EP1117781A2 - Proteines membranaires de canal humaines - Google Patents

Proteines membranaires de canal humaines

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Publication number
EP1117781A2
EP1117781A2 EP99948140A EP99948140A EP1117781A2 EP 1117781 A2 EP1117781 A2 EP 1117781A2 EP 99948140 A EP99948140 A EP 99948140A EP 99948140 A EP99948140 A EP 99948140A EP 1117781 A2 EP1117781 A2 EP 1117781A2
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EP
European Patent Office
Prior art keywords
mechp
seq
polynucleotide
sequence
sequences
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
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EP99948140A
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German (de)
English (en)
Inventor
Janice Au-Young
Olga Bandman
Y. Tom Tang
Roopa Reddy
Jennifer L. Hillman
Henry Yue
Preeti Lal
Neil C. Corley
Karl J. Guegler
Gina Gorgone
Mariah R. Baughn
Yalda Azimzai
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Incyte Corp
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Incyte Pharmaceuticals Inc
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Publication date
Priority claimed from US09/155,226 external-priority patent/US6207225B1/en
Application filed by Incyte Pharmaceuticals Inc filed Critical Incyte Pharmaceuticals Inc
Priority claimed from PCT/US1999/020468 external-priority patent/WO2000012711A2/fr
Publication of EP1117781A2 publication Critical patent/EP1117781A2/fr
Withdrawn legal-status Critical Current

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Definitions

  • This invention relates to nucleic acid and amino acid sequences of human membrane channel proteins and to the use of these sequences in the diagnosis, treatment, and prevention of cell proliferative, immune/inflammatory, transport/secretory, osmoregulatory, muscular, cardiovascular, and neurological disorders.
  • Channel proteins facilitate the transport of hydrophilic molecules across membranes by forming aqueous pores that can perforate a lipid bilayer.
  • Many channels consist of protein complexes formed by the assembly of multiple subunits, at least one of which is an integral membrane protein that contributes to formation of the pore. In some cases, the pore is constructed to selectively allow passage of only one or a few molecular species. Distinct types of membrane channels that differ greatly in their distribution and selectivity include: (1) aquaporins.
  • Aquaporins are channels that transport water and, in some cases, nonionic small solutes such as urea and glycerol. Water movement is important for a number of physiological processes including renal fluid filtration, aqueous humor generation in the eye, cerebrospinal fluid production in the brain, and appropriate hydration of the lung. A variety of aquaporins have been found in higher animals, plants and microorganisms.
  • the mammalian aquaporins appear to have selective expression in particular tissues, with AQPO localized to lens epithelium; AQP1 localized to many tissues including red blood cells, kidney, eye, lung, choroid plexus, bile duct, and vascular epithelium; AQP2 localized to the apical membrane of kidney collecting duct cells; AQP3 localized to kidney, colon, trachea, urinary bladder, skin, and sclera of eye; AQP4 localized to kidney, colon, trachea, stomach, skeletal muscle, spinal cord, brain, and retina; AQP5 localized to the apical membranes of exocrine tissues; AQP6 localized to kidney; and AQP7 localized to testis (King, L.S.
  • AQP9 is expressed in peripheral leukocytes, less abundantly in liver, even less in lung and spleen, and not at all in thymus tissue (Ishibashi, K. et al. (1998) Biochem. Biophys. Res. Commun. 244:268-274).
  • Aquaporins are members of the major intrinsic protein (MIP) family of membrane transporters. MIP family proteins are composed of four subunits, each of which may span the membrane six times, and have their N-and C-termini facing the cell cytoplasm. Proteins from bacteria, yeast, plants, and animals have been shown to be members of the MIP family (Reizer, J. et al. (1993) Crit. Rev. Biochem. 28:235-257). Aquaporin subunits are integral membrane proteins with six transmembrane regions and two conserved Asn-Pro-Ala (NPA) boxes (which are sometimes found as Asn-Pro-Ser) found in loop regions between the transmembrane regions (King, supra; Ishibashi, (1997) supra).
  • NPA Asn-Pro-Ala
  • Secreted and integral membrane proteins are transported from the cytoplasm to the endoplasmic reticulum (ER) through protein-conducting channels in the ER membrane.
  • the channel is used for both co- and post-translational translocation.
  • transport is initiated by the action of a cytoplasmic signal recognition particle (SRP) which recognizes a signal sequence on a growing, nascent polypeptide and binds the polypeptide and its ribosome complex to the ER membrane through an SRP receptor located on the membrane.
  • SRP cytoplasmic signal recognition particle
  • the post-translational process also requires a signal sequence on the protein to be translocated, but does not require an SRP.
  • the protein enters the channel and is driven across the ER membrane by the hydrolysis of adenosine triphosphate (ATP) by BiP, an ATPase and molecular chaperone in the ER lumen.
  • ATP adenosine triphosphate
  • the protein-conducting channel termed the Sec ⁇ lp complex
  • the Sec ⁇ lp complex is composed of multiple, probably two, heterotrimers of three membrane proteins, the alpha, beta, and gamma subunits of Sec ⁇ lp.
  • the Sec ⁇ lp complex forms a ring structure visible by electron microscopy (EM).
  • EM and quenching experiments indicate a channel diameter of 20 to 60 A.
  • Association of the Sec ⁇ lp complex with the ribosome and with the proteins Sec62p, Sec63p, Sec71p, Sec72p, BiP, and TRAM (translocating chain-associating membrane protein) is required for some of the channel's functions.
  • the Sec ⁇ lp alpha subunit contains ten membrane-spanning segments and has been found to line the path of the translocating polypeptide chain from one side of the membrane to the other.
  • the sequences of dog and rat Sec ⁇ lp alpha genes have been determined. Homologs of the mammalian Sec ⁇ lp alpha are found in the yeast Saccharomyces cerevisiae (Sec ⁇ lp) and in bacteria (SecYp). (See G ⁇ riich, D. et al. (1992) Cell 71 :489-503; Matlack, K.E.S. et al. (1998) Cell 92:381-390.)
  • Gap junctions are channels that function chemically and electrically to couple the cytoplasms of neighboring cells in many tissues. Gap junctions function as electrical synapses for intercellular propagation of action potentials in excitable tissues. In nonexcitable tissues, gap junctions have roles in tissue homeostasis, coordinated physiological response, metabolic cooperation, growth control, and the regulation of development and differentiation. Gap junctions help to synchronize heart and smooth muscle contraction, speed neural transmission, and propagate extracellular signals. Gap junctions can open and close in response to particular stimuli (e.g., pH, Ca +2 , and cAMP).
  • stimuli e.g., pH, Ca +2 , and cAMP
  • the effective pore size of a gap junction is approximately 1.5 nm, which enables small molecules (e.g., those under 1000 daltons) to diffuse freely through the pore.
  • Transported molecules include ions, small metabolites, and second messengers (e.g., Ca +2 and cAMP).
  • Each connexon is composed of six identical subunits called connexins. At least thirteen distinct connexin proteins exist, with each having similar structures but differing tissue distributions. Structurally, the connexins are integral membrane proteins with four putative membrane spanning regions and N- and C-termini oriented towards the cell cytoplasm. conserveed regions include the membrane spanning regions and two extracellular loops. The variable regions, which are two cytoplasmic loops and the C-terminal region, may be responsible for the regulation of different connexins. (See Hennemann, H. et al. (1992) J. Biol. Chem. 267: 17225-17233; PRINTS PR00206 connexin signature.)
  • Connexins have many disease associations. Female mice lacking connexin 37 (Cx37) are infertile due to the absence of the oocyte-granulosa cell signaling pathway. Mice lacking Cx43 die shortly after birth and show cardiac defects reminiscent of some forms of stenosis of the pulmonary artery in humans. Mutations in Cx32 are associated with the X-linked form of Charcot-Marie-Tooth disease, a motor and sensory neuropathy of the peripheral nervous system. Cx26 is expressed in the placenta, and Cx26-deficient mice show decreased transplacental transport of a glucose analog from the maternal to the fetal circulation.
  • Cx26 has been identified as the first susceptibility gene for non-syndromic sensorineural autosomal deafness.
  • Cx46 is expressed in lens fiber cells, and Cx46-deficient mice develop early-onset cataracts that resemble human nuclear cataracts.
  • Ion Channels The electrical potential of a cell is generated and maintained by controlling the movement of ions across the plasma membrane. The movement of ions requires ion channels, which form an ion-selective pore within the membrane. There are two basic types of ion channel: ion transporters and gated ion channels.
  • Ion transporters utilize the energy obtained from ATP hydrolysis to actively transport an ion against the ion's concentration gradient.
  • Gated ion channels allow passive flow of an ion down the ion's electrochemical gradient under restricted conditions. Together, these types of ion channels generate, maintain, and utilize an electrochemical gradient that is used in 1) electrical impulse conduction down the axon of a nerve cell, 2) transport of molecules into cells against concentration gradients, 3) initiation of muscle contraction, and 4) endocrine cell secretion.
  • Ion channels share common structural and mechanistic themes. The channel consists of four or five subunits or protein monomers that are arranged like a barrel in the plasma membrane.
  • Each subunit typically constists of six potential transmembrane segments (SI, S2, S3, S4, S5, and S6).
  • the center of the barrel forms a pore lined by ⁇ -helices or ⁇ -strands.
  • the side chains of the amino acid residues comprising the ⁇ -helices or ⁇ -strands establish the charge (cation or anion) selectivity of the channel.
  • the degree of selectivity, or what specific ions are allowed to pass through the channel depends on the diameter of the narrowest part of the pore.
  • Ion transporters generate and maintain the resting electrical potential of a cell. Utilizing the energy derived from ATP hydrolysis, they transport ions against the ion " s concentration gradient. These transmembrane ATPases are divided into three families.
  • the vacuolar (V) class of ion transporters includes H + pumps on intracellular organelles, such as lysosomes and Golgi. V-class ion transporters are responsible for generating the low pH within the lumen of these organelles that is required for function.
  • the coupling factor (F) class consists of H + pumps in the mitochondria. F-class ion transporters utilize a proton gradient to generate ATP from ADP and inorganic phosphate (P,).
  • the phosphorylated (P) class ion transporters including Na + -K * ATPase, Ca ⁇ 2 -ATPase, and H + -ATPase, are activated by a phosphorylation event.
  • P-class ion transporters are responsible for maintaining resting potential distributions such that cytosolic concentrations of Na" and Ca +2 are low and cytosolic concentration of K + is high.
  • the resting potential of the cell is utilized in many processes involving carrier proteins and gated ion channels. Carrier proteins utilize the resting potential to transport molecules into and out of the cell.
  • Amino acid and glucose transport into many cells is linked to sodium ion co-transport (symport) so that the movement of Na + down an electrochemical gradient drives transport of the other molecule up a concentration gradient.
  • cardiac muscle links transfer of Ca +2 out of the cell with transport of Na + into the cell (antiport).
  • Gated ion channels control ion flow by regulating the opening and closing of pores.
  • the ability to control ion flux through various gating mechanisms allows ion channels to mediate such diverse signaling and homeostatic functions as neuronal and endocrine signaling, muscle contraction, fertilization, and regulation of ion and pH balance.
  • Gated ion channels are categorized according to the manner of regulating the gating function.
  • Mechanically-gated channels open their pores in response to mechanical stress; voltage-gated channels (e.g., Na + , K + , Ca +2 , and Cl " channels) open their pores in response to changes in membrane potential; and ligand- gated channels (e.g., acetylcholine-, serotonin-, and glutamate- gated cation channels, and GABA- and glycine- gated chloride channels) open their pores in the presence of a specific ion, nucleotide, or neurotransmitter.
  • voltage-gated channels e.g., Na + , K + , Ca +2 , and Cl " channels
  • ligand- gated channels e.g., acetylcholine-, serotonin-, and glutamate- gated cation channels, and GABA- and glycine- gated chloride channels
  • the gating properties of a particular ion channel are sometimes modulated by association with auxiliary channel proteins and/or post translational modifications, such as phosphorylation.
  • auxiliary channel proteins and/or post translational modifications such as phosphorylation.
  • the pore forming subunits of voltage-gated and transmitter-gated cation channels form two distinct superfamilies of conserved multipass membrane proteins.
  • Voltage-gated Na + and K + channels are necessary for the function of electrically excitable cells such as nerve, endocrine, and muscle cells. Action potentials, which lead to neurotransmitter release and muscle contraction, arise from large, transient changes in the permeability of the membrane to Na + and K + ions. Depolarization of the membrane beyond the threshold level opens voltage-gated Na + channels. Sodium ions flow into the cell, further depolarizing the membrane and opening more voltage-gated Na + channels, thus propagating the depolarization down the length of the cell. Depolarization also opens voltage-gated K + channels. Consequently, potassium ions flow outward, leading to repolarization of the membrane.
  • Voltage-gated channels utilize charged residues in the fourth transmembrane segment (S4) to sense voltage change.
  • the open state lasts only about 1 millisecond, at which time the channel spontaneously converts into an inactive state that cannot be opened irrespective of the membrane potential.
  • Inactivation is mediated by the channel's N-terminus, which acts as a plug that closes the pore. The transition from an inactive to a closed state requires a return to resting potential.
  • Na + channels isolated from rat brain tissue are heterotrimeric complexes composed of a
  • the ⁇ 2 subunit is an integral membrane glycoprotein that contains an extracellular lg domain, and its association with ⁇ and ⁇ l subunits correlates with increased function of the channel, a change in the channel's gating properties, as well as an increase in whole cell capacitance (Isom, L.L. et al. (1995) Cell 83:433-442).
  • K + channels are located in all cell types, and may be regulated by voltage, ATP concentration, or second messengers such as Ca" ⁇ and cAMP.
  • K + channels are involved in protein synthesis, control of endocrine secretions, and the maintenance of osmotic equilibrium across membranes.
  • K + channels are responsible for setting resting membrane potential.
  • the cytosol contains non-diffusible anions and, to balance this net negative charge, the cell contains a Na + -K + pump and ion channels that provide the redistribution of Na + , K + , and Cl " .
  • the pump actively transports Na + out of the cell and K + into the cell in a 3:2 ratio. Ion channels in the plasma membrane allow K + and Cl " to flow by passive diffusion. Because of the high negative charge within the cytosol, Cl " flows out of the cell. The flow of K + is balanced by an electromotive force pulling K + into the cell, and a K + concentration gradient pushing K + out of the cell. Thus, the resting membrane potential is primarily regulated by K + flow (Salkoff, L. and T. Jegla (1995) Neuron 15:489-492).
  • K + pore-forming subunits generally have six transmembrane-spanning domains with a short region between the fifth and sixth transmembrane regions that senses membrane potential; and the amino and carboxy termini are located intracellularly.
  • the duration of ventricular action potential is controlled by a K + current.
  • the K + channel is central to the control of heart rate and rhythm.
  • K + channel dysfunctions are associated with a number of renal diseases including hypertension, hypokalemia, and the associated Barrier's syndrome and Getelman's syndrome, as well as neurological disorders including epilepsy.
  • K + channels have been implicated in Alzheimer's disease by observations that a significant component of senile plaques, beta amyloid or A beta, also blocks voltage-gated potassium channels in hippocampal neurons.
  • a significant component of senile plaques, beta amyloid or A beta also blocks voltage-gated potassium channels in hippocampal neurons.
  • Voltage-gated Ca” 2 channels are involved in presynaptic neurotransmitter release, and heart and skeletal muscle contraction.
  • the voltage-gated Ca +2 channels from skeletal muscle (L- type) and brain (N-type) have been purified and, though their functions differ dramatically, they have similar subunit compositions.
  • the channels are composed of three subunits.
  • the ⁇ , subunit forms the membrane pore and voltage sensor, while the ⁇ 2 ⁇ and ⁇ subunits modulate the voltage- dependence, gating properties, and the current amplitude of the channel.
  • These subunits are encoded by at least six ⁇ ,, one ⁇ 2 ⁇ , and four ⁇ genes.
  • a fourth subunit, ⁇ has been identified in skeletal muscle. (See Walker, D. et al. (1998) J. Biol. Chem. 273:2361-2367; Jay, S.D. et al. (1990) Science 248:490-492.)
  • Chloride channels are necessary in endocrine secretion and in regulation of cytosolic and organelle pH.
  • Cl ' enters the cell across a basolateral membrane through an Na + , K7C1 ' cotransporter, accumulating in the cell above its electrochemical equilibrium concentration.
  • Secretion of Cl ' from the apical surface in response to hormonal stimulation, leads to flow of Na" and water into the secretory lumen.
  • the cystic fibrosis transmembrane conductance regulator (CFTR) is a chloride channel encoded by the gene for cystic fibrosis, a common fatal genetic disorder in humans.
  • Loss of CFTR function decreases transepithelial water secretion and, as a result, the layers of mucus that coat the respiratory tree, pancreatic ducts, and intestine are dehydrated and difficult to clear. The resulting blockage of these sites leads to pancreatic insufficiency, "meconium ileus,” and devastating "chronic obstructive pulmonary disease” (Al-Awqati, Q. et al. (1992) J. Exp. Biol. 172:245-266).
  • H + -ATPase pumps that generate transmembrane pH and electrochemical differences by moving protons from the cytosol to the organelle lumen. If the membrane of the organelle is permeable to other ions, then the electrochemical gradient can be abrogated without affecting the pH differential. In fact, removal of the electrochemical barrier allows more H + to be pumped across the membrane, increasing the pH differential.
  • Cl " is the sole counterion of H + translocation in a number of organelles, including chromaffin granules, Golgi vesicles, lysosomes, and endosomes.
  • Functions that require a low vacuolar pH include uptake of small molecules such as biogenic amines in chromaffin granules, processing of vacuolar constituents such as pro-hormones by proteolytic enzymes, and protein degradation in lysosomes (Al-Awqati, supra).
  • Ligand-gated channels open their pores when an extracellular or intracellular mediator binds to the channel.
  • Neurotransmitter-gated channels are channels that open when a neurotransmitter binds to their extracellular domain. These channels exist in the postsynaptic membrane of nerve or muscle cells.
  • Chloride channels open in response to inhibitory neurotransmitters, such as ⁇ -aminobutyric acid (GABA) and glycine, leading to hyperpolarization of the membrane and the subsequent generation of an action potential.
  • GABA ⁇ -aminobutyric acid
  • Ligand-gated channels can be regulated by intracellular second messengers.
  • Calcium- activated K + channels are gated by internal calcium ions. In nerve cells, an influx of calcium during depolarization opens K + channels to modulate the magnitude of the action potential (Ishi, T.M. et al. (1997) Proc. Natl. Acad. Sci. USA 94:1 1651-1 1656).
  • Cyclic nucleotide-gated (CNG) channels are gated by cytosolic cyclic nucleotides. The best examples of these are the cAMP- gated Na " channels involved in olfaction and the cGMP-gated cation channels involved in vision.
  • Both systems involve ligand-activation of a G-protein coupled receptor which then alters the level of cyclic nucleotide within the cell.
  • binding of an odorant to the receptor activates adenylate cyclase, leading to a rise in cytosolic cAMP.
  • the cAMP binds to the cAMP-gated Na + channel causing an influx of Na + , depolarization of the membrane, and initiation of a nerve impulse that travels along the axon to the brain.
  • light activation of rhodopsin leads to activation of cGMP phosphodiesterase, which hydrolyzes cGMP.
  • CNG channels for example, consist of ⁇ and ⁇ subunits that differ from each other at the N-terminal cytoplasmic tail.
  • the central pore formed by the barrel arrangement is lined by an antiparallel ⁇ - sheet, the pore (P) region, contained within each subunit. This region also contains information specifying the ion selectivity for the channel.
  • P pore
  • a GYG tripeptide is involved in this selectivity (Ishi et al.. supra).
  • voltage-gated channels one of the transmembrane domains contains regularly spaced, positively charged amino acids that act as a voltage-sensor.
  • CNG channels a region in the C-terminal cytoplasmic domain acts as a cyclic nucleotide binding site (Za Moscow and Siegelbaum. supra). Ion channels also have a domain that functions in inactivation of the channel. In CNG K + channels, the inactivation domain is on the N- terminal cytoplasmic tail of the ⁇ -subunit. This domain acts as a tethered ball to block ion flow through the pore. This domain is also expressed as a separate protein, a glutamic acid-rich protein (GARP), by alternative splicing and may act as an independent regulator of pore activity (Sautter, A. et al. (1997) Molec. Brain Res. 48: 171-175).
  • GRIP glutamic acid-rich protein
  • Ion channels are essential to a wide range of physiological functions including neuronal signaling, muscle contraction, cardiac pacemaking, hormone secretion, and cell proliferation. Ion channels are expressed in a number of tissues where they are implicated in a variety of processes. CNG channels, while abundantly expressed in photoreceptor and olfactory sensory cells, are also found in kidney, lung, pineal, retinal ganglion cells, testis, aorta, and brain. Calcium-activated K + channels may be responsible for the vasodilatory effects of bradykinin in the kidney and for shunting excess K + from brain capillary endothelial cells into the blood.
  • Ion channels have been the target for many drug therapies.
  • Neurotransmitter-gated channels have been targeted in therapies for treatment of insomnia, anxiety, depression, and schizophrenia.
  • Voltage-gated channels have been targeted in therapies for arrhythmia, ischemic stroke, head trauma, and neurodegenerative disease (Taylor, C.P. and L.S. Narasimhan (1997) Adv. Pharmacol. 39:47-98).
  • the invention features substantially purified polypeptides, human membrane channel proteins, referred to collectively as “MECHP” and individually as “MECHP- 1,” “MECHP-2,” “MECHP-3,” “MECHP-4,” “MECHP-5,” “MECHP-6,” “MECHP-7,” “MECHP-8,” “MECHP-9,” “MECHP- 10,” “MECHP- 11,” “MECHP- 12,” “MECHP- 13 ,” “MECHP- 14,” “MECHP- 15,” “MECHP- 16", “MECHP- 17", and “MECHP- 18.”
  • the invention provides a substantially purified polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 1-18, and fragments thereof.
  • the invention further provides a substantially purified variant having at least 95% amino acid sequence identity to at least one of the amino acid sequences selected from the group consisting of SEQ ID NO: 1-18 and fragments thereof.
  • the invention also provides an isolated and purified polynucleotide encoding the polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 1-18 and fragments thereof.
  • the invention also includes an isolated and purified polynucleotide variant having at least 95% polynucleotide sequence identity to the polynucleotide encoding the polypeptide comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 1-18 and fragments thereof.
  • the invention provides an isolated and purified polynucleotide which hybridizes under stringent conditions to the polynucleotide encoding the polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 1-18 and fragments thereof.
  • the invention also provides an isolated and purified polynucleotide having a sequence which is complementary to the polynucleotide encoding the polypeptide comprising the amino acid sequence selected from the group consisting of SEQ ID NO: 1-18 and fragments thereof.
  • the invention also provides a method for detecting a polynucleotide in a sample containing nucleic acids, the method comprising the steps of (a) hybridizing the complement of the polynucleotide sequence to at least one of the polynucleotides of the sample, thereby forming a hybridization complex; and (b) detecting the hybridization complex, wherein the presence of the hybridization complex correlates with the presence of a polynucleotide in the sample.
  • the method further comprises amplifying the polynucleotide prior to hybridization.
  • the invention also provides an isolated and purified polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO: 19-36, and fragments thereof.
  • the invention further provides an isolated and purified polynucleotide variant having at least 95% polynucleotide sequence identity to the polynucleotide sequence selected from the group consisting of SEQ ID NO: 19-36 and fragments thereof.
  • the invention also provides an isolated and purified polynucleotide having a sequence which is complementary to the polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO: 19-36 and fragments thereof.
  • the invention further provides an expression vector containing at least a fragment of the polynucleotide encoding the polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 1-18 and fragments thereof.
  • the expression vector is contained within a host cell.
  • the invention also provides a method for producing a polypeptide, the method comprising the steps of: (a) culturing the host cell containing an expression vector containing at least a fragment of a polynucleotide under conditions suitable for the expression of the polypeptide; and (b) recovering the polypeptide from the host cell culture.
  • the invention also provides a pharmaceutical composition
  • a pharmaceutical composition comprising a substantially purified polypeptide having the amino acid sequence selected from the group consisting of SEQ ID NO: 1-18 and fragments thereof, in conjunction with a suitable pharmaceutical carrier.
  • the invention further includes a purified antibody which binds to a polypeptide selected from the group consisting of SEQ ID NO: 1-18 and fragments thereof.
  • the invention also provides a purified agonist and a purified antagonist to the polypeptide.
  • the invention also provides a method for treating or preventing a disorder associated with decreased expression or activity of MECHP, the method comprising administering to a subject in need of such treatment an effective amount of a pharmaceutical composition comprising a substantially purified polypeptide having the amino acid sequence selected from the group consisting of SEQ ID NO: 1-18 and fragments thereof, in conjunction with a suitable pharmaceutical carrier.
  • the invention also provides a method for treating or preventing a disorder associated with increased expression or activity of MECHP, the method comprising administering to a subject in need of such treatment an effective amount of an antagonist of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO: 1-18 and fragments thereof.
  • rat glutamic acid-rich protein (GI 2924369; SEQ ID NO:37), produced using the
  • FIG. 1 shows the amino acid sequence alignment among MECHP-2 (4094907; SEQ ID NO: 1
  • Drosophila voltage-gated potassium channel (GI 116443; SEQ ID NO:38), and P.. penicillatus potassium channel ⁇ -subunit (GI 1763619; SEQ ID NO:39), produced using the multisequence alignment program of LASERGENE software (DNASTAR, Madison WI).
  • FIGS 3A and 3B show the amino acid sequence alignment between MECHP-3 (518158;
  • P. penicillatus potassium channel ⁇ -subunit (GI 1763619; SEQ ID NO:39), produced using the multisequence alignment program of LASERGENE software.
  • Figures 5 A and 5B show the amino acid sequence alignment between MECHP-5 (922119; SEQ ID NO:5) and rat aquaporin 7 (GI 2350843; SEQ ID NO:41), produced using the multisequence alignment program of LASERGENE software.
  • FIGS 6A and 6B show the amino acid sequence alignment between MECHP-7
  • Figure 7 shows the amino acid sequence alignment between MECHP- 16 (2069907; SEQ ID NO: 16) and human beta subunit of Ca * activated K + channel (GI 1055345; SEQ ID NO:43), produced using the multisequence alignment program of LASERGENE software.
  • Figures 8A and 8B show the amino acid sequence alignment between MECHP- 17 (2243917: SEQ ID NO: 17) and a homolog of Caenorhabditis elegans K + channel protein (GI 3292929; SEQ ID NO:44), produced using the multisequence alignment program of LASERGENE software.
  • Figures 9A and 9B show the amino acid sequence alignment between MECHP- 18 (2597476; SEQ ID NO: 18) and human aquaporin 9 (GI 2887407; SEQ ID NO:45), produced using the multisequence alignment program of LASERGENE software.
  • Table 1 shows polypeptide and nucleotide sequence identification numbers (SEQ ID NOs), clone identification numbers (clone IDs), cDNA libraries, and cDNA fragments used to assemble full-length sequences encoding MECHP.
  • Table 2 shows features of each polypeptide sequence, including potential motifs, homologous sequences, and methods and algorithms used for identification of MECHP.
  • Table 3 shows the tissue-specific expression patterns of each nucleic acid sequence as determined by northern analysis, diseases, disorders, or conditions associated with these tissues, and the vector into which each cDNA was cloned.
  • Table 4 describes the tissues used to construct the cDNA libraries from which cDNA clones encoding MECHP were isolated.
  • Table 5 shows the tools, programs, and algorithms used to analyze MECHP, along with applicable descriptions, references, and threshold parameters.
  • MECHP refers to the amino acid sequences of substantially purified MECHP obtained from any species, particularly a mammalian species, including bovine, ovine, porcine, murine, equine, and preferably the human species, from any source, whether natural, synthetic, semi-synthetic, or recombinant.
  • agonist refers to a molecule which, when bound to MECHP, increases or prolongs the duration of the effect of MECHP. Agonists may include proteins, nucleic acids, carbohydrates, or any other molecules which bind to and modulate the effect of MECHP.
  • allelic variant is an alternative form of the gene encoding MECHP. Allelic variants may result from at least one mutation in the nucleic acid sequence and may result in altered mRNAs or in polypeptides whose structure or function may or may not be altered. Any given natural or recombinant gene may have none, one, or many allelic forms. Common mutational changes which give rise to allelic variants are generally ascribed to natural deletions, additions, or substitutions of nucleotides. Each of these types of changes may occur alone, or in combination with the others, one or more times in a given sequence.
  • altered nucleic acid sequences encoding MECHP include those sequences with deletions, insertions, or substitutions of different nucleotides, resulting in a polypeptide the same as MECHP or a polypeptide with at least one functional characteristic of MECHP. Included within this definition are polymorphisms which may or may not be readily detectable using a particular oligonucleotide probe of the polynucleotide encoding MECHP, and improper or unexpected hybridization to allelic variants, with a locus other than the normal chromosomal locus for the polynucleotide sequence encoding MECHP.
  • the encoded protein may also be "altered,” and may contain deletions, insertions, or substitutions of amino acid residues which produce a silent change and result in a functionally equivalent MECHP.
  • Deliberate amino acid substitutions may be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity, and/or the amphipathic nature of the residues, as long as the biological or immunological activity of MECHP is retained.
  • negatively charged amino acids may include aspartic acid and glutamic acid
  • positively charged amino acids may include lysine and arginine
  • amino acids with uncharged polar head groups having similar hydrophilicity values may include leucine, isoleucine, and valine; glycine and alanine; asparagine and glutamine; serine and threonine; and phenylalanine and tyrosine.
  • amino acid and amino acid sequence refer to an oligopeptide, peptide, polypeptide, or protein sequence, or a fragment of any of these, and to naturally occurring or synthetic molecules.
  • fragments refer to fragments of MECHP which are preferably at least 5 to about 15 amino acids in length, most preferably at least 14 amino acids, and which retain some biological activity or immunological activity of MECHP.
  • amino acid sequence is recited to refer to an amino acid sequence of a naturally occurring protein molecule
  • amino acid sequence and like terms are not meant to limit the amino acid sequence to the complete native amino acid sequence associated with the recited protein molecule.
  • Amplification relates to the production of additional copies of a nucleic acid sequence. Amplification is generally carried out using polymerase chain reaction (PCR) technologies well known in the art.
  • PCR polymerase chain reaction
  • antagonist refers to a molecule which, when bound to MECHP, decreases the amount or the duration of the effect of the biological or immunological activity of MECHP.
  • Antagonists may include proteins, nucleic acids, carbohydrates, antibodies, or any other molecules which decrease the effect of MECHP.
  • antibody refers to intact molecules as well as to fragments thereof, such as Fab, F(ab') 2 , and Fv fragments, which are capable of binding the epitopic determinant.
  • Antibodies that bind MECHP polypeptides can be prepared using intact polypeptides or using fragments containing small peptides of interest as the immunizing antigen.
  • the polypeptide or oligopeptide used to immunize an animal e.g., a mouse, a rat, or a rabbit
  • an animal e.g., a mouse, a rat, or a rabbit
  • RNA e.g., a mouse, a rat, or a rabbit
  • antigenic determinant refers to that fragment of a molecule (i.e., an epitope) that makes contact with a particular antibody.
  • an antigenic determinant may compete with the intact antigen (i.e.. the immunogen used to elicit the immune response) for binding to an antibody.
  • antisense refers to any composition containing a nucleic acid sequence which is complementary to the "sense” strand of a specific nucleic acid sequence. Antisense molecules may be produced by any method including synthesis or transcription. Once introduced into a cell, the complementary nucleotides combine with natural sequences produced by the cell to form duplexes and to block either transcription or translation. The designation “negative” can refer to the antisense strand, and the designation “positive” can refer to the sense strand.
  • biologically active refers to a protein having structural, regulatory, or biochemical functions of a naturally occurring molecule.
  • immunologically active refers to the capability of the natural, recombinant, or synthetic MECHP, or of any oligopeptide thereof, to induce a specific immune response in appropriate animals or cells and to bind with specific antibodies.
  • complementarity refers to the natural binding of polynucleotides by base pairing.
  • sequence 5' A-G-T 3'
  • complementary sequence 3' T-C-A 5'.
  • Complementarity between two single-stranded molecules may be “partial,” such that only some of the nucleic acids bind, or it may be “complete,” such that total complementarity exists between the single stranded molecules.
  • the degree of complementarity between nucleic acid strands has significant effects on the efficiency and strength of the hybridization between the nucleic acid strands. This is of particular importance in amplification reactions, which depend upon binding between nucleic acids strands, and in the design and use of peptide nucleic acid (PNA) molecules.
  • PNA peptide nucleic acid
  • composition comprising a given polynucleotide sequence and a “composition comprising a given amino acid sequence” refer broadly to any composition containing the given polynucleotide or amino acid sequence.
  • the composition may comprise a dry formulation or an aqueous solution.
  • Compositions comprising polynucleotide sequences encoding MECHP or fragments of MECHP may be employed as hybridization probes.
  • the probes may be stored in freeze-dried form and may be associated with a stabilizing agent such as a carbohydrate.
  • the probe may be deployed in an aqueous solution containing salts (e.g., NaCl), detergents (e.g., sodium dodecyl sulfate; SDS), and other components (e.g., Denhardt's solution, dry milk, salmon sperm DNA, etc.).
  • salts e.g., NaCl
  • detergents e.g., sodium dodecyl sulfate; SDS
  • other components e.g., Denhardt's solution, dry milk, salmon sperm DNA, etc.
  • Consensus sequence refers to a nucleic acid sequence which has been resequenced to resolve uncalled bases, extended using the XL-PCR kit (Perkin-Elmer, Norwalk CT) in the 5' and/or the 3' direction, and resequenced, or which has been assembled from the overlapping sequences of more than one Incyte Clone using a computer program for fragment assembly, such as the GELVIEW fragment assembly system (GCG, Madison WI). Some sequences have been both extended and assembled to produce the consensus sequence.
  • correlates with expression of a polynucleotide indicates that the detection of the presence of nucleic acids, the same or related to a nucleic acid sequence encoding MECHP, by northern analysis is indicative of the presence of nucleic acids encoding MECHP in a sample, and thereby correlates with expression of the transcript from the polynucleotide encoding MECHP.
  • a “deletion” refers to a change in the amino acid or nucleotide sequence that results in the absence of one or more amino acid residues or nucleotides.
  • the term “derivative” refers to the chemical modification of a polypeptide sequence, or a polynucleotide sequence. Chemical modifications of a polynucleotide sequence can include, for example, replacement of hydrogen by an alkyl, acyl, or amino group.
  • a derivative polynucleotide encodes a polypeptide which retains at least one biological or immunological function of the natural molecule.
  • a derivative polypeptide is one modified by glycosylation, pegylation, or any similar process that retains at least one biological or immunological function of the polypeptide from which it was derived.
  • similarity refers to a degree of complementarity. There may be partial similarity or complete similarity. The word “identity” may substitute for the word “similarity.”
  • a partially complementary sequence that at least partially inhibits an identical sequence from hybridizing to a target nucleic acid is referred to as “substantially similar.”
  • the inhibition of hybridization of the completely complementary sequence to the target sequence may be examined using a hybridization assay (Southern or northern blot, solution hybridization, and the like) under conditions of reduced stringency.
  • a substantially similar sequence or hybridization probe will compete for and inhibit the binding of a completely similar (identical) sequence to the target sequence under conditions of reduced stringency.
  • Percent identity refers to the percentage of sequence similarity found in a comparison of two or more amino acid or nucleic acid sequences. Percent identity can be determined electronically, e.g., by using the MEGALIGN program (DNASTAR) which creates alignments between two or more sequences according to methods selected by the user, e.g., the clustal method. (See, e.g., Higgins, D.G. and P.M. Sharp (1988) Gene 73:237-244.) Parameters for each method may be the default parameters provided by MEGALIGN or may be specified by the user. The clustal algorithm groups sequences into clusters by examining the distances between all pairs. The clusters are aligned pairwise and then in groups.
  • the percentage similarity between two amino acid sequences is calculated by dividing the length of sequence A, minus the number of gap residues in sequence A, minus the number of gap residues in sequence B, into the sum of the residue matches between sequence A and sequence B, times one hundred. Gaps of low or of no similarity between the two amino acid sequences are not included in determining percentage similarity. Percent identity between nucleic acid sequences can also be counted or calculated by other methods known in the art, e.g., the Jotun Hein method. (See, e.g., Hein, J. (1990) Methods Enzymol.
  • HACs Human artificial chromosomes
  • HACs are linear microchromosomes which may contain DNA sequences of about 6 kb to 10 Mb in size, and which contain all of the elements required for stable mitotic chromosome segregation and maintenance.
  • humanized antibody refers to antibody molecules in which the amino acid sequence in the non-antigen binding regions has been altered so that the antibody more closely resembles a human antibody, and still retains its original binding ability.
  • Hybridization refers to any process by which a strand of nucleic acid binds with a complementary strand through base pairing.
  • hybridization complex refers to a complex formed between two nucleic acid sequences by virtue of the formation of hydrogen bonds between complementary bases.
  • a hybridization complex may be formed in solution (e.g., C 0 t or Rot analysis) or formed between one nucleic acid sequence present in solution and another nucleic acid sequence immobilized on a solid support (e.g., paper, membranes, filters, chips, pins or glass slides, or any other appropriate substrate to which cells or their nucleic acids have been fixed).
  • insertion and “addition” refer to changes in an amino acid or nucleotide sequence resulting in the addition of one or more amino acid residues or nucleotides, respectively, to the sequence found in the naturally occurring molecule.
  • Immuno response can refer to conditions associated with inflammation, trauma, immune disorders, or infectious or genetic disease, etc. These conditions can be characterized by expression of various factors, e.g., cytokines, chemokines, and other signaling molecules, which may affect cellular and systemic defense systems.
  • factors e.g., cytokines, chemokines, and other signaling molecules, which may affect cellular and systemic defense systems.
  • microarray refers to an arrangement of distinct polynucleotides on a substrate.
  • element and “array element” in a microarray context, refer to hybridizable polynucleotides arranged on the surface of a substrate.
  • modulate refers to a change in the activity of MECHP. For example, modulation may cause an increase or a decrease in protein activity, binding characteristics, or any other biological, functional, or immunological properties of MECHP.
  • nucleic acid refers to a nucleotide, oligonucleotide, polynucleotide, or any fragment thereof. These phrases also refer to DNA or RNA of genomic or synthetic origin which may be single-stranded or double-stranded and may represent the sense or the antisense strand, to peptide nucleic acid (PNA), or to any DNA-like or RNA-like material.
  • fragment refers to those nucleic acid sequences which comprise a region of unique polynucleotide sequence that specifically identifies SEQ ID NO: 19-36, for example, as distinct from any other sequence in the same genome.
  • a fragment of SEQ ID NO: 19-36 is useful in hybridization and amplification technologies and in analogous methods that distinguish SEQ ID NO: 19-36 from related polynucleotide sequences.
  • a fragment of SEQ ID NO: 19-36 is at least about 15-20 nucleotides in length.
  • the precise length of the fragment of SEQ ID NO: 19-36 and the region of SEQ ID NO: 19-36 to which the fragment corresponds are routinely determinable by one of ordinary skill in the art based on the intended purpose for the fragment.
  • a fragment, when translated, would produce polypeptides retaining some functional characteristic, e.g., antigenicity, or structural domain characteristic, e.g., ATP-binding site, of the full-length polypeptide.
  • operably associated and operably linked refer to functionally related nucleic acid sequences.
  • a promoter is operably associated or operably linked with a coding sequence if the promoter controls the translation of the encoded polypeptide. While operably associated or operably linked nucleic acid sequences can be contiguous and in the same reading frame, certain genetic elements, e.g., repressor genes, are not contiguously linked to the sequence encoding the polypeptide but still bind to operator sequences that control expression of the polypeptide.
  • oligonucleotide refers to a nucleic acid sequence of at least about 6 nucleotides to 60 nucleotides, preferably about 15 to 30 nucleotides, and most preferably about 20 to 25 nucleotides, which can be used in PCR amplification or in a hybridization assay or microarray.
  • Oligonucleotide is substantially equivalent to the terms “amplimer,” “primer,” “oligomer,” and “probe,” as these terms are commonly defined in the art.
  • PNA protein nucleic acid
  • PNA refers to an antisense molecule or anti-gene agent which comprises an oligonucleotide of at least about 5 nucleotides in length linked to a peptide backbone of amino acid residues ending in lysine. The terminal lysine confers solubility to the composition. PNAs preferentially bind complementary single stranded DNA or RNA and stop transcript elongation, and may be pegylated to extend their lifespan in the cell. The term “sample” is used in its broadest sense.
  • a sample suspected of containing nucleic acids encoding MECHP, or fragments thereof, or MECHP itself may comprise a bodily fluid; an extract from a cell, chromosome, organelle, or membrane isolated from a cell; a cell; genomic DNA, RNA, or cDNA, in solution or bound to a substrate; a tissue; a tissue print; etc.
  • binding and “specifically binding” refer to that interaction between a protein or peptide and an agonist, an antibody, or an antagonist. The interaction is dependent upon the presence of a particular structure of the protein, e.g., the antigenic determinant or epitope, recognized by the binding molecule. For example, if an antibody is specific for epitope "A,” the presence of a polypeptide containing the epitope A, or the presence of free unlabeled A, in a reaction containing free labeled A and the antibody will reduce the amount of labeled A that binds to the antibody.
  • stringent conditions refers to conditions which permit hybridization between polynucleotides and the claimed polynucleotides.
  • Stringent conditions can be defined by salt concentration, the concentration of organic solvent, e.g., formamide, temperature, and other conditions well known in the art.
  • stringency can be increased by reducing the concentration of salt, increasing the concentration of formamide, or raising the hybridization temperature.
  • substantially purified refers to nucleic acid or amino acid sequences that are removed from their natural environment and are isolated or separated, and are at least about 60% free, preferably about 75% free, and most preferably about 90% free from other components with which they are naturally associated.
  • substitution refers to the replacement of one or more amino acids or nucleotides by different amino acids or nucleotides, respectively.
  • Substrate refers to any suitable rigid or semi-rigid support including membranes, filters, chips, slides, wafers, fibers, magnetic or nonmagnetic beads, gels, tubing, plates, polymers, microparticles and capillaries.
  • the substrate can have a variety of surface forms, such as wells, trenches, pins, channels and pores, to which polynucleotides or polypeptides are bound.
  • Transformation describes a process by which exogenous DNA enters and changes a recipient cell. Transformation may occur under natural or artificial conditions according to various methods well known in the art, and may rely on any known method for the insertion of foreign nucleic acid sequences into a prokaryotic or eukaryotic host cell.
  • the method for transformation is selected based on the type of host cell being transformed and may include, but is not limited to, viral infection, electroporation, heat shock, lipofection, and particle bombardment.
  • the term "transformed” cells includes stably transformed cells in which the inserted DNA is capable of replication either as an autonomously replicating plasmid or as part of the host chromosome, as well as transiently transformed cells which express the inserted DNA or RNA for limited periods of time.
  • a “variant" of MECHP polypeptides refers to an amino acid sequence that is altered by one or more amino acid residues.
  • the variant may have "conservative” changes, wherein a substituted amino acid has similar structural or chemical properties (e.g., replacement of leucine with isoleucine). More rarely, a variant may have "nonconservative” changes (e.g., replacement of glycine with tryptophan).
  • Analogous minor variations may also include amino acid deletions or insertions, or both.
  • Guidance in determining which amino acid residues may be substituted, inserted, or deleted without abolishing biological or immunological activity may be found using computer programs well known in the art, for example, LASERGENE software (DNASTAR).
  • variants when used in the context of a polynucleotide sequence, may encompass a polynucleotide sequence related to MECHP. This definition may also include, for example, "allelic” (as defined above), “splice,” “species,” or “polymorphic” variants.
  • a splice variant may have significant identity to a reference molecule, but will generally have a greater or lesser number of polynucleotides due to alternate splicing of exons during mRNA processing.
  • the corresponding polypeptide may possess additional functional domains or an absence of domains.
  • Species variants are polynucleotide sequences that vary from one species to another. The resulting polypeptides generally will have significant amino acid identity relative to each other.
  • a polymorphic variant is a variation in the polynucleotide sequence of a particular gene between individuals of a given species.
  • Polymorphic variants also may encompass "single nucleotide polymorphisms" (SNPs) in which the polynucleotide sequence varies by one base.
  • SNPs single nucleotide polymorphisms
  • the presence of SNPs may be indicative of, for example, a certain population, a disease state, or a propensity for a disease state.
  • the invention is based on the discovery of new human membrane channel proteins
  • MECHP the polynucleotides encoding MECHP
  • MECHP the polynucleotides encoding MECHP
  • use of these compositions for the diagnosis, treatment, or prevention of cell proliferative, immune/inflammatory, transport/secretory, osmoregulatory, muscular, cardiovascular, and neurological disorders.
  • Table 1 lists the Incyte clones used to assemble full length nucleotide sequences encoding MECHP. Columns 1 and 2 show the sequence identification numbers (SEQ ID NOs) of the polypeptide and nucleotide sequences, respectively. Column 3 shows the clone IDs of the Incyte clones in which nucleic acids encoding each MECHP were identified, and column 4 shows the cDNA libraries from which these clones were isolated. Column 5 shows Incyte clones and their corresponding cDNA libraries. Clones for which cDNA libraries are not indicated were derived from pooled cDNA libraries. The clones in column 5 were used to assemble the consensus nucleotide sequence of each MECHP and are useful as fragments in hybridization technologies.
  • SEQ ID NOs sequence identification numbers
  • column 1 references the SEQ ID NO; column 2 shows the number of amino acid residues in each polypeptide; column 3 shows potential phosphorylation sites; column 4 shows potential glycosylation sites; column 5 shows the amino acid residues comprising signature sequences and motifs; column 6 shows the identity of each polypeptide; and column 7 shows analytical methods used to identify each polypeptide through sequence homology and protein motifs.
  • MECHP- 1 has chemical and structural similarity with rat glutamic acid-rich protein (GI
  • MECHP- 1 and rat glutamic acid-rich protein share 15% overall identity.
  • BLAST analysis identifies regions of MECHP- 1 and rat glutamic acid-rich protein which share 27-30% identity. These regions extend from residue VI 2 through T163, P266 through G344, P461 through E548, and E653 through G709 in MECHP-1.
  • MECHP-2 has chemical and structural similarity with Drosophila voltage-gated potassium channel (GI 116443; SEQ ID NO:38) and P. penicillatus potassium channel ⁇ -subunit (GI 1763619; SEQ ID NO:39). In particular.
  • MECHP-2 shares 18% identity with Drosophila voltage-gated K + channel, and 17% identity with P. penicillatus K + channel ⁇ - subunit. In particular, MECHP-2 shares 27% identity with Drosophila voltage-gated potassium channel and P. penicillatus potassium channel ⁇ -subunit over the first 133 residues, from Ml through T133 in MECHP-2.
  • MECHP-3 has chemical and structural similarity with rat calcium-activated potassium channel rSK3 (GI 2564072; SEQ ID NO:40).
  • MECHP- 3 and rat rSK3 share 40% identity.
  • MECHP-3 and rat rSK3 also share a canonical ion pore (P) region, including a GYG potassium ion selectivity sequence, from residue W192 through G213 in MECHP-3.
  • P canonical ion pore
  • MECHP-4 has chemical and structural similarity with Drosophila voltage-gated potassium channel (GI 1 16443; SEQ ID NO:38) and P. penicillatus potassium channel ⁇ -subunit (GI 1763619; SEQ ID NO:39). In particular, MECHP-4 shares 28% identity with Drosophila voltage-gated K + channel, and 26% identity with P. penicillatus K + channel ⁇ -subunit, respectively. MECHP-4, Drosophila voltage-gated K + channel, and penicillatus K + channel ⁇ -subunit also share a GYG potassium ion selectivity sequence from residue G372 through G374 in MECHP-4. As shown in Figures 5A and 5B, MECHP-5 has chemical and structural similarity with rat aquaporin 7 (GI 2350843; SEQ ID NO:41). In particular, MECHP-5 and rat aquaporin 7 share 74% identity.
  • MECHP-7 has chemical and structural similarity with mouse connexin 30.3 (GI 192647; SEQ ID NO:42).
  • MECHP-7 and mouse connexin 30.3 share 84% identity.
  • MECHP- 16 has chemical and structural similarity with human beta subunit of Ca + activated K + channel (GI 1055345; SEQ ID NO:43).
  • MECHP- 16 and human beta subunit of Ca + activated K + channel share 40% identity.
  • MECHP- 17 has chemical and structural similarity with a homolog of C. elegans K + channel protein (GI 3292929; SEQ ID NO:44).
  • MECHP- 17 and the specified homolog of C. elegans K + channel protein share 47% identity.
  • MECHP- 18 has chemical and structural similarity with human aquaporin 9 (GI 2887407; SEQ ID NO:45).
  • MECHP- 18 and human aquaporin 9 share 46% identity.
  • the columns of Table 3 show the tissue-specificity and diseases, disorders, or conditions associated with nucleotide sequences encoding MECHP.
  • the first column of Table 3 lists the nucleotide SEQ ID NOs.
  • Column 2 lists tissue categories which express MECHP as a fraction of total tissue categories expressing MECHP.
  • Column 3 lists diseases, disorders, or conditions associated with those tissues expressing MECHP.
  • Column 4 lists the vectors used to subclone the cDNA library.
  • Northern analysis shows the expression of SEQ ID NO:34 in only 7 libraries, of which 6 (86%) are associated with cell proliferation. Two of these libraries are associated with brain tissue, one with pancreatic islet cells, one with kidney tissue, one with fetal lung tissue, one with ovarian tissue, and one with adrenal tissue.
  • Northern analysis shows the expression of SEQ ID NO:36 in only 3 libraries, one of which is associated with ovarian tumor tissue, one with developing lung tissue, and one with gastrointestinal tissue associated with inflammation.
  • MECHP neural and neuroendocrine tissue, most prominently the neural tissue-specific expression of SEQ ID NO:30.
  • Table 4 show descriptions of the tissues used to construct the cDNA libraries from which cDNA clones encoding MECHP were isolated.
  • Column 1 references the nucleotide SEQ ID NOs
  • column 2 shows the cDNA libraries from which these clones were isolated
  • column 3 shows the tissue origins and other descriptive information relevant to the cDNA libraries in column 2.
  • the following fragments of the nucleotide sequences encoding MECHP are useful, for example, in hybridization or amplification technologies to identify SEQ ID NO: 19-36, and to distinguish between SEQ ID NO: 19-36 and related polynucleotide sequences.
  • the useful fragments include the fragment of SEQ ID NO: 19 from about nucleotide 764 to about nucleotide 808; the fragment of SEQ ID NO:20 from about nucleotide 523 to about nucleotide 582; the fragment of SEQ ID NO:21 from about nucleotide 628 to about nucleotide 669; the fragment of SEQ ID NO:22 from about nucleotide 779 to about nucleotide 826; the fragment of SEQ ID NO:23 from about nucleotide 64 to about nucleotide 108; the fragment of SEQ ID NO:24 from about nucleotide 1 133 to about nucleotide 1 180; the fragment of SEQ ID NO:25 from about nucleotide 656 to about nucleotide 700; the fragment of SEQ ID NO:26 from about nucleotide 153 to about nucleotide 197; the fragment of SEQ ID NO:27 from about nucleotide 2160 to about nucleotide 22
  • polypeptides encoded by the fragments of SEQ ID NO: 19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:23, SEQ ID NO:24, SEQ ID NO:25, SEQ ID NO:26, SEQ ID NO:27, SEQ ID NO:28, SEQ ID NO:29, SEQ ID NO:30, SEQ ID NO:34, SEQ ID NO:35, AND SEQ ID NO:36 are useful, for example, as immunogenic peptides.
  • the invention also encompasses MECHP variants.
  • a preferred MECHP variant is one which has at least about 80%, more preferably at least about 90%, and most preferably at least about 95% amino acid sequence identity to the MECHP amino acid sequence, and which contains at least one functional or structural characteristic of MECHP.
  • the invention also encompasses polynucleotides which encode MECHP.
  • the invention encompasses a polynucleotide sequence comprising a sequence selected from the group consisting of SEQ ID NO: 19-36, which encodes MECHP.
  • the invention also encompasses a variant of a polynucleotide sequence encoding MECHP.
  • a variant polynucleotide sequence will have at least about 70%, more preferably at least about 85%. and most preferably at least about 95% polynucleotide sequence identity to the polynucleotide sequence encoding MECHP.
  • a particular aspect of the invention encompasses a variant of a sequence selected from the group consisting of SEQ ID NO: 19-36 which has at least about 70%, more preferably at least about 85%, and most preferably at least about 95% polynucleotide sequence identity to a sequence selected from the group consisting of SEQ ID NO: 19-36.
  • Any one of the polynucleotide variants described above can encode an amino acid sequence which contains at least one functional or structural characteristic of MECHP.
  • nucleotide sequences which encode MECHP and its variants are preferably capable of hybridizing to the nucleotide sequence of the naturally occurring MECHP under appropriately selected conditions of stringency, it may be advantageous to produce nucleotide sequences encoding MECHP or its derivatives possessing a substantially different codon usage, e.g., inclusion of non-naturally occurring codons. Codons may be selected to increase the rate at which expression of the peptide occurs in a particular prokaryotic or eukaryotic host in accordance with the frequency with which particular codons are utilized by the host.
  • RNA transcripts having more desirable properties such as a greater half-life, than transcripts produced from the naturally occurring sequence.
  • the invention also encompasses production of DNA sequences which encode MECHP and MECHP derivatives, or fragments thereof, entirely by synthetic chemistry.
  • the synthetic sequence may be inserted into any of the many available expression vectors and cell systems using reagents well known in the art.
  • synthetic chemistry may be used to introduce mutations into a sequence encoding MECHP or any fragment thereof.
  • polynucleotide sequences that are capable of hybridizing to the claimed polynucleotide sequences, and, in particular, to those shown in SEQ ID NO: 19-36, or to a fragment of SEQ ID NO: 19-36, under various conditions of stringency.
  • SEQ ID NO: 19-36 or to a fragment of SEQ ID NO: 19-36, under various conditions of stringency.
  • stringent salt concentration will ordinarily be less than about 750 mM NaCl and 75 mM trisodium citrate, preferably less than about 500 mM NaCl and 50 mM trisodium citrate, and most preferably less than about 250 mM NaCl and 25 mM trisodium citrate.
  • Low stringency hybridization can be obtained in the absence of organic solvent, e.g., formamide, while high stringency hybridization can be obtained in the presence of at least about 35% formamide, and most preferably at least about 50% formamide.
  • Stringent temperature conditions will ordinarily include temperatures of at least about 30°C, more preferably of at least about 37°C, and most preferably of at least about 42°C.
  • Varying additional parameters, such as hybridization time, the concentration of detergent, e.g., sodium dodecyl sulfate (SDS), and the inclusion or exclusion of carrier DNA, are well known to those skilled in the art.
  • concentration of detergent e.g., sodium dodecyl sulfate (SDS)
  • SDS sodium dodecyl sulfate
  • Various levels of stringency are accomplished by combining these various conditions as needed.
  • hybridization will occur at 30°C in 750 M NaCl, 75 mM trisodium citrate, and 1% SDS.
  • hybridization will occur at 37°C in 500 mM NaCl, 50 M trisodium citrate, 1% SDS, 35% formamide, and 100 ⁇ g/ml denatured salmon sperm DNA
  • hybridization will occur at 42°C in 250 mM NaCl, 25 mM trisodium citrate, 1% SDS, 50 % formamide, and 200 ⁇ g/ml ssDNA. Useful variations on these conditions will be readily apparent to those skilled in the art.
  • wash stringency conditions can be defined by salt concentration and by temperature. As above, wash stringency can be increased by decreasing salt concentration or by increasing temperature.
  • stringent salt concentration for the wash steps will preferably be less than about 30 mM NaCl and 3 mM trisodium citrate, and most preferably less than about 15 mM NaCl and 1.5 mM trisodium citrate.
  • Stringent temperature conditions for the wash steps will ordinarily include temperature of at least about 25°C, more preferably of at least about 42°C, and most preferably of at least about 68°C.
  • wash steps will occur at 25°C in 30 mM NaCl, 3 mM trisodium citrate, and 0.1% SDS. In a more preferred embodiment, wash steps will occur at 42°C in 15 mM NaCl, 1.5 mM trisodium citrate, and 0.1% SDS. In a most preferred embodiment, wash steps will occur at 68°C in 15 mM NaCl, 1.5 mM trisodium citrate, and 0.1% SDS. Additional variations on these conditions will be readily apparent to those skilled in the art.
  • Methods for DNA sequencing are well known in the art and may be used to practice any of the embodiments of the invention.
  • the methods may employ such enzymes as the Klenow fragment of DNA polymerase I, SEQUENASE (US Biochemical, Cleveland OH), Taq polymerase (Perkin-Elmer), thermostable T7 polymerase (Amersham Pharmacia Biotech, Piscataway NJ), or combinations of polymerases and proofreading exonucleases such as those found in the ELONGASE amplification system (Life Technologies, Gaithersburg MD).
  • sequence preparation is automated with machines such as the Robbins Hydra microdispenser (Robbins Scientific, Sunnyvale CA), Hamilton MICROLAB 2200 (Hamilton, Reno NV), Peltier Thermal Cycler 200 (PTC200; MJ Research, Watertown MA) and the ABI CATALYST 800 (Perkin- Elmer). Sequencing is then carried out using either ABI 373 or 377 DNA sequencing systems (Perkin-Elmer), the MEGABACE 1000 DNA sequencing system (Molecular Dynamics, Sunnyvale CA), or other systems known in the art. The resulting sequences are analyzed using a variety of algorithms which are well known in the art. (See, e.g., Ausubel, F.M. (1997) Short Protocols in Molecular Biology.
  • the nucleic acid sequences encoding MECHP may be extended utilizing a partial nucleotide sequence and employing various PCR-based methods known in the art to detect upstream sequences, such as promoters and regulatory elements.
  • PCR-based methods known in the art to detect upstream sequences, such as promoters and regulatory elements.
  • restriction-site PCR uses universal and nested primers to amplify unknown sequence from genomic DNA within a cloning vector.
  • Another method uses primers that extend in divergent directions to amplify unknown sequence from a circularized template.
  • the template is derived from restriction fragments comprising a known genomic locus and surrounding sequences.
  • a third method, capture PCR involves PCR amplification of DNA fragments adjacent to known sequences in human and yeast artificial chromosome DNA. (See, e.g., Lagerstrom, M. et al. (1991) PCR Methods Applic.
  • primers may be designed using commercially available software, such as OLIGO 4.06 primer analysis software (National Biosciences, Plymouth MN) or another appropriate program, to be about 22 to 30 nucleotides in length, to have a GC content of about 50% or more, and to anneal to the template at temperatures of about 68°C to 72°C.
  • commercially available software such as OLIGO 4.06 primer analysis software (National Biosciences, Plymouth MN) or another appropriate program, to be about 22 to 30 nucleotides in length, to have a GC content of about 50% or more, and to anneal to the template at temperatures of about 68°C to 72°C.
  • Genomic libraries may be useful for extension of sequence into 5' non-transcribed regulatory regions.
  • Capillary electrophoresis systems which are commercially available may be used to analyze the size or confirm the nucleotide sequence of sequencing or PCR products.
  • capillary sequencing may employ flowable polymers for electrophoretic separation, four different nucleotide-specific, laser-stimulated fluorescent dyes, and a charge coupled device camera for detection of the emitted wavelengths.
  • Output/light intensity may be converted to electrical signal using appropriate software (e.g., GENOTYPER and SEQUENCE NAVIGATOR, Perkin-Elmer), and the entire process from loading of samples to computer analysis and electronic data display may be computer controlled.
  • Capillary electrophoresis is especially preferable for sequencing small DNA fragments which may be present in limited amounts in a particular sample.
  • polynucleotide sequences or fragments thereof which encode MECHP may be cloned in recombinant DNA molecules that direct expression of MECHP, or fragments or functional equivalents thereof, in appropriate host cells. Due to the inherent degeneracy of the genetic code, other DNA sequences which encode substantially the same or a functionally equivalent amino acid sequence may be produced and used to express MECHP.
  • nucleotide sequences of the present invention can be engineered using methods generally known in the art in order to alter MECHP-encoding sequences for a variety of purposes including, but not limited to, modification of the cloning, processing, and/or expression of the gene product.
  • DNA shuffling by random fragmentation and PCR reassembly of gene fragments and synthetic oligonucleotides may be used to engineer the nucleotide sequences.
  • oligonucleotide-mediated site-directed mutagenesis may be used to introduce mutations that create new restriction sites, alter glycosylation patterns, change codon preference, produce splice variants, and so forth.
  • sequences encoding MECHP may be synthesized, in whole or in part, using chemical methods well known in the art.
  • chemical methods See, e.g., Caruthers, M.H. et al. (1980) Nucleic Acids Symp. Ser. 7:215-223, and Horn, T. et al. (1980) Nucleic Acids Symp. Ser. 7:225-232.
  • MECHP itself or a fragment thereof may be synthesized using chemical methods.
  • peptide synthesis can be performed using various solid-phase techniques. (See, e.g., Roberge, J.Y. et al.
  • Automated synthesis may be achieved using the ABI 431 A peptide synthesizer (Perkin-Elmer). Additionally, the amino acid sequence of MECHP, or any part thereof, may be altered during direct synthesis and/or combined with sequences from other proteins, or any part thereof, to produce a variant polypeptide.
  • the peptide may be substantially purified by preparative high performance liquid chromatography. (See, e.g, Chiez, R.M. and F.Z. Regnier (1990) Methods Enzymol. 182:392- 421.)
  • the composition of the synthetic peptides may be confirmed by amino acid analysis or by sequencing. (See, e.g., Creighton, T. (1984) Proteins. Structures and Molecular Properties. WH Freeman, New York NY.)
  • the nucleotide sequences encoding MECHP or derivatives thereof may be inserted into an appropriate expression vector, i.e., a vector which contains the necessary elements for transcriptional and translational control of the inserted coding sequence in a suitable host.
  • these elements include regulatory sequences, such as enhancers, constitutive and inducible promoters, and 5' and 3' untranslated regions in the vector and in polynucleotide sequences encoding MECHP.
  • Such elements may vary in their strength and specificity.
  • Specific initiation signals may also be used to achieve more efficient translation of sequences encoding MECHP. Such signals include the ATG initiation codon and adjacent sequences, e.g. the Kozak sequence.
  • Methods which are well known to those skilled in the art may be used to construct expression vectors containing sequences encoding MECHP and appropriate transcriptional and translational control elements. These methods include in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. (See, e.g., Sambrook, J. et al. (1989) Molecular Cloning. A Laboratory Manual, Cold Spring Harbor Press, Plainview NY, ch. 4, 8, and 16-17; Ausubel, F.M. et al. ( 1995) Current Protocols in Molecular Biology, John Wiley & Sons, New York NY, ch. 9, 13, and 16.)
  • a variety of expression vector/host systems may be utilized to contain and express sequences encoding MECHP. These include, but are not limited to, microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast transformed with yeast expression vectors; insect cell systems infected with viral expression vectors (e.g., baculovirus); plant cell systems transformed with viral expression vectors (e.g., cauliflower mosaic virus, CaMV, or tobacco mosaic virus, TMV) or with bacterial expression vectors (e.g., Ti or pBR322 plasmids); or animal cell systems.
  • the invention is not limited by the host cell employed.
  • a number of cloning and expression vectors may be selected depending upon the use intended for polynucleotide sequences encoding MECHP.
  • routine cloning, subcloning, and propagation of polynucleotide sequences encoding MECHP can be achieved using a multifunctional E. coli vector such as PBLUESCRIPT (Stratagene, La Jolla CA) or pSPORTl plasmid (Life Technologies). Ligation of sequences encoding MECHP into the vector's multiple cloning site disrupts the lacZ gene, allowing a colorimetric screening procedure for identification of transformed bacteria containing recombinant molecules.
  • these vectors may be useful for in vitro transcription, dideoxy sequencing, single strand rescue with helper phage, and creation of nested deletions in the cloned sequence.
  • vectors which direct high level expression of MECHP may be used.
  • vectors containing the strong, inducible T5 or T7 bacteriophage promoter may be used.
  • Yeast expression systems may be used for production of MECHP.
  • a number of vectors containing constitutive or inducible promoters such as alpha factor, alcohol oxidase, and PGH promoters, may be used in the yeast Saccharomyces cerevisiae or Pichia pastoris.
  • such vectors direct either the secretion or intracellular retention of expressed proteins and enable integration of foreign sequences into the host genome for stable propagation.
  • Plant systems may also be used for expression of MECHP. Transcription of sequences encoding MECHP may be driven by viral promoters, e.g., the 35S and 19S promoters of CaMV used alone or in combination with the omega leader sequence from TMV (Takamatsu, N. (1987) EMBO J. 3:17-311). Alternatively, plant promoters such as the small subunit of RUBISCO or heat shock promoters may be used. (See, e.g., Coruzzi, G. et al. (1984) EMBO J. 3:1671-1680; Broglie, R. et al. (1984) Science 224:838-843; and Winter, J. et al. (1991) Results Probl.
  • constructs can be introduced into plant cells by direct DNA transformation or pathogen-mediated transfection.
  • pathogen-mediated transfection See, e.g.. The McGraw Hill Yearbook of Science and Technology ( 1992) McGraw Hill, New York NY, pp. 191 - 196.
  • a number of viral-based expression systems may be utilized.
  • sequences encoding MECHP may be ligated into an adenovirus transcription/translation complex consisting of the late promoter and tripartite leader sequence. Insertion in a non-essential El or E3 region of the viral genome may be used to obtain infective virus which expresses MECHP in host cells.
  • transcription enhancers such as the Rous sarcoma virus (RSV) enhancer, may be used to increase expression in mammalian host cells.
  • SV40 or EBV-based vectors may also be used for high-level protein expression.
  • HACs Human artificial chromosomes
  • HACs may also be employed to deliver larger fragments of DNA than can be contained in and expressed from a plasmid.
  • HACs of about 6 kb to 10 Mb are constructed and delivered via conventional delivery methods (liposomes, polycationic amino polymers, or vesicles) for therapeutic purposes. (See, e.g., Harrington, J.J. et al. (1997) Nat. Genet. 15:345-355.)
  • sequences encoding MECHP can be transformed into cell lines using expression vectors which may contain viral origins of replication and/or endogenous expression elements and a selectable marker gene on the same or on a separate vector. Following the introduction of the vector, cells may be allowed to grow for about 1 to 2 days in enriched media before being switched to selective media.
  • the purpose of the selectable marker is to confer resistance to a selective agent, and its presence allows growth and recovery of cells which successfully express the introduced sequences.
  • Resistant clones of stably transformed cells may be propagated using tissue culture techniques appropriate to the cell type.
  • selection systems may be used to recover transformed cell lines. These include, but are not limited to, the herpes simplex virus thymidine kinase and adenine phosphoribosyltransferase genes, for use in tk or apr cells, respectively. (See, e.g., Wigler, M. et al. (1977) Cell 11:223-232; Lowy, I. et al. (1980) Cell 22:817-823.) Also, antimetabolite, antibiotic, or herbicide resistance can be used as the basis for selection.
  • dhfr confers resistance to methotrexate
  • neo confers resistance to the aminoglycosides neomycin and G-418
  • als or pat confer resistance to chlorsulfuron and phosphinotricin acetyltransferase, respectively.
  • markers can be used not only to identify transformants, but also to quantify the amount of transient or stable protein expression attributable to a specific vector system. (See. e.g., Rhodes, CA. (1995) Methods Mol. Biol. 55:121-131.) Although the presence/absence of marker gene expression suggests that the gene of interest is also present, the presence and expression of the gene may need to be confirmed. For example, if the sequence encoding MECHP is inserted within a marker gene sequence, transformed cells containing sequences encoding MECHP can be identified by the absence of marker gene function. Alternatively, a marker gene can be placed in tandem with a sequence encoding MECHP under the control of a single promoter. Expression of the marker gene in response to induction or selection usually indicates expression of the tandem gene as well.
  • host cells that contain the nucleic acid sequence encoding MECHP and that express MECHP may be identified by a variety of procedures known to those of skill in the art. These procedures include, but are not limited to, DNA-DNA or DNA-RNA hybridizations, PCR amplification, and protein bioassay or immunoassay techniques which include membrane, solution, or chip based technologies for the detection and/or quantification of nucleic acid or protein sequences.
  • Immunological methods for detecting and measuring the expression of MECHP using either specific polyclonal or monoclonal antibodies are known in the art. Examples of such techniques include enzyme-linked immunosorbent assays (ELISAs), radioimmunoassays (RIAs), and fluorescence activated cell sorting (FACS).
  • ELISAs enzyme-linked immunosorbent assays
  • RIAs radioimmunoassays
  • FACS fluorescence activated cell sorting
  • Means for producing labeled hybridization or PCR probes for detecting sequences related to polynucleotides encoding MECHP include oligolabeling, nick translation, end-labeling, or PCR amplification using a labeled nucleotide.
  • sequences encoding MECHP, or any fragments thereof may be cloned into a vector for the production of an mRNA probe.
  • RNA polymerase such as T7, T3, or SP6 and labeled nucleotides.
  • T7, T3, or SP6 an appropriate RNA polymerase
  • Suitable reporter molecules or labels which may be used for ease of detection include radionuclides, enzymes, fluorescent, chem i luminescent, or chromogenic agents, as well as substrates, cofactors, inhibitors, magnetic particles, and the like.
  • Host cells transformed with nucleotide sequences encoding MECHP may be cultured under conditions suitable for the expression and recovery of the protein from cell culture.
  • the protein produced by a transformed cell may be secreted or retained intracellularly depending on the sequence and/or the vector used.
  • expression vectors containing polynucleotides which encode MECHP may be designed to contain signal sequences which direct secretion of MECHP through a prokaryotic or eukaryotic cell membrane.
  • a host cell strain may be chosen for its ability to modulate expression of the inserted sequences or to process the expressed protein in the desired fashion.
  • Such modifications of the polypeptide include, but are not limited to, acetylation, carboxylation, glycosylation, phosphorylation, lipidation, and acylation.
  • Post-translational processing which cleaves a "prepro" form of the protein may also be used to specify protein targeting, folding, and/or activity.
  • Different host cells which have specific cellular machinery and characteristic mechanisms for post-translational activities (e.g., CHO, HeLa, MDCK, HEK293, and WI38), are available from the American Type Culture Collection (ATCC, Manassas VA) and may be chosen to ensure the correct modification and processing of the foreign protein.
  • natural, modified, or recombinant nucleic acid sequences encoding MECHP may be ligated to a heterologous sequence resulting in translation of a fusion protein in any of the aforementioned host systems.
  • a chimeric MECHP protein containing a heterologous moiety that can be recognized by a commercially available antibody may facilitate the screening of peptide libraries for inhibitors of MECHP activity.
  • Heterologous protein and peptide moieties may also facilitate purification of fusion proteins using commercially available affinity matrices.
  • Such moieties include, but are not limited to, glutathione S-transferase (GST), maltose binding protein (MBP), thioredoxin (Trx), calmodulin binding peptide (CBP), 6-His, FLAG, c-myc, and hemagglutinin (HA).
  • GST, MBP, Trx, CBP, and 6-His enable purification of their cognate fusion proteins on immobilized glutathione, maltose, phenylarsine oxide, calmodulin, and metal-chelate resins, respectively.
  • FLAG, c-myc, and hemagglutinin (HA) enable immunoaffinity purification of fusion proteins using commercially available monoclonal and polyclonal antibodies that specifically recognize these epitope tags.
  • a fusion protein may also be engineered to contain a proteolytic cleavage site located between the MECHP encoding sequence and the heterologous protein sequence, so that MECHP may be cleaved away from the heterologous moiety following purification. Methods for fusion protein expression and purification are discussed in Ausubel (1995, supra, ch 10). A variety of commercially available kits may also be used to facilitate expression and purification of fusion proteins.
  • synthesis of radiolabeled MECHP may be achieved in vitro using the TNT rabbit reticulocyte lysate or wheat germ extract systems (Promega). These systems couple transcription and translation of protein-coding sequences operably associated with the T7, T3, or SP6 promoters. Translation takes place in the presence of a radiolabeled amino acid precursor, preferably 35 S-methionine.
  • Fragments of MECHP may be produced not only by recombinant production, but also by direct peptide synthesis using solid-phase techniques. (See, e.g., Creighton, supra pp. 55-60.) Protein synthesis may be performed by manual techniques or by automation. Automated synthesis may be achieved, for example, using the ABI 431 A Peptide Synthesizer (Perkin-Elmer). Various fragments of MECHP may be synthesized separately and then combined to produce the full length molecule. THERAPEUTICS
  • MECHP Chemical and structural similarity, e.g., in the context of sequences and motifs, exists between regions of MECHP and human membrane channel proteins.
  • the expression of MECHP is closely associated with nervous, reproductive, and gastrointestinal tissues; fetal development; and neurological, immune/inflammatory, and cell proliferative disorders, including cancer. Therefore, MECHP appears to play a role in cell proliferative, immune/inflammatory, transport/secretory, osmoregulatory, muscular, cardiovascular, and neurological disorders.
  • MECHP appears to play a role in cell proliferative, immune/inflammatory, transport/secretory, osmoregulatory, muscular, cardiovascular, and neurological disorders.
  • MECHP or a fragment or derivative thereof may be administered to a subject to treat or prevent a disorder associated with decreased expression or activity of MECHP.
  • disorders include, but are not limited to, a cell proliferative disorder such as actinic keratosis, arteriosclerosis, atherosclerosis, bursitis, cirrhosis, hepatitis, mixed connective tissue disease (MCTD), myelofibrosis, paroxysmal nocturnal hemoglobinuria, polycythemia vera, psoriasis, primary thrombocythemia, and cancers including adenocarcinoma, leukemia, lymphoma, melanoma, myeloma, sarcoma, teratocarcinoma, and, in particular, cancers of the adrenal gland, bladder, bone, bone marrow, brain, breast, cervix, gall bladder, ganglia, gastrointestinal tract, heart, kidney, liver, lung
  • congenital, distal, and ocular congenital and metabolic myopathies, myotonia. peripheral nervous system disorders, dermatomyositis and polymyositis; inherited, metabolic, endocrine, and toxic myopathies; myasthenia gravis, periodic paralysis; mental disorders including depression and bipolar disorder, and mood, anxiety, and schizophrenic disorders; seasonal affective disorder (SAD); akathesia, amnesia, catatonia, diabetic neuropathy, tardive dyskinesia, dystonias, paranoid psychoses, postherpetic neuralgia, and Tourette's disorder; abnormalities in electrolytes such as calcium, phosphate, magnesium, and potasium; hypo- and hyperfunction of the thyroid, adrenal, parathyroid, and pituitary; and primary and metastatic neoplasms.
  • SAD seasonal affective disorder
  • akathesia amnesia, catatonia, diabetic neuropathy, tardive dyskinesia,
  • a vector capable of expressing MECHP or a fragment or derivative thereof may be administered to a subject to treat or prevent a disorder associated with decreased expression or activity of MECHP including, but not limited to, those described above.
  • a pharmaceutical composition comprising a substantially purified MECHP in conjunction with a suitable pharmaceutical carrier may be administered to a subject to treat or prevent a disorder associated with decreased expression or activity of MECHP including, but not limited to, those provided above.
  • an agonist which modulates the activity of MECHP may be administered to a subject to treat or prevent a disorder associated with decreased expression or activity of MECHP including, but not limited to, those listed above.
  • an antagonist of MECHP may be administered to a subject to treat or prevent a disorder associated with increased expression or activity of MECHP.
  • disorders may include, but are not limited to, those discussed above.
  • an antibody which specifically binds MECHP may be used directly as an antagonist or indirectly as a targeting or delivery mechanism for bringing a pharmaceutical agent to cells or tissue which express MECHP.
  • a vector expressing the complement of the polynucleotide encoding MECHP may be administered to a subject to treat or prevent a disorder associated with increased expression or activity of MECHP including, but not limited to, those described above.
  • any of the proteins, antagonists, antibodies, agonists, complementary sequences, or vectors of the invention may be administered in combination with other appropriate therapeutic agents. Selection of the appropriate agents for use in combination therapy may be made by one of ordinary skill in the art, according to conventional pharmaceutical principles.
  • the combination of therapeutic agents may act synergistically to effect the treatment or prevention of the various disorders described above. Using this approach, one may be able to achieve therapeutic efficacy with lower dosages of each agent, thus reducing the potential for adverse side effects.
  • An antagonist of MECHP may be produced using methods which are generally known in the art.
  • purified MECHP may be used to produce antibodies or to screen libraries of pharmaceutical agents to identify those which specifically bind MECHP.
  • Antibodies to MECHP may also be generated using methods that are well known in the art. Such antibodies may include, but are not limited to, polyclonal, monoclonal, chimeric, and single chain antibodies, Fab fragments, and fragments produced by a Fab expression library. Neutralizing antibodies (i.e., those which inhibit dimer formation) are especially preferred for therapeutic use.
  • various hosts including goats, rabbits, rats, mice, humans, and others may be immunized by injection with MECHP or with any fragment or oligopeptide thereof which has immunogenic properties.
  • various adjuvants may be used to increase immunological response.
  • adjuvants include, but are not limited to, Freund's, mineral gels such as aluminum hydroxide, and surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, KLH, and dinitrophenol.
  • BCG Bacilli Calmette-Guerin
  • Corvnebacterium parvum are especially preferable.
  • the oligopeptides, peptides, or fragments used to induce antibodies to MECHP have an amino acid sequence consisting of at least about 5 amino acids, and, more preferably, of at least about 10 amino acids. It is also preferable that these oligopeptides, peptides, or fragments are identical to a portion of the amino acid sequence of the natural protein and contain the entire amino acid sequence of a small, naturally occurring molecule. Short stretches of MECHP amino acids may be fused with those of another protein, such as KLH, and antibodies to the chimeric molecule may be produced.
  • Monoclonal antibodies to MECHP may be prepared using any technique which provides for the production of antibody molecules by continuous cell lines in culture. These include, but are not limited to, the hybridoma technique, the human B-cell hybridoma technique, and the EBV- hybridoma technique.
  • the hybridoma technique the human B-cell hybridoma technique
  • EBV- hybridoma technique See, e.g., Kohler, G. et al. (1975) Nature 256:495-497; Kozbor, D. et al. (1985) J. Immunol. Methods 81 :31-42; Cote, R.J. et al. (1983) Proc. Natl. Acad. Sci. USA 80:2026-2030; and Cole, S.P. et al. (1984) Mol. Cell Biol. 62:109-120.)
  • chimeric antibodies such as the splicing of mouse antibody genes to human antibody genes to obtain a molecule with appropriate antigen specificity and biological activity.
  • techniques developed for the production of “chimeric antibodies” such as the splicing of mouse antibody genes to human antibody genes to obtain a molecule with appropriate antigen specificity and biological activity, can be used.
  • techniques described for the production of single chain antibodies may be adapted, using methods known in the art, to produce MECHP-specific single chain antibodies.
  • Antibodies with related specificity, but of distinct idiotypic composition may be generated by chain shuffling from random combinatorial immunoglobulin libraries. (See, e.g., Burton D.R. (1991) Proc. Natl. Acad. Sci. USA 88: 10134- 10137.)
  • Antibodies may also be produced by inducing in vivo production in the lymphocyte population or by screening immunoglobulin libraries or panels of highly specific binding reagents as disclosed in the literature. (See, e.g., Orlandi, R. et al. (1989) Proc. Natl. Acad. Sci. USA 86: 3833-3837; Winter, G. et al. (1991) Nature 349:293-299.)
  • Antibody fragments which contain specific binding sites for MECHP may also be generated.
  • fragments include, but are not limited to, F(ab')2 fragments produced by pepsin digestion of the antibody molecule and Fab fragments generated by reducing the disulfide bridges of the F(ab')2 fragments.
  • Fab expression libraries may be constructed to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity. (See, e.g., Huse, W.D. et al. (1989) Science 246: 1275-1281.)
  • immunoassays may be used for screening to identify antibodies having the desired specificity.
  • Numerous protocols for competitive binding or immunoradiometric assays using either polyclonal or monoclonal antibodies with established specificities are well known in the art.
  • Such immunoassays typically involve the measurement of complex formation between MECHP and its specific antibody.
  • a two-site, monoclonal-based immunoassay utilizing monoclonal antibodies reactive to two non- interfering MECHP epitopes is preferred, but a competitive binding assay may also be employed (Pound, supra).
  • Various methods such as Scatchard analysis in conjunction with radioimmunoassay techniques may be used to assess the affinity of antibodies for MECHP.
  • K a is defined as the molar concentration of MECHP-antibody complex divided by the molar concentrations of free antigen and free antibody under equilibrium conditions.
  • the K a determined for a preparation of monoclonal antibodies, which are monospecific for a particular MECHP epitope, represents a true measure of affinity.
  • High-affinity antibody preparations with K a ranging from about 10 9 to 10 1 1/mole are preferred for use in immunoassays in which the MECHP-antibody complex must withstand rigorous manipulations.
  • Low-affinity antibody preparations with K a ranging from about 10 6 to 10 7 1/mole are preferred for use in immunopurification and similar procedures which ultimately require dissociation of MECHP, preferably in active form, from the antibody (Catty, D. (1988) Antibodies. Volume I: A Practical Approach. IRL Press, Washington DC; Liddell, J.E. and Cryer, A. ( 1991 ) A Practical Guide to Monoclonal Antibodies. John Wiley & Sons, New York NY).
  • polyclonal antibody preparations may be further evaluated to determine the quality and suitability of such preparations for certain downstream applications.
  • a polyclonal antibody preparation containing at least 1-2 mg specific antibody/ml, preferably 5-10 mg specific antibody/ml is preferred for use in procedures requiring precipitation of MECHP-antibody complexes.
  • Procedures for evaluating antibody specificity, titer, and avidity, and guidelines for antibody quality and usage in various applications, are generally available. (See, e.g., Catty, supra, and Coligan et al. supra.)
  • the polynucleotides encoding MECHP may be used for therapeutic purposes.
  • the complement of the polynucleotide encoding MECHP may be used in situations in which it would be desirable to block the transcription of the mRNA.
  • cells may be transformed with sequences complementary to polynucleotides encoding MECHP.
  • complementary molecules or fragments may be used to modulate MECHP activity, or to achieve regulation of gene function.
  • sense or antisense oligonucleotides or larger fragments can be designed from various locations along the coding or control regions of sequences encoding MECHP.
  • Expression vectors derived from retroviruses, adenoviruses, or herpes or vaccinia viruses, or from various bacterial plasmids may be used for delivery of nucleotide sequences to the targeted organ, tissue, or cell population. Methods which are well known to those skilled in the art can be used to construct vectors to express nucleic acid sequences complementary to the polynucleotides encoding MECHP. (See, e.g., Sambrook. supra; Ausubel, 1995. supra.) Genes encoding MECHP can be turned off by transforming a cell or tissue with expression vectors which express high levels of a polynucleotide, or fragment thereof, encoding MECHP.
  • Such constructs may be used to introduce untranslatable sense or antisense sequences into a cell. Even in the absence of integration into the DNA, such vectors may continue to transcribe RNA molecules until they are disabled by endogenous nucleases. Transient expression may last for a month or more with a non-replicating vector, and may last even longer if appropriate replication elements are part of the vector system.
  • modifications of gene expression can be obtained by designing complementary sequences or antisense molecules (DNA, RNA. or PNA) to the control, 5', or regulatory regions of the gene encoding MECHP.
  • Oligonucleotides derived from the transcription initiation site e.g., between about positions -10 and +10 from the start site, are preferred.
  • inhibition can be achieved using triple helix base-pairing methodology. Triple helix pairing is useful because it causes inhibition of the ability of the double helix to open sufficiently for the binding of polymerases, transcription factors, or regulatory molecules. Recent therapeutic advances using triplex DNA have been described in the literature. (See, e.g., Gee, J.E. et al. (1994) in Huber, B.E.
  • a complementary sequence or antisense molecule may also be designed to block translation of mRNA by preventing the transcript from binding to ribosomes.
  • Ribozymes enzymatic RNA molecules, may also be used to catalyze the specific cleavage of RNA.
  • the mechanism of ribozyme action involves sequence-specific hybridization of the ribozyme molecule to complementary target RNA, followed by endonucleolytic cleavage.
  • engineered hammerhead motif ribozyme molecules may specifically and efficiently catalyze endonucleolytic cleavage of sequences encoding MECHP.
  • RNA sequences of between 15 and 20 ribonucleotides, corresponding to the region of the target gene containing the cleavage site, may be evaluated for secondary structural features which may render the oligonucleotide inoperable.
  • the suitability of candidate targets may also be evaluated by testing accessibility to hybridization with complementary oligonucleotides using ribonuclease protection assays.
  • RNA molecules and ribozymes of the invention may be prepared by any method known in the art for the synthesis of nucleic acid molecules. These include techniques for chemically synthesizing oligonucleotides such as solid phase phosphoramidite chemical synthesis. Alternatively, RNA molecules may be generated by in vitro and in vivo transcription of DNA sequences encoding MECHP. Such DNA sequences may be incorporated into a wide variety of vectors with suitable RNA polymerase promoters such as T7 or SP6. Alternatively, these cDNA constructs that synthesize complementary RNA, constitutively or inducibly, can be introduced into cell lines, cells, or tissues.
  • RNA molecules may be modified to increase intracellular stability and half-life. Possible modifications include, but are not limited to, the addition of flanking sequences at the 5' and/or 3' ends of the molecule, or the use of phosphorothioate or 2' O-methyl rather than phosphodiesterase linkages within the backbone of the molecule.
  • Delivery by transfection, by liposome injections, or by polycationic amino polymers may be achieved using methods which are well known in the art. (See, e.g., Goldman, C.K. et al. (1997) Nat. Biotech. 15:462-466.)
  • any of the therapeutic methods described above may be applied to any subject in need of such therapy, including, for example, mammals such as dogs, cats, cows, horses, rabbits, monkeys, and most preferably, humans.
  • An additional embodiment of the invention relates to the administration of a pharmaceutical or sterile composition, in conjunction with a pharmaceutically acceptable carrier, for any of the therapeutic effects discussed above.
  • Such pharmaceutical compositions may consist of MECHP, antibodies to MECHP, and mimetics, agonists, antagonists, or inhibitors of MECHP.
  • the compositions may be administered alone or in combination with at least one other agent, such as a stabilizing compound, which may be administered in any sterile, biocompatible pharmaceutical carrier including, but not limited to, saline, buffered saline, dextrose, and water.
  • the compositions may be administered to a patient alone, or in combination with other agents, drugs, or hormones.
  • compositions utilized in this invention may be administered by any number of routes including, but not limited to, oral, intravenous, intramuscular, intra-arterial, intrameduUary, intrathecal, intraventricular, transdermal, subcutaneous, intraperitoneal, intranasal, enteral, topical, sublingual, or rectal means.
  • these pharmaceutical compositions may contain suitable pharmaceutically-acceptable carriers comprising excipients and auxiliaries which facilitate processing of the active compounds into preparations which can be used pharmaceutically. Further details on techniques for formulation and administration may be found in the latest edition of Remington's Pharmaceutical Sciences (Maack Publishing, Easton PA).
  • compositions for oral administration can be formulated using pharmaceutically acceptable carriers well known in the art in dosages suitable for oral administration.
  • Such carriers enable the pharmaceutical compositions to be formulated as tablets, pills, dragees. capsules, liquids, gels, syrups, slurries, suspensions, and the like, for ingestion by the patient.
  • compositions for oral use can be obtained through combining active compounds with solid excipient and processing the resultant mixture of granules (optionally, after grinding) to obtain tablets or dragee cores.
  • auxiliaries can be added, if desired.
  • Suitable excipients include carbohydrate or protein fillers, such as sugars, including lactose, sucrose, mannitol, and sorbitol; starch from corn, wheat, rice, potato, or other plants; cellulose, such as methyl cellulose, hydroxypropylmethyl-cellulose, or sodium carboxymethylcellulose; gums, including arabic and tragacanth; and proteins, such as gelatin and collagen.
  • disintegrating or solubilizing agents may be added, such as the cross-linked polyvinyl pyrrolidone, agar, and alginic acid or a salt thereof, such as sodium alginate.
  • Dragee cores may be used in conjunction with suitable coatings, such as concentrated sugar solutions, which may also contain gum arabic, talc, polyvinylpyrrolidone, carbopol gel, polyethylene glycol, and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures.
  • suitable coatings such as concentrated sugar solutions, which may also contain gum arabic, talc, polyvinylpyrrolidone, carbopol gel, polyethylene glycol, and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures.
  • Dyestuffs or pigments may be added to the tablets or dragee coatings for product identification or to characterize the quantity of active compound, i.e., dosage.
  • Push-fit capsules made of gelatin, as well as soft, sealed capsules made of gelatin and a coating, such as glycerol or sorbitol.
  • Push- fit capsules can contain active ingredients mixed with fillers or binders, such as lactose or starches, lubricants, such as talc or magnesium stearate, and, optionally, stabilizers.
  • the active compounds may be dissolved or suspended in suitable liquids, such as fatty oils, liquid, or liquid polyethylene glycol with or without stabilizers.
  • compositions suitable for parenteral administration may be formulated in aqueous solutions, preferably in physiologically compatible buffers such as Hanks' solution, Ringer's solution, or physiologically buffered saline.
  • Aqueous injection suspensions may contain substances which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dextran.
  • suspensions of the active compounds may be prepared as appropriate oily injection suspensions.
  • Suitable lipophilic solvents or vehicles include fatty oils, such as sesame oil, or synthetic fatty acid esters, such as ethyl oleate, triglycerides, or liposomes.
  • Non-lipid polycationic amino polymers may also be used for delivery.
  • the suspension may also contain suitable stabilizers or agents to increase the solubility of the compounds and allow for the preparation of highly concentrated solutions.
  • penetrants appropriate to the particular barrier to be permeated are used in the formulation.
  • penetrants are generally known in the art.
  • the pharmaceutical compositions of the present invention may be manufactured in a manner that is known in the art, e.g., by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping, or lyophilizing processes.
  • the pharmaceutical composition may be provided as a salt and can be formed with many acids, including but not limited to, hydrochloric, sulfuric, acetic, lactic, tartaric. malic, and succinic acids. Salts tend to be more soluble in aqueous or other protonic solvents than are the corresponding free base forms.
  • the preferred preparation may be a lyophilized powder which may contain any or all of the following: 1 M to 50 mM histidine, 0.1% to 2% sucrose, and 2% to 7% mannitol, at a pH range of 4.5 to 5.5, that is combined with buffer prior to use.
  • compositions After pharmaceutical compositions have been prepared, they can be placed in an appropriate container and labeled for treatment of an indicated condition.
  • labeling would include amount, frequency, and method of administration.
  • compositions suitable for use in the invention include compositions wherein the active ingredients are contained in an effective amount to achieve the intended purpose.
  • the determination of an effective dose is well within the capability of those skilled in the art.
  • the therapeutically effective dose can be estimated initially either in cell culture assays, e.g., of neoplastic cells or in animal models such as mice, rats, rabbits, dogs, or pigs.
  • An animal model may also be used to determine the appropriate concentration range and route of administration. Such information can then be used to determine useful doses and routes for administration in humans.
  • a therapeutically effective dose refers to that amount of active ingredient, for example MECHP or fragments thereof, antibodies of MECHP, and agonists, antagonists or inhibitors of MECHP, which ameliorates the symptoms or condition.
  • Therapeutic efficacy and toxicity may be determined by standard pharmaceutical procedures in cell cultures or with experimental animals, such as by calculating the ED 50 (the dose therapeutically effective in 50% of the population) or LD 50 (the dose lethal to 50% of the population) statistics.
  • the dose ratio of toxic to therapeutic effects is the therapeutic index, which can be expressed as the LD 50 /ED 50 ratio.
  • Pharmaceutical compositions which exhibit large therapeutic indices are preferred. The data obtained from cell culture assays and animal studies are used to formulate a range of dosage for human use.
  • the dosage contained in such compositions is preferably within a range of circulating concentrations that includes the ED 50 with little or no toxicity.
  • the dosage varies within this range depending upon the dosage form employed, the sensitivity of the patient, and the route of administration. The exact dosage will be determined by the practitioner, in light of factors related to the subject requiring treatment. Dosage and administration are adjusted to provide sufficient levels of the active moiety or to maintain the desired effect. Factors which may be taken into account include the severity of the disease state, the general health of the subject, the age, weight, and gender of the subject, time and frequency of administration, drug combination(s), reaction sensitivities, and response to therapy. Long-acting pharmaceutical compositions may be administered every 3 to 4 days, every week, or biweekly depending on the half-life and clearance rate of the particular formulation.
  • Normal dosage amounts may vary from about 0.1 ⁇ g to 100,000 ⁇ g, up to a total dose of about 1 gram, depending upon the route of administration.
  • Guidance as to particular dosages and methods of delivery is provided in the literature and generally available to practitioners in the art. Those skilled in the art will employ different formulations for nucleotides than for proteins or their inhibitors. Similarly, delivery of polynucleotides or polypeptides will be specific to particular cells, conditions, locations, etc. DIAGNOSTICS
  • antibodies which specifically bind MECHP may be used for the diagnosis of disorders characterized by expression of MECHP, or in assays to monitor patients being treated with MECHP or agonists, antagonists, or inhibitors of MECHP.
  • Antibodies useful for diagnostic purposes may be prepared in the same manner as described above for therapeutics. Diagnostic assays for MECHP include methods which utilize the antibody and a label to detect MECHP in human body fluids or in extracts of cells or tissues.
  • the antibodies may be used with or without modification, and may be labeled by covalent or non-covalent attachment of a reporter molecule.
  • a wide variety of reporter molecules, several of which are described above, are known in the art and may be used.
  • MECHP ELISAs, RIAs, and FACS
  • ELISAs ELISAs
  • RIAs RIAs
  • FACS fluorescence-activated cell sorting
  • normal or standard values for MECHP expression are established by combining body fluids or cell extracts taken from normal mammalian subjects, preferably human, with antibody to MECHP under conditions suitable for complex formation. The amount of standard complex formation may be quantitated by various methods, preferably by photometric means. Quantities of MECHP expressed in subject, control, and disease samples from biopsied tissues are compared with the standard values. Deviation between standard and subject values establishes the parameters for diagnosing disease.
  • the polynucleotides encoding MECHP may be used for diagnostic purposes.
  • the polynucleotides which may be used include oligonucleotide sequences, complementary RNA and DNA molecules, and PNAs.
  • the polynucleotides may be used to detect and quantitate gene expression in biopsied tissues in which expression of MECHP may be correlated with disease.
  • the diagnostic assay may be used to determine absence, presence, and excess expression of MECHP, and to monitor regulation of MECHP levels during therapeutic intervention.
  • hybridization with PCR probes which are capable of detecting polynucleotide sequences, including genomic sequences, encoding MECHP or closely related molecules may be used to identify nucleic acid sequences which encode MECHP.
  • the specificity of the probe whether it is made from a highly specific region, e.g., the 5' regulatory region, or from a less specific region, e.g., a conserved motif, and the stringency of the hybridization or amplification (maximal, high, intermediate, or low), will determine whether the probe identifies only naturally occurring sequences encoding MECHP, allelic variants, or related sequences.
  • Probes may also be used for the detection of related sequences, and should preferably have at least 50% sequence identity to any of the MECHP encoding sequences.
  • the hybridization probes of the subject invention may be DNA or RNA and may be derived from the sequence of SEQ ID NO: 19-36 or from genomic sequences including promoters, enhancers, and introns of the gene encoding MECHP.
  • Means for producing specific hybridization probes for DNAs encoding MECHP include the cloning of polynucleotide sequences encoding MECHP or MECHP derivatives into vectors for the production of mRNA probes.
  • Such vectors are known in the art, are commercially available, and may be used to synthesize RNA probes in vitro by means of the addition of the appropriate RNA polymerases and the appropriate labeled nucleotides.
  • Hybridization probes may be labeled by a variety of reporter groups, for example, by radionuclides such as 32 P or 35 S, or by enzymatic labels, such as alkaline phosphatase coupled to the probe via avidin/biotin coupling systems, and the like.
  • Polynucleotide sequences encoding MECHP may be used for the diagnosis of disorders associated with expression of MECHP.
  • disorders include, but are not limited to, a cell proliferative disorder such as actinic keratosis, arteriosclerosis, atherosclerosis, bursitis, cirrhosis, hepatitis, mixed connective tissue disease (MCTD), myelofibrosis, paroxysmal nocturnal hemoglobinuria, polycythemia vera, psoriasis, primary thrombocythemia, and cancers including adenocarcinoma, leukemia, lymphoma, melanoma, myeloma, sarcoma, teratocarcinoma, and, in particular, cancers of the adrenal gland, bladder, bone, bone marrow, brain, breast, cervix, gall bladder, ganglia, gastrointestinal tract, heart, kidney, liver, lung, muscle, ovary, pancrea
  • anemia asthma, atherosclerosis, autoimmune hemolytic anemia, autoimmune thyroiditis, autoimmune polyenodocrinopathy-candidiasis-ectodermal dystrophy (APECED), bronchitis, cholecystitis, contact dermatitis, Crohn's disease, atopic dermatitis, dermatomyositis, diabetes mellitus, emphysema, episodic lymphopenia with lymphocyte-toxins, erythroblastosis fetalis, erythema nodosum, atrophic gastritis, glomerulonephritis, Goodpasture's syndrome, gout, Graves' disease, Hashimoto's thyroiditis, hypereosinophilia, irritable bowel syndrome, multiple sclerosis, myasthenia gravis, myocardial or pericardial inflammation, osteoarthritis, osteoporosis, pancreatitis, polymyositis, p
  • the polynucleotide sequences encoding MECHP may be used in Southern or northern analysis, dot blot, or other membrane-based technologies; in PCR technologies; in dipstick, pin, and multiformat ELISA-like assays; and in microarrays utilizing fluids or tissues from patients to detect altered MECHP expression. Such qualitative or quantitative methods are well known in the art.
  • the nucleotide sequences encoding MECHP may be useful in assays that detect the presence of associated disorders, particularly those mentioned above.
  • the nucleotide sequences encoding MECHP may be labeled by standard methods and added to a fluid or tissue sample from a patient under conditions suitable for the formation of hybridization complexes. After a suitable incubation period, the sample is washed and the signal is quantitated and compared with a standard value. If the amount of signal in the patient sample is significantly altered in comparison to a control sample then the presence of altered levels of nucleotide sequences encoding MECHP in the sample indicates the presence of the associated disorder.
  • Such assays may also be used to evaluate the efficacy of a particular therapeutic treatment regimen in animal studies, in clinical trials, or to monitor the treatment of an individual patient.
  • a normal or standard profile for expression is established. This may be accomplished by combining body fluids or cell extracts taken from normal subjects, either animal or human, with a sequence, or a fragment thereof, encoding MECHP, under conditions suitable for hybridization or amplification. Standard hybridization may be quantified by comparing the values obtained from normal subjects with values from an experiment in which a known amount of a substantially purified polynucleotide is used. Standard values obtained in this manner may be compared with values obtained from samples from patients who are symptomatic for a disorder. Deviation from standard values is used to establish the presence of a disorder.
  • hybridization assays may be repeated on a regular basis to determine if the level of expression in the patient begins to approximate that which is observed in the normal subject.
  • the results obtained from successive assays may be used to show the efficacy of treatment over a period ranging from several days to months.
  • the presence of an abnormal amount of transcript (either under- or over-expressed) in biopsied tissue from an individual may indicate a predisposition for the development of the disease, or may provide a means for detecting the disease prior to the appearance of actual clinical symptoms.
  • a more definitive diagnosis of this type may allow health professionals to employ preventative measures or aggressive treatment earlier thereby preventing the development or further progression of the cancer.
  • oligonucleotides designed from the sequences encoding MECHP may involve the use of PCR. These oligomers may be chemically synthesized, generated enzymatically, or produced in vitro. Oligomers will preferably contain a fragment of a polynucleotide encoding MECHP, or a fragment of a polynucleotide complementary to the polynucleotide encoding MECHP, and will be employed under optimized conditions for identification of a specific gene or condition. Oligomers may also be employed under less stringent conditions for detection or quantitation of closely related DNA or RNA sequences.
  • Methods which may also be used to quantitate the expression of MECHP include radiolabeling or biotinylating nucleotides, coamplification of a control nucleic acid, and inte ⁇ olating results from standard curves.
  • radiolabeling or biotinylating nucleotides include radiolabeling or biotinylating nucleotides, coamplification of a control nucleic acid, and inte ⁇ olating results from standard curves.
  • the speed of quantitation of multiple samples may be accelerated by running the assay in an ELISA format where the oligomer of interest is presented in various dilutions and a spectrophotometric or colorimetric response gives rapid quantitation.
  • oligonucleotides or longer fragments derived from any of the polynucleotide sequences described herein may be used as targets in a microarray.
  • the microarray can be used to monitor the expression level of large numbers of genes simultaneously and to identify genetic variants, mutations, and polymo ⁇ hisms. This information may be used to determine gene function, to understand the genetic basis of a disorder, to diagnose a disorder, and to develop and monitor the activities of therapeutic agents.
  • Microarrays may be prepared, used, and analyzed using methods known in the art.
  • methods known in the art See, e.g., Brennan, T.M. et al. (1995) U.S. Patent No. 5,474,796; Schena, M. et al. (1996) Proc. Natl. Acad. Sci. 93:10614-10619; Baldeschweiler et al. (1995) PCT application W095/251 1 16; Shalon, D. et al. (1995) PCT application WO95/35505; Heller, R.A. et al. (1997) Proc. Natl. Acad. Sci. USA 94:2150-2155; and Heller, M.J. et al. (1997) U.S. Patent No. 5,605,662.
  • nucleic acid sequences encoding MECHP may be used to generate hybridization probes useful in mapping the naturally occurring genomic sequence.
  • the sequences may be mapped to a particular chromosome, to a specific region of a chromosome, or to artificial chromosome constructions, e.g., human artificial chromosomes (HACs), yeast artificial chromosomes (YACs), bacterial artificial chromosomes (BACs), bacterial PI constructions, or single chromosome cDNA libraries.
  • HACs human artificial chromosomes
  • YACs yeast artificial chromosomes
  • BACs bacterial artificial chromosomes
  • PI constructions or single chromosome cDNA libraries.
  • Fluorescent in situ hybridization may be correlated with other physical chromosome mapping techniques and genetic map data.
  • FISH Fluorescent in situ hybridization
  • Examples of genetic map data can be found in various scientific journals or at the Online Mendelian Inheritance in Man (OMIM) site. Correlation between the location of the gene encoding MECHP on a physical chromosomal map and a specific disorder, or a predisposition to a specific disorder, may help define the region of DNA associated with that disorder.
  • the nucleotide sequences of the invention may be used to detect differences in gene sequences among normal, carrier, and affected individuals.
  • In situ hybridization of chromosomal preparations and physical mapping techniques may be used for extending genetic maps. Often the placement of a gene on the chromosome of another mammalian species, such as mouse, may reveal associated markers even if the number or arm of a particular human chromosome is not known. New sequences can be assigned to chromosomal arms by physical mapping. This provides valuable information to investigators searching for disease genes using positional cloning or other gene discovery techniques.
  • any sequences mapping to that area may represent associated or regulatory genes for further investigation.
  • the nucleotide sequence of the subject invention may also be used to detect differences in the chromosomal location due to translocation, inversion, etc., among normal, carrier, or affected individuals.
  • MECHP its catalytic or immunogenic fragments, or oligopeptides thereof can be used for screening libraries of compounds in any of a variety of drug screening techniques.
  • the fragment employed in such screening may be free in solution, affixed to a solid support, borne on a cell surface, or located intracellularly. The formation of binding complexes between MECHP and the agent being tested may be measured.
  • Another technique for drug screening provides for high throughput screening of compounds having suitable binding affinity to the protein of interest.
  • This method large numbers of different small test compounds are synthesized on a solid substrate. The test compounds are reacted with MECHP, or fragments thereof, and washed. Bound MECHP is then detected by methods well known in the art. Purified MECHP can also be coated directly onto plates for use in the aforementioned drug screening techniques. Alternatively, non-neutralizing antibodies can be used to capture the peptide and immobilize it on a solid support.
  • the nucleotide sequences which encode MECHP may be used in any molecular biology techniques that have yet to be developed, provided the new techniques rely on properties of nucleotide sequences that are currently known, including, but not limited to, such properties as the triplet genetic code and specific base pair interactions.
  • RNA was purchased from Clontech or isolated from tissues described in Table 4. Some tissues were homogenized and lysed in guanidinium isothiocyanate, while others were homogenized and lysed in phenol or in a suitable mixture of denaturants, such as TRIZOL (Life Technologies), a monophasic solution of phenol and guanidine isothiocyanate. The resulting lysates were centrifuged over CsCl cushions or extracted with chloroform. RNA was precipitated from the lysates with either isopropanol or sodium acetate and ethanol, or by other routine methods.
  • poly(A+) RNA was isolated using oligo d(T)-coupled paramagnetic particles (Promega), OLIGOTEX latex particles (QIAGEN, Chatsworth CA), or an OLIGOTEX mRNA purification kit (QIAGEN).
  • RNA was provided with RNA and constructed the corresponding cDNA libraries.
  • cDNA was synthesized and cDNA libraries were constructed with the UNIZAP vector system (Stratagene) or SUPERSCRIPT plasmid system (Life Technologies), using the recommended procedures or similar methods known in the art. (See, e.g., Ausubel, 1997, supra, units 5.1-6.6.) Reverse transcription was initiated using oligo d(T) or random primers. Synthetic oligonucleotide adapters were ligated to double stranded cDNA, and the cDNA was digested with the appropriate restriction enzyme or enzymes.
  • cDNA was size-selected (300-1000 bp) using SEPHACRYL SI 000, SEPHAROSE CL2B. or SEPHAROSE CL4B column chromatography (Amersham Pharmacia Biotech) or preparative agarose gel electrophoresis.
  • cDNAs were ligated into compatible restriction enzyme sites of the polylinker of a suitable plasmid, e.g., PBLUESCRIPT plasmid (Stratagene), pSPORTl plasmid (Life Technologies), or pINCY (Incyte Pharmaceuticals, Palo Alto CA).
  • Recombinant plasmids were transformed into competent E. coli cells including XL 1 -Blue, XLl-BlueMRF, or SOLR from Stratagene or DH5 ⁇ , DH10B, or ElectroMAX DH10B from Life Technologies. II. Isolation of cDNA Clones
  • Plasmids were recovered from host cells by in vivo excision, using the UNIZAP vector system (Stratagene) or cell lysis. Plasmids were purified using at least one of the following: a Magic or WIZARD Minipreps DNA purification system (Promega); an AGTC Miniprep purification kit (Edge Biosystems, Gaithersburg MD); and QIAWELL 8 Plasmid, QIAWELL 8 Plus Plasmid, QIAWELL 8 Ultra Plasmid purification systems or the R.E.A.L. PREP 96 plasmid purification kit from QIAGEN. Following precipitation, plasmids were resuspended in 0.1 ml of distilled water and stored, with or without lyophilization, at 4°C.
  • plasmid DNA was amplified from host cell lysates using direct link PCR in a high-throughput format (Rao, V.B. (1994) Anal. Biochem. 216:1-14). Host cell lysis and thermal cycling steps were carried out in a single reaction mixture. Samples were processed and stored in 384-well plates, and the concentration of amplified plasmid DNA was quantified fluorometrically using PICOGREEN dye (Molecular Probes, Eugene OR) and a Fluoroskan II fluorescence scanner (Labsystems Oy, Helsinki, Finland). III.
  • cDNA sequencing reactions were processed using standard methods or high-throughput instrumentation such as the ABI CATALYST 800 (Perkin-Elmer) thermal cycler or the PTC-200 thermal cycler (MJ Research) in conjunction with the HYDRA microdispenser (Robbins Scientific) or the MICROLAB 2200 (Hamilton) liquid transfer system.
  • cDNA sequencing reactions were prepared using reagents provided by Amersham Pharmacia Biotech or supplied in ABI sequencing kits such as the ABI PRISM BIGDYE Terminator cycle sequencing ready reaction kit (Perkin-Elmer).
  • Electrophoretic separation of cDN A sequencing reactions and detection of labeled polynucleotides were carried out using the MEGABACE 1000 DNA sequencing system (Molecular Dynamics); the ABI PRISM 373 or 377 sequencing systems (Perkin-Elmer) in conjunction with standard ABI protocols and base calling software; or other sequence analysis systems known in the art. Reading frames within the cDNA sequences were identified using standard methods (reviewed in Ausubel, 1997, supra, unit 7.7). Some of the cDNA sequences were selected for extension using the techniques disclosed in Example V. The polynucleotide sequences derived from cDNA sequencing were assembled and analyzed using a combination of software programs which utilize algorithms well known to those skilled in the art.
  • Table 5 summarizes the tools, programs, and algorithms used and provides applicable descriptions, references, and threshold parameters.
  • the first column of Table 5 shows the tools, programs, and algorithms used, the second column provides brief descriptions thereof, the third column presents appropriate references, all of which are inco ⁇ orated by reference herein in their entirety, and the fourth column presents, where applicable, the scores, probability values, and other parameters used to evaluate the strength of a match between two sequences (the higher the score, the greater the homology between two sequences).
  • Sequences were analyzed using MACDNASIS PRO software (Hitachi Software Engineering, South San Francisco CA) and LASERGENE software (DNASTAR). Polypeptide sequence alignments were generated using the default parameters specified by the clustal algorithm as inco ⁇ orated into the MEGALIGN multisequence alignment program (DNASTAR), which also calculates the percent identity between aligned sequences.
  • the polynucleotide sequences were validated by removing vector, linker, and polyA sequences and by masking ambiguous bases, using algorithms and programs based on BLAST, dynamic programing, and dinucleotide nearest neighbor analysis. The sequences were then queried against a selection of public databases such as the GenBank primate, rodent, mammalian, vertebrate, and eukaryote databases, and BLOCKS to acquire annotation using programs based on BLAST, FASTA, and BLIMPS. The sequences were assembled into full length polynucleotide sequences using programs based on Phred, Phrap, and Consed, and were screened for open reading frames using programs based on GeneMark, BLAST, and FASTA.
  • HMM Hidden Markov Model
  • Northern analysis is a laboratory technique used to detect the presence of a transcript of a gene and involves the hybridization of a labeled nucleotide sequence to a membrane on which RNAs from a particular cell type or tissue have been bound. (See, e.g., Sambrook. supra, ch. 7; Ausubel, 1995, supra, ch. 4 and 16.)
  • % sequence identity x % maximum BLAST score 100 The product score takes into account both the degree of similarity between two sequences and the length of the sequence match. For example, with a product score of 40, the match will be exact within a 1% to 2% error, and, with a product score of 70, the match will be exact. Similar molecules are usually identified by selecting those which show product scores between 15 and 40, although lower scores may identify related molecules. The results of northern analyses are reported as a percentage distribution of libraries in which the transcript encoding MECHP occurred. Analysis involved the categorization of cDNA libraries by organ/tissue and disease.
  • the organ/tissue categories included cardiovascular, dermatologic, developmental, endocrine, gastrointestinal, hematopoietic/immune, musculoskeletal, nervous, reproductive, and urologic.
  • the disease/condition categories included cancer, inflammation/trauma, cell proliferation, neurological, and pooled. For each category, the number of libraries expressing the sequence of interest was counted and divided by the total number of libraries across all categories. Percentage values of tissue-specific and disease- or condition- specific expression are reported in the description of the invention. V. Extension of MECHP Encoding Polynucleotides
  • the full length nucleic acid sequences of SEQ ID NO: 19-36 was produced by extension of an appropriate fragment of the full length molecule using oligonucleotide primers designed from this fragment.
  • One primer was synthesized to initiate 5' extension of the known fragment, and the other primer, to initiate 3' extension of the known fragment.
  • the initial primers were designed using OLIGO 4.06 software (National Biosciences), or another appropriate program, to be about 22 to 30 nucleotides in length, to have a GC content of about 50% or more, and to anneal to the target sequence at temperatures of about 68°C to about 72°C. Any stretch of nucleotides which would result in hai ⁇ in structures and primer-primer dimerizations was avoided.
  • Selected human cDNA libraries were used to extend the sequence. If more than one extension was necessary or desired, additional or nested sets of primers were designed.
  • the concentration of DNA in each well was determined by dispensing 100 ⁇ l PICO GREEN quantitation reagent (0.25% (v/v) PICO GREEN; Molecular Probes, Eugene OR) dissolved in IX TE and 0.5 ⁇ l of undiluted PCR product into each well of an opaque fluorimeter plate (Corning Costar, Acton MA), allowing the DNA to bind to the reagent.
  • the plate was scanned in a Fluoroskan II (Labsystems Oy, Helsinki, Finland) to measure the fluorescence of the sample and to quantify the concentration of DNA.
  • a 5 ⁇ l to 10 ⁇ l aliquot of the reaction mixture was analyzed by electrophoresis on a 1 % agarose mini-gel to determine which reactions were successful in extending the sequence.
  • the extended nucleotides were desalted and concentrated, transferred to 384-well plates, digested with CviJI cholera virus endonuclease (Molecular Biology Research, Madison WI), and sonicated or sheared prior to religation into pUC 18 vector (Amersham Pharmacia Biotech).
  • CviJI cholera virus endonuclease Molecular Biology Research, Madison WI
  • sonicated or sheared prior to religation into pUC 18 vector
  • the digested nucleotides were separated on low concentration (0.6 to 0.8%) agarose gels, fragments were excised, and agar digested with Agar ACE (Promega).
  • Extended clones were religated using T4 ligase (New England Biolabs, Beverly MA) into pUC 18 vector (Amersham Pharmacia Biotech), treated with Pfu DNA polymerase (Stratagene) to fill-in restriction site overhangs, and transfected into competent E. coli cells. Transformed cells were selected on antibiotic-containing media, individual colonies were picked and cultured overnight at 37°C in 384- well plates in LB/2x carb liquid media. The cells were lysed, and DNA was amplified by PCR using Taq DNA polymerase
  • Step 1 94°C, 3 min
  • Step 2 94°C, 15 sec
  • Step 3 60°C, 1 min
  • Step 4 72°C, 2 min
  • Step 5 steps 2, 3, and 4 repeated 29 times
  • Step 6 72°C, 5 min
  • Step 7 storage at 4°C.
  • DNA was quantified by PICOGREEN reagent (Molecular Probes) as described above. Samples with low DNA recoveries were reamplified using the same conditions as described above.
  • nucleotide sequence of SEQ ID NO: 19-36 is used to obtain 5' regulatory sequences using the procedure above, oligonucleotides designed for such extension, and an appropriate genomic library.
  • Hybridization probes derived from SEQ ID NO: 19-36 are employed to screen cDNAs, genomic DNAs, or mRNAs. Although the labeling of oligonucleotides, consisting of about 20 base pairs, is specifically described, essentially the same procedure is used with larger nucleotide fragments. Oligonucleotides are designed using state-of-the-art software such as OLIGO 4.06 software (National Biosciences) and labeled by combining 50 pmol of each oligomer, 250 ⁇ Ci of [ 32 P]-adenosine triphosphate (Amersham Pharmacia Biotech), and T4 polynucleotide kinase (DuPont NEN, Boston MA).
  • the labeled oligonucleotides are substantially purified using a SEPHADEX G-25 superfine size exclusion dextran bead column (Amersham Pharmacia Biotech). An aliquot containing 10 7 counts per minute of the labeled probe is used in a typical membrane- based hybridization analysis of human genomic DNA digested with one of the following endonucleases: Ase I, Bgl II, Eco RI, Pst I, Xbal, or Pvu II (DuPont NEN).
  • a chemical coupling procedure and an ink jet device can be used to synthesize array elements on the surface of a substrate.
  • An array analogous to a dot or slot blot may also be used to arrange and link elements to the surface of a substrate using thermal, UV, chemical, or mechanical bonding procedures.
  • a typical array may be produced by hand or using available methods and machines and contain any appropriate number of elements.
  • nonhybridized probes are removed and a scanner used to determine the levels and patterns of fluorescence. The degree of complementarity and the relative abundance of each probe which hybridizes to an element on the microarray may be assessed through analysis of the scanned images.
  • Full-length cDNAs, Expressed Sequence Tags (ESTs), or fragments thereof may comprise the elements of the microarray. Fragments suitable for hybridization can be selected using software well known in the art such as LASERGENE software (DNASTAR). Full-length cDNAs, ESTs, or fragments thereof corresponding to one of the nucleotide sequences of the present invention, or selected at random from a cDNA library relevant to the present invention, are arranged on an appropriate substrate, e.g., a glass slide. The cDNA is fixed to the slide using, e.g., UV cross-linking followed by thermal and chemical treatments and subsequent drying. (See, e.g., Schena, M. et al.
  • Sequences complementary to the MECHP-encoding sequences, or any parts thereof, are used to detect, decrease, or inhibit expression of naturally occurring MECHP.
  • oligonucleotides comprising from about 15 to 30 base pairs is described, essentially the same procedure is used with smaller or with larger sequence fragments.
  • Appropriate oligonucleotides are designed using OLIGO 4.06 software (National Biosciences) and the coding sequence of MECHP.
  • a complementary oligonucleotide is designed from the most unique 5' sequence and used to prevent promoter binding to the coding sequence.
  • To inhibit translation, a complementary oligonucleotide is designed to prevent ribosomal binding to the MECHP-encoding transcript.
  • MECHP expression and purification of MECHP are achieved using bacterial or virus-based expression systems.
  • cDNA is subcloned into an appropriate vector containing an antibiotic resistance gene and an inducible promoter that directs high levels of cDNA transcription.
  • promoters include, but are not limited to, the trp-lac (tac) hybrid promoter and the T5 or T7 bacteriophage promoter in conjunction with the lac operator regulatory element.
  • Recombinant vectors are transformed into suitable bacterial hosts, e.g., BL21(DE3).
  • Antibiotic resistant bacteria express MECHP upon induction with isopropyl beta-D-thiogalactopyranoside (IPTG).
  • MECHP in eukaryotic cells is achieved by infecting insect or mammalian cell lines with recombinant Autographica californica nuclear polyhedrosis virus (AcMNPV), commonly known as baculovirus.
  • AcMNPV Autographica californica nuclear polyhedrosis virus
  • the nonessential polyhedrin gene of baculovirus is replaced with cDNA encoding MECHP by either homologous recombination or bacterial-mediated transposition involving transfer plasmid intermediates. Viral infectivity is maintained and the strong polyhedrin promoter drives high levels of cDNA transcription.
  • Recombinant baculovirus is used to infect Spodoptera frugiperda (Sf9) insect cells in most cases, or human hepatocytes, in some cases.
  • MECHP is synthesized as a fusion protein with, e.g., glutathione S-transferase (GST) or a peptide epitope tag, such as FLAG or 6-His, permitting rapid, single-step, affinity-based purification of recombinant fusion protein from crude cell lysates.
  • GST glutathione S-transferase
  • a peptide epitope tag such as FLAG or 6-His
  • FLAG an 8-amino acid peptide
  • 6-His a stretch of six consecutive histidine residues, enables purification on metal-chelate resins (QIAGEN). Methods for protein expression and purification are discussed in Ausubel (1995, supra, ch 10 and 16). Purified MECHP obtained by these methods can be used directly in the following activity assay.
  • Aquaporin activity of MECHP is demonstrated as the ability to induce osmotic water permeability in Xenopus laevis oocytes injected with MECHP cRNA (Ishibashi, K. et al. (1994) Proc. Natl. Acad. Sci. USA 91 :6269-6273).
  • Oocytes injected with water are used as the control.
  • Injected oocytes are given a hypotonic shock by being transferred from 200 mosM to 70 mosM modified Barth's buffer.
  • the increase in osmotic volume of the oocytes, observed at 24 °C by videomicroscopy, is proportional to the MECHP aquaporin activity in the injected oocytes.
  • Protein Transport Activity of MECHP is demonstrated as the ability to induce osmotic water permeability in Xenopus laevis oocytes injected with MECHP cRNA (Ishibashi, K. et al. (1994) Pro
  • Protein transport activity of MECHP is demonstrated by its ability to catalyze the translocation of newly synthesized preprolactin into proteoliposomes in an in vitro system (G ⁇ riich, D. and T.A. Rapoport (1993) Cell 75:615-630).
  • Proteoliposomes are prepared containing purified MECHP, purified dog Sec ⁇ lp beta and gamma, purified dog SRP receptor, and a mixture of phospholipids (phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, and phosphatidylinositol) corresponding approximately to those found in native microsomes.
  • the proteoliposomes are incubated in a wheat germ in vitro translation system in which a secretory protein (preprolactin) is synthesized in the presence of SRP and radioactive amino acids. After translation and synthesis of preprolactin, half of the sample is treated with 500 ⁇ g/ml proteinase K while the other half remains untreated. Any translocated preprolactin will be inaccessible to proteinase K while any untranslocated preprolactin will be degraded.
  • the amount of preprolactin in the samples with and without proteinase K treatment is determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis followed by phosphor image analysis. The amount of preprolactin protected from proteinase K digestion in the proteinase K-treated sample is proportional to the protein transport activity of MECHP. Gap Junction Activity of MECHP
  • Gap junction activity of MECHP is demonstrated as the ability to induce the formation of intercellular channels between paired Xenopus laevis oocytes injected with MECHP cRNA (Hennemann, supra).
  • MECHP cRNA oligonucleotide to MECHP to reduce background.
  • MECHP cRNA- injected oocytes are incubated overnight, stripped of vitelline membranes, and paired for recording of junctional currents by dual cell voltage clamp. The measured conductances are proportional to gap junction activity of MECHP.
  • Ion Channel Activity of MECHP Ion channel activity of MECHP is demonstrated using an electrophysiological assay for ion conductance.
  • MECHP can be expressed by transforming a mammalian cell line such as COS7, HeLa or CHO with a eukaryotic expression vector encoding MECHP.
  • Eukaryotic expression vectors are commercially available, and the techniques to introduce them into cells are well known to those skilled in the art.
  • a second plasmid which expresses any one of a number of marker genes, such as ⁇ -galactosidase, is co-transformed into the cells to allow rapid identification of those cells which have taken up and expressed the foreign DNA. The cells are incubated for 48-72 hours after transformation under conditions appropriate for the cell line to allow expression and accumulation of MECHP and ⁇ -galactosidase.
  • Transformed cells expressing ⁇ -galactosidase are stained blue when a suitable colorimetric substrate is added to the culture media under conditions that are well known in the art. Stained cells are tested for differences in membrane conductance due to potassium ions by electrophysiological techniques that are well known in the art. Untransformed cells, and/or cells transformed with either vector sequences alone or ⁇ -galactosidase sequences alone, are used as controls and tested in parallel. Cells expressing MECHP will have higher cation conductance relative to control cells. The contribution of MECHP to conductance can be confirmed by incubating the cells using antibodies specific for MECHP. The antibodies will bind to the extracellular side of MECHP. thereby blocking the pore in the ion channel, and the associated conductance.
  • Ion channel activity of MECHP is also measured as current flow across a MECHP- containing Xenopus oocyte membrane using the two-electrode voltage-clamp technique (Ishi et al., supra: Jegla, T. and L. Salkoff (1997) J. Neurosci. 17:32-44).
  • MECHP is subcloned into an appropriate Xenopus oocyte expression vector, such as pBF, and 0.5-5 ng of mRNA is injected into mature stage IV oocytes. Injected oocytes are incubated at 18°C for 1-5 days.
  • Electrode resistance is set at 2-5 M ⁇ and electrodes are filled with the intracellular solution lacking mediator. Experiments are performed at room temperature from a holding potential of 0 mV. Voltage ramps (2.5 s) from -100 to 100 mV are acquired at a sampling frequency of 500 Hz. Current measured is proportional to the activity of MECHP in the assay.
  • MECHP function is assessed by expressing the sequences encoding MECHP at physiologically elevated levels in mammalian cell culture systems.
  • cDNA is subcloned into a mammalian expression vector containing a strong promoter that drives high levels of cDNA expression.
  • Vectors of choice include pCMV SPORT (Life Technologies) and pCR3.1 (Invitrogen, Carlsbad C A), both of which contain the cytomegalovirus promoter.
  • 5- 10 ⁇ g of recombinant vector are transiently transfected into a human cell line, preferably of endothelial or hematopoietic origin, using either liposome formulations or electroporation.
  • 1-2 ⁇ g of an additional plasmid containing sequences encoding a marker protein are co-transfected.
  • Expression of a marker protein provides a means to distinguish transfected cells from nontransfected cells and is a reliable predictor of cDNA expression from the recombinant vector.
  • Marker proteins of choice include, e.g., Green Fluorescent Protein (GFP; Clontech), CD64, or a CD64-GFP fusion protein.
  • FCM Flow cytometry
  • FCM detects and quantifies the uptake of fluorescent molecules that diagnose events preceding or coincident with cell death. These events include changes in nuclear DNA content as measured by staining of DNA with propidium iodide; changes in cell size and granularity as measured by forward light scatter and 90 degree side light scatter; down-regulation of DNA synthesis as measured by decrease in bromodeoxyuridine uptake; alterations in expression of cell surface and intracellular proteins as measured by reactivity with specific antibodies; and alterations in plasma membrane composition as measured by the binding of fluorescein-conjugated Annexin V protein to the cell surface. Methods in flow cytometry are discussed in Ormerod, M.G. (1994) Flow Cytometry. Oxford, New York NY.
  • MECHP The influence of MECHP on gene expression can be assessed using highly purified populations of cells transfected with sequences encoding MECHP and either CD64 or CD64-GFP.
  • CD64 and CD64-GFP are expressed on the surface of transfected cells and bind to conserved regions of human immunoglobulin G (IgG).
  • Transfected cells are efficiently separated from nontransfected cells using magnetic beads coated with either human IgG or antibody against CD64 (DYNAL, Lake Success NY).
  • mRNA can be purified from the cells using methods well known by those of skill in the art. Expression of mRNA encoding MECHP and other genes of interest can be analyzed by northern analysis or microarray techniques. XII. Production of MECHP Specific Antibodies
  • MECHP substantially purified using polyacrylamide gel electrophoresis (PAGE; see, e.g., Harrington, M.G. (1990) Methods Enzymol. 182:488-495), or other purification techniques, is used to immunize rabbits and to produce antibodies using standard protocols.
  • PAGE polyacrylamide gel electrophoresis
  • the MECHP amino acid sequence is analyzed using LASERGENE software (DNASTAR) to determine regions of high immunogenicity, and a corresponding oligopeptide is synthesized and used to raise antibodies by means known to those of skill in the art.
  • LASERGENE software DNASTAR
  • Methods for selection of appropriate epitopes, such as those near the C-terminus or in hydrophilic regions are well described in the art. (See, e.g., Ausubel, 1995. supra, ch. 1 1.)
  • oligopeptides 15 residues in length are synthesized using an ABI 431 A peptide synthesizer (Perkin-Elmer) using fmoc-chemistry and coupled to KLH (Sigma-Aldrich, St. Louis
  • Resulting antisera are tested for antipeptide activity by, for example, binding the peptide to plastic, blocking with 1% BSA, reacting with rabbit antisera, washing, and reacting with radio-iodinated goat anti-rabbit IgG.
  • Naturally occurring or recombinant MECHP is substantially purified by immunoaffinity chromatography using antibodies specific for MECHP.
  • An immunoaffinity column is constructed by covalently coupling anti-MECHP antibody to an activated chromatographic resin, such as
  • Media containing MECHP are passed over the immunoaffinity column, and the column is washed under conditions that allow the preferential absorbance of MECHP (e.g., high ionic strength buffers in the presence of detergent).
  • the column is eluted under conditions that disrupt antibody/MECHP binding (e.g., a buffer of pH 2 to pH 3, or a high concentration of a chaotrope, such as urea or thiocyanate ion), and MECHP is collected.
  • MECHP or biologically active fragments thereof, are labeled with 125 I Bolton-Hunter reagent.
  • Bolton-Hunter reagent See, e.g., Bolton, A.E. and W.M. Hunter (1973) Biochem. J. 133:529-539.
  • Candidate molecules previously arrayed in the wells of a multi-well plate are incubated with the labeled
  • MECHP washed, and any wells with labeled MECHP complex are assayed. Data obtained using different concentrations of MECHP are used to calculate values for the number, affinity, and association of MECHP with the candidate molecules.
  • ABI FACTURA A program that removes vector sequences and masks Perkin-Elmer Applied Biosystems, ambiguous bases in nucleic acid sequences. Foster City, CA.
  • ABI/PARACEL FDF A Fast Data Finder useful in comparing and annotating Perkin-Elmer Applied Biosystems, Mismatch ⁇ 50% amino acid or nucleic acid sequences. Foster City, CA; Paracel Inc., Pasadena, CA.
  • ABI AutoAssembler A program that assembles nucleic acid sequences. Perkin-Elmer Applied Biosystems, Foster City, CA.
  • Phred A base-calling algorithm that examines automated Ewing, B. et al. ( 1998) Genome sequencer traces with high sensitivity and probability. Res. 8: 175-185; Ewing, B. and P. Green ( 1998) Genome Res. 8: 186- 194.
  • Motifs A program that searches amino acid sequences for patterns Bairoch et al. SU ⁇ ia; Wisconsin that matched those defined in Prosite. Package Program Manual, version 9, page M5I-59, Genetics Computer Group, Madison, WI.

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  • Peptides Or Proteins (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Preparation Of Compounds By Using Micro-Organisms (AREA)
  • Medicines That Contain Protein Lipid Enzymes And Other Medicines (AREA)

Abstract

L'invention concerne de nouvelles protéines membranaires de canal humaines (MECHP) et les polynucléotides qui identifient et codent pour MECHP. L'invention concerne également des vecteurs d'expression, des cellules hôtes, des anticorps, des agonistes et des antagonistes. L'invention concerne, en outre, des techniques de diagnostic, de traitement et de prévention des troubles associés à l'expression de MECHP.
EP99948140A 1998-09-02 1999-09-02 Proteines membranaires de canal humaines Withdrawn EP1117781A2 (fr)

Applications Claiming Priority (12)

Application Number Priority Date Filing Date Title
US09/155,226 US6207225B1 (en) 1996-03-26 1997-03-25 Solventless two-component strippable lacquer for metal surfaces
1997-05-16
US155226P 1998-09-02
US19128398A 1998-11-12 1998-11-12
US191283P 1998-11-12
US15522598P 1998-12-09 1998-12-09
US155225P 1998-12-09
US15521199P 1999-01-26 1999-01-26
US155211P 1999-01-26
US15526399P 1999-02-10 1999-02-10
US155263P 1999-02-10
PCT/US1999/020468 WO2000012711A2 (fr) 1998-09-02 1999-09-02 Proteines membranaires de canal humaines

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US7667013B2 (en) * 2004-03-31 2010-02-23 Daiichi Sankyo Company, Limited Gene encoding a guanine nucleotide exchange factor and the gene product thereof
JP5759664B2 (ja) * 2008-08-29 2015-08-05 花王株式会社 Ｃｎｇチャネル阻害剤

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