Isolated peptides corresponding to amino acid sequences of...

Details Isolated peptides corresponding to amino acid sequences of... Isolated peptides corresponding to amino acid sequences of...

1998-10-02

2004-04-20

Chan, Christina (Department: 1644)

Chemistry: natural resins or derivatives; peptides or proteins;

Peptides of 3 to 100 amino acid residues

25 or more amino acid residues in defined sequence

C530S325000, C530S326000, C530S328000, C530S350000, C514S012200, C514S013800, C514S015800, C514S885000, C424S185100, C424S450000, C424S085100, C424S085200, C424S282100, C424S283100

Reexamination Certificate

active

06723832

ABSTRACT:

FIELD OF THE INVENTION
This invention relates to HLA binding peptides derived from an antigen associated with cancer. These peptides bind to Class I and to Class II MHC molecules.
BACKGROUND AND PRIOR ART
It is fairly well established that many pathological conditions, such as infections, cancer, autoimmune disorders, etc., are characterized by the inappropriate expression of certain molecules. These molecules thus serve as “markers” for a particular pathological or abnormal condition. Apart from their use as diagnostic “targets”, i.e., materials to be identified to diagnose these abnormal conditions, the molecules serve as reagents which can be used to generate diagnostic and/or therapeutic agents. A by no means limiting example of this is the use of cancer markers to produce antibodies specific to a particular marker. Yet another non-limiting example is the use of a peptide which complexes with an MHC molecule, to generate cytolytic T cells against abnormal cells.
Preparation of such materials, of course, presupposes a source of the reagents used to generate these. Purification from cells is one laborious, far from sure method of doing so. Another preferred method is the isolation of nucleic acid molecules which encode a particular marker, followed by the use of the isolated encoding molecule to express the desired molecule.
To date, two strategies have been employed for the detection of such antigens, in e.g., human tumors. These will be referred to as the genetic approach and the biochemical approach. The genetic approach is exemplified by, e.g., dePlaen et al., Proc. Natl. Sci. USA 85: 2275 (1988), incorporated by reference. In this approach, several hundred pools of plasmids of a cDNA library obtained from a tumor are transfected into recipient cells, such as COS cells, or into antigen-negative variants of tumor cell lines which are tested for the expression of the specific antigen. The biochemical approach, exemplified by, e.g., O. Mandelboim, et al., Nature 369: 69 (1994) incorporated by reference, is based on acidic elution of peptides which have bound to MHC-class I molecules of tumor cells, followed by reversed-phase high performance liquid chromography (HPLC). Antigenic peptides are identified after they bind to empty MHC-class I molecules of mutant cell lines, defective in antigen processing, and induce specific reactions with cytotoxic T-lymphocytes. These reactions include induction of CTL proliferation, TNF release, and lysis of target cells, measurable in an MTT assay, or a
51
Cr release assay.
These two approaches to the molecular definition of antigens have the following disadvantages: first, they are enormously cumbersome, time-consuming and expensive; and second, they depend on the establishment of cytotoxic T cell lines (CTLS) with predefined specificity.
The problems inherent to the two known approaches for the identification and molecular definition of antigens is best demonstrated by the fact that both methods have, so far, succeeded in defining only very few new antigens in human tumors. See, e.g., van der Bruggen et al., Science 254: 1643-1647 (1991); Brichard et al., J. Exp. Med. 178: 489-495 (1993); Coulie, et al., J. Exp. Med. 180: 35-42 (1994); Kawakami, et al., Proc. Natl. Acad. Sci. USA 91: 3515-3519 (1994).
Further, the methodologies described rely on the availability of established, permanent cell lines of the cancer type under consideration. It is very difficult to establish cell lines from certain cancer types, as is shown by, e.g., Oettgen, et al., Immunol. Allerg. Clin. North. Am. 10: 607-637 (1990). It is also known that some epithelial cell type cancers are poorly susceptible to CTLs in vitro, precluding routine analysis. These problems have stimulated the art to develop additional methodologies for identifying cancer associated antigens.
One key methodology is described by Sahin, et al., Proc. Natl. Acad. Sci. USA 92: 11810-11913 (1995), incorporated by reference. Also, see U.S. Pat. No. 5,698,396, and patent application Ser. No. 08/479,328 filed Jan. 3, 1996. All three of these references are incorporated by reference. To summarize, the method involves the expression of cDNA libraries in a prokaryotic host. (The libraries are secured from a tumor sample). The expressed libraries are then immnoscreened with absorbed and diluted sera, in order to detect those antigens which elicit high titer humoral responses. This methodology is known as the SEREX method (“Serological identification of antigens by Recombinant Expression Cloning”). The methodology has been employed to confirm expression of previously identified tumor associated antigens, as well as to detect new ones. See the above referenced patent applications and Sahin, et al., supra, as well as Crew, et al., EMBO J 144: 2333-2340 (1995).
The SEREX methodology has been applied to esophageal cancer samples, and an antigen has now been identified, and its encoding nucleic acid molecule isolated and cloned. This is the subject of several patent applications, some of which are incorporated by reference. The antigen and truncated forms have been found to be reactive with antibodies in the serum of cancer patients. It has also been found that peptides derived form this molecule bind with MHC molecules, provoking both cytolytic T cell and helper T cell responses. These features of the invention are seen in the disclosure which follows.


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patent: 5804381 (1998-09-01), Chen et al.
patent: 9814464 (1998-04-01), None
US 5,811,519, 9/1998, Lethe et al. (withdrawn)
Rammensee et al. Immunogenetics. 41: 178-228, 1995.*
Chen et al. A testicular antigen aberrantly expressed in human cancers detected by autologous antibody screening,: Proc. Natl Academey Sciences USA94; 1914-1918 (Mar. 1997).
Futaki, et al., “Naturally processed HLA-DR 9/DR 53 (DR B1*0901/DR B4* 010)-bound peptides,” Immunogenics 42: 299-301 (1995).
Drijfhout, et al, “Detailed Motifs For Peptide Binding 10 HLC-A *0201 Derived From Large Random Sets of Peptides Using Cellular Binding Assay,” Human Immunology 43:1-12 (1995).
D'Amaro, et al., “A Computer Program For Predicting Possible Cytotoxic T Lymphocyte Epitopes Based on HLA-Class I Peptides Binding Motifs,” Human Immunol. 43: 13-18 (1995).
Kiyokawa et al., “Overexpression of ERK, an EPH Family Receptor Protein Tyrosine Kinase, in Various Human Tumors,”Canc. Res.,54:3645-3650 (Jul. 15, 1994).
Fazioli et al., “The ezrin-like family of tyrosine kinase sub trates: receptor specific pattern of tyrosine phosphorylation and relationship to malignant transformation,”Oncogene,8 (5) :1335-1345 (5/93).

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