Classifications

• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K31/00—Medicinal preparations containing organic active ingredients
  • A61K31/33—Heterocyclic compounds
  • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
  • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
  • A61K31/505—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim
  • A61K31/517—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim ortho- or peri-condensed with carbocyclic ring systems, e.g. quinazoline, perimidine
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K31/00—Medicinal preparations containing organic active ingredients
  • A61K31/33—Heterocyclic compounds
  • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
  • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
  • A61K31/47—Quinolines; Isoquinolines
  • A61K31/4709—Non-condensed quinolines and containing further heterocyclic rings
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K45/00—Medicinal preparations containing active ingredients not provided for in groups A61K31/00 - A61K41/00
  • A61K45/06—Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P35/00—Antineoplastic agents

Definitions

• the present technology is directed to methods useful in treating cancer, slowing growth of a tumor, reversing growth of a tumor, slowing growth of a neoplasm, reversing growth of a neoplasm, slowing proliferation of a neoplasm, and/or reversing proliferation of a neoplasm, for cancers, tumors, and neoplasms harboring a constitutively active variant of one or both of KRAS or HRAS, where the constitutively active variant is a gain of function mutation, a duplication, or a gene amplification.
• the present technology provides a method of treating a cancer in a subject, where the method includes administering to the subject an effective amount of a compound to treat the cancer; where the compound is at least one of darapladib, rilapladib, AA39-2, or ML256; and where the cancer harbors a constitutively active variant of one or both of KRAS or HRAS, wherein the constitutively active variant is a gain of function mutation, a duplication, or a gene amplification.
• the cancer may be the cancer exhibits elevated expression and/or activity of at least one of PLA2G7A and PAFAH2 compared to healthy control cells.
• the present technology provides a method of slowing or reversing growth of a tumor in a subject, the method comprising administering to the subject an effective amount of a compound; where the compound is at least one of darapladib, rilapladib, AA39-2, or ML256; wherein the effective amount is an amount effective to slow or reverse growth of the tumor; and wherein the tumor is of a cancer that harbors a constitutively active variant of one or both of KRAS or HRAS, wherein the constitutively active variant is a gain of function mutation, a duplication, or a gene amplification.
• the cancer may be the cancer exhibits elevated expression and/or activity of at least one of PLA2G7A and PAFAH2 compared to healthy control cells.
• the present technology provides a method of slowing or reversing growth of a neoplasm in a subject and/or slowing or reversing proliferation of the neoplasm in the subject, the method comprising administering to the subject an effective amount of a compound; where the compound is at least one of darapladib, rilapladib, AA39-2, or ML256; wherein the effective amount is an amount effective to slow or reverse growth of the neoplasm and/or slow or reverse proliferation of the neoplasm; and wherein the neoplasm is of a cancer that harbors a constitutively active variant of one or both of KRAS or HRAS, wherein the constitutively active variant is a gain of function mutation, a duplication, or a gene amplification. In any embodiment herein, it may be the cancer exhibits elevated expression and/or activity of at least one of PLA2G7A and PAFAH2 compared to healthy control cells.
• FIG. 2 provides immunoblots of vector/iKRas cells 24 h after introducing
• doxycycline according to the working examples.
• FIG. 11 illustrates lipid reporter response in cells treated with pathway inhibitors or a PAF-AH inducer, according to the working examples, providing reporter emission wavelength from 24 h treated cultures.
• FIG. 12 illustrates lipid reporter response in cells treated with pathway inhibitors or a PAF-AH inducer, according to the working examples, providing reporter emission wavelength in Atg5 double knock-out SV40LT MEF with or without transduced K-rasG12V.
• FIG. 13 provides the results of an intracellular endomembrane reporter assay for lysophospholipids, according to the working examples, where emission center wavelength from sensor in the inducible amplified iKRas line is compared to the single-allele knock-in line, eKRas.
• FIG. 15 provides the results of an intracellular endomembrane reporter assay for lysophospholipids, according to the working examples, where illustrated is the quantification of sensor emission wavelengths from vector/iKRas cells incubated with the indicated drugs during the 24 h induction period: 20 nM varespladib, MJ-33; 75 nM BEL; 500 nM MAFP; 50 nM darapladib, rilapladib, ML256, AA39-2; 800 nM PI 1; 1 pM TSI-01.
• FIG. 19 provides a similar quantification as in FIG. 18 but for iKRas cells treated with vehicle or darapladib (50 nM).
• FIG. 21 provides similarly as FIG. 20 but for the iKRas or eKRas cell lines exposed to 10 mM of each lipid.
• FIG. 26 illustrates the effect of darapladib on eKRas and wildtype (WT) MEF, according to the working examples.
• Cells were plated as described in the main text for viability testing.
• FIG. 27 illustrates the effect of group 7 sPLA2 targeting on cell survival, according to the working examples, providing the results of a survival study of mice injected with KP lung cells on Day 0 and treated with vehicle or darapladip (Darap, 10 mg/kg) daily (oral gavage) starting on Day 1 (Dl) or Day 6 (D6).
• Darap darapladip
• “about” will be understood by persons of ordinary skill in the art and will vary to some extent depending upon the context in which it is used. If there are uses of the term which are not clear to persons of ordinary skill in the art, given the context in which it is used,“about” will mean up to plus or minus 10% of the particular term - for example,“about 10 wt.%” would be understood to mean“9 wt.% to 11 wt.%.” It is to be understood that when “about” precedes a term, the term is to be construed as disclosing“about” the term as well as the term without modification by“about” - for example,“about 10 wt.%” discloses“9 wt.% to 11 wt.%” as well as disclosing“10 wt.%.”
• phrase“and/or” as used in the present disclosure will be understood to mean any one of the recited members individually or a combination of any two or more thereof - for example,“A, B, and/or C” would mean“A, B, C, A and B, A and C, or B and C.”
• a range includes each individual member.
• a group having 1-3 atoms refers to groups having 1, 2, or 3 atoms.
• a group having 1-5 atoms refers to groups having 1, 2, 3, 4, or 5 atoms, and so forth.
• Pharmaceutically acceptable salts of compounds described herein are within the scope of the present technology and include acid or base addition salts which retain the desired pharmacological activity and is not biologically undesirable (e.g., the salt is not unduly toxic, allergenic, or irritating, and is bioavailable).
• pharmaceutically acceptable salts can be formed with inorganic acids (such as hydrochloric acid, hydroboric acid, nitric acid, sulfuric acid, and phosphoric acid), organic acids (e.g.
• alginate formic acid, acetic acid, benzoic acid, gluconic acid, fumaric acid, oxalic acid, tartaric acid, lactic acid, maleic acid, citric acid, succinic acid, malic acid, methanesulfonic acid, benzenesulfonic acid, naphthalene sulfonic acid, and p-toluenesulfonic acid) or acidic amino acids (such as aspartic acid and glutamic acid).
• an acidic group such as for example, a carboxylic acid group
• it can form salts with metals, such as alkali and earth alkali metals (e.g.
• organic amines e.g. dicyclohexylamine, trimethylamine, triethylamine, pyridine, picoline, ethanolamine, diethanolamine,
• salts can be prepared in situ during isolation and purification of the compounds or by separately reacting the purified compound in its free base or free acid form with a suitable acid or base, respectively, and isolating the salt thus formed.
• Tautomers refers to isomeric forms of a compound that are in equilibrium with each other. The presence and concentrations of the isomeric forms will depend on the environment the compound is found in and may be different depending upon, for example, whether the compound is a solid or is in an organic or aqueous solution. For example, in aqueous solution, quinazolinones may exhibit the following isomeric forms, which are referred to as tautomers of each other:
• guanidines may exhibit the following isomeric forms in protic organic solution (e.g ., water), also referred to as tautomers of each other:
• Stereoisomers of compounds include all chiral, diastereomeric, and racemic forms of a structure, unless the specific stereochemistry is expressly indicated.
• compounds used in the present technology include enriched or resolved optical isomers at any or all asymmetric atoms as are apparent from the depictions.
• racemic and diastereomeric mixtures, as well as the individual optical isomers can be isolated or synthesized so as to be substantially free of their enantiomeric or diastereomeric partners, and these stereoisomers are all within the scope of the present technology.
• the compounds of the present technology may exist as solvates, especially hydrates. Hydrates may form during manufacture of the compounds or compositions comprising the compounds, or hydrates may form over time due to the hygroscopic nature of the compounds.
• Compounds of the present technology may exist as organic solvates as well, including DMF, ether, and alcohol solvates among others. The identification and preparation of any particular solvate is within the skill of the ordinary artisan of synthetic organic or medicinal chemistry.
• various publications, patents, and published patent specifications are referenced by an identifying citation. Also within this disclosure are Arabic numerals referring to referenced citations, the full bibliographic details of which are provided preceding the claims. The disclosures of these publications, patents, and published patent specifications are hereby incorporated by reference into the present disclosure. Definitions that are contained in text incorporated by reference are excluded to the extent that they contradict definitions in this disclosure.
• Stress-induced premature senescence is a tumor-suppressive mechanism that delays or aborts oncogenesis.
• Constitutive signaling through RAS/RAF important components of the mitogenic MAP kinase cascade, can trigger proliferation delay, apoptosis, 1, 2 3 4 5 6 ’ 7 8 and DNA damage responses 9 in vitro and in vivo 1 ’ 10, u ’ 12, 13 While this process may suppress tumor initiation, oncogene-induced senescence (OIS) can be detrimental since surviving cells lose genomic stability through, for example, oxidative damage and replication defects. 14, 15, 16, 17, 18 .
• endogenous mutant KRAS expression in the developing mouse embryo causes pre-malignant tissue defects: senescence, p21 wafl/ciP1 overexpression, DNA damage responses, mutant allele instability, and overall developmental delay. 19, 20, 21, 22 More recently, epithelial cells and fibroblasts have been used to recapitulate oncogene-induced damage; for example, innate inflammatory gene expression phenotypes (senescence
• sPLA2 secretory phospholipase A2
• SIR secretory phospholipase A2
• SASP senescence-associated secretory phenotype
• sPLA2s are directly involved in senescence. 26, 27, 28, 29 These observations prompted the inventors to evaluate the role of sPLA2s - a large serine hydrolase family, initially studied in animal venom and inflamed joints, that is integral to cardiovascular, lipid, and leukocyte signaling 30, 31, 32 - within the context of oncogenic RAS-induced damage.
• the inventors investigated the involvement of sPLA2s in a murine model of oncogenic RAS-induced damage.
• Constitutive KRAS or HRAS was introduced into SV40 mouse embryo fibroblasts (MEF) using a Tet-ON retroviral plasmid (amplification model, iKRas), or through endogenous recombination in mouse embryos (single allele model, eKRas).
• iKRas amplification model
• eKRas single allele model
• the oncogene amplified line exhibited unique and striking overexpression of p21 " afl/c p 1 ⁇ doxycycline-dose dependent arrest, senescence-associated markers, DNA damage, and SIR/SASP gene expression.
• group 7 includes pla2g7 , PLA2G7A, also known as lipoprotein-associated phospholipase A2 and pafah2 , PLA2G7B, also known as platelet-activating factor acetylhydrolase 2 showed activity that was upregulated upon RAS amplification.
• Cellular arrest, p21 " aH/cp 1 ⁇ anc j phosphorylated ERK were stimulated on exposure to a non-degradable group 7 substrate lipid.
• Knockdown of group 7 sPLA2 isoforms selectively killed the RAS mutants.
• darapladib a potent second generation group 7 enzyme inhibitor previously tested in clinical trials for atherosclerosis and Alzheimer’s, prevented lysophospholipid accumulation in the RAS-transformed cells, preferentially killed oncogenic raw-harboring lines, and prolonged survival in a Kras ⁇ ,l2l) p53 ⁇ ⁇ lung cancer model in mice.
• the present technology provides a method of treating a cancer in a subject, where the method includes administering to the subject an effective amount of a compound to treat the cancer; where the compound is at least one of darapladib, rilapladib, AA39-2, or ML256 (collectively or individually referred to as“a compound of the present technology” or the like; also referred to as“the compound”); and where the cancer harbors a constitutively active variant of one or both of KRAS or HRAS, wherein the constitutively active variant is a gain of function mutation, a duplication, or a gene amplification.
• the structural formulas for each of darapladib, rilapladib, AA39-2, and ML256 are provided below in Scheme 1
• the cancer may be the cancer exhibits elevated expression and/or activity of at least one of PLA2G7A and PAFAH2 compared to healthy control cells.
• the present technology provides a method of slowing or reversing growth of a tumor in a subject, the method comprising administering to the subject an effective amount of a compound; where the compound is at least one of darapladib, rilapladib, AA39-2, or ML256; wherein the effective amount is an amount effective to slow or reverse growth of the tumor; and wherein the tumor is of a cancer that harbors a constitutively active variant of one or both of KRAS or HRAS, wherein the constitutively active variant is a gain of function mutation, a duplication, or a gene amplification.
• the cancer may be the cancer exhibits elevated expression and/or activity of at least one of PLA2G7A and PAFAH2 compared to healthy control cells.
• the present technology provides a method of slowing or reversing growth of a neoplasm in a subject and/or slowing or reversing proliferation of the neoplasm in the subject, the method comprising administering to the subject an effective amount of a compound; where the compound is at least one of darapladib, rilapladib, AA39-2, or ML256; wherein the effective amount is an amount effective to slow or reverse growth of the neoplasm and/or slow or reverse proliferation of the neoplasm; and wherein the neoplasm is of a cancer that harbors a constitutively active variant of one or both of KRAS or HRAS, wherein the constitutively active variant is a gain of function mutation, a duplication, or a gene amplification. In any embodiment herein, it may be the cancer exhibits elevated expression and/or activity of at least one of PLA2G7A and PAFAH2 compared to healthy control cells.
• Effective amount refers to the amount of a compound or composition required to produce a desired effect. In any embodiment and/or aspect disclosed herein (for simplicity’s sake, hereinafter recited as“in any embodiment disclosed herein” or the like), the effective amount may be determined in relation to a subject.
• a“subject” or“patient” is a mammal, such as a cat, dog, rodent or primate. Typically the subject is a human, and, preferably, a human suffering from or suspected of suffering from a cancer, a tumor, and/or a neoplasm.
• the term“subject” and“patient” can be used interchangeably.
• an effective amount includes amounts or dosages that yield acceptable toxicity and bioavailability levels for therapeutic (pharmaceutical) use including, but not limited to, reduction of a tumor mass.
• the effective amount may be an amount effective in treating a cancer, treating a tumor, shrinking a tumor, treating a neoplasm, shrinking a neoplasm, and/or increasing subject survival.
• the effective amount of any embodiment herein including a compound of the present technology may be from about 0.01 pg to about 200 mg of the compound (such as about 160 mg of the compound).
• the effective amount of a compound of the present technology may be (in terms of mass of the compound/mass of patient) from 1 x 1CT 5 g/kg to 1 g/kg, 1 x 1CT 3 g/kg to 1.0 g/kg, 0.01 mg/kg to 100 mg/kg, 0.01 mg/kg to about 20 mg/kg, or, preferably, from 0.25 mg/kg to 10 mg/kg - thus, in any embodiment disclosed herein, the effective amount a compound of the present technology may be about 0.01 mg/kg, about 0.1 mg/kg, about 0.15 mg/kg, about 0.2 mg/kg, about 0.25 mg/kg, about 0.3 mg/kg, about 0.4 mg/kg, about 0.5 mg/kg, about 0.6 mg/kg/ about 0.7 mg/kg, about 0.8 mg/kg, about 0.9 mg/kg, about 1 mg/kg, about 2 mg/kg, about 3 mg/kg, about 4 mg/kg, about 5 mg/kg, about 6 mg/kg, about 7 mg/kg,
• a method of any embodiment disclosed herein may comprise administering a pharmaceutical composition to the subject, where the pharmaceutical composition includes the effective amount of the compound of the present technology as well as a pharmaceutically acceptable carrier or one or more excipients, fillers or agents (collectively referred to hereafter as“pharmaceutically acceptable carrier” unless otherwise indicated and/or specified).
• the present technology also provides pharmaceutical compositions and medicaments including a compound of any embodiment disclosed herein and a pharmaceutically acceptable carrier.
• the compositions may be used in the methods and treatments described herein (for ease of reference, the medicaments and pharmaceutical compositions of the present technology may collectively be referred to herein as“compositions” or“compositions of the present technology” or the like).
• the pharmaceutical composition may be packaged in unit dosage form.
• the unit dosage form is effective in treating a tumor by reducing a tumor when administered to a subject in need thereof.
• a unit dosage including a compound of the present technology will vary depending on patient considerations. Such considerations include, for example, age, protocol, condition, sex, extent of disease, contraindications, concomitant therapies and the like.
• An exemplary unit dosage based on these considerations may also be adjusted or modified by a physician skilled in the art.
• a unit dosage for a patient comprising a compound of the present technology may vary from 1 x ICG* g/kg to 1 g/kg, preferably, 1 x 10 _3 g/kg to 1.0 g/kg.
• Dosage of a compound of the present technology may also vary from (in terms of mass of the compound/mass of patient) 1 x 10 _5 g/kg to 1 g/kg, 1 x 10 _3 g/kg to 1.0 g/kg, 0.01 mg/kg to 100 mg/kg, 0.01 mg/kg to about 20 mg/kg, or, preferably, from 0.25 mg/kg to 10 mg/kg - thus, in any embodiment disclosed herein, the dosage may be about 0.01 mg/kg, about 0.1 mg/kg, about 0.15 mg/kg, about 0.2 mg/kg, about 0.25 mg/kg, about 0.3 mg/kg, about 0.4 mg/kg, about 0.5 mg/kg, about 0.6 mg/kg/ about 0.7 mg/kg, about 0.8 mg/kg, about 0.9 mg/kg, about 1 mg/kg, about 2 mg/kg, about 3 mg/kg, about 4 mg/kg, about 5 mg/kg, about 6 mg/kg, about 7 mg/kg, about 8 mg/kg, about 9
• Suitable unit dosage forms include, but are not limited to parenteral solutions, oral solutions, powders, tablets, pills, gelcaps, capsules, lozenges, suppositories, patches, nasal sprays, injectables, implantable sustained-release formulations, mucoadherent films, topical varnishes, lipid complexes, liquids, etc.
• compositions and medicaments may be prepared by mixing one or more compounds of the present technology with pharmaceutically acceptable carriers, excipients, binders, diluents or the like.
• Such compositions can be in the form of, for example, granules, powders, tablets, capsules, syrup, suppositories, injections, emulsions, elixirs, suspensions or solutions.
• the instant compositions can be formulated for various routes of administration, for example, by oral, parenteral, topical, rectal, nasal, vaginal administration, or via implanted reservoir.
• Parenteral or systemic administration includes, but is not limited to, subcutaneous, intravenous, intraperitoneal, and intramuscular, injections.
• the following dosage forms are given by way of example and should not be construed as limiting the instant present technology.
• powders, suspensions, granules, tablets, pills, capsules, gelcaps, and caplets are acceptable as solid dosage forms. These can be prepared, for example, by mixing one or more compounds of the instant present technology, or pharmaceutically acceptable salts or tautomers thereof, with at least one additive such as a starch or other additive.
• Suitable additives are sucrose, lactose, cellulose sugar, mannitol, maltitol, dextran, starch, agar, alginates, chitins, chitosans, pectins, tragacanth gum, gum arabic, gelatins, collagens, casein, albumin, synthetic or semi-synthetic polymers or glycerides.
• oral dosage forms can contain other ingredients to aid in administration, such as an inactive diluent, or lubricants such as magnesium stearate, or preservatives such as paraben or sorbic acid, or anti-oxidants such as ascorbic acid, tocopherol or cysteine, a disintegrating agent, binders, thickeners, buffers, sweeteners, flavoring agents or perfuming agents. Tablets and pills may be further treated with suitable coating materials known in the art.
• suitable coating materials known in the art.
• Liquid dosage forms for oral administration may be in the form of pharmaceutically acceptable emulsions, syrups, elixirs, suspensions, and solutions, which may contain an inactive diluent, such as water.
• Pharmaceutical formulations and medicaments may be prepared as liquid suspensions or solutions using a sterile liquid, such as, but not limited to, an oil, water, an alcohol, and combinations of these.
• Pharmaceutically suitable surfactants, suspending agents, emulsifying agents may be added for oral or parenteral administration, , and may include natural and modified cyclodextrin compounds.
• suspensions may include oils.
• oils include, but are not limited to, peanut oil, sesame oil, cottonseed oil, com oil and olive oil.
• Suspension preparation may also contain esters of fatty acids such as ethyl oleate, isopropyl myristate, fatty acid glycerides and acetylated fatty acid glycerides.
• Suspension formulations may include alcohols, such as, but not limited to, ethanol, isopropyl alcohol, hexadecyl alcohol, glycerol and propylene glycol.
• Ethers such as but not limited to, poly(ethyleneglycol), petroleum hydrocarbons such as mineral oil and petrolatum; aprotic solvents such as dimethyl sulfoxide; and/or water may also be used in suspension formulations.
• Injectable dosage forms generally include aqueous suspensions or oil suspensions which may be prepared using a suitable dispersant or wetting agent and a suspending agent. Injectable forms may be in solution phase or in the form of a suspension, which is prepared with a solvent or diluent. Acceptable solvents or vehicles include sterilized water, Ringer's solution, or an isotonic aqueous saline solution. Alternatively, sterile oils may be employed as solvents or suspending agents. Typically, the oil or fatty acid is non-volatile, including natural or synthetic oils, fatty acids, mono-, di- or tri-glycerides.
• the pharmaceutical formulation and/or medicament may be a powder suitable for reconstitution with an appropriate solution as described above.
• these include, but are not limited to, freeze dried, rotary dried or spray dried powders, amorphous powders, granules, precipitates, or particulates.
• the formulations may optionally contain stabilizers, pH modifiers, surfactants, bioavailability modifiers and combinations of these.
• Compounds of the present technology may be administered to the lungs by inhalation through the nose or mouth.
• suitable pharmaceutical formulations for inhalation include solutions, sprays, dry powders, or aerosols containing any appropriate solvents and optionally other compounds such as, but not limited to, stabilizers, antimicrobial agents, antioxidants, pH modifiers, surfactants, bioavailability modifiers and combinations of these.
• the carriers and stabilizers vary with the requirements of the particular compound, but typically include nonionic surfactants (Tweens, Pluronics, or polyethylene glycol), innocuous proteins like serum albumin, sorbitan esters, oleic acid, lecithin, amino acids such as glycine, buffers, salts, sugars or sugar alcohols.
• Aqueous and nonaqueous (e.g., in a fluorocarbon propellant) aerosols are typically used for delivery of compounds of the present technology by inhalation.
• Dosage forms for the topical (including buccal and sublingual) or transdermal administration of compounds of the present technology include powders, sprays, ointments, pastes, creams, lotions, gels, solutions, and patches.
• the active component may be mixed under sterile conditions with a pharmaceutically-acceptable carrier or excipient, and with any preservatives, or buffers, which may be required.
• Powders and sprays can be prepared, for example, with excipients such as lactose, talc, silicic acid, aluminum hydroxide, calcium silicates and polyamide powder, or mixtures of these substances.
• the ointments, pastes, creams and gels may also contain excipients such as animal and vegetable fats, oils, waxes, paraffins, starch, tragacanth, cellulose derivatives, polyethylene glycols, silicones, bentonites, silicic acid, talc and zinc oxide, or mixtures thereof.
• Absorption enhancers can also be used to increase the flux of the compounds of the present technology across the skin. The rate of such flux can be controlled by either providing a rate controlling membrane (e.g., as part of a transdermal patch) or dispersing the compound in a polymer matrix or gel.
• excipients and carriers are generally known to those skilled in the art and are thus included in the instant present technology. Such excipients and carriers are described, for example, in“Remingtons Pharmaceutical Sciences” Mack Pub. Co., New Jersey (1991), and “Remington: The Science and Practice of Pharmacy,” 20 th Edition, Editor: Alfonso R Gennaro, Lippincott, Williams & Wilkins, Baltimore (2000), each of which is incorporated herein by reference.
• the formulations of the present technology may be designed to be short-acting, fast releasing, long-acting, and sustained-releasing as described below.
• the pharmaceutical formulations may also be formulated for controlled release or for slow release.
• compositions may also comprise, for example, micelles or liposomes, or some other encapsulated form, or may be administered in an extended release form to provide a prolonged storage and/or delivery effect. Therefore, the pharmaceutical formulations and medicaments may be compressed into pellets or cylinders and implanted intramuscularly or subcutaneously as depot injections or as implants such as stents. Such implants may employ known inert materials such as silicones and biodegradable polymers.
• specific dosages may be adjusted depending on conditions of disease, the age, body weight, general health conditions, sex, and diet of the subject, dose intervals, administration routes, excretion rate, and combinations of drugs. Any of the above dosage forms containing effective amounts are well within the bounds of routine
• the compounds of the present technology can be administered to a patient at dosage levels in the range of about 0.1 to about 1,000 mg per day (discussed in further detail supra). For a normal human adult having a body weight of about 70 kg, a dosage in the range of about 0.01 to about 100 mg per kg of body weight per day is sufficient (discussed in further detail supra).
• the specific dosage used can vary or may be adjusted as considered appropriate by those of ordinary skill in the art.
• the dosage can depend on a number of factors including the requirements of the patient, the severity of the cancer associated with the tumor, and the pharmacological activity of the compound being used.
• the determination of optimum dosages for a particular patient is well known to those skilled in the art.
• Various assays and model systems can be readily employed to determine the therapeutic effectiveness of the treatment according to the present technology. Effectiveness of the compositions (as well as determination of effective amounts) and methods of the present technology may also be demonstrated by a decrease in the mass of a tumor, slowing the growth of a tumor, and/or increasing subject survival.
• test subjects will exhibit a 10%, 20%, 30%, 50% or greater reduction, up to a 75-90%, or 95% or greater, reduction, in one or more symptom(s) caused by, or associated with, the disorder in the subject, compared to placebo-treated or other suitable control subjects.
• a compound of the present technology is administered to a patient in an amount or dosage suitable for therapeutic use (e.g ., included in a pharmaceutical composition of any embodiment of the present technology).
• a unit dosage comprising a compound of the present technology will vary depending on patient considerations. Such considerations include, for example, age, protocol, condition, sex, extent of disease, contraindications, concomitant therapies and the like. An exemplary unit dosage based on these considerations can also be adjusted or modified by a physician skilled in the art.
• a unit dosage for a patient comprising a compound of the present technology can vary from 1 x lO -4 g/kg to 1 g/kg, preferably, 1 c lO -3 g/kg to 1.0 g/kg. Dosage of a compound of the present technology can also vary from 0.01 mg/kg to 100 mg/kg or, preferably, from 0.1 mg/kg to 10 mg/kg.
• a compound of the present technology can also be modified, for example, by the covalent attachment of an organic moiety or conjugate to improve pharmacokinetic properties, toxicity or bioavailability (e.g., increased in vivo half-life).
• the conjugate can be a linear or branched hydrophilic polymeric group, fatty acid group or fatty acid ester group.
• a polymeric group can comprise a molecular weight that can be adjusted by one of ordinary skill in the art to improve, for example, pharmacokinetic properties, toxicity or bioavailability.
• Exemplary conjugates can include a polyalkane glycol (e.g., polyethylene glycol (PEG), polypropylene glycol (PPG)), carbohydrate polymer, amino acid polymer or polyvinyl pyrolidone and a fatty acid or fatty acid ester group, each of which can independently comprise from about eight to about seventy carbon atoms.
• a polyalkane glycol e.g., polyethylene glycol (PEG), polypropylene glycol (PPG)
• carbohydrate polymer e.g., amino acid polymer or polyvinyl pyrolidone and a fatty acid or fatty acid ester group, each of which can independently comprise from about eight to about seventy carbon atoms.
• Conjugates for use with a compound of the present technology can also serve as linkers to, for example, any suitable substituents or groups, radiolabels (marker or tags), halogens, proteins, enzymes, polypeptides, other therapeutic agents (for example, a pharmaceutical or drug), nucleosides, dyes, oligonucleotides, lipids, phospholipids and/or liposomes.
• conjugates can include polyethylene amine (PEI), polyglycine, hybrids of PEI and polyglycine, polyethylene glycol (PEG) or methoxypoly ethylene glycol (mPEG).
• a conjugate can also link a compound of the present technology to, for example, a label (fluorescent or luminescent) or marker (radionuclide, radioisotope and/or isotope) to comprise a probe of the present technology.
• Conjugates for use with a compound of the present technology can, in one aspect, improve in vivo half-life.
• Other exemplary conjugates for use with a compound of the present technology as well as applications thereof and related techniques include those generally described by U.S. Patent No. 5,672,662, which is hereby incorporated by reference herein.
• the cancer may be (and/or the tumor may be of a cancer such as, and/or the neoplasm may be of a cancer such as) squamous cell carcinoma, soft tissue sarcoma, oral melanoma, acute lymphoblastic leukemia (ALL), acute myeloid leukemia (AML), adrenocortical carcinoma, AIDS-related cancers, Kaposi sarcoma (soft tissue sarcoma), AIDS-related lymphoma (lymphoma), anal cancer, appendix cancer, gastrointestinal carcinoid tumors, astrocytomas, atypical teratoid/rhabdoid tumor, basal cell carcinoma of the skin, bile duct cancer, bladder cancer, bone cancer (includes Ewing Sarcoma and Osteosarcoma and Malignant Fibrous Histiocytoma), brain tumors, breast cancer, bronchial tumors (lung cancer), Burkitt lymphoma
• ALL acute lymphoblastic leuk
• the cancer may be (and the tumor may be of a cancer such as, and the neoplasm may be of a cancer such as) a pancreatic cancer, a colorectal cancer, a hepatocellular cancer, a bile duct cancer, a soft tissue sarcoma, a blood or hematopoietic cell cancer, a breast cancer, a lung cancer, a uterine or cervical cancer, a thyroid cancer, a bladder cancer, a kidney cancer, a gastric cancer, an ovarian cancer, a brain cancer, a mesothelioma cancer, a skin cancer, a head and neck cancer, a neuroendocrine cancer or neoplasm, an esophagus cancer, a testicular cancer, a prostate cancer, or a thymus cancer.
• a pancreatic cancer such as, a colorectal cancer, a hepatocellular cancer, a bile duct cancer, a soft tissue sarcom
• the cancer may include (and/or the tumor may be of a cancer including, and/or the neoplasm may be of a cancer including) an adenocarcinoma, a uterine carcinoma, a squamous cell carcinoma, small cell carcinoma, a transitional carcinoma, a serous carcinoma, a clear-cell carcinoma, a mucinous adenocarcinoma, an undifferentiated carcinoma, a dedifferentiated carcinoma, a serous adenocarcinoma, or a combination of any two or more thereof.
• the administering may include local administration of the compound to a site in the subject including the cancer (such as a tumor) or local administration of the composition to a site in the subject including the cancer (such as a tumor).
• the administering may include oral, rectal, nasal, vaginal, transdermal, intravenous, intramuscular, or inhalation administration.
• the administering may include injection of the compound into the site in the subject including the cancer (such as a tumor) or proximal to the site in the subject including the cancer (such as a tumor).
• the compounds of the present technology may also be administered to a patient along with other conventional therapeutic agents that may be useful in the treatment of tumors or in vaccination.
• the administration may include oral administration, parenteral administration, or nasal administration. In any of these embodiments, the administration may include
• the administration may include oral administration.
• the methods of the present technology can also include administering, either sequentially or in combination with one or more compounds of the present technology, a conventional therapeutic agent in an amount that can potentially or synergistically be effective for the treatment of tumors or in vaccination.
• the administering may further include
• chemotherapeutic agent such as an alkylating agent; a nitrosourea; an antimetabolite; an anthracycline; a topoisomerase II inhibitor; a mitotic inhibitor; an anti estrogen; a progestin; an aromatase inhibitor; an anti-androgen; an LHRH agonist; a chemotherapeutic agent such as an alkylating agent; a nitrosourea; an antimetabolite; an anthracycline; a topoisomerase II inhibitor; a mitotic inhibitor; an anti estrogen; a progestin; an aromatase inhibitor; an anti-androgen; an LHRH agonist; a chemotherapeutic agent such as an alkylating agent; a nitrosourea; an antimetabolite; an anthracycline; a topoisomerase II inhibitor; a mitotic inhibitor; an anti estrogen; a progestin; an aromatase inhibitor; an anti-
• corticosteroid hormone a DNA alkylating agent; a taxane; a vinca alkaloid; a microtubule poison, or a combination of any two or more thereof.
• the DNA alkylating agent a taxane; a vinca alkaloid; a microtubule poison, or a combination of any two or more thereof.
• administering may further include administration of a chemotherapeutic agent such as busulfan, cisplatin, carboplatin, oxaliplatin, an octahedral platinum (IV) compound, chlorambucil, cyclophosphamide, ifosfamide, dacarbazine (DTIC), mechlorethamine (nitrogen mustard), melphalan, temozolomide, carmustine (BCNU), lomustine (CCNU), 5-fluorouracil,
• a chemotherapeutic agent such as busulfan, cisplatin, carboplatin, oxaliplatin, an octahedral platinum (IV) compound, chlorambucil, cyclophosphamide, ifosfamide, dacarbazine (DTIC), mechlorethamine (nitrogen mustard), melphalan, temozolomide, carmustine (BCNU), lomustine (CCNU), 5-fluorouracil,
• capecitabine 6-mercaptopurine, methotrexate, gemcitabine, cytarabine (ara-C), fludarabine, pemetrexed, daunorubicin, doxorubicin (Adriamycin), epirubicin, idarubicin, mitoxantrone, topotecan, irinotecan, etoposide (VP- 16), teniposide, paclitaxel, docetaxel, vinblastine, vincristine, vinorelbine, prednisone, dexamethasone, L-asparaginase, dactinomycin, thalidomide, tretinoin, imatinib (Gleevec), gefitinib (Iressa), erlotinib (Tarceva), rituximab (Rituxan), bevacizumab (Avastin), ipilimumab, nivolumab (O
• the administering of the chemotherapeutic agent may include local administration of of the chemotherapeutic agent to a site in the subject including the cancer.
• the administering of the chemotherapeutic agent may include oral, rectal, nasal, vaginal, transdermal, intravenous, intramuscular, or inhalation administration.
• the administering of the chemotherapeutic agent may include injection of the chemotherapeutic agent into the site in the subject including the cancer or proximal to the site in the subject including the cancer.
• the examples herein are provided to illustrate advantages of the present technology and to further assist a person of ordinary skill in the art with preparing or using the compounds and compositions of the present technology.
• the examples herein are also presented in order to more fully illustrate the preferred aspects of the present technology.
• the examples should in no way be construed as limiting the scope of the present technology, as defined by the appended claims.
• the examples can include or incorporate any of the variations, aspects, or embodiments of the present technology described above.
• the variations, aspects, or embodiments described above may also further each include or incorporate the variations of any or all other variations, aspects, or embodiments of the present technology.
• ImageJ or Fiji was used to analyze western blot film densities and to generate blot and immunofluorescence images, b-gal images, and wide field/confocal images (HDF5/Bio-Formats plugins). Chemical structures and cartoons were designed with ChemBioDraw Ultra 13.0. Figure and scheme layouts were designed with Adobe Illustrator CS6 vl6.0.3.
• MEF Primary mouse embryo fibroblasts
• MEF were derived from Lowe laboratory C57BL/6 mouse colonies at MSKCC. MEF were immortalized by SV40 large T antigen.
• 82 ’ Immortalized MEF were transduced by retrovirus packaged by a HEK293T line transfected with cDNA plasmids.
• cDNA inserts, empty (scramble) vector, mouse K-ras G12V 4B, or human H-ras G12V were cloned in front of a Tet-ON 3G pTURN construct 84 using a modified version of the retroviral plasmid vector pTRE-Tight (Clonetech).
• Plasmids were co-transfected with retrovirus packaging plasmids in HEK293T cells using Lipofectamine 2000 (Life).
• Retroviral transduction occurred through exposure of 0.45 pm filtered HEK conditioned medium (plus 4 pg/mL polybrene, Fisher TR1003G) to 6E5 target cells. Hygromycin (150 pg/mL, ThermoFisher 10687-010) was used for selection.
• a K-ras G12D knock-in line was prepared with self-excising retroviral Cre-recombinase 19, 84, 86 prior to infection with SV40LT.
• SV40LT MEF harboring constitutive Aktl or constitutive short-guide RNA against Pten were described previously.
• the SV40LT Atg5 knock-out line 82 was transduced by the pTURN plasmid. All cell lines were tested for mycoplasma prior to expansion and storage.
• macrophage/monocyte were from ATCC (TIB-71) and cultured in medium as indicated in the main text, but with the addition of 10% heat inactivated FBS.
• Malignant lines were cultured using the same medium and were gifts from research groups at Memorial Sloan Kettering Cancer Center and included the following: KP Lung, KrasG12Dlp53R270H invasive primary lung adenocarcinoma from mouse; Human PA-TU-8988T pancreatic adenocarcinoma, Human HCT-116 colon carcinoma, Human A549 lung adenocarcinoma, Human Panc-1 pancreatic ductal epithelioid adenocarcinoma.
• ThermoFisher 10313021 and the following final concentrations of additives: 4.75% v/v heat inactivated fetal bovine serum (FBS) (ThermoFisher 10082147), 88.5 U/mL Pen Strep
• ThermoFisher 15140122 3.54 mM GlutaMAX (ThermoFisher 35050061), 1.77 mM L- glutamine (ThermoFisher 25030081), and 35 mM HEPES (ThermoFisher 15630080).
• Routine passage was performed with TrypLE (ThermoFisher 12604013).
• Cell lines were not used after seven to eight passages out from liquid nitrogen storage; experiments were started after at least two passages out from liquid nitrogen storage. Cultured cells were routinely split prior to 80- 90% confluence. To supplement lipophilic drugs, the DMSO dissolved stock compound was pre-incubated with the appropriate volume of 37°C complete culture medium and gently mixed for 10 minutes.
• FBS lipoprotein deficient experiments
• FBS was replaced with the same final % LPDS (Sigma S5394). All pre-made solutions were sterile filtered (0.22 pm). Unless indicated otherwise, doxycycline (500 ng/mL) was added into media simultaneously with other test compounds.
• doxycycline 500 ng/mL was added into media simultaneously with other test compounds.
• a volume of fatty acid oil needed to make a 6 mM stock in 1 mL was transferred to a sterile Eppendorf purged with nitrogen gas. To this tube, 1 mL of 1 mM delipidated BSA (Fraction V fatty acid free BSA, Sigma A7030, Lot#5LBQ0873 V) was added.
• 1 mM delipidated BSA Fraction V fatty acid free BSA, Sigma A7030, Lot#5LBQ0873 V
• the tube was placed into an auto-mixer at 1000 rpm, 37°C, for 30 minutes (Eppendorf ThermoMixer C).
• the resulting stock PUFA-BSA was sterile filtered with a 0.22 pm PES membrane.
• the stock was aliquoted, nitrogen purged, and stored at -20°C until use.
• Culture medium supplemented with the PUFA mix contained 5 pM docosahexanoic acid (Sigma D2534), 5 pM arachidonic acid (EMD 181198), and 2.5 pM each of linoleic acid (LA) (Sigma L1376) and linolenic acid (ALA) (Sigma L2376).
• Delipidated BSA was supplemented in the control condition.
• ThermoFisher T 10794 containing 24 pL of the trypsinized cell suspension. 18 fields were imaged; the cytometer output was given in cells/mL. Output was gated for cell/particle size so that the final count did not include particles at or below 7 pm, which was taken to reflect background debris from culture. An upper gating threshold was set at 34 pm to include size doubling of the measured 17 pm average.
• nano-reporter was removed by rinsing in complete medium and the stored test media was re-added to the dish for the 5-h incubation period.
• Near-infrared hyperspectral microscopy 87 was performed on live attached cells to obtain fluorescence emission maps from endomembrane vesicles. 88 Briefly, a 730 nm continuous wave diode laser was pumped through fibers to a lOOx oil objective to excite the fluorescent reporters inside attached cells. Collected emission was stored as a hyperspectral imaging cube of encoded wavelengths rectified between 1100 and 1200 nm. The center wavelength for each pixel in the cube was obtained by fitting a Lorentzian function in
• PEZGS0416/PEZGS0816 were treated as described.
• cells were fixed for 15 minutes at RT by 3.7% paraformaldehyde (using a 4°C 37% stock added dropwise to the warm culture).
• Fixative was inactivated by 10-minute incubation with 75 mM ammonium chloride in lx PBS.
• the ICC protocol was modified depending on target: Nuclear - secondary incubation was increased to 2 h; non-nuclear endomembrane - reduction to 2% fixative, permeabilization for 10 minutes in 100% -20°C methanol, followed by one rinse and blocking as described.
• the following primary antibodies were used: anti-HRIg (1 : 100, Cell Signaling 2619S), anti-phospho-H2A.X (1 :300, Cell Signaling 9718), anti-PLA2g7 (1 :50, Proteintech 15526-1-AP), anti-PAFAH2 (1 :50, Proteintech 10085-1-AP); secondary antibodies were chosen from the following:
• Alexa488/568 goat anti-mouse Alexa568 anti-rabbit IgG (Life Technologies A11001/Al 1004 & A11011), goat anti-rabbit IgG Super Clonal 555/647 (Invitrogen A27040/A27039), or goat anti-rat IgG 555/647 (Life Technologies 21247/21434).
• Lysate was pooled into an Eppendorf on wet ice and set to mix for 30 minutes at 4°C. Lysate was homogenized through a 26G needle with 5 full strokes, and then spun at 16,000 ref for 20 minutes in a 4°C centrifuge. RT Bradford reagent (BioRad 5000205) was mixed 1 : 1 with deionized water diluted samples containing either a BSA standard the sample lysate. Absorbance was measured at 595 nm in a Tecan Infinite M1000 Pro plate reader. Loading buffer consisted of lx Laemmli Buffer/2-Mercaptoethanol (BioRad
• Blot sandwiches comprised a 0.2 pm PVDF membrane (BioRad 1620174) pre incubated in methanol followed by transfer buffer (BioRad 10026938) held between buffer wetted-stack paper (BioRad) and the gel.
• a Trans-Blot Turbo transfer system BioRad 1704150 was used on the 7-minute Midi-Turbo setting. Blot membranes were cut and immediately rinsed in lx TBS, then moved into a blocking solution (3% w/v BSA in lx TBS-T) (BioRad 1706435; Sigma P1379) and agitated at RT for 1.5 h.
• Antibodies were as follows: anti-Coxl (1 :500, Cell Signaling 9896), anti-Cox2 (1 : 1000, Cell Signaling 12282), anti-p38 MAPK (1 : 1300, Cell Signaling 8690), anti-phospho-p38 MAPK T180/Y182 (1 :500, Cell Signaling 4511), anti-ATF-2 (1 : 1000, Cell Signaling 9226), anti- phospho-ATF-2 T69/T71 (1 : 1000, Cell Signaling 5112), anti-TBP (1 : 1500, Cell Signaling 44059), anti-cPLA2 (1 : 1000, Cell Signaling 5249), anti-phospho-cPLA2 S505 (1 :750, Cell Signaling 53044), anti-phospho-IkBa S32 (1 :500, Cell Signaling 2859), anti-IkBa (1 : 1000, Cell Signaling 4812) anti-NF-kB p65 (1 : 1000, Selleckchem.com A5075), anti-phospho-NF-kB p65
• Pan-sPLA2/PAF-AH Activity and Total Lipid Hydroperoxides were used per chromogenic assay.
• commercial enzyme activity-based kits for sPLA2 (Cayman 765001), PAF-AH assay (Cayman 760901), or Lipid hydroperoxides (LPO) (Cayman 705003) were used per
• glycerophospholipid/sphingolipid reverse phase for sterol/glycerolipid
• Quantitation used an MRM method under positive and negative electrospray modes.
• Raw data was reported as Mol%, or ng/mL of the lipid species normalized to the absolute total lipid abundance (ng/mL) detected by the mass spectrometer.
• Reported data is Mol% divided by the total adherent cell count from a parallel-treated plate, calculated as a Fold change versus control: (iKRas/Vector)-l.
• siRNA Knockdown Transient knockdown of MEF lines was achieved by plating target cells to reach 80-90% confluence on the day of assay. For extended experiments, cells were plated to reach 40-50% confluence on treatment day.
• siRNA and target well two Eppendorf tubes were each filled with 150 pL of serum- and antibiotic-free DMEM. The transfection cocktail was made by transferring siRNA into one tube such that the final volume in the target well was 45 nM. Into the other tube, 9 pL of RNAiMAX (Thermofisher 13778) was added. The siRNA volume was added to the RNAiMAX volume and mixed by pipetting.
• the cocktail was incubated at RT for 10 minutes and then added, dropwise, to a target well containing 2 mL of fresh complete medium. Plates were swirled to mix and incubated at 37°C for 48 h. Doxycycline and other compounds were added after the first 24 h of exposure to siRNA: a 1 mL aliquot of the wells’ contents was removed, mixed with the compounds, and returned.
• siRNA was as follows: Universal negative controls (Sigma SICOOl/002 WDAA), pla2g7 #1 (Sigma NM_013737 SASI_Mm01_00162678), pla2g7 #2 (Sigma NM_013737 SASI_Mm01_00162677), pafah2 #1 (Sigma NM_133880 SASI_Mm01_00180435), pafah2 #2 (Sigma NM_133880 SASI_Mm01_00180436).
• LDH Lactate Dehydrogenase
• Luminescence was measured using a Tecan Infinite M1000 Pro plate reader (Tecan Group Ltd.). Results from the assays were calculated as a percentage of the non-treated control.
• the reported EC so of darapladib ranges from 10 - 1000 nM, depending on the cell type and downstream marker used.
• the enzyme ICso ranges from 1 - 10 nM.
• CxB Cholera Toxin Subunit B Labeling.
• Cells were plated onto chamber slides or glass bottom dishes. Cells were pulsed as previously described with an Alexa647-ssDNA coated reporter alone or in combination with cholera toxin subunit B (CTxB, 0.5 pg) (ThermoFisher C22843). Media was removed and cells were triple rinsed in room temperature (RT) lx HBSS. At the final time point, cells were fixed in situ by adding, dropwise, microscopy-grade paraformaldehyde (EMS 15714-S) onto culture medium and gently swirled to generate a final concentration of 2% v/v.
• EMS 15714-S microscopy-grade paraformaldehyde
• Tubes were mixed by pipetting and left to incubate at room temperature for 10 minutes. Cells were plated to reach 50-60% confluence on the day of transfection. See Girotti M, Banting G.“TGN38-green fluorescent protein hybrid proteins expressed in stably transfected eukaryotic cells provide a tool for the real-time, in vivo study of membrane traffic pathways and suggest a possible role for ratTGN38.” Journal of cell science 109 (Pt 12), 2915-2926 (1996). The cocktail mix was added dropwise to the cells growing in complete medium. The dish was swirled, and then incubated at 37°C for 36 hours. After this period, cells were washed and allowed to rest for 2 hours before treatment and imaging.
• RNA Sequencing (RNAseq). To ensure adequate starting material, two biological replicates each of vector and K-ras Gi2i were grown in 6-well plates so that three wells were dedicated for each replicate. On the day of extraction, media was aspirated and 500 pL of Trizol LS reagent (Thermo 10296010) was pipetted into each well. Plates were placed on wet ice, and the contents of each well were agitated and scraped with a rubber policeman to ensure all material was homogenous before transfer into a pre-cooled 2 mL Eppendorf (Fisher 05-402- 24C). Samples were flash frozen in isopropanol/dry ice slurry and stored at -80°C until processing by the MSKCC Integrated Genomics Operation (IGO): extraction, poly- A
• Downstream bioinformatics was performed by the MSKCC Bioinformatics Core (BIC) using a standard delivery pipeline for alignment, clustering, Htseq counts, and differential expression.
• PC-SUV Vesicle and ANS Assay 500 mg of Soy bean phosphatidylcholine (Lipoid) was dissolved in 200 pL of ethanol; 25 pL of ethanol-lipid solution was injected into 750 pL of deionized water. The resulting MLV dispersion was extruded four times with a manual extruder through a 200 nm membrane. The resulting small unilamellar vesicle (SUV) size was -160 nm. See Portnoy E, el al.“Indocyanine Green Liposomes for Diagnosis and Therapeutic Monitoring of Cerebral Malaria.” Theranostics 6, 167-176 (2016).
• ANS assay a 100 mM stock of 8- anilino-l-naphthalenesulfonic acid ammonium salt (Sigma 10417-F) was dissolved in deionized water. A stock solution of sodium dodecyl sulfate, SDS (Fisher BP 166- 100), was generated in deionized water. The assay was prepared by first mixing an excess working concentration of 2 mM ANS with 1 mM SUV (calculation based on total lipid) in lx PBS. To this mixture the vehicle blank, SDS, or reporter was added. As a control, ANS was mixed with SDS or reporter in the absence of SUV.
• SDS sodium dodecyl sulfate
• RT3GEPIR miR-E vector backbone was used to clone in shRNA targeting sequences (two per gene target) against Renilla luciferase (vector control), pla2g 7, or pafah2.
• shRNA inserts were 22 bases long. Plasmid DNA was generated and supplied by the Gene Editing and Screening Core at MSKCC in part using an algorithm for shRNA generation. See Pelossof R, et al.“Prediction of potent shRNAs with a sequential classification algorithm.” Nature Biotechnology 35, 350-353 (2017). Plasmid amplification was performed using Machl competent bacteria inoculated onto 100 mm LB Agar plates (Teknova LI 11002).
• Bacterial stocks were first expanded using manufacturer instructions (Zymo Research T3002) followed by storage at -80°C. Transformation of plasmids into bacteria took place on wet ice: 20 pL of competent Machl was mixed gently with 250 pg of DNA. This volume was drop pipetted onto 37°C pre-warmed 100 mm LB Agar plus Carbenicillin (200 pg) plates (Teknova LI 046) and was followed by bead rolling. Plates were incubated in a dry 37°C incubator for 18 hours or until robust colonies formed.
• Colonies were amplified by inoculating a single transformant colony into 3 mL Terrific Broth plus 200 pg Carbenicillin (Teknova T7510; plus 100 pg Carbenicillin, Fisher AAJ67159AD). Culture tubes with loose fitting caps were incubated 15 hours at 37°C with shaking (225 rpm). For archiving, 900 pL was taken from the resulting cloudy broth and was mixed 1 :1 with 50% sterile glycerol and frozen at -80°C. The remaining broth (or full volume if archiving was not performed) was spun down (6800 ref, 3 minutes, 15°C) for mini-prep (Qiagen 27106).
• Retroviral packaging was achieved using a Phoenix-AMPHO cell line derived from the HEK293T (ATCC CRL3213). Phoenix was expanded then frozen as aliquots at passage 3 in liquid nitrogen; for use, 2.5E6 Phoenix cells were thawed into basal growth medium as described elsewhere, supplemented with 10% heat inactivated FBS but without antibiotics, onto 60 mm plates 24 hours before transfection to achieve -80% confluence. Fresh medium was replaced at 12 hours post seeding. The transfection cocktail made up for each 60 mm dish was: 6 pg plasmid DNA diluted into 1 mL growth medium without FB S/antibiotics followed by a 1 : 1 ratio DNA:PLUS reagent
• ThermoFisher 15338100 and gentle mixing. Mix was incubated at room temperature for 10 minutes followed by the addition of 20 pL Lipofectamine LTX (ThermoFisher 15338100); this mix was incubated for 25 minutes at room temperature. 2 mL of conditioned medium from Phoenix dishes ready for transfection was mixed with 2 mL fresh medium without antibiotics.
• filtered viral supernatant was buffered with 10% v/v HEPES (ThermoFisher 15630106) and 25% v/v fresh complete growth medium.
• the filtered viral supernatant was snap frozen and stored in sealed conical tubes at -80°C.
• Target MEF lines were infected with virus by first plating 5E5 target cells per 100 mm dish overnight in complete medium with 5% FBS. Frozen viral supernatant was rapidly but incompletely thawed in a 37°C water bath.
• a transduction cocktail was made by diluting 4 mL of viral supernatant with 1 mL fresh medium supplemented with 5% FBS.
• Polybrene was then added to a final concentration of 4 pg/mL, and the cocktail was gently mixed and incubated at room temperature for 10 minutes.
• Transduction cocktail was added to aspirated target cell plates. Dishes were incubated at 37°C for 8 hours, after which fresh 5% FBS supplemented medium was added to bring the dish volume up to 10 mL. Incubation was continued for an additional 36 hours or until cells reached 90% confluence. Conditioned medium was washed off completely using HBSS and complete medium and then target cells were split into new dishes to achieve 80-90% confluence two days later for the start of dual antibiotic selection.
• iKRas/mirG7 or iKRas/mirAH2 versus Renilla control overexpressed RasG12V and had reduced levels of group 7 or pafah2 protein; however, the control lines showed elevated inflammatory lipid contents when assayed by nanosensor and showed elevated PAFAH activity when assayed with a kit.
• iKRas harboring knockdown lines showed no distinct change in nanosensor response and assay of PAFAH reported elevated activity in cell lysate and conditioned culture medium (data not shown). For these reasons, stable inducible shRNA was not reported and instead transient RNAi was used.
• Nano-reporter was prepared as described; 88 in brief, raw nanotube (SWCNT) was suspended with single-stranded DNA (ssDNA) sequence 5’- CTTCCCTTC-3’ (IDT Technologies) and subjected to Aqueous Two Phase (ATP) separation to purify the (9,4) chirality. Stock solutions were kept at 4°C. For confocal imaging, 1 pmole of Alexa647-ssDNA (5’-CTTCCCTTCTT/iSpl8//3AlexF647N/-3 ⁇ IDT Technologies) was used to generate the reporter.
• SWCNT single-stranded DNA sequence 5’- CTTCCCTTC-3’
• ATP Aqueous Two Phase
• Dispersion of 1 mg raw SWCNT (Nanolntegris, HiPco) with 1 mg ssDNA dissolved in 0.1 M NaCl was achieved by sonicating (2 mm stepped probe, Sonics and Materials Inc., Pulse: 1-minute ON, 15 seconds OFF) the mixture for 30 minutes in a -20°C cold block.
• the resulting suspension was benchtop centrifuged for 10 minutes at 30,000 ref.
• the supernatant was ultra-centrifuged for 30 minutes at 171,180 ref.
• the resulting supernatant was spin-filtered (Millipore Amicon, 100 kDa) three times against deionized water, re-suspended, and then centrifuged for 10 minutes, 30,000 ref.
• Darapladib (Selleckchem S7520), Rilapladib (MCE HY-102004/CS-0022446), ML256 (gift), AA39-2 (gift), Pl l (Cayman 17507), TSI-01 (Cayman 17628), methylcarbamyl PAF C-16 (Cayman 60908), ( ⁇ )-a-Tocopherol (Sigma T3251), phosphocholine chloride calcium salt tetrahydrate (Sigma P0378), linoleic acid (Sigma L1376), 1-C16 ether MG (Avanti 999971),
• a cell line derived from a KrasG12D/+; Trp53-/- (KP) GEMM lung tumor was infected with a retroviral luciferase (Luc)-GFP construct, and 5000 KP tumor cells resuspended in 400 pL of PBS were tail vein injected into 7 week old Female C57BL/6 mice. 90 Mice were randomized into various study cohorts before treatment with vehicle or darapladib. Treatments were administered by oral gavage once per day, Monday through Friday.
• mice that did not die with disease-related morbidities by Day 73 post-xenograft were monitored for tumor formation by bioluminescence imaging (BLI) on a Xenogen IVIS Spectrum (Caliper Life Sciences) and their weight changes were evaluated. Bioluminescence positive mice remained in the study while bioluminescence negative mice were euthanized, and their lungs were harvested for histology. Tissues were rinsed and fixed in 4°C buffered 4% paraformaldehyde for 24-48 hours and moved to 4°C 70% ethanol for long term storage, embedding, sectioning, and staining (H&E, anti-GFP primary antibody, anti-Ki-67 primary antibody).
• H&E anti-GFP primary antibody, anti-Ki-67 primary antibody
• mice from the Day 73 survivor group were harvested and evaluated by histology. Tissues negative for histological dysplasia were excluded from final study analysis; tissues positive for histological dysplasia were kept in the final study analysis. Each cohort’s N value was adjusted to reflect histology results before final analysis.
• One treatment cohort mouse negative for bioluminescence was labelled as an outlier in the final analysis due to a very early death (Day 24) without disease-related morbidity, and one treatment cohort mouse positive for lung bioluminescence was euthanized once its weight dropped but before disease-related death (Day 91) to keep a reasonable study timeline.
• FIG. 2 To investigate the signaling changes in these two models, a 24 h immunoblot was performed on cell lysates (FIG. 2). The immunoblot showed oncogenic RAS over-expression and downstream ERKl/2 phosphorylation in iKRas cells. Notably, phospho-p53 showed no significant increase; however, p21 wafl/ciP1 expression was elevated and maintained expression throughout doxycycline treatment (FIG. 3). Compared to the amplified RAS cells, in eKRas endogenous RAS cells the ERK phosphorylation was not detectible and p21 wafl/ci P 1 was barely detectible.
• FIG. 4 shows the quantification of immunofluorescence from an acute double-strand break marker, gH2A.C.
• an assay for the genotoxic stress markers, phospho-JNK and phospho-ATF-2 was performed (FIG. 5). All stress markers were elevated in iKRas cells, but not eKRas or control.
• the inventors assessed whether RAS mutant cells exhibited a difference in senescence markers. Keeping with a two-marker minimum for stress-induced senescence, the inventors assayed for senescence-associated b-galactosidase and heterochromatin foci (HRIg). Both of these assays reported elevated senescence-associated marker expression only in iKRas cells after 72 h in culture (FIG. 6). In the case of the eKRas cells, b-Gal signal was stochastic.
• RNA sequencing of 24 h induced cell cultures, as well as immunoblots for representative SIR/SASP markers reported the upregulation of an innate inflammatory response. Based on previous findings of SIR and SASP phenotypes from long-term cell culture, 23, 28, 33, 34, 35, 36, 37 our profiling indicated that iKRas, but not eKRas cells, modeled a stress and damage response to amplified oncogenic RAS.
• Oncogenic RAS stress triggers Group 7 sPLA2 activity.
• Chromogenic enzyme assays were run using two lipid substrates: diheptanoyl- phosphatidylcholine (PC), a substrate of most cancer-associated sPLA2 isoforms known to-date, or platelet activating factor (PAF), a substrate of group 7 and 8 sPLA2 isoforms (also known as platelet activating factor acetylhydrolases, PAF-AHs).
• PC diheptanoyl- phosphatidylcholine
• PAF platelet activating factor
• PAF-AHs platelet activating factor acetylhydrolases
• results were consistent with a 32-fold amplification of pla2g7 RNA.
• Group 7B and group 8 enzymes were not similarly over-expressed in iKRas cells.
• Lipid dysregulation in iKRas endomembrane is due to PLA2G7 activity and oxidized phospholipid.
• group 7A sPLA2 is a normal component of animal serum lipoproteins
• the inventors surmised that iKRas cells may exhibit dysregulated intracellular lipid metabolism related to the endogenous activity of this circulatory enzyme.
• Lipid dysregulation in cellular endosomal organelles was assessed using a previously-validated nanosensor that measures soluble lipids by a shift in its near infrared emission towards smaller (bluer) values in the endosomal lumen of live cells.
• 39, 40 The inventors first queried whether the sensors would respond to the substrates/products of sPLA2 enzymes. 39 The reporter was confirmed to be pH- insensitive and membrane bilayer-impermeable.
• lysophosphatidylserine lysoPS
• Additional sensitivities e.g. to very-long chain lysoPC and PC, were observed at lipid concentrations far above their endogenous critical micelle concentrations (pM-nM, above this point free solubility is negligible).
• the lipid nanosensor was introduced into the culture medium of RAS- or vector-transformed cell lines. Near-infrared hyperspectral microscopy was utilized to acquire the fluorescence spectra of the nanosensor spatially within iKRas, iHRas, eKRas, vector control cells, and MEFs harboring mutations in the parallel PI3K pathway. The data were fitted to determine the center wavelength of the nanosensor emission band, which was then mapped back over the brightfield images of the cells and plotted in a histogram. Using this method, the average sensor emission wavelength 24 h and 72 h after oncogenic RAS induction was measured.
• the average sensor emission wavelength 24 h after culturing immortalized MEFs harboring myristoylated (constitutive) Aktl (myrAktl) or short guide RNA to knockout Pten was also measured (FIG. 10). It was found that only the constitutive RAS mutants exhibited significantly blue-shifted responses, as compared to either vector or signaling control cells. eKRas cells exhibited a minor blue-shift that was significantly less than the shift in iKRas cells.
• Pharmacologic inhibitors of MAPK pathway effectors such as RAF, MEK, and ERK, (TAK-632, trametinib, and GDC-0994, respectively) significantly diminished the lipid nanosensor response in iKRas relative to vector, as compared to
• Darapladib and rilapladib are potent and reversible PLA2G7A inhibitors, while ML256 is a covalent inhibitor of PLA2G7A and AA39-2 is a covalent inhibitor of PLA2G7B.
• the other PLA2 inhibitors that were unable to attenuate the lipid reporter response in iKRas cells included varespladib, which inhibits PLA2G2/5/10/12 isoforms, MJ-33, a transition state analog of arachi donate 43 that reportedly inactivates PRDX6 and PLA2G15, BEL, an inhibitor of PLA2G6, MAFP, an inhibitor of cytosolic PLA2G4, PI 1, an inhibitor of PLA2G8, and TSI-01, an inhibitor of PAF biosynthesis. Consistent with group 7 activity in RAS-damaged cells, the PLA2G7A stimulator and anti-inflammatory drug, dexamethasone, 44 increased the reporter response in the vector line (FIG. 14).
• iKRas lipid dysregulation was potentially caused by membrane phospholipid oxidation.
• live cell cultures were stained with the redox dye methylene blue, which showed elevated cellular staining. This result supports an elevated intracellular oxidizing environment.
• iKRas cells were then incubated with lipophilic a-tocopherol (Vitamin E), a common membrane antioxidant. 45 The reporter response was abrogated in cells pre-incubated with Vitamin E (FIG. 15),
• AA arachidonic acid
• DHA docosahexaenoic acid
• Electron microscopy of oncogenic RAS-amplified cells were conducted to further investigate the lipid dysregulation phenotype.
• Transmission electron microscopy (TEM) showed the presence of unusual lamellar-like structures in iKRas and iHRas lines (FIG. 17). These structures appear to resemble lamellar bodies. 47 These images further support lipid dysregulation within the lumen of endosomal and/or secretory endomembrane compartments and these images also support intracellular retention of PLA2G7 as an important component of oncogenic RAS- induced damage.
• iKRas cell lysates and conditioned media were prepared for LC-MS/MS of glycerophospholipids, sterols, glycerolipids, and sphingolipids. It was found that lysoPAF and lysoPC species were enriched in the conditioned media of the mutant cultures, as compared to the vector control.
• the iKRas cell lysates contained less total saturated/unsaturated phospholipids, plasmalogen phospholipids, and ether phospholipids, but they contained more lysophospholipids than the vector control.
• Group 7 sPLA2 substrate and product lipids differentially affect cell proliferation.
• sPLA2 enzyme isoforms have been described as both tumor suppressors and tumor promoters
• 48, 4 ⁇ l 5(1 5 L 52 53 iKRas cells were interrogated using two representative lipids - a group 7 sPLA2 substrate, and a product.
• the vector control cells were incubated with increasing concentrations of 16:0 lysoPC, a group 7 sPLA2 product, and 16:0 methylcarbamyl PAF (cPAF), a substrate.
• cPAF 16:0 methylcarbamyl PAF
• the group 7 sPLA2 substrate, cPAF exhibited a mild stimulatory effect on control cell proliferation at both sub-critical and critical micelle concentrations (CMC similar to lysoPC). Therefore, in the vector control cells, intracellular accumulation of the group 7 sPLA2 product affected proliferation to a greater extent than the enzyme substrate.
• lysoPC promoted either a negligible arresting effect or a reduced arresting effect
• cPAF promoted a potent arresting effect on both iKRas and eKRas cells (FIG. 21). Therefore, the data from these studies support that intracellular accumulation of the group 7 substrate is significantly more cytostatic than the product lipid.
• eKRas cells were much more sensitive to the substrate lipid absent significant RAS- related damage or group 7 activity.
• PAF- R PAF receptor
• Group 7 sPLA2 knockdown kills oncogenic KRAS-harboring cells.
• group 7 sPLA2 To assess whether a function of group 7 sPLA2 is to remove deleterious PAF-analog lipid species, the inventors assessed whether knockdown of group 7 would modulate p21 wafl/ciP1 expression.
• Commercial siRNAs targeting the group 7 sPLA2 genes were incubated with iKRas cells. The inventors immunoblotted lysates to assess the impact of genetic knockdown on arrest, where it was found that phospho-ERK and p21 wafl/ci P 1 expression disappeared, supporting that oncogene-induced arrest required group 7 expression.
• removal of group 7 enzymes should permit greater accumulation of damage-inducing PAF analogs, an expectation seemingly inconsistent with the finding that cPAF lipid substrate alone promotes phospho-ERK and p21 wafi/cipi expression.
• group 7 sPLA2 enzymes clear away cytostatic/cytotoxic phospholipids
• the inventors assessed whether group 7 knockdown would affect cell proliferation and survival. As before, cells were maintained in culture medium supplemented with PETFAs and siRNAs.
• a syngeneic KrasG12D/+; Trp53-/- (KP) transplant model of non-small cell lung cancer was used.
• 54, 55 Luciferized cells derived from a GEMM lung tumor were administered intravenously into WT C57BL/6 mice.
• group 7 transcripts are expressed and amplified in a wide variety of human cancers, including pancreatic cancer. Almost all these cancers show overexpression and amplification of kras and hras transcripts, including tissues that frequently harbor the point-mutated and constitutive form of RAS.
• inflammation-related lipid dysregulation that contributes to cell survival in RAS-mutant tumors was investigated. While various sPLA2 isoforms have been discovered in malignant cells and tissues that harbor oncogenic ras , 48, 49, 50, 51, 52, 53 a direct relationship between these inflammatory mediators and RAS is a nascent area of research in non-leukocyte models.
• p21 aH/cp 1 ⁇ pre-mature senescence markers, as well as markers of DNA damage and stress (gH2A.C, phospho-JNK, and phospho-ATF-2) that in total support the link between gene amplification and in vivo carcinogenicity from oncogenic RAS in the developing mouse. 19, 20, 21, 22 Coupled with the upregulation of senescence markers, SIR/SASP gene and protein upregulation indicated that iKRas cells modelled an inflammatory phenotype.
• eKRas the single-allele hyperproliferative mutant cell line, showed none of the same signs of damage as in the iKRas cells beyond minor elevation in p21 wafl/ci P 1 expression.
• Unbiased biochemical profiling allowed the inventors to identify a unique bioactive enzyme isoform of the broad secreted Pla2 gene family, PLA2G7, as a mediator of the damage. Confocal imaging showed substantial overexpression of group 7A sPLA2, while RNAseq reported a 32-fold elevation of Pla2g7 gene expression but not that of Pafah2 (group 7B), its homolog. Using a nanosensor which detects lipids in the endosomal lumen of living cells, the inventors explored lipid dysregulation in this system.
• a fluorescent nanosensor to benchmark lipid accumulation, the inventors found that oncogenic RAS amplification induces substantial lipid dysregulation in the intracellular endosomal compartments as well as endomembrane trafficking defects. Only specific inhibitors of group 7 sPLA2 and RAS-ERK signaling abrogated the lipid dysregulation. Using the nanosensor, the inventors found partial intracellular lipid dysregulation in eKRas, the endogenous mutant; however, eKRas showed no significant stress response or group 7A expression.
• inflammation inducible group 7A isoforms may require the highly-elevated stress of RAS amplification for expression, even though these isoforms are paradoxically inactivated by direct oxidative attack. 62
• the inventors further investigated the source and identity of the lipids involved in the aberrant accumulation. It was found that culture medium-derived polyunsaturated fatty acids (PUFA) were necessary for intracellular lipid dysregulation, which is expected, as membrane- active enzymes in the Pla2 family play an important role in PUFA release 46, 63 while group 7 enzymes selectively attack membrane lipids with oxidized PUFA. 64, 65, 66, 67 The sensitivity of intracellular lipid dysregulation on PUFA loading and lipophilic anti-oxidant treatment is consistent with the membrane damage responsive role of group 7 enzymes.
• PUFA culture medium-derived polyunsaturated fatty acids
• group 7 sPLA2 enzyme catalysis are soluble lysophospholipids and oxidized fatty acids; this catalytic activity should stop when the enzymes are degraded.
• the inventors attempts to block endolysosomal degradation had no influence on lipid dysregulation (FIG. 23). Without being bound by theory, this can be explained by the fact that group 7 enzymes are acid-labile and inactivated at acidic pH 68 ’ 69 while endomembrane compartments in Ras-transformed fibroblasts are alkaline 70 and support enzyme activity.
• a link between inflammatory group 7A activity and RAS-mediated survival was tested with the use of a non-degradable PAF-analog substrate lipid.
• the inventors evidenced a link between an important marker of oncogene-induced growth delay, p21 wafl/ci P 1 , and intracellular accumulation of this cytostatic substrate lipid class.
• group 7 gene silencing did not abrogate p21 wafl/ci P 1 expression, while chemical inhibition of available group 7 enzymes promoted p21 wafl/ci P 1 expression.
• the inventors showed group 7 gene silencing selectively killed RAS-damaged, but not control, cells.
• Fibroblasts including embryonic lines, are an often-used model system to study ms- transformation and, more recently, SIR/SASP phenomena induced by senescence-associated stresses. Fibroblasts can synthesize canonical PAF under specific conditions or generate IL-6 in the presence of critical micelle concentrations of exogenous PAF lipid. 71, 72 Here, the inventors found RAS overexpression led to elevated IL-6 levels in cell lysates, supporting that damage through oncogenic RAS amplification stimulates conserved inflammatory responses.
• PLA2G7A is a soluble lipoprotein-associated serine hydrolase derived largely from leukocytes
• PLA2G7B (pafah2 ) transfers from cytosol to ER membranes and was first described as an oxidant detoxifier in liver, 65 ’ 77 erythrocytes, 78 and the yeast S. pom he M Both enzymes are thought to act at the aqueous side of the membrane-water interface where most substrates are located, although it is possible activity against cytosolic substrates is relevant. At least part of this activity is endomembrane localized to endosomal compartments.
• group 7 inhibitors can selectively kill RAS-overexpressing cells.
• the most developed compound for these stress enzymes is darapladib, a group 7A and 7B inhibitor, which reached Phase 3 trials before failing to meet its intended cardiovascular clinical endpoint. While darapladib is safe and apparently side-effect-free in vivo , most cells harbor the group 7B enzyme for its housekeeper enzymatic functions. Therefore, blanket inhibition could selectively affect cell types where membrane damage is significant, or turnover is slow.
• Many human neoplasms overexpress or amplify RAS, including the point mutation leading to constitutive signaling.
• Tuveson DA et al. Endogenous oncogenic K-ras(G12D) stimulates proliferation and widespread neoplastic and developmental defects. Cancer Cell 5, 375-387 (2004). Chen X, et al. Endogenous expression of Hras(G12V) induces developmental defects and neoplasms with copy number imbalances of the oncogene. Proceedings of the National Academy of Sciences of the United States of America 106, 7979-7984 (2009). Guerra C, et al. Tumor induction by an endogenous K-ras oncogene is highly dependent on cellular context. Cancer Cell 4, 111-120 (2003).
• Thevenin AF Monillas ES, Winget JM, Czymmek K, Bahnson BJ. Trafficking of platelet-activating factor acetylhydrolase type II in response to oxidative stress.
• Phospholipase A2 Mediates Human Esophageal Adenocarcinoma Cell Growth and Proliferation via ERK 1/2 Pathway. Anticancer Research 33, 1337-1342 (2013).
• Ruscetti M et al. NK cell-mediated cytotoxicity contributes to tumor control by a cytostatic drug combination. Science (New York, NY) 362, 1416-1422 (2016).
• Human serum acid-labile factor is an acylhydrolase that inactivates platelet-activating factor. Federation proceedings 42, 3120-3122 (1983).
• the Utilization of Extracellular Proteins as Nutrients Is Suppressed by mTORCl. Cell 162, 259-270 (2015).
• a method of treating a cancer in a subject comprising administering to the
• the cancer harbors a constitutively active variant of one or both of KRAS or HRAS, wherein the
• constitutively active variant is a gain of function mutation, a duplication, or a gene amplification; optionally wherein the cancer exhibits elevated expression and/or activity of at least one of PLA2G7A and PAFAH2 compared to healthy control cells.
• the cancer is a pancreatic cancer, a colorectal cancer, a hepatocellular cancer, a bile duct cancer, a soft tissue sarcoma, a blood or hematopoietic cell cancer, a breast cancer, a lung cancer, a uterine or cervical cancer, a thyroid cancer, a bladder cancer, a kidney cancer, a gastric cancer, an ovarian cancer, a brain cancer, a mesothelioma cancer, a skin cancer, a head and neck cancer, a neuroendocrine cancer or neoplasm, an esophagus cancer, a testicular cancer, a prostate cancer, or a thymus cancer.
• the cancer comprises an adenoma, an adenocarcinoma, a uterine carcinoma, a squamous cell carcinoma, a small cell carcinoma, a transitional carcinoma, a serous carcinoma, a clear-cell carcinoma, a mucinous adenocarcinoma, an undifferentiated carcinoma, a dedifferentiated carcinoma, a serous adenocarcinoma, a sarcoma, a myeloma, a leukemia, a lymphoma, a dysplastic lesion, or a combination of any two or more thereof.
• a chemotherapeutic agent selected from the group consisting of an alkylating agent; a nitrosourea; an antimetabolite; an anthracycline; a topoisomerase II inhibitor; a mitotic inhibitor; an anti-estrogen; a progestin; an aromatase inhibitor; an anti-androgen; an LHRH agonist; a corticosteroid hormone; a DNA alkylating agent; a taxane; a vinca alkaloid; a microtubule poison, and a combination of any two or more thereof.
• a chemotherapeutic agent selected from the group consisting of an alkylating agent; a nitrosourea; an antimetabolite; an anthracycline; a topoisomerase II inhibitor; a mitotic inhibitor; an anti-estrogen; a progestin; an aromatase inhibitor; an anti-androgen; an LHRH agonist; a corticosteroid
• a chemotherapeutic agent selected from the group consisting of busulfan, cisplatin, carboplatin, oxaliplatin, an octahedral platinum (IV) compound, chlorambucil, cyclophosphamide, ifosfamide, dacarbazine (DTIC), mechlorethamine (nitrogen mustard), melphalan, temozolomide, carmustine (BCNU), lomustine (CCNU), 5-fluorouracil, capecitabine, 6-mercaptopurine, methotrexate, gemcitabine, cytarabine (ara-C), fludarabine, pemetrexed, daunorubicin, doxorubicin (Adriamycin), epirubicin, idarubicin, mitoxantrone, topotecan, irinotecan, etoposide (VP-
• a chemotherapeutic agent selected from the group consisting of busulfan, c
• administration intravenous administration, or intramuscular administration.
• a method of slowing or reversing growth of a tumor in a subject comprising administering to the subject an effective amount of a compound; wherein the compound is at least one of darapladib, rilapladib, AA39-2, or ML256; wherein the effective amount is an amount effective to slow or reverse growth of the tumor; and wherein the tumor is of a cancer that harbors a constitutively active variant of one or both of KRAS or HRAS, wherein the constitutively active variant is a gain of function mutation, a duplication, or a gene amplification; optionally wherein the cancer exhibits elevated expression and/or activity of at least one of PLA2G7A and PAFAH2 compared to healthy control cells.
• the tumor is of a cancer selected from a pancreatic cancer, a colorectal cancer, a hepatocellular cancer, a bile duct cancer, a soft tissue sarcoma, a blood or hematopoietic cell cancer, a breast cancer, a lung cancer, a uterine or cervical cancer, a thyroid cancer, a bladder cancer, a kidney cancer, a gastric cancer, an ovarian cancer, a brain cancer, a mesothelioma cancer, a skin cancer, a head and neck cancer, a neuroendocrine cancer or neoplasm, an esophagus cancer, a testicular cancer, a prostate cancer, or a thymus cancer.
• a cancer selected from a pancreatic cancer, a colorectal cancer, a hepatocellular cancer, a bile duct cancer, a soft tissue sarcoma, a blood or hematopoietic cell cancer, a breast cancer,
• the tumor is of a cancer comprising an adenoma, an adenocarcinoma, a uterine carcinoma, a squamous cell carcinoma, a small cell carcinoma, a transitional carcinoma, a serous carcinoma, a clear-cell carcinoma, a mucinous adenocarcinoma, an undifferentiated carcinoma, a dedifferentiated carcinoma, a serous adenocarcinoma, a sarcoma, a myeloma, a leukemia, a lymphoma, a dysplastic lesion, or a combination of any two or more thereof.
• T The method of any one of Paragraphs O-S, wherein the method comprises administering to the subject (in terms of mass of the compound/mass of the subject) about 0.25 mg/kg to about 10 mg/kg of the compound.
• a chemotherapeutic agent selected from the group consisting of an alkylating agent; a nitrosourea; an antimetabolite; an anthracycline; a topoisomerase II inhibitor; a mitotic inhibitor; an anti-estrogen; a progestin; an aromatase inhibitor; an anti-androgen; an LHRH agonist; a corticosteroid hormone; a DNA alkylating agent; a taxane; a vinca alkaloid; a microtubule poison, and a combination of any two or more thereof.
• a chemotherapeutic agent selected from the group consisting of an alkylating agent; a nitrosourea; an antimetabolite; an anthracycline; a topoisomerase II inhibitor; a mitotic inhibitor; an anti-estrogen; a progestin; an aromatase inhibitor; an anti-androgen; an LHRH agonist; a corticosteroid
• a chemotherapeutic agent selected from the group consisting of busulfan, cisplatin, carboplatin, oxaliplatin, an octahedral platinum (IV) compound, chlorambucil, cyclophosphamide, ifosfamide, dacarbazine (DTIC), mechlorethamine (nitrogen mustard), melphalan, temozolomide, carmustine (BCNU), lomustine (CCNU), 5-fluorouracil, capecitabine, 6-mercaptopurine, methotrexate, gemcitabine, cytarabine (ara-C), fludarabine, pemetrexed, daunorubicin, doxorubicin (Adriamycin), epirubicin, idarubicin, mitoxantrone, topotecan, irinotecan, etoposide (VP-
• a chemotherapeutic agent selected from the group consisting of busulfan, c
• AA The method of any one of Paragraphs O-Z, wherein the administering comprises oral administration, intravenous administration, or intramuscular administration.
• AD A method of slowing or reversing growth of a neoplasm in a subject and/or slowing or reversing proliferation of the neoplasm in the subject, the method comprising
• a compound where the compound is at least one of darapladib, rilapladib, AA39-2, or ML256; wherein the effective amount is an amount effective to slow or reverse growth of the neoplasm and/or slow or reverse proliferation of the neoplasm; and wherein the neoplasm is of a cancer that harbors a constitutively active variant of one or both of KRAS or HRAS, wherein the
• constitutively active variant is a gain of function mutation, a duplication, or a gene amplification; optionally wherein the cancer exhibits elevated expression and/or activity of at least one of PLA2G7A and PAFAH2 compared to healthy control cells.
• pancreatic cancer a colorectal cancer, a hepatocellular cancer, a bile duct cancer, a soft tissue sarcoma, a blood or hematopoietic cell cancer, a breast cancer, a lung cancer, a uterine or cervical cancer, a thyroid cancer, a bladder cancer, a kidney cancer, a gastric cancer, an ovarian cancer, a brain cancer, a mesothelioma cancer, a skin cancer, a head and neck cancer, a neuroendocrine cancer or neoplasm, an esophagus cancer, a testicular cancer, a prostate cancer, or a thymus cancer.
• an adenoma comprising an adenoma, an adenocarcinoma, a uterine carcinoma, a squamous cell carcinoma, a small cell carcinoma, a transitional carcinoma, a serous carcinoma, a clear cell carcinoma, a mucinous adenocarcinoma, an undifferentiated carcinoma, a dedifferentiated carcinoma, a serous adenocarcinoma, a sarcoma, a myeloma, a leukemia, a lymphoma, a dysplastic lesion, or a combination of any two or more thereof.
• administering in terms of mass of the compound/mass of the subject) about 0.01 mg/kg to about 20 mg/kg of the compound.
• administering in terms of mass of the compound/mass of the subject) about 0.25 mg/kg to about 10 mg/kg of the compound.
• a chemotherapeutic agent selected from the group consisting of an alkylating agent; a nitrosourea; an antimetabolite; an anthracycline; a
• topoisomerase II inhibitor a mitotic inhibitor; an anti-estrogen; a progestin; an aromatase inhibitor; an anti-androgen; an LHRH agonist; a corticosteroid hormone; a DNA alkylating agent; a taxane; a vinca alkaloid; a microtubule poison, and a combination of any two or more thereof.
• a chemotherapeutic agent selected from the group consisting of busulfan, cisplatin, carboplatin, oxaliplatin, an octahedral platinum (IV) compound, chlorambucil, cyclophosphamide, ifosfamide, dacarbazine (DTIC), mechlorethamine (nitrogen mustard), melphalan, temozolomide, carmustine (BCNU), lomustine (CCNU), 5-fluorouracil, capecitabine, 6-mercaptopurine, methotrexate, gemcitabine, cytarabine (ara-C), fludarabine, pemetrexed, daunorubicin, doxorubicin (Adriamycin), epirubicin, idarubicin, mitoxantrone, topotecan, irinotecan, etoposide (VP- 16), teniposide, paclitaxel, docetaxel, vinblast
• AP The method of any one of Paragraphs AD-AO, wherein the administering comprises oral administration, intravenous administration, or intramuscular administration.

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