinea pigs, monkeys, humans, etc., more preferably a human.
  • the words “right”, “left”, “lower” and “upper” designate directions in the drawings to which reference is made.
  • nucleic acids or polypeptide sequences e.g., BMP9 mutant polypeptides and polynucleotides that encode them
  • sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same, when compared and aligned for maximum correspondence, as measured using one of the following sequence comparison algorithms or by visual inspection.
  • sequence comparison typically one sequence acts as a reference sequence, to which test sequences are compared.
  • test and reference sequences are input into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated.
  • sequence comparison algorithm then calculates the percent sequence identity for the test sequence(s) relative to the reference sequence, based on the designated program parameters.
  • Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Nat’l. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, WI), or by visual inspection (see generally, Current Protocols in Molecular Biology, F.M. Ausubel et al., eds., Current Protocols, a joint venture between Greene Publishing Associates, Inc. and John Wiley & Sons, Inc., (1995 Supplement) (Ausubel)).
  • BLAST and BLAST 2.0 algorithms are described in Altschul et al. (1990) J. Mol. Biol. 215: 403-410 and Altschul et al. (1997) Nucleic Acids Res. 25: 3389-3402, respectively.
  • Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information.
  • This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al, supra).
  • HSPs high scoring sequence pairs
  • T is referred to as the neighborhood word score threshold (Altschul et al, supra).
  • These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them.
  • the word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased.
  • Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always > 0) and N (penalty score for mismatching residues; always ⁇ 0).
  • M forward score for a pair of matching residues; always > 0
  • N penalty score for mismatching residues; always ⁇ 0.
  • a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached.
  • the BLAST algorithm parameters W, T and X determine the sensitivity and speed of the alignment.
  • the BLASTP program uses as defaults a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad. Sci. USA 89:10915 (1989)).
  • the BLAST algorithm In addition to calculating percent sequence identity, the BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul, Proc. Nat’l. Acad. Sci. USA 90:5873-5787 (1993)).
  • One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance.
  • a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.1, more preferably less than about 0.01, and most preferably less than about 0.001.
  • a further indication that two nucleic acid sequences or polypeptides are substantially identical is that the polypeptide encoded by the first nucleic acid is immunologically cross reactive with the polypeptide encoded by the second nucleic acid, as described below.
  • a polypeptide is typically substantially identical to a second polypeptide, for example, where the two peptides differ only by conservative substitutions.
  • Another indication that two nucleic acid sequences are substantially identical is that the two molecules hybridize to each other under stringent conditions.
  • isolated means a biological component (such as a nucleic acid, peptide or protein) has been substantially separated, produced apart from, or purified away from other biological components of the organism in which the component naturally occurs, i.e., other chromosomal and extrachromosomal DNA and RNA, and proteins.
  • Nucleic acids, peptides and proteins that have been “isolated” thus include nucleic acids and proteins purified by standard purification methods.
  • isolated nucleic acids, peptides and proteins can be part of a composition and still be isolated if the composition is not part of the native environment of the nucleic acid, peptide, or protein.
  • the term also embraces nucleic acids, peptides and proteins prepared by recombinant expression in a host cell as well as chemically synthesized nucleic acids.
  • polynucleotide synonymously referred to as “nucleic acid molecule”, “nucleotides” or “nucleic acids”, refers to any polyribonucleotide or polydeoxyribonucleotide, which can be unmodified RNA or DNA or modified RNA or DNA.
  • Polynucleotides include, without limitation single- and double-stranded DNA, DNA that is a mixture of single- and double-stranded regions, single- and doublestranded RNA, and RNA that is mixture of single- and double-stranded regions, hybrid molecules comprising DNA and RNA that can be single-stranded or, more typically, double-stranded or a mixture of single- and double-stranded regions.
  • polynucleotide refers to triple-stranded regions comprising RNA or DNA or both RNA and DNA.
  • the term polynucleotide also includes DNAs or RNAs containing one or more modified bases and DNAs or RNAs with backbones modified for stability or for other reasons.
  • Modified bases include, for example, tritylated bases and unusual bases such as inosine.
  • polynucleotide embraces chemically, enzymatically or metabolically modified forms of polynucleotides as typically found in nature, as well as the chemical forms of DNA and RNA characteristic of viruses and cells.
  • Polynucleotide also embraces relatively short nucleic acid chains, often referred to as oligonucleotides.
  • vector is a replicon in which another nucleic acid segment can be operably inserted so as to bring about the replication or expression of the segment.
  • the term “host cell” refers to a cell comprising a nucleic acid molecule of the invention.
  • the “host cell” can be any type of cell, e.g., a primary cell, a cell in culture, or a cell from a cell line.
  • a “host cell” is a cell transfected or transduced with a nucleic acid molecule of the invention.
  • a “host cell” is a progeny or potential progeny of such a transfected or transduced cell.
  • a progeny of a cell may or may not be identical to the parent cell, e.g., due to mutations or environmental influences that can occur in succeeding generations or integration of the nucleic acid molecule into the host cell genome.
  • the term “expression” as used herein, refers to the biosynthesis of a gene product.
  • the term encompasses the transcription of a gene into RNA.
  • the term also encompasses translation of RNA into one or more polypeptides, and further encompasses all naturally occurring post-transcriptional and post-translational modifications.
  • the expressed polypeptide can be within the cytoplasm of a host cell, into the extracellular milieu such as the growth medium of a cell culture or anchored to the cell membrane.
  • the peptide sequences described herein are written according to the usual convention whereby the N-terminal region of the peptide is on the left and the C-terminal region is on the right. Although isomeric forms of the amino acids are known, it is the L- form of the amino acid that is represented unless otherwise expressly indicated.
  • the term “reduced osteogenic activity”, when used in reference to the mutant BMP9 polypeptides, means that the mutant BMP9 polypeptides have less osteogenic activity as compared to the wild type BMP9 polypeptide, e.g., a wild type BMP9 polypeptide comprising the amino acid sequence of SEQ ID NO: 29 or the parent BMP9 polypeptide from which the isolated mutant BMP9 polypeptide was made.
  • the term “reduced osteogenic activity”, when used in reference to the mutant pro-BMP9 polypeptides, means that the mutant pro-BMP9 polypeptides have less osteogenic activity as compared to the wild type pro-BMP9 polypeptide, e.g., a wild type BMP9 polypeptide comprising the amino acid sequence of SEQ ID NO: 29 or the parent pro-BMP9 polypeptide from which the isolated mutant pro-BMP9 polypeptide was made.
  • the term “eliminated osteogenic activity”, when used in reference to the mutant BMP9 polypeptides, means that the mutant BMP9 polypeptides do not have any osteogenic activity, or are incapable of activating any pathways leading to osteogenic activity in a cell.
  • the term “eliminated osteogenic activity”, when used in reference to the mutant pro-BMP9 polypeptides, means that the mutant pro-BMP9 polypeptides do not have any osteogenic activity, or are incapable of activating any pathways leading to osteogenic activity in a cell. Osteogenic activity can be measured by alkaline phosphatase (ALP) activity and/or by osteogenic marker gene expression (e.g., SP7 or alkaline phosphatase), as indicated herein.
  • ALP alkaline phosphatase
  • osteogenic marker gene expression e.g., SP7 or alkaline phosphatase
  • the invention generally relates to isolated BMP9 or pro-BMP9 mutant polypeptides, nucleic acids and expression vectors encoding the isolated BMP9 or pro-BMP9 mutant polypeptides, recombinant cells containing the vectors, and compositions comprising the isolated BMP9 or pro-BMP9 mutant polypeptides.
  • PAH pulmonary arterial hypertension
  • the isolated BMP9 or pro-BMP9 mutant polypeptides of the invention possess one or more desirable functional properties, including but not limited to activating endothelial cell signaling activity through pSMADl, pSMAD5, and/or pSMAD8, reduced or eliminated osteogenic activity, reduced or eliminated pSMAD3 activity, increased expression levels, increased stability (i.e., increased in vitro or in vivo stability), increased ability to purify, and/or increased ability to produce.
  • the invention relates to isolated BMP9 mutant polypeptides, wherein the isolated BMP9 mutant polypeptide comprises endothelial cell signaling activity through pSMADl/5/8 and reduced or eliminated osteogenic cell signaling activity, and wherein the isolated BMP9 mutant polypeptide comprises an amino acid sequence having at least 98% sequence identity with the amino acid sequence of SEQ ID NO: 29.
  • the isolated mutant BMP9 polypeptide is in the form of a homodimer.
  • isolated pro-BMP9 mutant polypeptides wherein the isolated pro-BMP9 mutant polypeptide comprises endothelial cell signaling activity through pSMADl/5/8 and reduced or eliminated osteogenic activity, and wherein the isolated pro-BMP9 mutant polypeptide comprises a growth factor domain comprising an amino acid sequence having at least 98% sequence identity with the amino acid sequence of SEQ ID NO: 29.
  • the isolated mutant pro-BMP9 polypeptide is in the form of a homodimer.
  • a homodimer of pro-BMP9 is composed of four subunits i.e. two prodomains and two growth factor domains.
  • the isolated BMP9 mutant polypeptide comprises at least one amino acid substitution at an amino acid position selected from 333, 346, 347, 401, 402, 408, 412, 416, or 418.
  • the isolated BMP9 mutant polypeptide can have one, two, three, four, five, six, seven, eight, nine, or ten amino acid substitutions at an amino acid position selected from 333, 346, 347, 401, 402, 408, 412, 416, or 418.
  • the isolated BMP9 mutant polypeptide comprises at least one amino acid substitution at an amino acid position selected from 346 and 347.
  • the isolated BMP9 mutant polypeptide comprises an amino acid substitution at amino acid position 346.
  • the isolated BMP9 mutant polypeptide comprises an amino acid substitution at amino acid position 347.
  • the isolated mutant BMP9 polypeptide is in the form of a homodimer.
  • the isolated pro-BMP9 mutant polypeptide comprises at least one amino acid substitution at an amino acid position selected from 333, 346, 347, 401, 402, 408, 412, 416, and 418.
  • the isolated pro-BMP9 mutant polypeptide can have one, two, three, four, five, six, seven, eight, nine, or ten amino acid substitutions at an amino acid position selected from 333, 346, 347, 401, 402, 408, 412, 416, or 418.
  • the isolated pro-BMP9 mutant polypeptide comprises at least one amino acid substitution at an amino acid position selected from 346 and 347.
  • the isolated pro-BMP9 mutant polypeptide comprises an amino acid substitution at amino acid position 346.
  • the isolated pro-BMP9 mutant polypeptide comprises an amino acid substitution at amino acid position 347.
  • the amino acid substitution can be a R333A, R333N, I346W, I346F, A347R, A347M, A347Q, A347K, A347E, I401L, S402M, S402I, S402H, D408I, P412Y, P412W, P412L, P412H, P412F, Y416R, Y416P, Y416N, Y418V, Y418L, or Y418I substitution, or any combination thereof.
  • the amino acid substitution is an I346W substitution.
  • the amino acid substitution is an A347Q substitution.
  • the amino acid substitution is an A347E substitution.
  • the isolated BMP9 mutant polypeptide comprises at least one amino acid substitution at one of the following amino acid positions: a) amino acid position 333, wherein the amino acid substitution is selected from an R333 A or R333N substitution; b) amino acid position 346, wherein the amino acid substitution is selected from an I346W or I346F substitution; c) amino acid position 347, wherein the amino acid substitution is selected from an A347R, A347M, A347Q, A347K or A347E substitution; d) amino acid position 401, wherein the amino acid substitution is an I401L substitution; e) amino acid position 402, wherein the amino acid substitution is selected from an S402M, S402I or S402H substitution; f) amino acid position 408, wherein the amino acid substitution is a D408I substitution; g) amino acid position 412, wherein the amino acid substitution is selected from a P412Y, P412W, P412L, P412H or
  • the isolated mutant BMP9 polypeptide is in the form of a homodimer.
  • the isolated pro-BMP9 mutant polypeptide comprises at least one amino acid substitution at one of the following amino acid positions: a) amino acid position 333, wherein the amino acid substitution is selected from an R333 A or R333N substitution; b) amino acid position 346, wherein the amino acid substitution is selected from an I346W or I346F substitution; c) amino acid position 347, wherein the amino acid substitution is selected from an A347R, A347M, A347Q, A347K or A347E substitution; d) amino acid position 401, wherein the amino acid substitution is an I401L substitution; e) amino acid position 402, wherein the amino acid substitution is selected from an S402M, S402I or S402H substitution; f) amino acid position 408, wherein the amino acid substitution is a D408I substitution; g) amino acid position 412, wherein the amino acid substitution is selected from a P412Y, P412W, P412L, P412
  • the isolated BMP9 mutant polypeptide comprises at least one amino acid substitution at one of the following amino acid positions: a) amino acid position 346, wherein the amino acid substitution is selected from an I346W or I346F substitution; b) amino acid position 347, wherein the amino acid substitution is selected from an A347R, A347M, A347Q, A347K or A347E substitution; c) amino acid position 401, wherein the amino acid substitution is an I401L substitution; d) amino acid position 402, wherein the amino acid substitution is selected from an S402M, S402I or S402H substitution; e) amino acid position 408, wherein the amino acid substitution is a D408I substitution; f) amino acid position 412, wherein the amino acid substitution is a P412H substitution; g) amino acid position 416, wherein the amino acid substitution is selected from a Y416R, Y416P or Y416N substitution; and/or h
  • the isolated mutant BMP9 polypeptide is in the form of a homodimer.
  • the isolated pro-BMP9 mutant polypeptide comprises at least one amino acid substitution at one of the following amino acid positions: a) amino acid position 346, wherein the amino acid substitution is selected from an I346W or I346F substitution; b) amino acid position 347, wherein the amino acid substitution is selected from an A347R, A347M, A347Q, A347K or A347E substitution; c) amino acid position 401, wherein the amino acid substitution is an 140 IL substitution; d) amino acid position 402, wherein the amino acid substitution is selected from an S402M, S402I or S402H substitution; e) amino acid position 408, wherein the amino acid substitution is a D408I substitution; f) amino acid position 412, wherein the amino acid substitution is a P412H substitution; g) amino acid position 416, wherein the amino acid substitution is selected from a Y416R, Y416P or Y416N substitution; and/or
  • the isolated BMP9 mutant polypeptide comprises at least one amino acid substitution at one of the following amino acid positions: a) amino acid position 346, wherein the amino acid substitution is an I346F or I346W substitution; b) amino acid position 347, wherein the amino acid substitution is selected from an A347Q or A347E substitution; c) amino acid position 401, wherein the amino acid substitution is an 140 IL substitution; d) amino acid position 402, wherein the amino acid substitution is an S402I substitution; e) amino acid position 408, wherein the amino acid substitution is a D408I substitution; f) amino acid position 416, wherein the amino acid substitution is a Y416N substitution; and/or g) amino acid position 418, wherein the amino acid substitution is a Y418I substitution.
  • the isolated mutant BMP9 polypeptide is in the form of a homodimer.
  • the isolated pro-BMP9 mutant polypeptide comprises at least one amino acid substitution at one of the following amino acid positions: a) amino acid position 346, wherein the amino acid substitution is an I346F or I346W substitution; b) amino acid position 347, wherein the amino acid substitution is selected from an A347Q or A347E substitution; c) amino acid position 401, wherein the amino acid substitution is an I401L substitution; d) amino acid position 402, wherein the amino acid substitution is an S402I substitution; e) amino acid position 408, wherein the amino acid substitution is a D408I substitution; f) amino acid position 416, wherein the amino acid substitution is a Y416N substitution; and/or g) amino acid position 418, wherein the amino acid substitution is a Y418I substitution.
  • the isolated BMP9 mutant polypeptide amino acid sequence is selected from one of SEQ ID NOs: 30-54.
  • the amino acid sequence of the isolated BMP9 mutant polypeptide is SEQ ID NO: 32.
  • the amino acid sequence of the isolated BMP9 mutant polypeptide is SEQ ID NO: 36.
  • the amino acid sequence of the isolated BMP9 mutant polypeptide is SEQ ID NO: 38.
  • the isolated mutant BMP9 polypeptide is in the form of a homodimer.
  • the isolated pro-BMP9 mutant polypeptide is a noncovalent complex of a polypeptide having the amino acid sequence of SEQ ID NO: 55 and a polypeptide having an amino acid sequence selected from one of SEQ ID NOs: 30-54.
  • the isolated pro-BMP9 mutant polypeptide is a noncovalent complex of a polypeptide having the amino acid sequence of SEQ ID NO: 55 and a polypeptide having an amino acid sequence of SEQ ID NO: 32.
  • the isolated pro-BMP9 mutant polypeptide is a noncovalent complex of a polypeptide having the amino acid sequence of SEQ ID NO: 55 and a polypeptide having an amino acid sequence of SEQ ID NO: 36.
  • the isolated pro-BMP9 mutant polypeptide is a noncovalent complex of a polypeptide having the amino acid sequence of SEQ ID NO: 55 and a polypeptide having an amino acid sequence of SEQ ID NO: 38.
  • mutant BMP9 or pro-BMP9 polypeptides of the invention activate endothelial cell signaling through pSMAD 1/5/8.
  • mutant polypeptides that showed similar or greater phosphorylation of SMAD1 relative to a wild type BMP9 as a control were selected for further screening.
  • the endothelial cell signaling activity of the isolated mutant BMP9 polypeptide is measured based on induction of SMAD1 phosphorylation in an endothelial cell.
  • the endothelial cell signaling activity of the isolated mutant pro-BMP9 polypeptide is measured based on induction of SMAD1 phosphorylation in an endothelial cell.
  • the endothelial cell is a human cell. In one embodiment, the endothelial cell is a lung cell. In a further embodiment, the endothelial cell is a human lung cell line (e.g. HULEC-5a). In still further embodiments, the induction of SMAD1 phosphorylation is measured in a human lung cell line (e.g. HULEC-5a) after treatment with the isolated mutant BMP9 polypeptide for Cup at 37°C, 5.0% CO2. In still further embodiments, the induction of SMAD1 phosphorylation is measured in a human lung cell line (e.g. HULEC-5a) after treatment with the isolated mutant pro-BMP9 polypeptide for Cup at 37°C, 5.0% CO 2 .
  • a human lung cell line e.g. HULEC-5a
  • Levels of SMAD1 phosphorylation induced by isolated BMP9 or pro-BMP9 mutant polypeptides may be compared to levels of SMAD1 phosphorylation induced by wild type BMP9 or pro-BMP9 polypeptides (e.g. BMP9 comprising an amino acid sequence of SEQ ID NO: 29).
  • the isolated mutant BMP9 polypeptide induces phosphorylation of SMAD1 to a similar extent as that induced by a wild type BMP9 polypeptide.
  • the isolated mutant BMP9 polypeptide induces phosphorylation of SMAD1 to a greater extent than that induced by a wild type BMP9 polypeptide.
  • the isolated mutant pro-BMP9 polypeptide induces phosphorylation of SMAD1 to a similar extent as that induced by a wild type pro-BMP9 polypeptide. In one embodiment, the isolated mutant pro-BMP9 polypeptide induces phosphorylation of SMAD1 to a greater extent than that induced by a wild type pro-BMP9 polypeptide.
  • phosphorylation of SMAD1 induced by the isolated mutant BMP9 polypeptide is at least 95%, 100%, 105%, 110%, 115%, 120%, 125%, 130%, 135%, 140%, 145% or 150% of phosphorylation of SMAD1 induced by a wild type BMP9 polypeptide.
  • the E max for phosphorylation of SMAD1 induced by the isolated mutant BMP9 polypeptide is at least 95%, 100%, 105%, 110%, 115%, 120%, 125%, 130%, 135%, 140%, 145% or 150% of the E max for phosphorylation of SMAD1 that is induced by a wild type BMP9 polypeptide.
  • the E max for phosphorylation of SMAD1 induced by the isolated mutant BMP9 polypeptide is at least 100% of the E max for phosphorylation of SMAD1 that is induced by a wild type BMP9 polypeptide.
  • phosphorylation of SMAD1 induced by the isolated mutant BMP9 polypeptide is at least 90% of phosphorylation of SMAD1 induced by a wild type BMP9 polypeptide, when human lung cell lines (e.g. HULEC-5a) are treated with both polypeptides at a concentration of 4 nM of the growth factor domain.
  • phosphorylation of SMAD1 induced by the isolated mutant pro-BMP9 polypeptide is at least 95%, 100%, 105%, 110%, 115%, 120%, 125%, 130%, 135%, 140%, 145% or 150% of phosphorylation of SMAD1 induced by a wild type pro-BMP9 polypeptide.
  • the Em ax for phosphorylation of SMAD1 induced by the isolated mutant pro-BMP9 polypeptide is at least 95%, 100%, 105%, 110%, 115%, 120%, 125%, 130%, 135%, 140%, 145% or 150% ofthe E ⁇ for phosphorylation of SMAD1 that is induced by a wild type pro-BMP9 polypeptide.
  • the E max for phosphorylation of SMAD1 induced by the isolated mutant pro-BMP9 polypeptide is at least 100% of the E max for phosphorylation of SMAD1 that is induced by a wild type pro-BMP9 polypeptide.
  • phosphorylation of SMAD1 induced by the isolated mutant pro-BMP9 polypeptide is at least 90% of phosphorylation of SMAD1 induced by a wild type pro-BMP9 polypeptide, when human lung cell lines (e.g. HULEC-5a) are treated with both polypeptides at a concentration of 4 nM of the growth factor domain.
  • human lung cell lines e.g. HULEC-5a
  • mutant polypeptides that showed comparable or lesser phosphorylation of SMAD3 relative to a wild type BMP9 as a control were selected for further screening.
  • the endothelial cell signaling activity of the isolated mutant BMP9 polypeptide is measured based on induction of SMAD3 phosphorylation in an endothelial cell. In other embodiments, the endothelial cell signaling activity of the isolated mutant pro-BMP9 polypeptide is measured based on induction of SMAD3 phosphorylation in an endothelial cell.
  • the endothelial cell is a human cell.
  • the endothelial cell is a lung cell.
  • the endothelial cell is a human lung cell line (e.g. HULEC-5a).
  • the induction of SMAD3 phosphorylation is measured in a human lung cell line (e.g. HULEC-5a) after treatment with the isolated mutant BMP9 polypeptide for Cup at 37°C, 5.0% CO2. In still further embodiments, the induction of SMAD3 phosphorylation is measured in a human lung cell line (e.g. HULEC-5a) after treatment with the isolated mutant pro-BMP9 polypeptide for Cup at 37°C, 5.0% CO2.
  • Levels of SMAD3 phosphorylation induced by isolated BMP9 or pro-BMP9 mutant polypeptides may be compared to levels of SMAD3 phosphorylation induced by wild type BMP9 or pro-BMP9 polypeptides (e.g. BMP9 comprising an amino acid sequence of SEQ ID NO: 29).
  • the isolated mutant BMP9 polypeptide induces phosphorylation of SMAD3 to a similar extent as that induced by a wild type BMP9 polypeptide.
  • the isolated mutant BMP9 polypeptide induces phosphorylation of SMAD3 to a lesser extent than that induced by a wild type BMP9 polypeptide.
  • the isolated mutant pro-BMP9 polypeptide induces phosphorylation of SMAD3 to a similar extent as that induced by a wild type pro-BMP9 polypeptide. In one embodiment, the isolated mutant pro-BMP9 polypeptide induces phosphorylation of SMAD3 to a lesser extent than that induced by a wild type pro-BMP9 polypeptide.
  • phosphorylation of SMAD3 induced by the isolated mutant BMP9 polypeptide is at most 200%, 175%, 150%, 125%, 100%, 75% or 50% of phosphorylation of SMAD3 induced by a wild type BMP9 polypeptide.
  • the E max for phosphorylation of SMAD3 induced by the isolated mutant BMP9 polypeptide is at most 200%, 175%, 150%, 125%, 100%, 75% or 50% of the E max for phosphorylation of SMAD3 that is induced by a wild type BMP9 polypeptide.
  • the E max for phosphorylation of SMAD3 induced by the isolated mutant BMP9 polypeptide is at most 200% of the E max for phosphorylation of SMAD3 that is induced by a wild type BMP9 polypeptide. In some embodiments, phosphorylation of SMAD3 induced by the isolated mutant BMP9 polypeptide is at most 210% of phosphorylation of SMAD3 induced by a wild type BMP9 polypeptide, when human lung cell lines (e.g. HULEC-5a) are treated with both polypeptides at a concentration of 4 nM of the growth factor domain.
  • human lung cell lines e.g. HULEC-5a
  • phosphorylation of SMAD3 induced by the isolated mutant BMP9 polypeptide is at most 70% of phosphorylation of SMAD3 induced by a wild type BMP9 polypeptide, when human lung cell lines (e.g. HULEC-5a) are treated with both polypeptides at a concentration of 4 nM of the growth factor domain.
  • phosphorylation of SMAD3 induced by the isolated mutant pro-BMP9 polypeptide is at most 200%, 175%, 150%, 125%, 100%, 75% or 50% of phosphorylation of SMAD3 induced by a wild type pro-BMP9 polypeptide.
  • the E max for phosphorylation of SMAD3 induced by the isolated mutant pro-BMP9 polypeptide is at most 200%, 175%, 150%, 125%, 100%, 75% or 50% of the E max for phosphorylation of SMAD3 that is induced by a wild type pro-BMP9 polypeptide.
  • the E max for phosphorylation of SMAD3 induced by the isolated mutant pro-BMP9 polypeptide is at most 200% of the E max for phosphorylation of SMAD3 that is induced by a wild type pro-BMP9 polypeptide. In some embodiments, phosphorylation of SMAD3 induced by the isolated mutant pro-BMP9 polypeptide is at most 210% of phosphorylation of SMAD3 induced by a wild type pro-BMP9 polypeptide, when human lung cell lines (e.g. HULEC-5a) are treated with both polypeptides at a concentration of 4 nM of the growth factor domain.
  • human lung cell lines e.g. HULEC-5a
  • phosphorylation of SMAD3 induced by the isolated mutant pro-BMP9 polypeptide is at most 70% of phosphorylation of SMAD3 induced by a wild type pro-BMP9 polypeptide, when human lung cell lines (e.g. HULEC-5a) are treated with both polypeptides at a concentration of 4 nM of the growth factor domain.
  • Isolated mutant BMP9 and pro-BMP9 polypeptides of the invention comprise reduced or eliminated osteogenic activity.
  • screening for non-osteogenic mutants was carried out based on the detection of ALP activation and/or activity in C2C12 cells, or based on the expression of Osterix (Osx/SP7) in human mesenchymal stem cells (hMSCs).
  • the isolated mutant BMP9 polypeptides of the invention comprise reduced osteogenic activity.
  • the isolated mutant pro-BMP9 polypeptides of the invention comprise reduced osteogenic activity.
  • the isolated mutant BMP9 polypeptides of the invention comprise eliminated osteogenic activity.
  • the isolated mutant pro-BMP9 polypeptides of the invention comprise eliminated osteogenic activity.
  • the osteogenic activity of the isolated mutant BMP9 polypeptide is measured based on the induction of alkaline phosphatase expression in a cell.
  • the osteogenic activity of the isolated mutant pro-BMP9 polypeptide is measured based on the induction of alkaline phosphatase expression in a cell.
  • the alkaline phosphatase expression is estimated based on expression of alkaline phosphatase mRNA and/or protein levels. In one embodiment, the alkaline phosphatase expression is estimated based on measurement of mRNA levels.
  • the alkaline phosphatase expression is estimated based on measurement of protein levels (e.g. by an enzymatic assay).
  • the cell is a C2C12 cell line.
  • the alkaline phosphatase mRNA expression is measured in a C2C12 cell line after treatment with the isolated mutant BMP9 polypeptide for 48 hrs at 37°C, 5.0% CO2.
  • the alkaline phosphatase mRNA expression is measured in a C2C12 cell line after treatment with the isolated mutant pro-BMP9 polypeptide for 48 hrs at 37°C, 5.0% CO2.
  • the alkaline phosphatase protein expression in a C2C12 cell line is measured by an enzymatic assay after treatment with the isolated mutant BMP9 polypeptide for 5 days at 37°C, 5.0% CO2. In some embodiments, the alkaline phosphatase protein expression in a C2C12 cell line is measured by an enzymatic assay after treatment with the isolated mutant pro-BMP9 polypeptide for 5 days at 37°C, 5.0% CO 2 .
  • the isolated mutant BMP9 polypeptide comprises reduced osteogenic activity in human cells. In some embodiments, the isolated mutant BMP9 polypeptide comprises eliminated osteogenic activity in human cells. In some embodiments, the isolated mutant pro-BMP9 polypeptide comprises reduced osteogenic activity in human cells. In some embodiments, the isolated mutant pro-BMP9 polypeptide comprises eliminated osteogenic activity in human cells. In some embodiments, the osteogenic activity of the isolated mutant BMP9 polypeptide is measured based on the induction of Osterix (Osx/SP7) expression in a human cell line. In other embodiments, the osteogenic activity of the isolated mutant pro-BMP9 polypeptide is measured based on the induction of Osterix (Osx/SP7) expression in a human cell line.
  • the Osterix (Osx/SP7) expression is estimated based on expression of alkaline phosphatase mRNA and/or protein levels. In one embodiment, the Osterix (Osx/SP7) expression is estimated based on measurement of mRNA levels. In another embodiment, the Osterix (Osx/SP7) expression is estimated based on measurement of protein levels.
  • the cell is a pre-osteoblastic cell line. In further embodiments, the pre- osteoblastic cells are human mesenchymal stem cells (e.g. PoieticsTM hMSCs).
  • the Osterix (Osx/SP7) mRNA expression is measured in hMSCs after treatment with the isolated mutant BMP9 polypeptide for 12 hrs at 37°C, 5.0% CO2. In some embodiments, the Osterix (Osx/SP7) mRNA expression is measured in hMSCs after treatment with the isolated mutant pro-BMP9 polypeptide for 12 hrs at 37°C, 5.0% CO 2 .
  • Osteogenic activity induced by isolated BMP9 or pro-BMP9 mutant polypeptides may be compared to osteogenic activity induced by wild type BMP9 or pro-BMP9 polypeptides (e.g. BMP9 comprising an amino acid sequence of SEQ ID NO: 29).
  • the osteogenic activity induced by the isolated mutant BMP9 polypeptide is at most 10% of the osteogenic activity induced by a wild type BMP9 polypeptide.
  • the osteogenic activity induced by the isolated mutant BMP9 polypeptide is at most 5% of the osteogenic activity induced by a wild type BMP9 polypeptide.
  • the E max of osteogenic activity induced by the isolated mutant BMP9 polypeptide is at most 10% of the E max of osteogenic activity induced by a wild type BMP9 polypeptide in human cells. In some embodiments, the E max of osteogenic activity induced by the isolated mutant BMP9 polypeptide is at most 5% of the E max of osteogenic activity induced by a wild type BMP9 polypeptide in human cells. In certain such embodiments, osteogenic activity in hMSCs is measured by levels of Osterix (Osx/SP7) mRNA expression.
  • osteogenic activity induced by the isolated mutant BMP9 polypeptide is at most 10% of the osteogenic activity induced by a wild type BMP9 polypeptide in a C2C12 cell line. In some embodiments, osteogenic activity induced by the isolated mutant BMP9 polypeptide is at most 5% of the osteogenic activity induced by a wild type BMP9 polypeptide in a C2C12 cell line. In certain such embodiments, osteogenic activity in a C2C12 cell line is measured by levels of alkaline phosphatase protein (e.g. by an enzymatic assay) in cells treated with both polypeptides at a concentration of 25 nM of the growth factor domain.
  • alkaline phosphatase protein e.g. by an enzymatic assay
  • osteogenic activity induced by the isolated mutant BMP9 polypeptide is 0% of the osteogenic activity induced by a wild type BMP9 polypeptide in a C2C12 cell line.
  • osteogenic activity in a C2C12 cell line is measured by levels of alkaline phosphatase protein (e.g. by an enzymatic assay) in cells treated with both polypeptides at a concentration of 25 nM of the growth factor domain.
  • the osteogenic activity induced by the isolated mutant pro-BMP9 polypeptide is at most 10% of the osteogenic activity induced by a wild type pro-BMP9 polypeptide.
  • the osteogenic activity induced by the isolated mutant pro-BMP9 polypeptide is at most 5% of the osteogenic activity induced by a wild type pro-BMP9 polypeptide. In some embodiments, the E max of osteogenic activity induced by the isolated mutant pro-BMP9 polypeptide is at most 10% of the E max of osteogenic activity induced by a wild type pro-BMP9 polypeptide in human cells. In some embodiments, the E max of osteogenic activity induced by the isolated mutant pro-BMP9 polypeptide is at most 5% of the E max of osteogenic activity induced by a wild type pro-BMP9 polypeptide in human cells.
  • osteogenic activity in hMSCs is measured by levels of Osterix (Osx/SP7) mRNA expression.
  • osteogenic activity induced by the isolated mutant pro-BMP9 polypeptide is at most 10% of the osteogenic activity induced by a wild type pro-BMP9 polypeptide in a C2C12 cell line.
  • osteogenic activity induced by the isolated mutant pro-BMP9 polypeptide is at most 5% of the osteogenic activity induced by a wild type pro-BMP9 polypeptide in a C2C12 cell line.
  • osteogenic activity in a C2C12 cell line is measured by levels of alkaline phosphatase protein (e.g.
  • osteogenic activity induced by the isolated mutant pro-BMP9 polypeptide is 0% of the osteogenic activity induced by a wild type pro-BMP9 polypeptide in a C2C12 cell line.
  • osteogenic activity in a C2C12 cell line is measured by levels of alkaline phosphatase protein (e.g. by an enzymatic assay) in cells treated with both polypeptides at a concentration of 25 nM of the growth factor domain.
  • the invention relates to an isolated nucleic acid encoding an isolated BMP9 mutant polypeptide of the invention.
  • the invention relates to an isolated nucleic acid encoding an isolated pro-BMP9 mutant polypeptide of the invention.
  • the coding sequence of a protein can be changed (e.g., replaced, deleted, inserted, etc.) without changing the amino acid sequence of the protein. Accordingly, it will be understood by those skilled in the art that nucleic acid sequences encoding isolated BMP9 or pro-BMP9 mutant polypeptides of the invention can be altered without changing the amino acid sequences of the proteins.
  • the invention in another general aspect, relates to a vector comprising an isolated nucleic acid encoding an isolated BMP9 mutant polypeptide of the invention.
  • the invention in a further general aspect, relates to a vector comprising an isolated nucleic acid encoding an isolated pro-BMP9 mutant polypeptide of the invention.
  • Any vector known to those skilled in the art in view of the present disclosure can be used, such as a plasmid, a cosmid, a phage vector or a viral vector.
  • the vector is a recombinant expression vector such as a plasmid.
  • the vector can include any element to establish a conventional function of an expression vector, for example, a promoter, ribosome binding element, terminator, enhancer, selection marker, and origin of replication.
  • the promoter can be a constitutive, inducible, or repressible promoter.
  • a number of expression vectors capable of delivering nucleic acids to a cell are known in the art and can be used herein for production of an antibody or antigen-binding fragment thereof in the cell. Conventional cloning techniques or artificial gene synthesis can be used to generate a recombinant expression vector according to embodiments of the invention.
  • the invention relates to a host cell comprising an isolated nucleic acid encoding a BMP9 mutant polypeptide of the invention.
  • the invention relates to a host cell comprising an isolated nucleic acid encoding a pro-BMP9 mutant polypeptide of the invention.
  • Any host cell known to those skilled in the art in view of the present disclosure can be used for recombinant expression of BMP9 or pro-BMP9 mutant polypeptides of the invention.
  • the host cells are E. coli TGI or BL21 cells (for expression of, e.g., an scFv or Fab antibody), CHO-DG44 or CHO-K1 cells or HEK293 cells (for expression of, e.g., a full-length IgG antibody).
  • the recombinant expression vector is transformed into host cells by conventional methods such as chemical transfection, heat shock, or electroporation, where it is stably integrated into the host cell genome such that the recombinant nucleic acid is effectively expressed.
  • the invention in another general aspect, relates to a method of producing an isolated BMP9 mutant polypeptide of the invention, comprising culturing a cell comprising a nucleic acid encoding the BMP9 mutant polypeptide under conditions to produce a BMP9 mutant polypeptide of the invention, and recovering the BMP9 mutant polypeptide from the cell or cell culture (e.g., from the supernatant).
  • the invention relates to a method of producing an isolated pro-BMP9 mutant polypeptide of the invention, comprising culturing a cell comprising a nucleic acid encoding the pro-BMP9 mutant polypeptide under conditions to produce a pro-BMP9 mutant polypeptide of the invention, and recovering the pro-BMP9 mutant polypeptide from the cell or cell culture (e.g., from the supernatant).
  • Expressed BMP9 or pro-BMP9 mutant polypeptides can be harvested from the cells and purified according to conventional techniques known in the art and as described herein.
  • the invention in another general aspect, relates to a pharmaceutical composition, comprising an isolated BMP9 mutant polypeptide of the invention and a pharmaceutically acceptable carrier.
  • the invention in a further general aspect, relates to a pharmaceutical composition, comprising an isolated pro-BMP9 mutant polypeptide of the invention and a pharmaceutically acceptable carrier.
  • pharmaceutical composition as used herein means a product comprising a BMP9 or pro-BMP9 mutant polypeptide of the invention together with a pharmaceutically acceptable carrier. BMP9 or pro-BMP9 mutant polypeptides of the invention and compositions comprising them are also useful in the manufacture of a medicament for therapeutic applications mentioned herein.
  • the term “carrier” refers to any excipient, diluent, filler, salt, buffer, stabilizer, solubilizer, oil, lipid, lipid containing vesicle, microsphere, liposomal encapsulation, or other material well known in the art for use in pharmaceutical formulations. It will be understood that the characteristics of the carrier, excipient or diluent will depend on the route of administration for a particular application.
  • the term “pharmaceutically acceptable carrier” refers to a non-toxic material that does not interfere with the effectiveness of a composition according to the invention or the biological activity of a composition according to the invention. According to particular embodiments, in view of the present disclosure, any pharmaceutically acceptable carrier suitable for use in a polypeptide pharmaceutical composition can be used in the invention.
  • the formulation of pharmaceutically active ingredients with pharmaceutically acceptable carriers is known in the art, e.g., Remington: The Science and Practice of Pharmacy (e.g. 21st edition (2005), and any later editions).
  • additional ingredients include: buffers, diluents, solvents, tonicity regulating agents, preservatives, stabilizers, and chelating agents.
  • One or more pharmaceutically acceptable carrier can be used in formulating the pharmaceutical compositions of the invention.
  • the pharmaceutical composition is a liquid formulation.
  • a preferred example of a liquid formulation is an aqueous formulation, i.e., a formulation comprising water.
  • the liquid formulation can comprise a solution, a suspension, an emulsion, a microemulsion, a gel, and the like.
  • An aqueous formulation typically comprises at least 50% w/w water, or at least 60%, 70%, 75%, 80%, 85%, 90%, or at least 95% w/w of water.
  • the pharmaceutical composition can be formulated as an injectable which can be injected, for example, via an injection device (e.g., a syringe or an infusion pump).
  • the injection can be delivered subcutaneously, intramuscularly, intraperitoneally, intravitreally, or intravenously, for example.
  • the pharmaceutical composition is a solid formulation, e.g., a freeze-dried or spray-dried composition, which can be used as is, or whereto the physician or the patient adds solvents, and/or diluents prior to use.
  • Solid dosage forms can include tablets, such as compressed tablets, and/or coated tablets, and capsules (e.g., hard or soft gelatin capsules).
  • the pharmaceutical composition can also be in the form of sachets, dragees, powders, granules, lozenges, or powders for reconstitution, for example.
  • the dosage forms may be immediate release, in which case they can comprise a water-soluble or dispersible carrier, or they can be delayed release, sustained release, or modified release, in which case they can comprise water-insoluble polymers that regulate the rate of dissolution of the dosage form in the gastrointestinal tract or under the skin.
  • the pharmaceutical composition can be delivered intranasally, intrabuccally or sublingually.
  • the pH in an aqueous formulation can be between pH 3 and pH 10.
  • the pH of the formulation is from about 7.0 to about 9.5. In another embodiment of the invention, the pH of the formulation is from about 3.0 to about 7.0.
  • the pharmaceutical composition comprises a buffer.
  • buffers include: arginine, aspartic acid, bicine, citrate, disodium hydrogen phosphate, fumaric acid, glycine, glycylglycine, histidine, lysine, maleic acid, malic acid, sodium acetate, sodium carbonate, sodium dihydrogen phosphate, sodium phosphate, succinate, tartaric acid, tricine, and tris(hydroxymethyl)-aminomethane, and mixtures thereof.
  • the buffer can be present individually or in the aggregate, in a concentration from about 0.01 mg/ml to about 50 mg/ml, for example from about 0.1 mg/ml to about 20 mg/ml. Pharmaceutical compositions comprising each one of these specific buffers constitute alternative embodiments of the invention.
  • the pharmaceutical composition comprises a preservative.
  • preservatives include: benzethonium chloride, benzoic acid, benzyl alcohol, bronopol, butyl 4-hydroxybenzoate, chlorobutanol, chlorocresol, chlorohexidine, chlorphenesin, o-cresol, m-cresol, p-cresol, ethyl 4- hydroxybenzoate, imidurea, methyl 4-hydroxybenzoate, phenol, 2-phenoxyethanol, 2- phenylethanol, propyl 4-hydroxybenzoate, sodium dehydroacetate, thiomerosal, and mixtures thereof.
  • the preservative can be present individually or in the aggregate, in a concentration from about 0.01 mg/ml to about 50 mg/ml, for example from about 0.1 mg/ml to about 20 mg/ml.
  • Pharmaceutical compositions comprising each one of these specific preservatives constitute alternative embodiments of the invention.
  • the pharmaceutical composition comprises an isotonic agent.
  • an isotonic agent such as sodium chloride
  • an amino acid such as glycine, histidine, arginine, lysine, isoleucine, aspartic acid, tryptophan, and threonine
  • an alditol such as glycerol, 1,2- propanediol propyleneglycol), 1,3-propanediol, and 1,3-butanediol
  • polyethyleneglycol e.g. PEG400
  • Another example of an isotonic agent includes a sugar.
  • Non-limiting examples of sugars may be mono-, di-, or polysaccharides, or water- soluble glucans, including for example fructose, glucose, mannose, sorbose, xylose, maltose, lactose, sucrose, trehalose, dextran, pullulan, dextrin, cyclodextrin, alpha and beta-HPCD, soluble starch, hydroxyethyl starch, and sodium carboxymethylcellulose.
  • an isotonic agent is a sugar alcohol, wherein the term “sugar alcohol” is defined as a C(4-8) hydrocarbon having at least one -OH group.
  • sugar alcohols include mannitol, sorbitol, inositol, galactitol, dulcitol, xylitol, and arabitol.
  • the isotonic agent can be present individually or in the aggregate, in a concentration from about 0.01 mg/ml to about 50 mg/ml, for example from about 0.1 mg/ml to about 20 mg/ml. Pharmaceutical compositions comprising each one of these specific isotonic agents constitute alternative embodiments of the invention.
  • the pharmaceutical composition comprises a chelating agent.
  • chelating agents include citric acid, aspartic acid, salts of ethylenediaminetetraacetic acid (EDTA), and mixtures thereof.
  • the chelating agent can be present individually or in the aggregate, in a concentration from about 0.01 mg/ml to about 50 mg/ml, for example from about 0.1 mg/ml to about 20 mg/ml.
  • Pharmaceutical compositions comprising each one of these specific chelating agents constitute alternative embodiments of the invention.
  • the pharmaceutical composition comprises a stabilizer.
  • stabilizers include one or more aggregation inhibitors, one or more oxidation inhibitors, one or more surfactants, and/or one or more protease inhibitors.
  • the pharmaceutical composition comprises a stabilizer, wherein said stabilizer is carboxy-/hydroxy cellulose and derivates thereof (such as HPC, HPC-SL, HPC-L and HPMC), cyclodextrins, 2-methylthioethanol, polyethylene glycol (such as PEG 3350), polyvinyl alcohol (PVA), polyvinyl pyrrolidone, salts (such as sodium chloride), sulphur-containing substances such as monothioglycerol), or thioglycolic acid.
  • the stabilizer can be present individually or in the aggregate, in a concentration from about 0.01 mg/ml to about 50 mg/ml, for example from about 0.1 mg/ml to about 20 mg/ml. Pharmaceutical compositions comprising each one of these specific stabilizers constitute alternative embodiments of the invention.
  • the pharmaceutical composition comprises one or more surfactants, preferably a surfactant, at least one surfactant, or two different surfactants.
  • surfactant refers to any molecules or ions that are comprised of a water-soluble (hydrophilic) part, and a fat-soluble (lipophilic) part.
  • the surfactant can, for example, be selected from the group consisting of anionic surfactants, cationic surfactants, nonionic surfactants, and/or zwitterionic surfactants.
  • the surfactant can be present individually or in the aggregate, in a concentration from about 0.1 mg/ml to about 20 mg/ml. Pharmaceutical compositions comprising each one of these specific surfactants constitute alternative embodiments of the invention.
  • the pharmaceutical composition comprises one or more protease inhibitors, such as, e.g., EDTA, and/or benzamidine hydrochloric acid (HC1).
  • the protease inhibitor can be present individually or in the aggregate, in a concentration from about 0.1 mg/ml to about 20 mg/ml.
  • Pharmaceutical compositions comprising each one of these specific protease inhibitors constitute alternative embodiments of the invention.
  • the invention relates to a method of producing a pharmaceutical composition comprising a BMP9 mutant polypeptide of the invention, comprising combining a BMP9 mutant polypeptide with a pharmaceutically acceptable carrier to obtain the pharmaceutical composition.
  • the invention relates to a method of producing a pharmaceutical composition comprising a pro-BMP9 mutant polypeptide of the invention, comprising combining a pro-BMP9 mutant polypeptide with a pharmaceutically acceptable carrier to obtain the pharmaceutical composition.
  • the invention in another general aspect, relates to a method of treating a vascular disease and/or a respiratory disease in a subject in need thereof, comprising administering to the subject an isolated BMP9 mutant polypeptide or a pharmaceutical composition of the invention.
  • the invention in a further general aspect, relates to a method of treating a vascular disease and/or a respiratory disease in a subject in need thereof, comprising administering to the subject an isolated pro-BMP9 mutant polypeptide or a pharmaceutical composition of the invention.
  • the pharmaceutical composition comprises a therapeutically effective amount of an isolated BMP9 or pro-BMP9 mutant polypeptide.
  • therapeutically effective amount refers to an amount of an active ingredient or component that elicits the desired biological or medicinal response in a subject.
  • a therapeutically effective amount can be determined empirically and in a routine manner, in relation to the stated purpose.
  • a therapeutically effective amount means an amount of the BMP9 or pro-BMP9 mutant polypeptide that modulates a response (i.e., activated endothelial cell signaling activity) in a subject in need thereof.
  • a therapeutically effective amount means an amount of the BMP9 or pro-BMP9 mutant polypeptide that results in treatment of a disease, disorder, or condition; prevents or slows the progression of the disease, disorder, or condition; or reduces or completely alleviates symptoms associated with the disease, disorder, or condition.
  • Examples of some of the effects of administration of a BMP9 or pro-BMP9 mutant polypeptide for the treatment of PAH can include, but is not limited to, improvements in mean pulmonary arterial pressure (mPAP) reduction, reduction in right ventricular hypertrophy, reduction in right ventricular pressure, and reduction in muscularization.
  • mPAP mean pulmonary arterial pressure
  • the disease, disorder or condition to be treated is a vascular disease and/or a respiratory disease.
  • the vascular disease can, for example, be selected from the group consisting of pulmonary hypertension (PH), pulmonary arterial hypertension (PAH), idiopathic pulmonary fibrosis (IPF), pulmonary venous occlusive disease (PVOD), hereditary haemorrhagic telangiectasia, atherosclerosis, and hepatopulmonary syndrome.
  • PH pulmonary hypertension
  • PAH pulmonary arterial hypertension
  • IPF idiopathic pulmonary fibrosis
  • PVOD pulmonary venous occlusive disease
  • hereditary haemorrhagic telangiectasia atherosclerosis
  • atherosclerosis and hepatopulmonary syndrome.
  • the respiratory disease can, for example, be selected from the group consisting of an obstructive lung disease (e.g., chronic obstructive pulmonary disease (COPD), chronic bronchitis, and emphysema), a pulmonary vascular disease (e.g., pulmonary edema and pulmonary hemorrhage), a respiratory failure or respiratory distress syndrome (e.g., acute lung injury), an acute respiratory disease syndrome (ARDS), COVID 19, and an interstitial lung disease (ILD) (e.g., idiopathic pulmonary fibrosis).
  • COPD chronic obstructive pulmonary disease
  • COPD chronic obstructive pulmonary disease
  • pulmonary vascular disease e.g., pulmonary edema and pulmonary hemorrhage
  • a respiratory failure or respiratory distress syndrome e.g., acute lung injury
  • ARDS acute respiratory disease syndrome
  • COVID interstitial lung disease
  • the vascular disease is pulmonary arterial hypertension (PAH
  • the therapeutically effective amount or dosage can vary according to various factors, such as the disease, disorder or condition to be treated, the means of administration, the target site, the physiological state of the subject (including, e.g., age, body weight, health), whether the subject is a human or an animal, other medications administered, and whether the treatment is prophylactic or therapeutic. Treatment dosages are optimally titrated to optimize safety and efficacy.
  • compositions described herein are formulated to be suitable for the intended route of administration to a subject.
  • the compositions described herein can be formulated to be suitable for intravenous, subcutaneous, or intramuscular administration.
  • the terms “treat,” “treating,” and “treatment” are all intended to refer to an amelioration or reversal of at least one measurable physical parameter related to a cancer and/or an inflammatory disease, disorder or condition, which is not necessarily discernible in the subject, but can be discernible in the subject.
  • the terms “treat,” “treating,” and “treatment,” can also refer to causing regression, preventing the progression, or at least slowing down the progression of the disease, disorder, or condition.
  • “treat,” “treating,” and “treatment” refer to an alleviation, prevention of the development or onset, or reduction in the duration of one or more symptoms associated with the disease, disorder, or condition, such as a tumor or more preferably a cancer.
  • “treat,” “treating,” and “treatment” refer to prevention of the recurrence of the disease, disorder, or condition. In a particular embodiment, “treat,” “treating,” and “treatment” refer to an increase in the survival of a subject having the disease, disorder, or condition. In a particular embodiment, “treat,” “treating,” and “treatment” refer to elimination of the disease, disorder, or condition in the subject.
  • compositions used in the treatment of a vascular disease or a respiratory disease are provided.
  • Example 1 Identification of BMP9 positions involved in BMPR2-ActRIIb selective binding, and BMP9 mutant library generation.
  • the epitope on BMP9 contacted by ActRIIb can be defined based on the ternary structure of BMP9/Alkl/ActRIIb. Because of the structural similarity between BMPR2 and ActRII as shown in Figure 1, the epitope contacted by BMPR2 can be estimated based on the common epitope (core epitope), i.e., residues contacted by identical residues as defined above and Figure 1.
  • core epitope i.e., residues contacted by identical residues as defined above and Figure 1.
  • the deduced core epitope is shown in Figure 2.
  • the residues surrounding the core epitope are residues that likely contribute to binding to BMPR2 and ActRIIb but differentially. Mutational analysis of these positions thus can reveal their different contributions to binding to these two receptors. These residues are shown in Figure 3.
  • mutants each position mutated to all other 18 amino acids except Cys
  • BMPR2 binding was designed to assess each position’s contribution to BMPR2 binding.
  • mutants were synthesized in mammalian expression constructs in the following format: prodomain - 6His - BMP9mut, see, e.g., the WT BMP9 sequence below with each portion of the polypeptide identified (the prodomain is underlined, the 6His portion is not underlined, and the mature BMP9 portion of the polypeptide is bolded and underlined).
  • Example 2 Small scale expression and purification of a BMP9 mutant library.
  • [00130] 518 mutant BMP9 constructs were co-expressed with furin at 2 mL small scale in Expi-293 cells for 6 days. Supernatants were harvested and His-tagged BMP9 proteins were purified using NiNTA resin, eluted in 250 mM imidazole and dialyzed in PBS.
  • BMP9 concentration in these fractions was determined using a ligand binding MSD assay (Alkl capture followed by Sulfo-Tag Goat anti-Human BMP-9 detection). 212 (out of 518 expression constructs) BMP9 mutants showed an expression level superior to 2 nM in these assays and were progressed to screening (FIG. 4).
  • Example 3 Screening of BMP9 mutants for pSMADl and pSMAD3 activity in HULEC-5a cells.
  • Example 4 Screening BMP9 mutant polypeptides for Alkaline Phosphatase activation in C2C12 cells.
  • Mouse muscle, C2C12, cells were plated in 96 well plates at 20,000 cells per well and allowed to recover overnight. The following day, the growth media was removed and replaced with treatments of internally generated BMP9 mutant polypeptides. The treatments were diluted to a concentration of either 0. InM or InM in growth media. The cells were treated for forty eight hours in an incubator set at 37°C, 5.0% CO2.
  • RNA concentrations were determined for a representative number of samples using the Trinean DropSense spectrophotometer. The sample’s concentrations were then averaged and used for normalization purposes for cDNA conversion.
  • a cDNA library was generated from the extracted RNA using ThermoFisher’s SuperScript IV VILO master mix (ThermoFisher; Waltham, MA). This mix contains reverse transcriptase, proprietary recombinant RNase inhibitor, helper proteins, stabilizer proteins, oligo(dt)18, random hexamer primers, MgCl and dNTPs. This system can handle up to 2.5 pg of RNA template. Based on measured RNA concentration, samples were tested in a range of 82 to 450 ng. The RNA templates and master mix were combined and placed in a thermocycler using the following program: ten minutes at 25°C (primer annealing), ten minutes at 50°C (reverse transcription), five minutes at 85°C (terminate enzyme).
  • cDNA concentrations were determined for a representative number of samples using the Trinean DropSense spectrophotometer. The sample’s concentrations were then averaged and used for normalization purposes for TaqMan gene expression assay. Gene expression was measured using a combination of TaqMan fast advance master mix, specific gene primers/FAM probe mix, and the RT-PCR instrument ViiA 7. Gene expression was measured for AlpL, ID1, Sp7 and the housekeeping GAPDH. lOOng of cDNA was combined with the specific primer/probe sets and master mix. The solution was placed in RT-PCR machine and subjected to forty cycles of twenty seconds at 95°C (polymerase activation), one second at 95°C (denaturation), twenty seconds at 60°C (annealing/ extension) .
  • ACT Delta cycling times
  • Example 5 Confirmation of Alkaline Phosphatase and pSMAD activities induced by selected BMP9 mutant polypeptides.
  • HULEC-5a The capacity of mutants harboring a reduced Alkaline phosphatase activity to induce SMAD1 and SMAD3 phosphorylation was evaluated in human lung cells.
  • HULEC-5a were placed in 96 well plates at 50,000 cells per well and allowed to recover overnight. The following day, the growth media was removed and replaced with treatments of internally generated BMP9 mutant polypeptides. The treatments were diluted in base media, MCDB 131, and tested in a titration range of 0.002 nM to 2 nM. The cells were treated for one hour in an incubator set at 37°C, 5.0% CO2.
  • 25 potential non-osteogenic mutants were selected using the following criteria: (1) no detectable ALP activity in C2C12; (2) pSMAD 1 activity equal or higher than WT in HULEC-5a; and (3) pSMAD3 activity comparable to or lower than WT in HULEC-5a (FIG. 9).
  • Example 6 Confirmation of osteogenic potential in human mesenchymal stem cells (hMSCs) for BMP9 mutant polypeptides.
  • BMP-9 has been shown to be one of the most effective of the bone morphogenic protein family to induce osteoblastic lineage-specific differentiation in progenitor cells.
  • a commonly used human pre-osteoblastic progenitor cell population bone marrow derived mesenchymal stem cells (hMSCs) are primary human cells capable of osteogenic differentiation.
  • hMSCs bone marrow derived mesenchymal stem cells
  • PoieticsTM hMSCs are isolated from normal (non-diabetic) adult human bone marrow withdrawn from bilateral punctures of the posterior iliac crests of normal volunteers.
  • Cellular differentiation has been monitored by measuring early osteogenic markers such as alkaline phosphatase (Aik Phos) activity and/or gene expression of other markers such as Osterix, or RUNX2.
  • Aik Phos (ALPL) gene expression has been found to have a higher background level and less of a fold increase that occurs later, day 7-14 in human cells.
  • Osterix (Osx/SP7) is an osteoblast-specific transcription factor which activates a repertoire of genes during differentiation of preosteoblasts into mature osteoblasts and osteocytes.
  • hMSCs respond to BMP-9 on Day 2 with increased SP7 (>100 fold) supporting its use as the primary osteogenic marker for in vitro assays.
  • the cells were allowed to incubate over night at 37°C, 5% CO2. After overnight incubation, the cells were stimulated with the BMP9 mutant polypeptides and wild type rhBMP9 in osteogenic media (MSC BM Basal Media (Cat# PT-3238; Lonza); hMSC Osteogenic BulletKit (Lonza); differentiation basal medium- osteogenic (Cat # PT-3924; Lonza); and hMSC SQ kit-Osteo (Cat # PT-4120; Lonza)) used for stimulation. Dose curves of all BMP9 mutant polypeptides were run.
  • RNA from the cell lysates was isolated in PLA buffer. Reverse transcription of the RNA to cDNA was performed using Vilo Reverse-Transcription Protocol on an Applied Biosystems SimpliAmp ThermoCycler (Applied Biosystems; Foster City, CA). Quantitative PCR was performed on the cDNA samples using Taqman on a ViiA7 PCR machine (Applied Biosystems) using TaqMan PCR primer probes for SP7 and the housekeeper gene GAPDH. The results are shown in FIGs. 10A-10B.

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Abstract

L'invention concerne des polypeptides mutants BMP9 et pro-BMP9 isolés. L'invention concerne également des acides nucléiques codant pour les polypeptides mutants BMP9 et pro-BMP9 isolés, des compositions comprenant les polypeptides mutants BMP9 et pro-BMP9 isolés, ainsi que des procédés de production des polypeptides mutants BMP9 et pro-BMP9 et l'utilisation des polypeptides mutants BMP9 et pro-BMP9 pour traiter ou prévenir des maladies vasculaires et/ou des maladies respiratoires, telles que l'hypertension artérielle pulmonaire (HTAP)
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