USPatent applicationPatented

Autophagy as a therapeutic target for intracranial aneurysm

Granted 15 Oct 2024 · 5 office actions

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Abstract

Disclosed here are uses of autophagy inhibitors for treating a subject at risk of suffering from an aneurysm. The present disclosure demonstrates that autophagy plays a role in THSD1-mediated focal adhesion stability and aneurysm formation and characterizes molecular targets for therapeutic intervention.

Description

25 parts
›CROSS-REFERENCE

The present application claims priority to U.S. Provisional Application Ser. No. 63/296,820, filed Jan. 5, 2022; U.S. Provisional Application Ser. No. 63/296,817, filed Jan. 5, 2022; U.S. Provisional Application Ser. No. 63/296,821, filed Jan. 5, 2022; and U.S. Provisional Application Ser. No. 63/296,825, filed Jan. 5, 2022, the contents of each being hereby incorporated by reference in their entirety.

›FIELD OF THE INVENTION

The present disclosure relates to the characterization of molecular targets for treating intracranial aneurysms (IA). Intracranial aneurysm (IA) is a cerebrovascular disease that predominantly occurs in the cerebral artery and is characterized by pathologic dilatation of blood vessels. Each intracranial aneurysm (IA) is a weakened area in a cerebral artery wall that leads to abnormal dilatation and rupture causing subarachnoid hemorrhage (SAH), a major cause of hemorrhagic stroke. A rupture of IA induces a subarachnoid hemorrhage (SAH), a type of hemorrhagic stroke that frequently leads to death or severe disability. Due to early age of onset and high mortality, SAH accounts for >25% of years lost for all stroke victims under the age of 65 years. Despite treatment advances, SAH mortality rate is 40% and only half of survivors return to independent life.

There is a critical unmet need for understanding the genetic and molecular basis for IA to improve clinical outcomes through early therapeutic intervention.

›SUMMARY

This Summary is provided to introduce a selection of concepts in a simplified form that are further described below in the Detailed Description. This Summary is not intended to identify key or essential features of the claimed subject matter, nor is it intended to be used to limit the scope of the claimed subject matter. Other features, details, utilities, and advantages of the claimed subject matter will be apparent from the following written Detailed Description including those aspects illustrated in the accompanying drawings and defined in the appended claims.

In some aspects, the present disclosure demonstrates that autophagy plays a role in THSD1-mediated focal adhesion stability and aneurysm formation. Briefly, the present disclosure provides that THSD1 can be a new, endothelial-specific, mechanosensory protein that regulates the autophagy pathway.

In some aspects, the disclosure provides a therapeutic method to treat a subject at risk of suffering from an aneurysm comprised of administering to said subject a therapeutically effective dose of an autophagy inhibitor. The autophagy inhibitor can be a phagophore inhibitor, a autophagosome inhibitor, an autolysosome inhibitor, or an inhibitor of the autophagosome-lysosome fusion. In some cases, the autophagy inhibitor is selected from the group consisting of wortmannin, chloroquine, clomipramine, 3-Methyladenine, Bafilomycin A1, Pepstatin A, and Pepstatin E-64-d. The aneurysm can be any aneurysm, and in some cases it is an intracranial aneurysm in others it is an aortic aneurysm. In some cases, the subject carries a variant affecting the expression of a Thrombospondin Type 1 Domain Containing 1 (THSD1) gene. The variant can be in a coding region, in a control sequence, or in a non-coding region of the Thrombospondin Type 1 Domain Containing 1 (THSD1) gene. In some cases the variant has a single codon substitution in at least one THSD1 allele relative to NCBI Reference Sequence: NP_061146.1. In specific cases, the single codon substitution is L5F, R460W, E466G, G600E, P639L. T653I, or S775P. In some instances the therapeutically effective dose of the autophagy inhibitor is administered systemically, and the systemic administration can include, but it is not limited to: (i) intravenous; (ii) intra-arterial; (iii) subcutaneous; or (iv) intraperitoneal. In other cases, the therapeutically effective dose of the autophagy inhibitor is administered locally. The local administration can include, but is not limited to, (i) intracranial; (ii) intra-ocular; (iii) intra-nasal; (iv) intrathecal or (v) intra-vascular. In preferred instances the subject is a human.

In some aspects the disclosure describes an autophagy inhibitor for use in a method of treating an aneurysm in a subject. The disclosure provides for a use of an autophagy inhibitor in the manufacture of a medicament for the treatment of an aneurysm, such as intracranial aneurysm (IA) or aortic aneurysm (AA). The disclosure provides for a use of an autophagy inhibitor for the treatment of an aneurysm, such as intracranial aneurysm (IA) or aortic aneurysm (AA). The autophagy inhibitor can be a phagophore inhibitor, an autophagosome inhibitor, an autolysosome inhibitor, or an inhibitor that blocks the autophagosome-lysosome fusion. In some instances the autophagy inhibitor is selected from the group consisting of wortmannin, chloroquine, clomipramine, 3-Methyladenine, Bafilomycin A1, Pepstatin A, or Pepstatin E-64-d. The aneurysm can be an intracranial aneurysm or an aortic aneurysm. The subject can carry a variant affecting the expression of a Thrombospondin Type 1 Domain Containing 1 (THSD1) gene. Such variants can be in a coding region, in a control sequence, or in a non-coding region of the Thrombospondin Type 1 Domain Containing 1 (THSD1) gene. In some cases, the variant in the THSD1 gene is a single codon substitution in at least one THSD1 allele, such as L5F, R460W, E466G, G600E. P639L, T653I, or S775P. In some instances the therapeutically effective dose of the autophagy inhibitor is administered systemically, and the systemic administration can include, but it is not limited to: (i) intravenous; (ii) intra-arterial; (iii) subcutaneous; or (iv) intraperitoneal. In other cases, the therapeutically effective dose of the autophagy inhibitor is administered locally. The local administration can include, but is not limited to, (i) intracranial; (ii) intra-ocular; (iii) intra-nasal; (iv) intrathecal or (v) intra-vascular. In preferred instances the subject is a human.

The present disclosure also provides for a kit(s) comprising any one of the autophagy inhibitors described herein and instructions for use thereof.

›BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fec.

The foregoing and other features and advantages of the present invention will be more fully understood from the following detailed description of illustrative embodiments taken in conjunction with the accompanying drawings in which:

FIG. 1 A ( FIG. 1 A ) illustrates simplified pedigrees of three IA families (NR4748, NR4931, and NR5704). Specifically, FIG. 1 A illustrates Intracranial Aneurysm (IA) affected (black), aortic aneurysm (AA) affected (half black), unaffected individuals >45 (white), and individuals with unknown/unclear status (gray symbols).

FIG. 1 B ( FIG. 1 B ) depicts patient-identified THSD1 variants identified in the pedigrees of the families from FIG. 1 B . The black bar represents the 853 amino acids of the WT version of the THSD1 gene. The diagram lists 8 variants found in patients affected by IA and AA, namely L5F, R450X, R460W, E466G, G600E, P639L, T653I, S775P. The back boxes illustrate the relative position of the signal peptide (SP), thrombospondin type 1 domain (TSP1), and transmembrane (TM) domains of THSD1.

FIG. 2 ( FIG. 2 ) is a drawing depicting an intracranial aneurysm. An intracranial aneurysm, also known as a brain aneurysm, is a cerebrovascular disorder in which weakness in the wall of a cerebral artery or vein causes a localized dilation or ballooning of the blood vessel.

FIG. 3 ( FIG. 3 ) is a drawing depicting a model of autophagy pathway that degrades focal adhesion.

FIG. 4 a through FIG. 4 f ( FIG. 4 a - 4 f ) are experimental results depicting that loss-of-function of THSD1 activates endothelial autophagy. Legend: P/E: Pepstatin A and E-64-d.

FIG. 5 a through FIG. 5 b ( FIG. 5 a - 5 b ) are experimental results depicting that autophagy inhibition rescues focal adhesion defects in THSD1-deficient endothelial cells.

FIG. 6 a through FIG. 6 c ( FIG. 6 a - 6 c ) are experimental results depicting that autophagy inhibition rescues cerebrovascular integrity defects in Thsd1-deficient zebrafish.

FIG. 7 ( FIG. 7 ) are experimental results depicting that loss-of-function of Thsd1 promotes IA formation in circle of Willis in mice.

FIG. 8 a through FIG. 8 c ( FIG. 8 a - 8 c ) are experimental results depicting that loss-of-function of Thsd1 reduces FA number in intimal endothelial cells in circle of Willis in mice.

FIG. 9 A through FIG. 9 C are protein alignments between human and zebrafish THSD1.

FIG. 10 is a sequence alignment illustrating three rare variants of thsd1 conserved between humans and fish.

FIG. 11 is a graph charting the results of treatment of a model organism with conserved sequences demonstrating that autophagy inhibitors rescued intracranial hemorrhage. Three exemplary inhibitors disclosed on this chart include 3-MA, Wortmannin, and Verteporfin.

It should be understood that the drawings are not necessarily to scale, and that like reference numbers refer to like features.

›INCORPORATION BY REFERENCE

All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.

›DETAILED DESCRIPTIONS · 1 of 2

In the following description, numerous specific details are set forth to provide a more thorough understanding of the present invention. However, it will be apparent to one of skill in the art that the present invention may be practiced without one or more of these specific details. In other instances, features and procedures well known to those skilled in the art have not been described in order to avoid obscuring the invention. The terms used herein are intended to have the plain and ordinary meaning as understood by those of ordinary skill in the art.

The rupture of an intracranial aneurysm frequently causes a subarachnoid hemorrhage (SAH), a type of stroke characterized by high morbidity and mortality. Specifically, the present disclosure demonstrates with data from three large IA/SAH families with at least 4 affected individuals where whole exome sequencing has been performed to identify rare variants that segregate with disease. For each family, whole exome sequencing has been performed on at least 15 family members, irrespective of their IA status.

Previously, it has been reported that deleterious Thrombospondin-type 1 domain-containing protein 1 (THSD1) rare variants caused disease in both familial and sporadic cases with supporting evidence from animal models. Of note, whole exome sequencing of large IA families identified (some members of the affected family are shown in the pedigree of FIG. 1 A ) a THSD1 nonsense mutation that segregated in all nine (9) affected and was absent in 13 unaffected family members. It was further discovered that eight (8) THSD1 rare missense variants in 507 unrelated patients/probands where each perturbed THSD1 cell adhesion activity.

These rare variants were highly enriched in case-control studies in comparison to ethnically matched controls. It was found that Thsd1 loss-of-function leads to brain hemorrhage and premature death in both zebrafish and mice. Further, Thsd1 heterozygous and null mice developed IA and suffered SAH. The study further demonstrated that THSD1 is highly expressed in endothelial cells of the cerebrovasculature, is important for cell adhesion, promotes nascent focal adhesion assembly via Talin interactions, and potentially regulates downstream signaling. For further description of this work see. Z. Xu, D. Kim, et al., NeuroMolecular Medicine (2019) 21:325-343; T. Santiago-Sim, D. Kim, et al., Stroke. 2016; 47:3005-3013. DOI: 10.1161/STROKEAHA.116.014161); Yan-Ning Rui and D. Kim, et al., Cell Physiol Biochem 2017; 43:2200-2211; each of which incorporated by reference in their entireties). However the study did not provide any insights on the THSD1 molecular pathways.

To further study the role of THSD1 in IA/SAH, additional analysis of whole exome sequencing of the IA families described in FIG. 1 was conducted. The detailed analysis identified a THSD1 nonsense mutation that segregated in all 9 affected and was absent in 13 unaffected family members. Notably, the exome sequencing analysis uncovered multiple signaling pathways that appeared to be affected by THSD1 expression: Integrin, Src, PI3/AKT/mTor, and Rho signaling that are functionally linked to Focal Adhesion Kinase (FAK) signaling as well as TGFβ signaling (see Table 1, discussed in Example 1). The present disclosure contemplates that THSD1 regulated genes may contribute to IA pathogenesis and that modulating their function may be beneficial as an IA treatment or in other diseases with aberrant THSD1 expression.

The present disclosure considered the differentially expressed genes and characterized autophagy pathways as contributors to IA development and potential targets for therapy. The present disclosure also contemplates that mutations in genes other than THSD1 that affect the autophagy pathway could render a subject at risk of suffering an IA. The present disclosure characterizes in detail the autophagy pathway as a novel molecular target for the treatment of subjects at risk of developing an aneurysm.

In some aspects, the present disclosure provides the molecular characterization of autophagy in the IA pathology. Autophagy is a catabolic process that degrades intracellular cargos. The autophagosome, a double membrane-bound vesicle with microtubule-associated protein 1A/1B-light chain 3 (LC3) protein associated on both sides, engulfs cytoplasmic constituents and later fuses with lysosome for degradation. In comparison to starvation-induced bulk autophagy, selective autophagy plays an important role in controlling organelle homeostasis. NBR1-mediated or Src-mediated selective autophagy were found to degrade FA via distinct mechanisms. NBR1 as a cargo receptor bridges LC3 to paxillin, a universal marker for FA, whereas SRC kinase promotes the direct interaction of LC3 and paxillin in a phosphorylation-dependent manner. However, the upstream signaling that determines the temporospatial degradation of FA remained unclear. The present disclosure considered different stages of autophagy pathway as potentially providing therapeutic targets for treatment of a genetic aneurysm in subjects at risk.

In some aspects, the present disclosure demonstrates that THSD1, as a transmembrane protein, is the upstream regulator of the selective autophagy cascade in endothelial cells. The disclosure contemplates that the THSD1-autophagy-FA axis regulates cerebrovascular integrity, and this is impaired in subjects that are prone or at risk of suffering an aneurysm particularly an intracranial aneurysm.

In some aspects, the present disclosure provides a method to treat a subject at risk of suffering from an aneurysm comprised of administering to said subject a therapeutically effective dose of a compound that modulates autophagy biogenesis. Examples of such compounds considered by the disclosure include: vertepofin, chloroquine, and/or clomipramine. Vertepofin was reported to inhibit autophagosome biogenesis, while chloroquine and clomipramine were reported to inhibit autophagosome-lysosome fusion. Autophagosome biogenesis and autophagosome-lysosome fusion are two sequential steps in autophagy. In many instances the subject carries a variant affecting the expression of a Thrombospondin Type 1 Domain Containing 1 (THSD1) gene. The variant can be in a coding region of the THSD1 gene, in a control sequence of a non-coding region of the THSD1 gene, or in any other suitable region. In some instances, the variant in the THSD1 gene is a single codon substitution in at least one THSD1 allele, such as the exemplary variants identified and described in FIG. 1 B , which include single codon substitutions at codon L5F, R460W, E466G, G600E, P639L, T653I, S775P.

›DETAILED DESCRIPTIONS · 2 of 2

Methods of Treating Intracranial Aneurysms

The methods, compositions, and uses of this disclosure may comprise a treatment method to arrest, reverse, or ameliorate an aneurysm, e.g., an intracranial aneurysm. In some cases, the therapeutic effect is achieved by administrating a therapeutically-effective dose of a autophagy inhibitor.

Wherein an autophagy inhibitor is utilized, the inhibitor may be of any suitable kind as long as it leads to autophagy inhibition. For instance, the inhibitor may block a phagophore (see FIG. 3 ; illustrating 3MA as an exemplary inhibitor of a phagophore), it may block an autophagosome (see FIG. 3 ; illustrating 3MA as an exemplary inhibitor of an autophagosome), or it may block an autolysosome (see FIG. 3 ; illustrating P/E—i.e., Pepstatin A and E-64-d—, as an exemplary inhibitors of an autophagosome).

The treatment may comprise treating a subject (e.g. a patient at risk of having an intracranial aneurysm due to the presence of a THSD1 genetic variant or an animal with a similar genetic variant). The disease may be a weakness in a blood vessel in the brain that balloons and fills with blood, for example, a brain aneurysm (also called a cerebral aneurysm or an intracranial aneurysm) is a ballooning arising from a weakened area in the wall of a blood vessel in the brain. The subject may be a human.

Treatment may be provided to the subject before clinical onset of disease. For instance, in specific cases, treatment may be provided upon the identification of a THSD1 variant in a subject, before the onset of a disease. Treatment may be provided to the subject after clinical onset of disease. Treatment may be provided to the subject after 1 day, 1 week, 6 months, 12 months, or 2 years after clinical onset of the disease. Treatment may be provided to the subject for more than 1 day, 1 week, 1 month, 6 months, 12 months, 2 years or more after clinical onset of disease. Treatment may be provided to the subject for less than 1 day, 1 week, 1 month, 6 months, 12 months, or 2 years after clinical onset of the disease. Treatment may also include treating a human in a clinical trial. Because of the genetic aspect of IA, treatment may be provided through the lifetime of a subject that is afflicted with a THSD1 variant that may lead to subarachnoid hemorrhage. In some aspects, treatment will be prescribed to prevent IA in a subject that carries a THSD1 variant associated with IA.

A treatment can comprise administering to a subject a pharmaceutical composition, such as one or more of the pharmaceutical compositions described throughout the disclosure. A treatment can comprise modulating the levels of autophagy in vivo. A treatment may comprise administering a suitable level of an autophagy inhibitor for reducing bulge's in the wall of a blood vessel and preventing Subarachnoid hemorrhage.

Further, there are many risk factors for the development of intracranial aneurysms, both inherited and acquired. Females are more prone to aneurysm rupture, with SAH times more common in women. The prevalence of aneurysms is increased in certain genetic diseases; the classic example is autosomal dominant polycystic kidney disease (ADPKD), but other diseases such as Ehlers-Danlos syndrome, neurofibromatosis, a1-antitrypsin deficiency also demonstrate a link.

In ADPKD, 10% to 15% of patients develop intracranial aneurysms. Marfan's Syndrome was once thought to be linked to intracranial aneurysm formation, but recent evidence suggests that this may not be true. Aneurysms also run in families in the absence of an identified genetic disorder, with a prevalence of 7% to 20% in first or second degree relatives of patients who have suffered a SAH. FIG. 1 A discloses a large family with variants in the THSD1 gene that have been causally linked to IA.

Autophagy Inhibitors

The methods, compositions, and uses of this disclosure may comprise a treatment method to prevent, arrest, reverse, or ameliorate an intracranial aneurysm. In some cases, the therapeutic effect is achieved by administrating a therapeutically-effective dose of a autophagy inhibitor.

Autophagy is a conserved lysosomal-dependent catabolic process that maintains the cellular homeostasis by recycling misfolded proteins and damaged organelles. It involves a series of ordered events (initiation, nucleation, elongation, lysosomal fusion and degradation) that are tightly regulated/controlled by diverse cell signals and stress. Autophagy begins with the nucleation of phagophores, which then expand to give rise to the double-membrane autophagosomes. Autophagosomes ultimately fuse with lysosomes, where the cytosolic cargoes are degraded. How the phagophore is generated and grows into a sealed autophagosome is still not clear in detail, but inhibitors of each step have been identified.

A number of therapeutics exist that modulate the various stages of autophagy initiation (e.g., ULK kinase inhibitors), nucleation (e.g., Vps34 inhibitors), elongation (e.g., ATG4 inhibitors), phagophore domain (e.g., ATG5), and lysosome fusion (e.g., chloroquine, hydroxyl chloroquine, etc.). See FIG. 3 for an schematic of exemplary stages. Also a number of small molecules reported to induce autophagy by targeting mammalian target of rapamycin (e.g., rapamycin analogs) or adenosine 5′-monophosphate-activated protein kinase (e.g., sulforaphane). Thus, many potential therapeutic targets exist in the autophagy pathway that could be harnessed for developing new therapies that can be used to prevent aneurysms in individuals carrying genetic mutations known to lead to aneurysms. See, e.g., the individuals from FIG. 1 A .

In some embodiments, an intracranial aneurysm is susceptible to treatment with an autophagy inhibitor of TABLE 1. Non-limiting examples of autophagy inhibitors include wortmannin, chloroquine and clomipramine. Vertepofin was reported to inhibit autophagosome biogenesis, while chloroquine and clomipramine were reported to inhibit autophagosome-lysosome fusion. Autophagosome biogenesis and autophagosome-lysosome fusion are two sequential steps in autophagy. A more comprehensive list of autophagy inhibitors include:

›Definitions

All of the functionalities described in connection with one embodiment of the methods, devices or instruments described herein are intended to be applicable to the additional embodiments of the methods, devices and instruments described herein except where expressly stated or where the feature or function is incompatible with the additional embodiments. For example, where a given feature or function is expressly described in connection with one embodiment but not expressly mentioned in connection with an alternative embodiment, it should be understood that the feature or function may be deployed, utilized, or implemented in connection with the alternative embodiment unless the feature or function is incompatible with the alternative embodiment.

Note that as used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “a cell” refers to one or more cells, and reference to “the system” includes reference to equivalent steps, methods and devices known to those skilled in the art, and so forth. Furthermore, terms such as “first,” “second,” “third,” etc., merely identify one of a number of steps, components, functions, and/or points of reference as disclosed herein, and likewise do not necessarily limit embodiments of the present disclosure to any particular configuration or orientation.

Subjects can be humans, non-human primates such as chimpanzees, and other apes and monkey species; farm animals such as cattle, horses, sheep, goats, swine; domestic animals such as rabbits, dogs, and cats; laboratory animals including rodents, such as rats, mice and guinea pigs, and the like. A subject can be of any age. Subjects can be, for example, elderly adults, adults, adolescents, pre-adolescents, children, toddlers, infants.

As used in the specification and claims of this application, the term “administering” includes any method which is effective to result in delivery of an autophagy inhibitor to the subject.

As used in this specification, the term “aneurysm” refers to broad classes of aneurysm, including aneurysms: abdominal aortic, thoracic aortic, and cerebral.

As used in this specification, the term “cerebral aneurysm” or “intracranial aneurysm” (also known as a brain aneurysm) is a weak or thin spot on an artery in the brain that balloons or bulges out and fills with blood. The bulging aneurysm can put pressure on the nerves or brain tissue. It may also burst or rupture, spilling blood into the surrounding tissue (called a hemorrhage). An unruptured aneurysm usually causes no symptoms. A key symptom of a ruptured aneurysm is a sudden, severe headache. Treatments for an unruptured aneurysm include medications to control blood pressure and procedures to prevent a future rupture.

As used in this specification, the term “abdominal aortic” aneurysm (AAA) is a bulge or swelling in the aorta, the main blood vessel that runs from the heart down through the chest and tummy. An AAA can be dangerous if it is not spotted early on. It can get bigger over time and could burst (rupture), causing life-threatening bleeding.

As used in this specification, the term “abdominal aortic” aneurysm (AAA) is a bulge or swelling in the aorta, the main blood vessel that runs from the heart down through the chest and tummy. An AAA can be dangerous if it is not spotted early on. It can get bigger over time and could burst (rupture), causing life-threatening bleeding.

As used in this specification, the term “thoracic aortic” aneurysm is an abnormal widening or ballooning of a portion of an artery due to weakness in the wall of the blood vessel. A thoracic aortic aneurysm occurs in the part of the body's largest artery (the aorta) that passes through the chest.

As used in the specification and claims of this application, the term “at risk” or more specifically a “subject at risk of developing an intracranial aneurysm” is a subject afflicted with a genetic variant, e.g., THSD1 variant, that causes the subarachnoid hemorrhage seen when an aneurysm ruptures.

The term DNA “control sequences” refers collectively to promoter sequences, polyadenylation signals, transcription termination sequences, upstream regulatory domains, origins of replication, internal ribosome entry sites, nuclear localization sequences, enhancers, and the like, which collectively provide for the replication, transcription and translation of a coding sequence in a recipient cell.

Where a range of values is provided, it is understood that each intervening value, between the upper and lower limit of that range and any other stated or intervening value in that stated range is encompassed within the invention. The upper and lower limits of these smaller ranges may independently be included in smaller ranges, and are also encompassed within the invention, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the invention.

›EMBODIMENTS

EMBODIMENT 1. A method for treating a subject at risk of suffering from an aneurysm comprised of administering to said subject a therapeutically effective dose of an autophagy inhibitor.

EMBODIMENT 2. The method of embodiment 1, wherein the autophagy inhibitor is a phagophore inhibitor.

EMBODIMENT 3. The method of embodiment 1, wherein the autophagy inhibitor is a autophagosome inhibitor.

EMBODIMENT 4. The method of embodiment 1, wherein the autophagy inhibitor blocks the autophagosome-lysosome fusion.

EMBODIMENT 5. The method of embodiment 1, wherein the autophagy inhibitor is an autolysosome inhibitor.

EMBODIMENT 6. The method of embodiment 1, wherein the autophagy inhibitor is selected from the group consisting of wortmannin, chloroquine, clomipramine, 3-Methyladenine, Bafilomycin A1, Pepstatin A, and Pepstatin E-64-d.

EMBODIMENT 7. The method of embodiment 6, wherein the autophagy inhibitor is wortmannin
EMBODIMENT 8. The method of embodiment 6, wherein the autophagy inhibitor is chloroquine
EMBODIMENT 9. The method of embodiment 6, wherein the autophagy inhibitor is clomipramine
EMBODIMENT 10. The method of embodiment 6, wherein the autophagy inhibitor is 3-Methyladenine
EMBODIMENT 11. The method of embodiment 6, wherein the autophagy inhibitor is Bafilomycin A1
EMBODIMENT 12. The method of embodiment 6, wherein the autophagy inhibitor is Pepstatin A
EMBODIMENT 13. The method of embodiment 6, wherein the autophagy inhibitor is Pepstatin E-64-d
EMBODIMENT 14. The method of embodiment 1, wherein the aneurysm is an intracranial aneurysm
›EMBODIMENT 15. The method of embodiment 1, wherein the aneurysm is an aortic aneurysm

EMBODIMENT 16. The method of embodiment 1, wherein the subject carries a variant affecting the expression of a Thrombospondin Type 1 Domain Containing 1 (THSD1) gene.

EMBODIMENT 17. The method of embodiment 16, wherein the variant is in a coding region of the Thrombospondin Type 1 Domain Containing 1 (THSD1) gene.

EMBODIMENT 18. The method of embodiment 16, wherein the variant is in a control sequence of a non-coding region of the Thrombospondin Type 1 Domain Containing 1 (THSD1) gene.

EMBODIMENT 19. The method of embodiment 1, wherein the variant in the THSD1 gene is a single codon substitution in at least one THSD1 allele.

EMBODIMENT 20. The method of embodiment 1, wherein the single codon substitution is L5F, R460W, E466G, G600E, P639L, T653I, or S775P.

EMBODIMENT 21. The method of embodiment 1, wherein the therapeutically effective dose of the autophagy inhibitor is administered systemically.

EMBODIMENT 22. The method of embodiment 21, wherein systemic administration includes, but is not limited to: (i) intravenous; (ii) intra-arterial; (iii) subcutaneous; or (iv) intraperitoneal.

EMBODIMENT 23. The method of embodiment 1, wherein the therapeutically effective dose of the autophagy inhibitor is administered locally.

EMBODIMENT 24. The method of embodiment 23, wherein local administration includes, but is not limited to, (i) intracranial; (ii) intra-ocular; (iii) intra-nasal; (iv) intrathecal or (v) intra-vascular.

›EMBODIMENT 25. The method of embodiment 1, wherein the subject is a human

EMBODIMENT 26. An autophagy inhibitor for use in a method of treating an aneurysm in a subject.

EMBODIMENT 27. The autophagy inhibitor of embodiment 26, wherein the autophagy inhibitor is a phagophore inhibitor.

EMBODIMENT 28. The autophagy inhibitor of embodiment 26, wherein the autophagy inhibitor is an autophagosome inhibitor.

EMBODIMENT 29. The autophagy inhibitor of embodiment 26, wherein the autophagy inhibitor is an autolysosome inhibitor.

EMBODIMENT 30. The autophagy inhibitor of embodiment 26, wherein the autophagy inhibitor blocks the autophagosome-lysosome fusion.

EMBODIMENT 31. The autophagy inhibitor of embodiment 26, wherein the autophagy inhibitor is selected from the group consisting of wortmannin, chloroquine, clomipramine, 3-Methyladenine, Bafilomycin A1, Pepstatin A, or Pepstatin E-64-d.

EMBODIMENT 32. The autophagy inhibitor of embodiment 31, wherein the autophagy inhibitor is wortmannin.

EMBODIMENT 33. The autophagy inhibitor of embodiment 31, wherein the autophagy inhibitor is chloroquine.

EMBODIMENT 34. The autophagy inhibitor of embodiment 31, wherein the autophagy inhibitor is clomipramine.

EMBODIMENT 35. The autophagy inhibitor of embodiment 31, wherein the autophagy inhibitor is 3-Methyladenine.

EMBODIMENT 36. The autophagy inhibitor of embodiment 31, wherein the autophagy inhibitor is Bafilomycin A1.

EMBODIMENT 37. The autophagy inhibitor of embodiment 31, wherein the autophagy inhibitor is Pepstatin A.

EMBODIMENT 38. The autophagy inhibitor of embodiment 31, wherein the autophagy inhibitor is Pepstatin E-64-d.

EMBODIMENT 39. The autophagy inhibitor of embodiment 26, wherein the aneurysm is an intracranial aneurysm.

EMBODIMENT 40. The autophagy inhibitor of embodiment 26, wherein the aneurysm is an aortic aneurysm.

EMBODIMENT 41. The autophagy inhibitor of embodiment 26, wherein the subject carries a variant affecting the expression of a Thrombospondin Type 1 Domain Containing 1 (THSD1) gene.

EMBODIMENT 42. The autophagy inhibitor of embodiment 41, wherein the variant is in a coding region of the Thrombospondin Type 1 Domain Containing 1 (THSD1) gene.

EMBODIMENT 43. The autophagy inhibitor of embodiment 41, wherein the variant is in a control sequence of a non-coding region of the Thrombospondin Type 1 Domain Containing 1 (THSD1) gene.

EMBODIMENT 44. The autophagy inhibitor of embodiment 41, wherein the variant in the THSD1 gene is a single codon substitution in at least one THSD1 allele.

EMBODIMENT 45. The autophagy inhibitor of embodiment 44, wherein the single codon substitution is L5F, R460W, E466G, G600E, P639L, T653I, or S775P.

EMBODIMENT 46. The autophagy inhibitor of embodiment 26, wherein the therapeutically effective dose of the autophagy inhibitor is administered systemically.

EMBODIMENT 47. The autophagy inhibitor of embodiment 46, wherein systemic administration includes, but is not limited to: (i) intravenous; (ii) intra-arterial; (iii) subcutaneous; or (iv) intraperitoneal.

EMBODIMENT 48. The autophagy inhibitor of embodiment 26, wherein the therapeutically effective dose of the autophagy inhibitor is administered is administered locally.

EMBODIMENT 49. The autophagy inhibitor of embodiment 48, wherein local administration includes, but is not limited to, (i) intracranial; (ii) intra-ocular; (iii) intra-nasal; (iv) intrathecal or (v) intra-vescular.

›EMBODIMENT 50. The autophagy inhibitor of embodiment 26, wherein the subject is a human

EMBODIMENT 51. The use of an autophagy inhibitor of any one of embodiments 26-50 in the manufacture of a medicament for the treatment of an aneurysm.

EMBODIMENT 52. A kit comprising an autophagy inhibitor of any one of embodiments 26-50 and instructions for use thereof.

›EXAMPLES · 1 of 3

The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use the present invention, and are not intended to limit the scope of what the inventors regard as their invention, nor are they intended to represent or imply that the experiments below are all of or the only experiments performed. It will be appreciated by persons skilled in the art that numerous variations and/or modifications may be made to the invention as shown in the specific aspects without departing from the spirit or scope of the invention as broadly described. The present aspects are, therefore, to be considered in all respects as illustrative and not restrictive.

The practice of some molecular techniques described herein may employ, unless otherwise indicated, techniques and descriptions of molecular biology (including recombinant techniques), cell biology, biochemistry, and genetic engineering technology, which are within the skill of those who practice in the art. Such techniques and descriptions can be found in standard laboratory manuals such as Westerfield, M. (2000). The zebrafish book. A guide for the laboratory use of zebrafish ( Danio rerio ). 4th ed., Univ. of Oregon Press, Eugene; all of which are herein incorporated in their entirety by reference for all purposes.

Example 1: Molecular Dissection of THSD1 Function in Vascular Endothelial Cells from Global Transcriptomics

Genetic factors play a significant role in IA pathogenesis as illustrated by family studies and several IA predisposing syndromes. 7%-20% of all patients have a known family history and a family history is the strongest risk factor for disease. Excluding syndromes that account for less than 1% of all IA cases, candidate IA genes have been primarily identified by genome-wide association studies and more recently, by whole exome sequencing in affected families. Yet, little is known about the genetic causes of IA providing minimum insight for the understanding and development of therapeutic targets that could treat the disease.

Single-family genetic studies are a powerful tool to identify candidate high-risk genetic variants. FIG. 1 A illustrates a large family pedigree studied as part of the present disclosure to identify novel candidate genes whose rare variants cause intracranial aneurysm. Specifically, we studied three large IA/SAH families with at least 4 affected individuals where whole exome sequencing has been performed to identify rare variants that segregate with disease. For each family, whole exome sequencing has been performed on at least 15 family members, irrespective of their IA status.

Deleterious Thrombospondin-type 1 domain-containing protein 1 (THSD1) rare variants cause disease in both familial and sporadic cases with supporting evidence from animal models. THSD1 is predominantly expressed in vascular endothelial cells. The work identified deleterious variants in thrombospondin-type 1 domain-containing protein 1 (THSD1) that can cause IA and SAH. Initial characterization of Thsd1 in two vertebrate models including zebrafish and mice lead to the discovery that THSD1 mediated cerebral hemorrhage is located in subarachnoid space in mice. For further description of this work see. Z. Xu, D. Kim, et al., NeuroMolecular Medicine (2019) 21:325-343; T. Santiago-Sim, D. Kim, et al., Stroke. 2016; 47:3005-3013. DOI: 10.1161/STROKEAHA.116.014161); Yan-Ning Rui and D. Kim, et al., Cell Physiol Biochem 2017; 43:2200-2211; each of which incorporated by reference).

However, the mechanism of action utilized by the discovered THSD1 variants to drive disease remained elusive. Further, there was little information describing genes and pathways regulated by THSD1 using global transcriptomics that could be used to inform the mechanism of action of THSD1. Thus, on its own the identification of THSD1 in the context of AI was not sufficient to inform a therapeutic strategy.

The present disclosure contemplated that THSD1 regulated genes may contribute to IA pathogenesis and that modulating their function may be beneficial as an IA treatment or in other diseases with aberrant THSD1 expression. The present disclosure provides results from global transcriptome profiling in human vascular endothelial cells upon THSD1 knockdown that identifies THSD1-regulated specific genes and pathways that are critical for mediating its function, providing potential targets for therapeutic intervention in IA.

The instant disclosure provides RNAseq experiments in two THSD1 knock-down endothelial cell lines. The RNAseq results from both cell lines support the evidence that THSD1 regulates multiple signaling pathways: Integrin, Src, PI3/AKT/mTor, and Rho signaling that are functionally linked to Focal Adhesion Kinase (FAK) signaling. A few of these pathways were selected for further analysis and characterization.

Materials and Methods

Cell Culture

HEK293T cells were maintained in DMEM medium (Corning, 10-013-CV) containing 10% fetal bovine serum (Invitrogen, 10082147), 100 IU penicillin, and 100 μg/ml streptomycin. Transfections of small interfering RNAs and plasmid DNA were performed using lipofectamine 2000 (Life Technologies, 11668027) according to the manufacturer's instructions. Alternatively, for cells such as endothelial cells that are hard to transfect, we will utilize lentiviral system to generate stable cell lines.

Knock-Down Experiments

Knockdown experiments in human vascular endothelial cells were performed using two distinct cell lines [HUVECs and Human brain microvascular endothelial cells (HBMECs)] using four siRNAs (two control siRNAs and two THSD1-specific siRNAs) to minimize erroneous findings due to off-target effects.

Transcriptome Profiling

Bioinformatic analyses of the global transcriptome were performed on rRNA-depleted RNA samples by RNA-Seq. Table 1 illustrates results of the analysis. As shown on Table 1, THSD1 regulates multiple signaling pathways: Integrin, Src, PI3/AKT/mTor, and Rho signaling that are functionally linked to Focal Adhesion Kinase (FAK) signaling) as well as TGFβ signaling.

›EXAMPLES · 2 of 3

We identified a number of genes that are affected by the lack of THSD1 in the knock-down cell lines and are likely regulated by THSD1. A subset of these genes likely contributes to disease pathobiology and may be targets for therapeutic intervention. Table 2. Describes genes differentially expressed in THSD1 knockdowns.

Table 3. lists genes differentially expressed in THSD1 knockdown HUVECs.

Bioinformatic analyses highlighted a potential role for the Src Signaling pathway, and other pathways, in the pathology of IA. We evaluated the potential link to the Src signaling pathway below.

Example 2: THSD1 Negatively Regulates Autophagy, which Impairs Cerebrovascular Integrity and Contributes to IA Development

Intracranial aneurysm (IA) is a weakened area in the wall of cerebral artery that leads to a bulging in a brain blood vessel. The rupture of IA causes aneurysmal subarachnoid hemorrhage (SAH), a devastating form of stroke. More than 30% will die due to SAH and more than half of survivors will never return to independent living. Unfortunately, there are no treatments for IA except open or endovascular surgery. Attempts to find new therapeutic avenues are greatly hindered by the lack of knowledge of the gene(s) and pathways responsible for IA development and growth.

Autophagy is a catabolic process that degrades intracellular cargos. The autophagosome, a double membrane-bound vesicle with LC3 protein associated on both sides, engulfs cytoplasmic constituents and later fuses with lysosome for degradation. In comparison to starvation-induced bulk autophagy, selective autophagy plays an important role in controlling organelle homeostasis. Although it is believed that SRC kinase promotes the direct interaction of LC3 and paxillin in a phosphorylation-dependent manner, the upstream signaling that determines the temporospatial degradation of FA remains unclear. The disclosure contemplates that THSD1 is the upstream regulator of the selective autophagy cascade in endothelial cells and that the THSD1-autophagy-FA axis regulates cerebrovascular integrity, and this is impaired in IA patients.

Materials and Methods

Cell Culture

HEK293T cells were maintained in DMEM medium (Corning, 10-013-CV) containing 10% fetal bovine serum (Invitrogen, 10082147), 100 IU penicillin, and 100 μg/ml streptomycin. Transfections of small interfering RNAs and plasmid DNA were performed using lipofectamine 2000 (Life Technologies, 11668027) according to the manufacturer's instructions. Alternatively, for cells such as endothelial cells that are hard to transfect, we will utilize lentiviral system to generate stable cell lines.

Western Blot

Cells were lysed in 1% Triton lysis buffer and sonicated briefly before centrifuged at 18506 g for 30 min at 4° C. Total cell lysates were added by 2×SDS sample buffer and then subjected to discontinuous SDS-PAGE analysis. Proteins were transferred to nitro-cellulose membranes using a Bio-Rad (Hercules, CA) mini transfer apparatus followed by blocking with 5% nonfat milk. Primary antibodies and secondary antibodies were used usually at 1:1000 and 1:10000 dilutions respectively before using an Odyssey system to detect the fluorescence signal.

Immunofluorescence

Cells were grown on glass coverslips in the DMEM medium for 16 h before fixed with 4% formaldehyde-phosphate-buffered saline (Electronic Microscopy Sciences, 15710; Fisher Scientific, BP399-500) for 10 min. Cells were incubated with primary antibodies against focal adhesion markers such as paxillin overnight at 4° C. after 1 h blocking by 5% goat serum. Secondary antibodies conjugated with Alexa Fluor 488 or 594 were used to visualize the localization. Image was taken with a Leica Confocal Microscope and processed by ImageJ and GraphPad 7 software for statistical analysis.

Intracranial Hemorrhage in Zebrafish

Anti-sense morpholinos against thsd1, atg5 or talin was injected into one-cell stage zebrafish singly or in combination to silence the gene accordingly. At day 2 to day 3, embryos will be checked under regular optical microscope. Embryos with intracranial hemorrhages will be counted and imaged by Olympus microscope.

MicroFil Injection in Mice

Prepare MicroFil (Flow Tech, Inc. Carver, MA) casting solution according to the manufacturer's instruction: Mix 5 ml of MV diluent with 4 ml of filtered MV-112 compound (yellow). Add 450 μl (5%) of catalyst (MV curing agent). Use 10 ml syringe to inject MicroFil mixture into the left ventricle after the blood was flushed out by saline. Inject MicroFil mixture slowly into the left ventricle at approximately 3 ml/min.

En Face Immunostaining of Circle of Willis in Mice

For en face immunostaining, isolated intracerebral arteries were dissected out from the brain with micro-needle and micro-scissors under the stereomicroscope. For immunofluorescent staining, tissue samples were washed in phosphate buffered saline (PBS), blocked with 5% goat scrum in PBST (0.1% Triton-X in PBS), then incubated with primary antibodies followed by the appropriate fluorescent-labeled secondary antibodies.

The IA-causing gene THSD1 is required for focal adhesion stability.

The present disclosure contemplates that THSD1 may be a new endothelial-specific, mechanosensory protein that regulates autophagy pathway. FIG. 3 is a schematic model of autophagy pathway for focal adhesion degradation. Autophagy related genes (ATGx) are highlighted in black letters; drugs that inhibit different stages of autophagy are highlighted in red. Paxillin is a marker for focal adhesion. Out of the exemplary drugs depicted in FIG. 3 . 3-Methyladenine (3-MA) is used to inhibit and study the mechanism of autophagy (lysosomal self-degradation) and apoptosis under various conditions. 3-MA inhibits autophagy by blocking autophagosome formation via the inhibition of type III Phosphatidylinositol 3-kinases (PI-3K). Bafilomycin A1 (BafA1), a macrolide antibiotic, is a known inhibitor of the latter stages of autophagy, inhibiting fusion between autophagosomes and lysosomes by inhibiting vacuolar H+ ATPase. P/E refers to Pepstatin A and E-64-d. Both are lysosome protease inhibitors.

›EXAMPLES · 3 of 3

Autophagy activity impairs cerebrovascular integrity and promotes IA formation, likely via destabilization of focal adhesion.

To evaluate the molecular effect of THSD1 on endothelial autophagy signaling activity in human tissue samples the level of LC3 lipidation and p62 turnover were measured with Western blot and immunostaining in THSD1-deficient endothelial cells, so as to predict the IA progression and rupture. Collectively. FIGS. 4 a - 4 f illustrate increased LC3 puncta formation and reduced p62 level in THSD1-deficient endothelial cells. Representative images of GFP-LC3 puncta formation ( FIG. 4 a ) and quantification ( FIG. 4 b ) upon THSD1 knockdown are shown. The flux value is calculated as the difference imposed by P/E treatment ( FIG. 4 c ). The level of p62 ( FIG. 4 d ) is detected by western and quantified in ( FIG. 4 e ). THSD1 knockdown efficiency is confirmed by western in ( FIG. 4 f ). *P<0.05 and **P<0.01. Scale bar: 10 mm.

Collectively. FIGS. 5 a - 5 b demonstrate that autophagy inhibition rescues focal adhesion defects in human THSD1-deficient endothelial cells. Representative images of FA indicated by co-staining of paxillin (green) and actin (red) upon THSD1 and/or ATG5 knockdown are shown in ( FIG. 4 a ) and quantified in ( FIG. 4 b ). **P<0.01. Scale bar: 5 mm. As shown in FIGS. 5 a - 5 b . ATG5 knockdown rescues defective FA in THSD1-deficient primary endothelial cells.

Conclusion

These result support that the IA-causing gene THSD1 negatively regulates autophagy pathway in human cells. This raises a novel concept that autophagy may play a pathogenic role in IA disease.

›Example 3: In-Vivo Autophagy Inhibition Rescues Cerebrovascular Integrity Defects

In-Vivo Zebrafish Model

Intracranial aneurysm and hemorrhage are tightly associated with compromised cerebrovascular integrity. Recently, zebrafish have gained additional popularity as a vertebrate model organism for studying the cerebrovasculature. Since zebrafish embryos are transparent, intracranial hemorrhage can be directly observed using a standard microscope. Furthermore, zebrafish fecundity and rapid development permits rapid phenotypic evaluation as intracranial hemorrhage in zebrafish fry are detectable as early as 2-3 days post fertilization. Importantly, gain-of-function and loss-of-function approaches are well established in zebrafish that include morpholino and mRNA injections and more recently, through applications of CRISPR/Cas9 technology.

Collectively, FIGS. 6 a - 6 c demonstrate that autophagy inhibition rescues cerebrovascular integrity defects in an in-vivo model, namely Thsd1-deficient zebrafish. FIGS. 6 a - 6 c show that knockdown of atg5 rescues intracranial hemorrhage in Thsd1-deficient zebrafish. A prominent cerebral hemorrhage phenotype was observed in thsd1 knockdown zebrafish ( FIG. 6 a ). Atg5 knockdown ameliorated Thsd1-dependent hemorrhage incidents (comparing grey bars in FIG. 6 b ), which was prohibited by further knockdown of talin I (comparing the third and fourth bar in FIG. 6 c ). For each MO injection, 76-92 embryos were analyzed. *p<0.05.

In-Vivo Mammalian Model

To interrogate the consequence of Thsd1 loss in mammals, we used the Thsd1 knockout mouse that contains a knockin of a fluorescent Venus reporter. Thsd1 Venus/+ and Thsd1 Venus/Venus mice survived to weaning age in expected Mendelian ratios. However, brain magnetic resonance imagings revealed mild to severe dilatation of cerebral ventricles, consistent with hydrocephalus in a subset of mutant mice as young as 8 weeks (not shown here, previously reported). FIG. 7 illustrates that loss-of-function of Thsd1 promotes IA formation in circle of Willis in mice. FIG. 7 shows that IAs were visualized by Microfil including a PCA (top), a left Pcom (middle), and a right ICA (bottom) as indicated by arrows. n=10.

Collectively. FIGS. 8 a - 8 c demonstrate that loss-of-function of Thsd1 reduces FA number in intimal endothelial cells in mouse circle of Willis. As shown in FIGS. 8 a - 8 c , in control ( FIG. 8 a , panel a1) or Thsd1-deficient mice ( FIG. 8 a , panel a2). FAs in the endothelium of circle of Willis and morphology of endothelial cells were revealed by paxillin (green) and VE-cadherin (red), respectively, which were further quantified in ( FIG. 8 b ). Arrows indicate the locations of FAs in enlarged pictures. ( FIG. 8 c ) The FA number was not significantly affected in Thsd1-deficient primary smooth muscle cells from circle of Willis. **=p<0.01. n.s.: not significant. Scale bar: 1 μm. In conclusion. Focal adhesion is compromised in Thsd1-deficient mice.

Collectively, the data from two distinct animal models, a mammalian and a non-mammalian animal model demonstrates that autophagy plays a role in THSD1-mediated focal adhesion stability and IA formation.

Example 4: Treatment of Subjects with Unruptured Intracranial Aneurysm Bulges In-Vivo with an Inhibitor of Autophagosome Biogenesis

In-Vivo Zebrafish Model

Vertepofin is dissolved in DMSO as 10 mM. The working concentration of vertepofin is 10 uM. Both control and Thsd1-deficient zebrafish will be treated at 1 dpf (day post fertilization) for 24 hours and hemorrhage incidence will be counted at 2 dpf (n>80 for each genotype X treatment). The zebrafish model is well known for its case-of-use in drug evaluation in vivo as drugs can be directly added to embryo water. Similarly, we will treat Thsd1-deficient zebrafish with other two drugs including chloroquine and clomipramine. The working concentration for each is 100 uM and 10 uM, respectively.

Example 5: Genetic Engineering of Non-Human Animal Models Encoding Distinct THSD1 Rare Variants for In-Vivo Assessment of Efficacy of Various Autophagy Inhibitors

Identified Conserved Sequences Suitable for Assessing Cross Species Efficacies of Treatments:

A protein alignment between human and zebrafish THSD1 was performed. See FIG. 9 illustrates the result of the alignment with black color indicating identical amino acids and the grey color indicating similar amino acids between humans and zebra fish. The alignment underscored that three rare variants of THSD1 identified in the aforementioned examples were conserved between human and zebrafish. The conserved amino acids include R450, R460 and T653. See, e.g., FIG. 10 . The conserved amino acids were used as a rational for generating animal models of the human condition. The following constructs were generated:

Mutations R449X, R459W and T665I were found to be conserved between human and zebrafish. Subsequently, the nucleic acid constructs encoding these sequences were introduced into zebrafish thsd1 by PCR mutagenesis. Specifically, the thsd1 variant or the WT sequence was subcloned into pCS2+ zebrafish vector for expression. These constructs were used as tools to study cerebrovascular integrity mediated by thsd1 WT and rare variants in the zebrafish animal model selected to model a human condition.

In-Vivo Zebrafish Model

To test the hypothesis that autophagy inhibition could treat intracranial hemorrhage in-vivo 80-120 different zebrafish animals genetically engineered as described in Table 5 were treated with three distinct autophagy inhibitors, namely, 3-MA, wortmannin, or verteporfin. Control (DMSO) or other known autophagy inhibitors including 3-MA (10 mM), wortmannin (50 nM), and verteporfin (1 uM) were added to embryo water at 1 dpf for 24 hours. All embryos were injected by thsd1-MO and the hemorrhagic incidence was counted under microscope. For each injection, around 80-120 embryos were injected. *p<0.05, **p<0.01, n.s. means not significant. See FIG. 11 .

The data demonstrates a body of work that first identified and studied a large number of human families with a disease. After significant effort in contacting individuals and sequencing the families shown in FIG. 1 A , the present disclosure first identified THSD1 as a gene associated with sub-cranial hemorrhage. In specific cases, a single codon substitution was identified as responsible for the phenotype L5F, R460W, E466G, G600E, P639L, T653I, or S775P. The inventors developed a plethora of nucleic acid constructs, cell lines, and transgenic animal models to study the condition. Subsequently, a detailed characterization of molecular pathways whose transcription was disturbed in the disease condition was used to identify potential druggable targets and pathways for treatment. One such pathway was autophagy. Three distinct autophagy inhibitors were tested including 3-MA (10 mM), wortmannin (50 nM), and verteporfin (1 uM) and its ability to treat subjects, particularly its ability to treat subjects susceptible to an aneurism rupture was tested by counting the hemorrhagic incidence under the microscope on an animal model. The results illustrate that autophagy inhibition provides a treatment for modulating the rupture of an aneurysm in vivo.

›Example 6: Kits

The disclosure contemplates kits comprising an autophagy inhibitor selected from the group consisting of wortmannin, chloroquine, clomipramine, 3-Methyladenine, Bafilomycin A1, Pepstatin A, and Pepstatin E-64-d and instructions for use of the same in the treatment of a condition disclosure herein. Specifically, the disclosure contemplates use of these drugs in treating an intracranial aneurysm.

While this invention is satisfied by embodiments in many different forms, as described in detail in connection with preferred embodiments of the invention, it is understood that the present disclosure is to be considered as exemplary of the principles of the invention and is not intended to limit the invention to the specific embodiments illustrated and described herein. Numerous variations may be made by persons skilled in the art without departure from the spirit of the invention. The scope of the invention will be measured by the appended claims and their equivalents. The abstract and the title are not to be construed as limiting the scope of the present invention, as their purpose is to enable the appropriate authorities, as well as the general public, to quickly determine the general nature of the invention. In the claims that follow, unless the term “means” is used, none of the features or elements recited therein should be construed as means-plus-function limitations pursuant to 35 U.S.C. § 112, 6.

›Tables in the description — 5
TABLE 1 — Exemplary Autophagy Inhibitors
Product NameActivity
AS 1842856Potent and selective Foxo1 inhibitor;
suppresses autophagy
AutophinibPotent VPS34 inhibitor
AzithromycinAutophagy inhibitor; antibiotic
Bafilomycin A1H+-ATPase (vacuolar) inhibitor;
also inhibits autophagy
(±)-Bay K 8644L-type Ca2+ channel activator;
inhibits autophagy
ChloroquineInhibits apoptosis and autophagy
diphosphate
ClomipramineInhibits autophagosome-lysosome fusion
Concanamycin AH+-ATPase (vacuolar) inhibitor
DBeQSelective p97 ATPase inhibitor; blocks
autophagosome maturation
Pepstatin E 64dCathepsin inhibitor; interferes with
autolysosomal digestion
EdaravoneAutophagy inhibitor; also anti-ischemic
and antioxidant
GW 4064Selective farnesoid X receptor (FXR)
agonist; suppresses autophagy in
nutrient-deprived hepatocytes
HydroxychloroquineAutophagy inhibitor; also TLR9 inhibitor
sulfate
LY 294002Prototypical PI 3-kinase inhibitor; inhibits
hydrochlorideautophagic sequestration
Mdivi 1Autophagy inhibitor; also selective
dynamin inhibitor
3-MethyladenineClass III PI 3-kinase inhibitor; also
inhibits autophagy
ML 240ATP-competitive inhibitor of p97 ATPase;
impairs autophagosome maturation
MRT 67307Autophagy inhibitor; also salt inducible
dihydrochloridekinase (SIK) inhibitor
MRT 68601Potent TBK1 inhibitor; also inhibits
hydrochlorideautophagy
MRT 68921Autophagy inhibitor; potent ULK
dihydrochlorideinhibitor
NMS 873Potent and selective p97 ATPase (VCP)
allosteric inhibitor
NocodazoleMicrotubule inhibitor; inhibits
autophagosome-lysosome fusion
Pepstatin AProtease inhibitor; interferes with
autolysosomal digestion
Spautin 1Inhibits autophagy; USP10 and
USP13 inhibitor
TaxolPromotes assembly and inhibits
disassembly of microtubules
VertepofinInhibits autophagosome biogenesis
Vinblastine sulfateDisrupts microtubules; inhibits
autophagosome maturation
WortmanninPotent, irreversible inhibitor of PI 3-kinase.
Also inhibitor of PLK1
Xanthohumolp97 ATPase (VCP) inhibitor;
impairs autophagosome maturation
TABLE 2 — Genes differentially expressed in THSD1 knockdowns; human brain microvascular endothelial cells and HUVECs, combined
DescriptionGenes
Differential Expression uponALOX5AP, ARL17B, CTSS, GUK1,
THSD1 Loss Upregulated genesIFNAR2, LAMC2, NHLRC4, NISCH,
OLFML3, PSMD11, PUM2, SLC37A1,
SMAP1, SNORA27, TMEM50B,
UBAP2, ZNF780A
Differential Expression uponABCG2, ADAMTS1, AQP1, BCAP31,
THSD1 Loss DownregulatedCDC45, CHCHD7, DMD, ENOX2,
genesFAM219A, FGF2, FGFR1OP2, GOS2,
GJA4, IGFBP3, INAFM1, MAP2, MGP,
NOL3, NPR1, NVL, PPHLN1,
SERPINB2, SETBP1, (THSD1),
TMEM107, ZNF185
TABLE 3 — Differentially Expressed Genes in THSD1 Knockdown HUVECs
Ensembl GeneGene NamelogFClogCPMLRPValueFDR
ENSG00000136114THSD1−2.074.85141.121.52E−322.15E−28
ENSG00000265107GJA5−3.813.42137.131.13E−318.01E−28
ENSG00000130066SAT1−1.748.37128.151.04E−294.92E−26
ENSG00000111341MGP−1.466.50112.093.42E−261.21E−22
ENSG00000187513GJA4−2.294.32102.474.39E−241.25E−20
ENSG00000284057AP001273.28.67−0.9971.343.00E−177.11E−14
ENSG00000170323FABP4−2.096.3666.293.90E−167.91E−13
ENSG00000125266EFNB2−1.287.7763.281.79E−153.18E−12
ENSG00000113389NPR3−3.161.2556.874.65E−147.35E−11
ENSG00000134668SPOCD11.165.4554.031.97E−132.80E−10
ENSG00000118777ABCG2−2.384.9251.457.36E−139.50E−10
ENSG00000203812HIST2H2AA34.210.2050.591.14E−121.35E−09
ENSG00000272921AC005832.4−8.85−0.7248.912.69E−122.93E−09
ENSG00000078018MAP2−1.064.8448.513.29E−123.34E−09
ENSG00000115884SDC1−1.533.2348.333.61E−123.42E−09
ENSG00000139278GLIPR11.136.5347.734.89E−124.34E−09
ENSG00000101335MYL91.094.7647.076.83E−125.71E−09
ENSG00000181634TNFSF151.645.1045.621.43E−111.13E−08
ENSG00000122861PLAU1.035.5843.853.55E−112.65E−08
ENSG00000107551RASSF4−1.105.0743.683.86E−112.74E−08
ENSG00000274611TBC1D3−7.97−1.5243.135.12E−113.46E−08
ENSG00000149591TAGLN1.812.5442.716.35E−114.10E−08
ENSG00000171435KSR21.183.9038.395.80E−103.58E−07
ENSG00000153165RGPD34.26−1.4837.479.26E−105.48E−07
ENSG00000251569AC093899.27.32−2.2034.853.55E−092.02E−06
ENSG00000163083INHBB−2.572.1834.753.75E−092.05E−06
ENSG00000272949AC093668.2−7.24−2.1533.676.51E−093.43E−06
ENSG00000152217SETBP1−1.783.7533.178.42E−094.27E−06
ENSG00000119900OGFRL10.856.5932.791.03E−085.02E−06
ENSG00000082684SEMA5B−4.57−1.6232.231.37E−086.26E−06
ENSG00000169604ANTXR10.985.9132.241.36E−086.26E−06
ENSG00000137573SULF1−1.275.0331.881.64E−087.29E−06
ENSG00000115232ITGA41.353.2930.822.83E−081.22E−05
ENSG00000058085LAMC21.065.7130.054.21E−081.76E−05
ENSG00000022567SLC45A4−1.353.0729.705.04E−081.99E−05
ENSG00000172602RND1−1.741.6429.715.03E−081.99E−05
ENSG00000103426CORO7-PAM164.38−1.4829.027.16E−082.75E−05
ENSG00000120217CD2741.354.2128.778.14E−083.04E−05
ENSG00000116667C1orf21−0.994.4227.881.29E−074.70E−05
ENSG00000169129AFAP1L2−2.163.1627.671.44E−075.10E−05
ENSG00000138646HERC5−1.851.4727.511.56E−075.29E−05
ENSG00000197646PDCD1LG21.073.5827.551.53E−075.29E−05
ENSG00000064651SLC12A20.737.0526.912.13E−077.03E−05
ENSG00000171388APLN0.859.8526.023.39E−070.000109
ENSG00000175426PCSK11.512.6825.803.79E−070.00012
ENSG00000057019DCBLD20.916.7825.674.05E−070.000125
ENSG00000008517IL320.696.1125.524.37E−070.000132
ENSG00000138685FGF2−1.205.7225.215.15E−070.000152
ENSG00000065308TRAM20.678.1025.045.60E−070.000162
ENSG00000137507LRRC32−0.877.2224.746.57E−070.000187
ENSG00000129116PALLD0.696.2724.567.22E−070.000201
ENSG00000129521EGLN3−1.850.0924.447.66E−070.000209
ENSG00000125954CHURC1-FNTB−6.59−2.6724.258.46E−070.000227
ENSG00000152402GUCY1A21.901.3124.208.68E−070.000228
ENSG00000169429CXCL81.224.6223.661.15E−060.000297
ENSG00000164683HEY1−1.253.4923.301.38E−060.000345
ENSG00000176907TCIM0.953.7723.311.38E−060.000345
ENSG00000082126MPP40.764.7623.081.56E−060.000379
ENSG00000163637PRICKLE2−0.993.7623.061.57E−060.000379
ENSG00000148143ZNF4620.724.9522.921.69E−060.0004
ENSG00000139289PHLDA10.637.0022.222.43E−060.000566
ENSG00000028137TNFRSF1B−0.996.1422.022.69E−060.000617
ENSG00000139629GALNT60.665.9821.942.82E−060.000635
ENSG00000117586TNFSF40.667.4321.803.03E−060.000672
ENSG00000256514AP003419.11.680.9121.473.60E−060.000787
ENSG00000240583AQP1−1.843.4321.273.99E−060.000858
ENSG00000115252PDE1A−2.040.5721.174.20E−060.00089
ENSG00000178695KCTD12−0.718.9420.994.62E−060.000965
ENSG00000173535TNFRSF10C−0.656.6920.894.87E−060.001002
ENSG00000156298TSPAN7−1.503.2220.815.08E−060.001031
ENSG00000037280FLT4−0.956.2220.665.48E−060.001066
ENSG00000118515SGK11.026.1920.705.37E−060.001066
ENSG00000171105INSR−0.825.2020.675.47E−060.001066
ENSG00000128917DLL4−1.066.9920.555.81E−060.001116
ENSG00000164284GRPEL20.715.8320.286.70E−060.001268
ENSG00000130449ZSWIM60.846.2220.206.96E−060.0013
ENSG00000165029ABCA1−1.204.8620.187.06E−060.001303
ENSG00000143127ITGA10−0.954.8420.087.43E−060.001336
ENSG00000187720THSD40.775.6820.087.43E−060.001336
ENSG00000073008PVR0.697.3419.908.14E−060.001422
ENSG00000107731UNC5B−1.583.9019.938.03E−060.001422
ENSG00000122786CALD10.719.3119.898.21E−060.001422
ENSG00000110092CCND10.778.2619.768.76E−060.0015
ENSG00000154734ADAMTS1−1.323.6519.669.23E−060.001561
ENSG00000142178SIK11.162.1119.629.46E−060.001581
ENSG00000168843FSTL51.550.3519.539.92E−060.001638
ENSG00000121858TNFSF10−0.944.9219.411.05E−050.001722
ENSG00000169213RAB3B0.715.4719.351.09E−050.001754
ENSG00000166670MMP101.616.0019.291.12E−050.00179
ENSG00000138347MYPN2.35−1.1219.031.29E−050.002029
ENSG00000145247OCIAD20.765.6218.901.38E−050.002126
ENSG00000160801PTH1R−2.70−1.6718.891.38E−050.002126
ENSG00000184113CLDN5−0.917.7318.881.39E−050.002126
ENSG00000152518ZFP36L2−0.626.8718.761.48E−050.002235
ENSG00000171617ENC10.876.9218.561.64E−050.002457
ENSG00000166833NAV20.615.3718.421.77E−050.00262
ENSG00000177076ACER2−1.053.1118.281.91E−050.002793
ENSG00000154928EPHB11.072.2818.162.03E−050.002915
ENSG00000162407PLPP3−0.995.1918.162.03E−050.002915
ENSG00000099204ABLIM1−0.738.3118.112.09E−050.002957
ENSG00000177606JUN0.687.5918.092.10E−050.002957
ENSG00000170006TMEM1540.745.4818.032.17E−050.003026
ENSG00000118762PKD2−0.615.4617.912.32E−050.003197
ENSG00000108387‘SEPT4−1.64−0.2217.452.96E−050.004038
ENSG00000170891CYTL10.913.8317.253.28E−050.004439
ENSG00000175040CHST20.884.5817.173.42E−050.004583
ENSG00000167037SGSM1−1.411.3317.153.45E−050.004587
ENSG00000185070FLRT20.707.6017.093.57E−050.004694
ENSG00000180304OAZ2−0.566.8216.784.20E−050.005473
ENSG00000257093KIAA1147−0.597.2416.714.36E−050.005628
ENSG00000184897H1FX−0.586.2816.644.53E−050.005794
ENSG00000075426FOSL20.576.6616.524.80E−050.006094
ENSG00000105825TFPI20.577.1416.405.13E−050.006449
ENSG00000135318NT5E0.617.6216.385.18E−050.00645
ENSG00000127533F2RL31.231.0616.345.30E−050.006492
ENSG00000205683DPF31.212.9816.345.30E−050.006492
ENSG00000105499PLA2G4C0.763.6816.295.44E−050.006599
ENSG00000167984NLRC30.992.8216.026.26E−050.007507
ENSG00000168685IL7R1.301.7916.006.32E−050.007507
ENSG00000172985SH3RF30.645.0516.006.34E−050.007507
ENSG00000108551RASD11.212.5515.956.49E−050.00762
ENSG00000081087OSTM10.675.6615.816.99E−050.008139
ENSG00000128849CGNL1−0.786.4615.617.78E−050.008985
ENSG00000133816MICAL20.697.5815.597.87E−050.009013
ENSG00000132965ALOX5AP2.25−1.6115.558.04E−050.009132
ENSG00000084734GCKR−2.84−1.7115.368.89E−050.009794
ENSG00000108854SMURF20.537.9415.388.81E−050.009794
ENSG00000111859NEDD90.526.2715.368.89E−050.009794
ENSG00000154678PDE1C0.893.9915.378.84E−050.009794
ENSG00000033867SLC4A70.587.0315.339.05E−050.009889
ENSG00000152207CYSLTR2−2.45−0.5615.259.42E−050.010156
ENSG00000188452CERKL1.260.9115.259.44E−050.010156
ENSG00000105357MYH141.430.1915.209.66E−050.010323
ENSG00000185432METTL7A−1.013.6615.179.83E−050.010418
ENSG00000004799PDK4−1.182.6115.120.0001010.010639
ENSG00000122694GLIPR20.654.8815.100.0001020.010655
ENSG00000213402PTPRCAP−3.20−2.4015.080.0001030.010665
ENSG00000115902SLC1A4−0.694.8514.960.000110.011119
ENSG00000169248CXCL111.350.9014.970.0001090.011119
ENSG00000189367KIAA04081.83−0.7914.960.000110.011119
ENSG00000102755FLT1−0.778.5314.900.0001140.011449
ENSG00000135905DOCK100.625.3014.860.0001160.01158
ENSG00000079102RUNX1T1−0.824.5014.830.0001180.011588
ENSG00000153208MERTK0.585.5314.830.0001180.011588
ENSG00000198435NRARP−0.635.0514.820.0001180.011588
ENSG00000141682PMAIP11.024.2514.800.000120.01165
ENSG00000011347SYT7−1.86−0.0914.710.0001260.012144
ENSG00000135842FAM129A−1.241.6614.520.0001390.013339
ENSG00000020577SAMD4A0.625.9414.470.0001430.013504
ENSG00000143153ATP1B10.745.5414.470.0001420.013504
ENSG00000177666PNPLA2−0.556.3614.430.0001450.013671
ENSG00000085276MECOM−0.537.3314.390.0001480.013802
ENSG00000111145ELK3−0.648.6414.390.0001490.013802
ENSG00000140675SLC5A2−5.88−3.1814.340.0001520.014056
ENSG00000005108THSD7A−0.615.9914.270.0001590.014543
ENSG00000157613CREB3L11.041.7614.230.0001620.014743
ENSG00000163584RPL22L1−0.615.3014.180.0001660.015011
ENSG00000169418NPR1−1.453.0114.120.0001710.015403
ENSG00000131016AKAP120.5910.2914.070.0001760.015751
ENSG00000141298SSH20.556.7513.980.0001840.016299
ENSG00000163131CTSS0.962.7513.980.0001850.016299
ENSG00000026508CD440.695.5413.940.0001890.016335
ENSG00000136404TM6SF10.694.2513.920.000190.016335
ENSG00000144583‘MARCH40.825.5313.950.0001880.016335
ENSG00000175899A2M−1.562.4113.920.0001910.016335
ENSG00000176749CDK5R11.012.8913.940.0001890.016335
ENSG00000258984UBE2F-SCLY3.28−1.9413.880.0001940.016538
ENSG00000136960ENPP2−1.141.3513.860.0001970.016639
ENSG00000140416TPM10.618.6513.810.0002020.016977
ENSG00000112541PDE10A−0.923.0913.760.0002080.017288
ENSG00000198286CARD110.595.9013.760.0002080.017288
ENSG00000108825PTGES3L-1.90−0.9113.670.0002180.017886
AARSD1
ENSG00000185650ZFP36L10.516.8213.660.0002190.017886
ENSG00000188290HES4−1.302.2013.660.0002190.017886
ENSG00000114631PODXL20.664.0513.620.0002240.018189
ENSG00000106852LHX60.944.2013.590.0002270.018332
ENSG00000171115GIMAP8−0.637.6613.560.0002310.018514
ENSG00000189120SP61.041.7713.540.0002340.018568
ENSG00000265972TXNIP−1.353.7413.540.0002340.018568
ENSG00000154639CXADR0.574.9813.510.0002370.018606
ENSG00000169242EFNA1−0.756.2313.520.0002370.018606
ENSG00000204304PBX2−0.725.8013.490.000240.018755
ENSG00000157557ETS20.566.5913.450.0002440.018975
ENSG00000105855ITGB81.013.6713.440.0002460.018999
ENSG00000144802NFKBIZ0.884.3313.370.0002550.019615
ENSG00000204262COL5A20.518.2213.330.0002620.019978
ENSG00000163092XIRP22.56−0.5413.310.0002640.020085
ENSG00000049540ELN−2.37−1.7213.230.0002750.020704
ENSG00000166341DCHS10.507.0613.240.0002740.020704
ENSG00000115414FN10.6912.3013.170.0002840.021259
ENSG00000094880CDC23−0.635.4913.100.0002950.021903
ENSG00000164647STEAP1−0.674.3313.100.0002960.021903
ENSG00000119681LTBP20.489.5413.030.0003060.022511
ENSG00000107562CXCL122.40−1.4612.980.0003140.022927
ENSG00000138448ITGAV0.558.7612.960.0003180.022927
ENSG00000160223ICOSLG−0.723.6112.950.000320.022927
ENSG00000163644PPM1K−0.643.9312.960.0003180.022927
ENSG00000186575NF20.586.5312.950.0003190.022927
ENSG00000109906ZBTB16−1.081.1212.940.0003220.022986
ENSG00000144476ACKR3−0.774.0612.890.000330.023468
ENSG00000136011STAB2−3.99-2.8012.860.0003350.023698
ENSG00000074181NOTCH3−1.011.4712.840.0003380.023798
ENSG00000168916ZNF608−0.635.1512.720.0003620.025298
ENSG00000076351SLC46A10.822.7712.710.0003640.025315
ENSG00000151474FRMD4A0.537.3112.660.0003740.025951
ENSG00000139508SLC46A3−1.454.0812.580.000390.026876
ENSG00000131386GALNT15−1.700.1612.530.0004010.027499
ENSG00000101017CD40−0.654.4212.490.0004090.027854
ENSG00000270316BORCS7-ASMT−6.14−3.0012.490.000410.027854
ENSG00000141668CBLN22.750.1912.480.0004120.027879
ENSG00000146072TNFRSF210.476.6412.440.0004190.028234
ENSG00000183287CCBE11.061.3912.390.0004320.028931
ENSG00000029534ANK1−1.370.0112.370.0004360.029068
ENSG00000124593AL365205.1−0.903.1812.350.000440.029134
ENSG00000281028AC104662.2−6.09−3.0412.350.0004410.029134
ENSG00000187942LDLRAD2−0.763.4112.330.0004460.029332
ENSG00000071246VASH1−0.667.7612.300.0004530.029655
ENSG00000269307AC010463.1−6.06−3.0612.270.0004610.030027
ENSG00000050405LIMA10.477.2612.260.0004630.030037
ENSG00000259171AL163636.2−1.371.5812.250.0004650.030049
ENSG00000048740CELF20.496.2312.180.0004830.030936
ENSG00000116774OLFML30.991.4512.180.0004820.030936
ENSG00000182240BACE2−0.567.5212.170.0004860.030971
ENSG00000204767FAM196B0.773.3912.150.000490.031102
ENSG00000211448DIO22.26−1.8412.140.0004940.031198
ENSG00000151468CCDC3−1.170.7212.110.0005010.031481
ENSG00000196498NCOR20.527.4912.090.0005060.031651
ENSG00000049130KITLG0.705.1612.070.0005120.031901
ENSG00000137033IL33−1.944.4012.060.0005160.031997
ENSG00000130635COL5A10.528.5812.030.0005240.032215
ENSG00000133056PIK3C2B−0.675.9012.030.0005220.032215
ENSG00000116741RGS20.793.0212.020.0005280.0323
ENSG00000129757CDKN1C−0.952.0511.980.0005360.032564
ENSG00000179195ZNF664−0.666.9911.990.0005350.032564
ENSG00000185924RTN4RL1−2.85−2.5411.970.0005420.032704
ENSG00000189060H1F0−0.506.4411.960.0005430.032704
ENSG00000255767AC108488.25.64−3.3511.950.0005480.032834
ENSG00000108691CCL20.565.0511.890.0005660.033765
ENSG00000106069CHN20.832.5211.870.0005710.033914
ENSG00000132702HAPLN21.073.2811.850.0005750.033914
ENSG00000183691NOG1.960.8711.850.0005750.033914
ENSG00000105738SIPA1L30.535.3711.840.0005780.033924
ENSG00000154096THY1−1.730.3711.840.000580.033924
ENSG00000140937CDH110.585.5011.800.0005920.034495
ENSG00000127241MASP1−1.60−0.5011.770.0006010.034815
ENSG00000164574GALNT100.477.1811.770.0006030.034815
ENSG00000259112NDUFC2-5.59−3.3811.750.0006090.035044
KCTD14
ENSG00000109046WSB1−0.578.5911.720.0006190.035055
ENSG00000130054FAM155B1.73−1.2811.720.0006190.035055
ENSG00000133401PDZD2−0.683.7211.720.0006180.035055
ENSG00000284041AC073111.3−5.87−3.1811.720.0006190.035055
ENSG00000115008IL1A1.561.1311.670.0006340.035722
ENSG00000185737NRG3−0.862.5011.660.0006380.035834
ENSG00000196923PDLIM70.577.1511.640.0006440.036026
ENSG00000187583PLEKHN11.60−1.0711.620.0006520.036337
ENSG00000135324MRAP2−0.973.2111.570.0006720.037286
ENSG00000158186MRAS0.564.2711.550.0006780.037503
ENSG00000092969TGFB21.403.4111.540.0006820.037523
ENSG00000158373HIST1H2BD1.950.5611.530.0006840.037523
ENSG00000118946PCDH171.003.0611.490.00070.038238
ENSG00000067798NAV30.645.2411.480.0007050.038357
ENSG00000143344RGL10.816.4811.460.000710.03848
ENSG00000188042ARL4C0.653.9711.430.0007230.039053
ENSG00000162772ATF30.981.9611.410.0007310.039331
ENSG00000164104HMGB2−0.507.5111.380.0007420.039771
ENSG00000138411HECW20.477.3111.360.0007490.03998
ENSG00000142627EPHA20.497.5711.330.0007630.040464
NSG00000258947TUBB30.627.5511.330.0007610.040464
ENSG00000183775KCTD161.30−0.1211.300.0007730.040837
ENSG00000114948ADAM230.555.1511.260.0007930.041703
ENSG00000114315HES1−0.495.5611.220.0008110.042315
ENSG00000138772ANXA30.655.8511.220.0008080.042315
ENSG00000270276HIST2H4B−1.49−0.1311.210.0008130.042315
ENSG00000213694S1PR30.714.7811.160.0008350.043284
ENSG00000150687PRSS230.449.7011.150.0008410.043462
ENSG00000095303PTGS10.624.2811.120.0008520.043854
ENSG00000146674IGFBP3−0.931.5911.110.000860.04411
ENSG00000109436TBC1D90.456.6611.090.0008680.044376
ENSG00000274933TBC1D3I3.01−2.3211.070.0008790.044738
ENSG00000116678LEPR−0.624.6011.040.0008930.044947
ENSG00000156642NPTN−0.656.3711.040.0008920.044947
ENSG00000198720ANKRD13B0.534.4511.030.0008950.044947
ENSG00000228144AC078927.15.57−3.5011.040.0008910.044947
ENSG00000256966AL513165.22.50−2.2411.010.0009070.045379
ENSG00000156920ADGRG43.17−2.8910.970.0009260.046138
ENSG00000171877FRMD50.664.1510.920.000950.047183
ENSG00000164946FREM11.210.1710.870.0009750.048254
ENSG00000159640ACE−0.995.6410.860.0009820.048417
ENSG00000176771NCKAP51.300.3610.840.0009930.048822
ENSG00000198513ATL11.003.2210.830.0009990.048942
ENSG00000100234TIMP3−0.983.1310.820.0010060.049108
TABLE 4
Ensembl GeneGene SymbollogFClogCPMLRPValueFDR
ENSG00000117152RGS4−1.596.0788.465.18E−217.37E−17
ENSG00000272949AC093668.28.74−0.8064.639.02E−166.40E−12
ENSG00000283088AC010487.3−8.71−0.8560.766.45E−153.05E−11
ENSG00000136114THSD1−1.514.7358.412.13E−147.56E−11
ENSG00000146674IGFBP3−2.592.5054.841.31E−133.72E−10
ENSG00000284057AP001273.28.19−1.3052.155.15E−131.22E−09
ENSG00000133101CCNA1−1.314.7645.041.93E−113.92E−08
ENSG00000078018MAP2−1.314.9843.564.11E−117.29E−08
ENSG00000240583AQP1−2.373.9341.781.02E−101.61E−07
ENSG00000008517IL321.066.4539.732.92E−104.15E−07
ENSG00000154734ADAMTS1−1.553.8238.764.78E−106.18E−07
ENSG00000068489PRR11−1.006.1937.141.10E−091.30E−06
ENSG00000118777ABCG2−1.753.4436.141.84E−091.87E−06
ENSG00000168542COL3A12.681.6436.271.72E−091.87E−06
ENSG00000138180CEP55−0.996.1935.712.30E−092.17E−06
ENSG00000272414FAM47E-4.42−1.0535.522.52E−092.24E−06
STBD1
ENSG00000264187AC055811.27.52−1.8935.392.70E−092.26E−06
ENSG00000072571HMMR−1.095.7034.953.39E−092.67E−06
ENSG00000112984KIF20A−1.036.2134.594.07E−093.05E−06
ENSG00000126787DLGAP5−0.966.8634.155.09E−093.62E−06
ENSG00000081087OSTM11.105.5633.068.93E−096.04E−06
ENSG00000117399CDC20−1.026.4032.401.25E−088.08E−06
ENSG00000100292HMOX10.946.8331.531.96E−081.21E−05
ENSG00000134057CCNB1−0.946.9531.402.10E−081.24E−05
ENSG00000143228NUF2−1.065.0130.902.71E−081.48E−05
ENSG00000166851PLK1−1.036.1730.912.70E−081.48E−05
ENSG00000108691CCL21.385.3329.455.74E−082.86E−05
ENSG00000132470ITGB4−1.943.6929.415.84E−082.86E−05
ENSG00000164104HMGB2−0.867.3529.545.47E−082.86E−05
ENSG00000163661PTX3−1.017.7129.116.85E−083.24E−05
ENSG00000145386CCNA2−1.016.4529.037.12E−083.26E−05
ENSG00000142945KIF2C−0.955.3628.798.07E−083.58E−05
ENSG00000146678IGFBP1−2.510.4528.449.65E−084.15E−05
ENSG00000137812KNL1−1.095.8128.261.06E−074.44E−05
ENSG00000138182KIF20B−1.015.8128.101.15E−074.67E−05
ENSG00000080986NDC80−1.055.1527.561.52E−075.90E−05
ENSG00000136928GABBR2−0.956.0327.441.62E−075.90E−05
ENSG00000137804NUSAP1−0.956.0827.461.60E−075.90E−05
ENSG00000273294C1QTNF3-7.05−2.2827.451.62E−075.90E−05
AMACR
ENSG00000131747TOP2A−0.978.0926.972.07E−077.35E−05
ENSG00000087586AURKA−0.865.6726.902.14E−077.42E−05
ENSG00000094880CDC23−0.935.4926.822.24E−077.43E−05
ENSG00000161888SPC24−1.084.3526.812.25E−077.43E−05
ENSG00000066279ASPM−1.186.8926.712.36E−077.62E−05
ENSG00000198901PRC1−0.916.8526.113.23E−070.000102
ENSG00000088325TPX2−0.867.2825.963.49E−070.000108
ENSG00000138778CENPE−1.036.4025.444.58E−070.000136
ENSG00000140525FANCI−0.855.8725.434.60E−070.000136
ENSG00000111206FOXM1−0.806.6125.294.94E−070.000143
ENSG00000076382SPAG5−0.835.8125.105.46E−070.000155
ENSG00000170312CDK1−0.956.0325.055.59E−070.000156
ENSG00000161800RACGAP1−0.885.4724.906.04E−070.000162
ENSG00000168078PBK−0.935.3724.916.02E−070.000162
ENSG00000146072TNFRSF210.886.4224.776.45E−070.00017
ENSG00000134690CDCA8−1.055.2524.597.11E−070.000184
ENSG00000148773MKI67−1.177.9924.069.33E−070.000237
ENSG00000102575ACP5−3.552.8124.039.50E−070.000237
ENSG00000024526DEPDC1−0.995.6123.901.02E−060.000249
ENSG00000099937SERPIND1−1.852.8723.801.07E−060.000258
ENSG00000276612FP565260.2−6.67−2.6123.741.10E−060.000261
ENSG00000118193KIF14−1.045.0423.641.16E−060.000266
ENSG00000175063UBE2C−1.035.1823.651.16E−060.000266
ENSG00000123485HJURP−0.924.9823.461.28E−060.000286
ENSG00000157456CCNB2−0.845.6123.411.31E−060.000286
ENSG00000163584RPL22L1−0.905.9523.411.31E−060.000286
ENSG00000117724CENPF−0.967.4422.282.35E−060.000506
ENSG00000100297MCM5−0.866.3022.122.56E−060.000535
ENSG00000105357MYH144.21−0.6122.152.53E−060.000535
ENSG00000138160KIF11−0.956.3422.012.71E−060.000558
ENSG00000093009CDC45−1.004.5521.972.77E−060.000562
ENSG00000185070FLRT20.768.2921.872.92E−060.000584
ENSG00000116774OLFML31.522.3021.783.06E−060.000603
ENSG00000123689G0S2−1.972.2921.723.15E−060.000613
ENSG00000167900TK1−0.765.6821.563.43E−060.000655
ENSG00000184661CDCA2−0.934.8721.543.46E−060.000655
ENSG00000013810TACC3−0.766.3621.523.50E−060.000655
ENSG00000101057MYBL2−0.786.0021.423.70E−060.000682
ENSG00000112742TTK−1.035.1421.293.95E−060.000719
ENSG00000163808KIF15−1.044.7421.004.59E−060.000826
ENSG00000011426ANLN−1.017.2320.775.19E−060.00091
ENSG00000265107GJA5−6.45−2.7720.775.19E−060.00091
ENSG00000121152NCAPH−0.964.7920.735.28E−060.000915
ENSG00000114631PODXL21.263.2020.675.44E−060.000932
ENSG00000129173E2F8−1.044.5720.505.97E−060.00101
ENSG00000101335MYL90.825.3620.466.10E−060.00102
ENSG00000164109MAD2L1−0.925.5420.326.55E−060.001082
ENSG00000104738MCM4−0.926.6320.276.74E−060.0011
ENSG00000169679BUB1−0.995.9320.117.32E−060.001182
ENSG00000073111MCM2−0.825.7619.947.98E−060.00126
ENSG00000165480SKA3−0.994.5719.957.95E−060.00126
ENSG00000075218GTSE1−0.895.4019.818.54E−060.001333
ENSG00000267618AC004223.36.30−2.8619.788.70E−060.001344
ENSG00000163131CTSS1.443.2919.609.54E−060.001458
ENSG00000089685BIRC5−0.776.2919.529.98E−060.001508
ENSG00000178999AURKB−0.984.8519.361.08E−050.001618
ENSG00000186193SAPCD2−0.874.8019.321.10E−050.001632
ENSG00000071539TRIP13−0.845.4819.221.17E−050.001707
ENSG00000156504FAM122B−0.844.7119.181.19E−050.001722
ENSG00000165092ALDH1A10.696.1619.141.21E−050.001741
ENSG00000123975CKS2−0.805.7119.021.29E−050.001764
ENSG00000135476ESPL1−0.974.7619.091.25E−050.001764
ENSG00000173597SULT1B1−0.977.0119.021.29E−050.001764
ENSG00000189431RASSF10−3.28−1.9419.031.29E−050.001764
ENSG00000237649KIFC1−0.935.3119.051.27E−050.001764
ENSG00000122966CIT−0.815.4618.931.36E−050.001836
ENSG00000117650NEK2−0.854.4818.901.38E−050.001846
ENSG00000100526CDKN3−0.934.1018.771.47E−050.001954
ENSG00000156970BUB1B−0.935.8418.681.55E−050.002039
ENSG00000284041AC073111.3−6.19−2.9618.661.57E−050.002041
ENSG00000115163CENPA−1.063.8718.251.94E−050.002507
ENSG00000269891ARHGAP19-6.14−2.9718.052.15E−050.002751
SLIT1
ENSG00000065328MCM10−1.014.1817.992.22E−050.002822
ENSG00000125378BMP40.746.1117.972.25E−050.002823
ENSG00000079616KIF22−0.755.6517.892.35E−050.002915
ENSG00000151640DPYSL40.984.0917.872.36E−050.002915
ENSG00000053747LAMA3−0.874.2317.672.62E−050.003214
ENSG00000154175ABI3BP−0.845.1817.652.65E−050.003219
ENSG00000183856IQGAP3−0.815.1017.632.68E−050.003226
ENSG00000198826ARHGAP11A−0.926.0817.482.91E−050.003475
ENSG00000228716DHFR−0.746.1617.442.97E−050.003512
ENSG00000076003MCM6−0.846.1017.393.05E−050.003576
ENSG00000173166RAPH1−0.945.5817.283.22E−050.003754
ENSG00000123473STIL−0.904.9217.233.31E−050.003819
ENSG00000117595IRF61.523.3417.103.55E−050.004062
ENSG00000146918NCAPG2−0.775.9417.063.63E−050.004089
ENSG00000164647STEAP1−0.835.0717.073.61E−050.004089
ENSG00000196878LAMB3−0.854.4717.033.67E−050.004108
ENSG00000171241SHCBP1−0.865.5817.013.72E−050.004126
ENSG00000150630VEGFC−0.964.7816.893.95E−050.004353
ENSG00000090889KIF4A−0.775.7516.624.56E−050.004974
ENSG00000121621KIF18A−0.924.2716.614.59E−050.004974
ENSG00000101447FAM83D−0.885.4016.544.77E−050.005136
ENSG00000169604ANTXR11.034.6216.474.93E−050.005267
ENSG00000096060FKBP5−0.686.9016.315.38E−050.005672
ENSG00000167434CA4−4.19−2.6916.315.39E−050.005672
ENSG00000163092XIRP21.931.4416.295.43E−050.005675
ENSG00000104147OIP5−1.142.9116.255.56E−050.005762
ENSG00000119403PHF19−0.646.0116.195.74E−050.005868
ENSG00000211448DIO21.640.5516.205.71E−050.005868
ENSG00000185432METTL7A−0.905.2016.115.99E−050.006078
ENSG00000105499PLA2G4C1.033.4716.096.05E−050.006091
ENSG00000139734DIAPH3−0.805.4716.016.30E−050.0063
ENSG00000163453IGFBP70.687.6515.926.60E−050.006561
ENSG00000140416TPM10.648.2715.876.77E−050.006677
ENSG00000109805NCAPG−0.776.2615.737.30E−050.007153
ENSG00000137807KIF23−0.785.9515.667.59E−050.007335
ENSG00000179195ZNF664−0.886.9015.667.58E−050.007335
ENSG00000144554FANCD2−0.874.5915.577.95E−050.007632
ENSG00000101003GINS1−0.834.7915.518.19E−050.007811
ENSG00000137310TCF19−0.814.9215.358.92E−050.008445
ENSG00000115008IL1A1.970.9015.329.06E−050.008525
ENSG00000163751CPA31.341.7015.309.18E−050.008576
ENSG00000197632SERPINB2−1.603.0615.219.61E−050.008924
ENSG00000133119RFC3−0.804.5215.169.87E−050.009103
ENSG00000140545MFGE80.735.9015.120.000100860.009244
ENSG00000101188NTSR1−1.162.7915.080.000103120.009391
ENSG00000171848RRM2−1.186.8715.060.000103940.009404
ENSG00000185480PARPBP−0.794.4415.050.000104670.009411
ENSG00000140675SLC5A24.89−2.9914.820.000118080.010484
ENSG00000151725CENPU−0.744.6714.830.000117770.010484
ENSG00000168243GNG42.60−1.7414.780.000120620.010643
ENSG00000173207CKS1B−0.735.3814.770.00012140.010646
ENSG00000010292NCAPD2−0.627.0414.640.000129880.011319
ENSG00000173281PPP1R3B0.646.9814.610.00013190.011425
ENSG00000164611PTTG1−0.645.6014.580.000134450.011569
ENSG00000167261DPEP22.79−2.0114.570.000135180.011569
ENSG00000184445KNTC1−0.705.3714.550.000136410.011604
ENSG00000012048BRCA1−0.904.7714.490.000140560.011791
ENSG00000092853CLSPN−0.874.9514.490.00014110.011791
ENSG00000203668CHML−0.705.1314.490.000140870.011791
ENSG00000101868POLA1−0.844.6814.450.000143750.011893
ENSG00000122694GLIPR20.705.1214.450.0001440.011893
ENSG00000149591TAGLN1.241.9114.370.000150510.012359
ENSG00000280537AC068946.12.14−1.1514.350.000151840.012397
ENSG00000105011ASF1B−0.914.7214.280.000157210.012762
ENSG00000105889STEAP1B−0.834.6414.200.000164420.013271
ENSG00000124721DNAH81.613.8214.170.000167170.013341
ENSG00000130816DNMT1−0.607.0414.170.000166710.013341
ENSG00000162645GBP20.606.1514.140.000169430.013447
ENSG00000058804NDC1−0.715.9714.030.000180260.014227
ENSG00000145604SKP2−0.675.3314.000.00018250.014324
ENSG00000123219CENPK−0.714.8113.980.000185130.014341
ENSG00000136824SMC2−0.816.0813.970.000185750.014341
ENSG00000188517COL25A12.38−1.6113.970.000185640.014341
ENSG00000107984DKK1−0.635.8513.950.000187620.01437
ENSG00000204262COL5A20.618.7313.950.000188140.01437
ENSG00000162063CCNF−0.675.3113.890.000193520.014701
ENSG00000258064AC073612.1−6.56−2.6913.760.000208160.01573
ENSG00000120802TMPO−0.667.4413.640.000221610.016569
ENSG00000163507CIP2A−0.825.1413.640.00022120.016569
ENSG00000186185KIF18B−0.864.3513.610.000225010.016735
ENSG00000149503INCENP−0.865.2213.410.000250510.018535
ENSG00000167601AXL−0.557.3313.280.000268060.019731
ENSG00000139618BRCA2−0.914.4913.190.000281850.020639
ENSG00000163554SPTA12.18−0.6713.160.000286630.020881
ENSG00000100311PDGFB0.826.7013.080.000297820.021586
ENSG00000106069CHN20.943.2712.980.000315470.022542
ENSG00000239389PCDHA136.39−2.8012.990.000313020.022542
ENSG00000258947TUBB30.597.1012.970.000315770.022542
ENSG00000144354CDCA7−0.744.9912.940.00032120.022815
ENSG00000123080CDKN2C−0.814.0012.930.000324140.022909
ENSG00000103489XYLT11.132.6912.830.000340940.023859
ENSG00000178538CA8−1.710.7112.830.000340880.023859
ENSG00000163535SGO2−0.805.3012.810.000344810.024012
ENSG00000133110POSTN−1.113.0512.780.000350750.024306
ENSG00000035499DEPDC1B−0.854.2412.750.000356160.024325
ENSG00000150540HNMT0.804.0512.750.00035570.024325
ENSG00000176890TYMS−0.616.9912.750.000355220.024325
ENSG00000261459AC002310.5−6.20−2.9512.710.000363110.024681
ENSG00000117593DARS2−0.675.5412.680.000369550.024999
ENSG00000111341MGP−0.576.6712.650.000375990.025314
ENSG00000058085LAMC20.754.7312.570.000392220.026282
ENSG00000103257SLC7A5−0.714.7412.490.000408950.027275
ENSG00000214357NEURL1B−1.410.8612.460.00041510.027556
ENSG00000258555SPECC1L-6.16−2.9612.370.000436120.028683
ADORA2A
ENSG00000268643AC006486.1−6.10−3.0212.370.000435840.028683
ENSG00000186871ERCC6L−0.973.8012.310.000451560.029562
ENSG00000128944KNSTRN−0.645.2712.260.000462730.029611
ENSG00000134222PSRC1−0.893.8712.280.000458030.029611
ENSG00000142731PLK4−0.894.9112.270.000461220.029611
ENSG00000147536GINS4−0.854.1412.280.000457410.029611
ENSG00000267022AC067968.1−2.73−1.1212.260.000461770.029611
ENSG00000155093PTPRN21.400.7312.230.000470290.029846
ENSG00000188229TUBB4B−0.698.3912.230.000470610.029846
ENSG00000215252GOLGA8B0.684.4612.210.000475360.030013
ENSG00000149573MPZL2−0.675.4012.200.000478770.030095
ENSG00000129195PIMREG−0.794.0712.180.000483880.030282
ENSG00000152104PTPN14−0.607.1712.160.000487770.030391
ENSG00000197457STMN32.813.3112.140.000493730.030629
ENSG00000168874ATOH80.843.7012.130.000495930.030631
ENSG00000255073ZFP91-CNTF−5.43−3.4512.100.000505470.031085
ENSG00000188486H2AFX−0.636.2712.020.000526460.032209
ENSG00000213297ZNF625-ZNF201.410.9312.010.000528280.032209
ENSG00000102007PLP2−0.556.2711.970.000539670.032496
ENSG00000135842FAM129A−1.023.2911.970.000539850.032496
ENSG00000168843FSTL51.093.0411.980.000538340.032496
ENSG00000178878APOLD1−0.893.5811.940.000550820.033017
ENSG00000113368LMNB1−0.666.7011.920.000555120.033135
ENSG00000137473TTC291.72−0.2011.880.00056640.033666
ENSG00000148848ADAM121.251.7911.860.000572720.0339
ENSG00000114346ECT2−0.685.9711.840.000580630.034226
ENSG00000196739COL27A10.575.9711.770.000602450.03522
ENSG00000258677AC022826.2−1.79−0.9111.770.000601750.03522
ENSG00000129810SGO1−0.893.5211.750.000608460.035425
ENSG00000198830HMGN2−0.538.4211.730.000613370.035566
ENSG00000174371EXO1−0.933.7311.690.000628710.036307
ENSG00000127564PKMYT1−0.903.5211.660.000637060.03664
ENSG00000100368CSF2RB0.555.7711.640.000643940.036738
ENSG00000135451TROAP−0.734.1011.640.000643850.036738
ENSG00000092470WDR76−0.724.4011.600.000659670.037485
ENSG00000143401ANP32E−0.566.7811.580.000667310.037768
ENSG00000257411AC034102.21.930.7511.540.00068090.038384
ENSG00000146670CDCA5−0.725.0211.500.000697680.039175
ENSG00000167325RRM1−0.576.8911.470.000708460.039623
ENSG00000152253SPC25−0.893.8211.460.000712210.039677
ENSG00000122952ZWINT−0.715.5311.430.000723530.04015
ENSG00000121966CXCR41.025.4411.400.000732560.040493
ENSG00000101224CDC25B−0.566.3311.380.000741610.040707
ENSG00000136490LIMD20.605.2311.380.000742160.040707
ENSG00000127528KLF2−0.824.4611.350.000752670.041125
ENSG00000151388ADAMTS120.853.4511.340.000758790.041163
ENSG00000154839SKA1−0.874.2011.340.000759170.041163
ENSG00000119969HELLS−0.654.7711.300.000775920.041911
ENSG00000108055SMC3−0.536.6811.280.000781720.042065
ENSG00000125695AC046185.15.80−3.2011.240.000798910.042828
ENSG00000146411SLC2A121.262.0911.230.000805060.042888
ENSG00000159167STC1−0.934.5411.230.000806070.042888
ENSG00000181634TNFSF150.785.8111.190.000822120.043579
ENSG00000111665CDCA3−0.783.9711.160.000835180.044106
ENSG00000067141NEO1−2.49−2.0611.100.000862970.045237
ENSG00000099282TSPAN150.666.2111.100.000862890.045237
ENSG00000120256LRP110.575.8610.970.000927650.048365
ENSG00000145990GFOD1−0.595.4710.960.000932850.048365
ENSG00000166250CLMP−1.022.4710.960.000930280.048365
ENSG00000072501SMC1A−0.596.9410.940.000938940.048504
ENSG00000112378PERP−0.597.1810.920.000950530.048925
ENSG00000077152UBE2T−0.674.4910.900.000963650.049243
ENSG00000198553KCNRG1.57−0.5510.900.000960420.049243
ENSG00000120337TNFSF180.874.8410.870.000979640.049881
TABLE 5
1pCS2 + zf-thsd1-WT-CT2FLAG
(for full rescue, positive control)
2pCS2 + zf-thsd1-R449X-CT2FLAG
(corresponding to R450X in human)
3pCS2 + zf-thsd1-R459W-CT2FLAG
(corresponding to R460W in human)
4pCS2 + zf-thsd1-T665I-CT2FLAG
(corresponding to T653I in human)

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Classifications

17 codes
IPC · International Patent Classification
Section A — Human necessities
  • A61P9/10
  • A61P9/00
  • A61K38/10
  • A61K31/55
  • A61K31/5377
  • A61K31/52
  • A61K31/517
  • A61K31/506
  • A61K31/5025
  • A61K31/496
  • A61K31/4706
  • A61K31/404
  • A61K31/37
  • A61K31/351
  • A61B17/12
Section C — Chemistry; metallurgy
  • C07K14/495
  • C12N5/071

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Sergio Coffa
art unit 1658 · TC 1600
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