`Beaulieu et al .
`
`( 10 ) Patent No . :
`( 45 ) Date of Patent :
`
`US 9 , 891 , 223 B2
`* Feb . 13 , 2018
`
`US009891223B2
`
`( 54 ) METHOD OF ASSAYING LEUKOCYTE
`ELASTASE INHIBITOR FOR THE IN VITRO
`DIAGNOSIS OF COLORECTAL CANCER
`( 75 ) Inventors : Corinne Beaulieu , Rillieux la Pape
`( FR ) ; Jean - Philippe Charrier , Tassin
`la Demi - Lune ( FR ) ; Genevieve
`Choquet - Kastylevsky , Francheville
`( FR ) ; Odile Mejan - Letourneur , Lyons
`( FR ) ; Dominique Rolland , Saint Genis
`les Ollieres ( FR )
`( 73 ) Assignee : BIOMERIEUX , Marcy l ' Etoile ( FR )
`Subject to any disclaimer , the term of this
`( * ) Notice :
`patent is extended or adjusted under 35
`U . S . C . 154 ( b ) by 0 days .
`This patent is subject to a terminal dis
`claimer .
`( 21 ) Appl . No . :
`12 / 452 , 035
`( 22 ) PCT Filed :
`Jul . 10 , 2008
`PCT / FR2008 / 051291
`( 86 ) PCT No . :
`$ 371 ( c ) ( 1 ) ,
`( 2 ) , ( 4 ) Date : Dec . 14 , 2009
`( 87 ) PCT Pub . No . : W02009 / 024691
`PCT Pub . Date : Feb . 26 , 2009
`Prior Publication Data
`US 2010 / 0129828 A1 May 27 , 2010
`Foreign Application Priority Data
`( 30 )
`Jul . 19 , 2007 ( FR ) .
`. . . . . . . . . 07 05202
`( 51 )
`Int . Ci .
`GOIN 33 / 53
`( 2006 . 01 )
`GOIN 30 / 72
`( 2006 . 01 )
`( 2006 . 01 )
`GOIN 33 / 574
`U . S . CI .
`CPC . GOIN 33 / 57419 ( 2013 . 01 ) ; GOIN 2333 / 811
`( 2013 . 01 )
`( 58 ) Field of Classification Search
`None
`See application file for complete search history .
`References Cited
`U . S . PATENT DOCUMENTS
`4 , 529 , 931 A
`7 / 1985 Kuhns
`5 , 002 , 870 A
`3 / 1991 Leavitt et al .
`5 , 223 , 789 A
`6 / 1993 Katsuyama et al .
`5 , 344 , 760 A
`9 / 1994 Harvey . . . . . . . . . . . . . . GOIN 33 / 6872
`435 / 7 . 1
`5 , 360 , 715 A
`11 / 1994 Leavitt et al .
`6 , 001 , 632 A
`12 / 1999 Braxton et al .
`6 , 291 , 205 B1
`9 / 2001 Tuite et al .
`6 , 451 , 528 B1
`9 / 2002 Carr et al .
`6 , 518 , 411 B12 / 2003 Murray et al .
`8 , 029 , 979 B2
`10 / 2011 Schneider - Mergener et al .
`
`2002 / 0160382 Al 10 / 2002 Lasek et al .
`2003 / 0082533 A1
`5 / 2003 Yue et al .
`2003 / 0087818 A1
`5 / 2003 Jiang et al .
`2003 / 0109690 Al 6 / 2003 Ruben et al .
`2003 / 0172388 Al
`9 / 2003 Fujise et al .
`2004 / 0157278 A1
`8 / 2004 Astle et al .
`2004 / 0191782 AL 9 / 2004 Wang
`2004 / 0197930 A1 *
`10 / 2004 Rosenfeld et al .
`2005 / 0181398 A1
`8 / 2005 Fung et al .
`2005 / 02 14826 AL
`9 / 2005 Mor et al .
`2006 / 0003359 Al 1 / 2006 Feinberg et al .
`2006 / 0179496 A1
`8 / 2006 Burgess et al .
`2006 / 0205014 A1 *
`9 / 2006 Dotan . . . . . . . . . . . . . . . . . . GOIN 33 / 569
`435 / 7 . 1
`
`. . . . . . . . . . .
`436 / 510
`
`2007 / 0020707 A11 / 2007 Holten - Andersen et al .
`2009 / 0239794 AL
`9 / 2009 Soudeyns et al .
`2011 / 0104701 Al
`5 / 2011 Ataman - Onal et al .
`
`AT
`CN
`EP
`EP
`EP
`FR
`
`JP
`WO
`WO
`WO
`WO
`wo
`WO
`
`FOREIGN PATENT DOCUMENTS
`500 719 A1
`3 / 2006
`1396182 A
`2 / 2003
`0 496 174 AL
`7 / 1992
`1 724 586 A2
`11 / 2006
`1 775 590 A1
`4 / 2007
`2 581 456 AL 11 / 1986
`2 - 287266 A
`11 / 1990
`4 - 64068 A
`2 / 1992
`2001 - 069971 A
`3 / 2001
`95 / 16462 A1 6 / 1995
`WO 00 / 33083 A1 6 / 2000
`WO 00 / 50588 A2
`8 / 2000
`01 / 31019 A2
`5 / 2001
`01 / 071357 A2
`9 / 2001
`WO 02 / 20731 Al
`3 / 2002
`( Continued )
`OTHER PUBLICATIONS
`Friedman et al . , Proteomics 2004 , 4 , 793 - 811 . *
`Giusti et al . , Proteomics May 2007 , 7 ( 10 ) : 1634 - 1643 . *
`Guo et al . , J Mol . Med . , 2004 , 82 : 768 - 774 . *
`Kim et al . , Annals Clin . Lab . Sci . 2003 , 33 ( 1 ) : 32 - 38 . *
`May 13 , 2011 Restriction and Election of Species Requirement
`issued in U . S . Appl . No . 12 / 452 , 038 .
`Sep . 1 , 2011 Office Action issued in U . S . Appl . No . 12 / 452 , 038 .
`Nov . 16 , 2011 Election of Species Requirement issued in U . S . Appl .
`No . 12 / 452 , 037 .
`Sep . 15 , 2011 Restriction and Election of Species Requirement
`issued in
`U . S . Appl . No . 12 / 452 , 042 .
`Oct . 28 , 2011 Office Action issued in U . S . Appl . No . 12 / 452 , 042 .
`Aug . 1 , 2011 Restriction and Election of Species Requirement
`issued in U . S . Appl . No . 12 / 452 , 034 .
`Oct . 27 , 2011 Office Action issued in U . S . Appl . No . 12 / 452 , 034 .
`Oct . 28 , 2011 Restriction Requirement issued in U . S . Appl . No .
`12 / 452 , 047 .
`
`( Continued )
`Primary Examiner – Hong Sang
`( 74 ) Attorney , Agent , or Firm — Oliff PLC
`( 57 )
`ABSTRACT
`The present invention relates to a method for the in vitro
`diagnosis of colorectal cancer by determining the presence
`of the Leukocyte Elastase Inhibitor tumor marker in a
`biological sample taken from a patient suspected of having
`colorectal cancer . Said method can be used for early diag
`nosis , screening , therapeutic follow - up and prognosis , and
`also for relapse diagnosis in relation to colorectal cancer .
`15 Claims , 12 Drawing Sheets
`
`*
`
`( 65 )
`
`( 52 )
`
`( 56 )
`
`Geneoscopy Exhibit 1048, Page 1
`
`
`
`US 9 , 891 , 223 B2
`Page 2
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`( 56 )
`
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`WO
`W0
`WO
`WO
`WO
`wo
`WO
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`References Cited
`FOREIGN PATENT DOCUMENTS
`WO 03 / 065003 A2
`8 / 2003
`WO 03 / 087831 A2 10 / 2003
`WO 2004 / 073730 A1
`9 / 2004
`WO 2005 / 015218 A1
`2 / 2005
`WO 2005 / 015219 AL
`2 / 2005
`WO 2005 / 015226 AL
`2 / 2005
`WO 2005015218 A1 *
`2 / 2005
`WO 2005015219 A1 *
`2 / 2005
`05 / 035003 A2
`4 / 2005
`05 / 060996 A2
`7 / 2005
`WO 2005 / 083440 A2
`9 / 2005
`WO 2006 / 015079 A2
`2 / 2006
`WO 2006 / 074360 A2
`7 / 2006
`WO 2007 / 002535 A2
`1 / 2007
`WO 2007 / 005578 A1 1 / 2007
`WO 2007020522 A2 *
`2 / 2007
`WO 2007 / 068985 A2
`6 / 2007
`WO 2007 / 140352 A2 12 / 2007
`WO 2008 / 021290 A2
`2 / 2008
`WO 2008 / 028968 A2
`3 / 2008
`WO 2008 / 036981 Al
`3 / 2008
`
`OTHER PUBLICATIONS
`SCORE sequence search result # 1 , Geneseq Database , “ 20110423 _
`191537 _ us - 12 - 452 - 038 - 2 . rag ” Apr . 23 , 2011 .
`Bruce et al . , Cancer - Wide Tissue Microanay Survey of Ezrin and
`Merlin Expression , Proc Amer Assoc Cancer Res , vol . 46 , Abstract
`# 424 , 2005 .
`Gould et al . , " cDNA Cloning and Sequencing of the Protein
`Tyrosine Kinase Substrate , Ezrin , Reveals Homology to Band 4 . 1 , "
`The EMBO Journal , vol . 8 , No . 13 , pp . 4133 - 4142 , 1989 .
`Etzioni et al . , “ The Case for Early Detection , " Nature Review , vol .
`3 , Internet pp . 1 - 10 , Apr . 2003 .
`Mercer , “ Use of Multiple Markers to Enhance Clinical Utility , "
`Immunol Ser . , vol . 53 , pp . 39 - 54 , 1990 .
`Delanote et al . , “ Plastins : Versatile Modulators of Actin Organiza
`tion
`in
`( patho ) physiological
`Cellular
`Processes , ”
`Acta
`Pharmacologica Sinica , vol . 26 , No . 7 , pp . 769 - 779 , Jul . 2005 .
`Hasselblatt et al . , “ Identification of Novel Diagnostic Markers for
`Choroid Plexus Tumors , ” Am . J . Surg Pathol , vol . 30 , No . 1 , pp .
`66 - 74 , Jan . 2006 .
`Lin et al . , “ Identification of I - Plastin , a Human Fimbrin Isoform
`Expressed in Intestine and Kidney , ” Molecular and Cellular Biol
`ogy , vol . 14 , No . 4 , pp . 2457 - 2467 , Apr . 1994 .
`Carroll et al . , “ Liver Fatty Acid - Binding Protein : A Marker for
`Studying Cellular Differentiation in Gut Epithelial Neoplasms , "
`Gastroenterology , vol . 99 , pp . 1727 - 1735 , 1999 .
`Kayser et al . , “ Primary Colorectal Carcinomas and their
`Intrapulmonary Metastases : Clinical , Glyco - , Immuno - and Lectin
`Histochemical , Nuclear and Syntactic Structure Analysis with
`Emphasis on Correlation with Period of Occurrence of Metastases
`and Survival , ” APMIS , vol . 110 , pp . 435 - 446 , 2002 .
`Kuusela et al . , " Comparison of CA 19 - 9 and Carcinoembryonic
`Antigen ( CEA ) Levels in the Serum of Patients with Colorectal
`Diseases , ” Br . J . Cancer , vol . 49 , pp . 135 - 139 , 1984 .
`Pelsers et al . , “ Fatty Acid - Binding Proteins as Plasma Markers of
`Tissue Injury , " Clinica Chimica Acta , vol . 352 , pp . 15 - 35 , 2005 .
`Iurisci et al . , " Concentrations of Galectin - 3 in the Sera of Normal
`Controls and Cancer Patients , ” Clinical Cancer Research , vol . 6 , pp .
`1389 - 1393 , Apr . 2000 .
`Niederkofler et al . , “ Novel Mass Spectrometric Immunoassays for
`the Rapid Structural Characterization of Plasma Apolipoproteins , "
`Journal of Lipid Research , vol . 44 , pp . 630 - 639 , 2003 .
`Hortin , “ The MALDI - TOF Mass Spectrometric View of the Plasma
`Proteome and Pepetidome , " Clinical Chemistry , vol . 52 , No . 7 , pp .
`1223 - 1237 , 2006 .
`Hachem , “ Serum Apolipoproteins A - I , A - II and B
`in Hepatic
`Metastases Comparison with other Liver Diseases : Hepatomas and
`Cirrhosis , " J . Clin . Chem . Clin . Biochem . , vol . 24 , pp . 161 - 166 ,
`1986 .
`
`Remold - O ' Donnell et al . , “ Sequence and Molecular Characteriza
`tion of Human Monocyte / Neutrophil Elastase Inhibitor , ” Proc . Natl .
`Acad . Sci . vol . 89 , pp . 5635 - 5639 , Jun . 1992 .
`Cooley et al . , “ The Serpin MNEI Inhibits Elastase - Like and
`Chymotrypsin - Like Proteases through Efficient Reactions at Two
`Active Sites , " Biochemistry , vol . 40 , pp . 15762 - 15770 , 2001 .
`Algrain et al , “ Ezrin Contains Cytoskeleton and Membrane Binding
`Domains Accounting for its Proposed Role as a Membrane
`Cytoskeletal Linker , " The Journal of Cell Biology , vol . 120 , No . 1 ,
`pp . 129 - 139 , Jan . 1993 .
`Jiang et al . , “ Cytokine Regulation of Ezrin Expression in the Human
`Colon Cancer Cell Line HT29 , " Anticancer Research , vol . 16 , pp .
`861 - 866 , 1996 .
`Hiscox et al , “ Ezrin Regulates Cell - Cell and Cell - Matrix Adhesion ,
`A Possible Role with E - Cadherin / B - Catenin , ” Journal of Cell Sci
`ence , vol . 112 , pp . 3081 - 3090 , 1999 .
`Xiao et al . , " An Approach to Studying Lung Cancer - Related Pro
`teins in Human Blood , ” Molecular & Cellular Proteomics , vol . 4 ,
`pp . 1480 - 1486 , 2005 .
`Anders et al . , “ Aminoacyclases , ” Advances in Pharmacology , vol .
`27 , pp . 431 - 448 , 1994 .
`Lorentz et al . , " A New Method for the Assay of Aminoacylase :
`Elaboration of a Fixed - Incubation Method for Routine Measure
`ments , ” Clinics Chimica Acta , vol . 63 , pp . 263 - 269 , 1975 .
`Lorentz et al , “ Clinical Application of a New Method for the
`Determination of Aminoacylase in Human Serum , " Clinica Chimica
`Acta , vol . 63 , pp . 271 - 274 , 1975 .
`Cook et al , “ Human Aminoacylase - 1 , " The Journal of Biological
`Chemistry , vol . 268 , No . 23 , pp . 17010 - 17017 , 1993 .
`Miller et al . , “ Lack of Expression of Aminoacylae - 1 in Small Cell
`Lung Cancer , ” The Journal of Clinical Investigation , Inc . , vol . 83 ,
`pp . 2120 - 2124 , Jun . 1989 .
`Balabanov et al . , “ Tumour - Related Enzyme Alterations in the Clear
`Cell Type of Human Renal Cell Carcinoma Identified by Two
`dimensional Gel Electrophoresis , ” Eur . J . Biochem . , vol . 268 , pp .
`5977 - 5980 , 2001 .
`Chan et al , “ Human Liver Fatty Acid Binding Protein cDNA and
`Amino Acid Sequence , " The Journal of Biological Chemistry , vol .
`260 , No . 5 , pp . 2629 - 2632 , 1985 .
`Das et al . , “ Expression Pattern of Fatty Acid - Binding Proteins in
`Human Normal and Cancer Prostate Cells and Tissues , " Clinical
`Cancer Research , vol . 7 , 1706 - 1715 , Jun . 2001 .
`Stulik et al . , “ Proteome Study of Colorectal Carcinogenesis , ” Elec
`trophoresis , vol . 22 , pp . 3019 - 3025 , 2001 .
`Yamazaki et al . , “ Liver Fatty Acid - Binding Protein is a New
`Prognostic Factor for Hepatic Resection of Colorectal Cancer
`Metastases , ” Journal of Surgical Oncology , vol . 72 , pp . 83 - 87 , 1999 .
`Sweetser et al . , “ The Human and Rodent Intestinal Fatty Acid
`Binding Protein Genes , " The Journal of Biological Chemistry , vol .
`262 , No . 33 , pp . 16060 - 16071 , 1987
`Pelsers et al , “ Intestinal - Type and Liver - Type Fatty Acid - Binding
`Protein in the Intestine . Tissue Distribution and Clinical Utility ” ,
`Clinical Biochemistry , vol . 36 , pp . 529 - 535 , 2003 .
`Xiao et al , “ Dietary Exposure to Soy or Whey Proteins Alters
`Colonic Global Gene Expression Profiles During Rat Colon
`Tumorigenesis , " Molecular Cancer , vol . 4 , No . 1 , pp . 1 - 17 , Jan . 11 ,
`2005 .
`Engwegen et al . , “ Identification of Serum Proteins Discriminating
`Colorectal Cancer Patients and Healthy Controls Using Surface
`Enhanced Laser Desorption Ionisation - Time of Flight Mass Spec
`trometry , " World J . Gastrenterol , vol . 12 , No . 10 , pp . 1536 - 1544 ,
`Mar . 14 , 2006 .
`Zhang et al . , “ Three Biomarkers Identified from Serum Proteomic
`Analysis for the Detection of Early Stage Ovarian Cancer , ” Cancer
`Research , vol . 64 , pp . 5882 - 5890 , Aug . 15 , 2004 .
`Lin et al . , “ Human Plastin Genes , " The Journal of Biological
`Chemistry , vol . 268 , No . 4 , pp . 2781 - 2792 , 1993 .
`Lavabre - Bertrand et al . , “ Plasma Proteasome Level is a Potential
`Marker in Patients with Solid Tumors and Hemopoietic Malignan
`cies , ” Cancer , vol . 92 , No . 10 , pp . 2493 - 2500 , Nov . 15 , 2001 .
`Schwartz , “ Enzymes as Prognostic Markers and Therapeutic Indi
`cators in Patients with Cancer , ” Clinica Chimica Acta , vol . 206 , pp .
`77 - 82 , 1992 .
`
`Geneoscopy Exhibit 1048, Page 2
`
`
`
`US 9 , 891 , 223 B2
`Page 3
`
`( 56 )
`
`References Cited
`OTHER PUBLICATIONS
`McCool et al . , “ Roles of Calreticulin and Calnexin During Mucin
`Synthesis in LS180 and HT29 / A1 Human Colonic Adenocarcinoma
`Cells , ” Biochem . J . , vol . 341 , pp . 593 - 600 , 1999 .
`Motoo et al . , “ Serum Levels of Pancreatitis - Associated Protein in
`Digestive Diseases with Special Reference to Gastrointestinal Can
`cer , ” Digestive Diseases and Sciences , vol . 44 , No . 6 , pp . 1142
`1147 , Jun . 1999 .
`Abe et al . , “ Preparation of Recombinant MK - 1 / EP - CAM and Estab
`lishment of an ELISA System for Determining Soluble MK - 1 / EP
`CAM Levels in Sera of Cancer Patients , ” Journal of Immunological
`Methods , vol . 270 , pp . 227 - 233 , 2002 .
`Katayama et al . , “ Soluble E - Cadherin Fragments Increased in
`Circulation of Cancer Patients , ” Br . J . Cancer , vol . 69 , pp . 580 - 585 ,
`1994 .
`Wilmanns et al . , “ Soluble Serum E - Cadherin as a Marker of Tumour
`Progression in Colorectal Cancer Patients , ” Clinical & Experimen
`tal Metastasis , vol . 21 , pp . 75 - 78 , 2004 .
`Gold et al . , “ Specific Carcinoembryonic Antigens of the Human
`Digestive System , ” J . Exp . Med . , pp . 467 - 481 , 1965 .
`Kim et al . , “ Gastrointestinal Tract Cancer Screening Using Fecal
`Carcinoembryonic Antigen , ” Annals of Clinical & Laboratory Sci
`ence , vol . 33 , No . 1 , pp . 32 - 38 , 2003 .
`Holmgren et al . , “ Detection by Monoclonal Antibody of Carbohy
`drate Antigen CA 50 in Serum of Patients with Carcinoma , ” British
`Medical Journal , vol . 288 , pp . 1479 - 1482 , May 19 , 1984 .
`Klug et al . , Monoclonal Anitbody Immunoradiometric Assay for An
`Antigenic Determinant ( CA 72 ) on a Novel Pancarcinoma Antigen
`( TAG - 72 ) , Int . J . Cancer , vol . 38 , pp . 661 - 669 , 1986 .
`Holland et al . , “ Testosterone Serica : Posible Marcador En El Cancer
`Colorrectal , ” Medicine ( Buenos Aires ) , vol . 53 , pp . 117 - 123 , 1993 .
`Model et al . , “ Detection of Methylated DNA in Plasma from
`Colorectal Cancer Patients and Controls by Real - Time PCR Analy
`sis of Septin 9 , ” World Congress on Gastrointestinal Cancer , Jul .
`2006 .
`Ebert et al . , " Aristaless - like Homeobox - 4 Gene Methylation is a
`Potential Marker for Colorectal Adenocarcinomas , ” Gastroenterol
`ogy , vol . 131 , pp . 1418 - 1430 , 2006 .
`Bianco et al . , “ Identification of Cripto - 1 as a Novel Serologic
`Marker for Breast and Colon Cancer , ” Clin . Cancer Res . , vol . 12 ,
`No . 17 , pp . 5158 - 5164 , Sep . 1 , 2006 .
`Mori et al . , " Two - Dimensional Electrophoresis Database of Fluo
`rescence - Labeled Proteins of Colon Cancer Cells , " Journal of
`Chromatography B , vol . 823 , pp . 82 - 97 , 2005 .
`Duffy et al . , “ Tumour Markers in Colorectal Cancer : European
`Group on Tumour Markers ( EGTM ) Guidelines for Clinical Use , "
`European Journal of Cancer , vol . 43 , pp . 1348 - 1360 , 2007 .
`Rouzier et al . , “ Immunocytochemical Detection of Bone Marrow
`Micrometastases in Colorectal Carcinoma Patients , Using A Mono
`clonal Antibody to Villin , ” Cytometry ( Communications in Clinical
`Cytometry ) , vol . 46 , pp . 281 - 289 , 2001 .
`Nishizuka et al . , “ Diagnostic Markers that Distinguish Colon and
`Ovarian Adenocarcinomas : Identification by Genomic , Proteomic ,
`and Tissue Array Profiling , ” Cancer Research , vol . 63 , pp . 5243
`5250 , Sep . 1 , 2003 .
`Wang et al . , Proteomic Dissection of the Molecular Mechanisms
`Underlying Hepatic
`Metastasis
`in
`Colorectal
`Cancer ,
`XP009093529 , Database Accession No . PREV200600505326 ,
`AGA Abstracts , p . A - 676 , W1533 , Apr . 2006 .
`Mori et al . , A Genome - Wide Search Identifies Epigenetic Silencing
`of Somatostatin , Tachykinin - 1 , and 5 other Genes in Colon Cancer ,
`Gastroenterology , vol . 131 , pp . 797 - 808 , 2006 .
`Database WPI Week 200777 , Thomson Scientific , London , GB ; AN
`2007 - 817830 , XP002464797 & CN 1 967 246 ( Proteome Analysis
`Research Center ) May 23 , 2007 , Abstract .
`Fujiwara et al . , Global Gene Expression Analysis of Rat Colon
`Cancers Induced by a Food - Borne Carcinogen , 2 - amino - 1 - methyl
`6 - phenylimidazo ( 4 , 5 - b ) pyridine , Carcinogenesis , vol . 25 , No . 8 , pp .
`1495 - 1505 , 2004 .
`
`Dorudi et al . , “ E - Cadherin Expression in Colorectal Cancer , " >
`American Journal of Pathology , vol . 142 , No . 4 , pp . 981 - 986 , Apr .
`1993
`Lawrie et al . , “ Liver Fatty Acid Binding Protein Expression in
`Colorectal Neoplasia , " British Journal of Cancer , vol . 90 , pp .
`1955 - 1960 , 2004 .
`Mar . 18 , 2009 International Search Report Issued in International
`Application No . PCT / FR2008 / 051291 .
`Feb . 23 , 2009 International Search Report Issued in International
`Application No . PCT / FR2008 / 051289 .
`Feb . 18 , 2009 International Search Report Issued in International
`Application No . PCT / FR2008 / 051295 .
`Jan . 16 , 2009 International Search Report Issued in International
`Application No . PCT / FR2008 / 051298 .
`Mar . 27 , 2009 International Search Report Issued in International
`Application No . PCT / FR2008 / 051290 .
`Mar . 6 , 2009 International Search Report Issued in International
`Application No . PCT / FR2008 / 051293 .
`Mar . 5 , 2009 International Search Report Issued in International
`Application No . PCT / FR2008 / 051292 .
`U . S . Appl . No . 12 / 452 , 038 , filed Dec . 14 , 2009 , in the name of
`Monique Arpin et al .
`U . S . Appl . No . 12 / 452 , 037 , filed Dec . 14 , 2009 , in the name of
`Yasemin Ataman - Onal et al .
`U . S . Appl . No . 12 / 452 , 042 , filed Dec . 14 , 2009 , in the name of
`Monique Arpin et al .
`U . S . Appl . No . 12 / 452 , 048 , filed Dec . 14 , 2009 , in the name of
`Jean - Philippe Charrier et al .
`U . S . Appl . No . 12 / 452 , 034 , filed Dec . 14 , 2009 , in the name of
`Yasemin Ataman - Onal et al .
`U . S . Appl . No . 12 / 452 , 047 , filed Dec . 14 , 2009 , in the name of
`Yasemin Ataman - Onal et al .
`Kaetzel et al . ; “ Protein disulphide - isomerase from human placenta
`and rat liver — Purification and immunological characterization with
`monoclonal antibodies ; " Biochem . J . ; 1987 ; pp . 39 - 47 ; vol . 241 , No .
`1 ; Great Britain .
`Kozaki et al . ; “ Tissue Distribution of Erpol and Association of Its
`Increased Expression with IgG Production in Hybridoma Cells ; " >
`Experimental Cell Research ; 1994 ; pp . 348 - 358 ; vol . 213 , No . 2 ;
`Academic Press , Inc .
`Leys et al . ; “ Expression and prognostic significance of
`prothymosin - a and Erp57 in human gastric cancer ; " Surgery ; 2007 ;
`pp . 41 - 50 ; vol . 141 , No . 1 ; Mosby Co . , St . Louis , MO , U . S . A .
`International Search Report dated Nov . 25 , 2009 in International
`Application No . PCT / FR2009 / 051361 ( with translation ) .
`Feb . 12 , 2009 International Search Report Issued in International
`Application No . PCT / FR2008 / 051294 .
`Feb . 3 , 2012 Office Action issued in U . S . Appl . No . 12 / 452 , 048 .
`Feb . 1 , 2012 Office Action issued in U . S . Appl . No . 12 / 452 , 037 .
`Jan . 9 , 2012 Office Action issued in U . S . Appl . No . 12 / 452 , 047 .
`Otsuka et al . “ Differential Expression of L - Plastin Gene in Human
`Colorectal Cancer Progression and Metastasis , ” Biochemical and
`Biophysical Research Communications , vol . 289 , No . 4 , pp . 876
`881 , 2001 .
`Sass et al . , “ Mutations in ACY1 , the Gene Encoding Aminoacylase
`1 , Cause a Novel Inborn Error of Metabolism ” , The American
`Journal of Human Genetics , Mar . 2006 , vol . 78 , pp . 401 - 409 .
`Tockman et al . , “ Considerations in Bringing a Cancer Biomarker to
`Clinical Application ” , Cancer Research , May 1 , 1992 , vol . 52 , pp .
`2711s - 2718s .
`Freeman et al . , “ APO - AII is an Elevated Biomarker of Chronic
`Non - Human Primate Ethanol Self - Administration ” , Alcohol &
`Alcoholism , Mar . 2006 , vol . 41 , No . 3 , pp . 300 - 305 .
`Stierum et al . ; Proteome analysis reveals novel proteins associated
`with proliferation and differentiation of colorectal cancer cell line
`Caco - 2 ; Biochemica et Biophysica Acta ; 2003 ; pp . 73 - 91 ; vol . 1650 ,
`No . 1 - 2 .
`Elsevier Publishing , “ Human PDIA1 tryptic peptideSEQ ID 33 ; " >
`Retrieved from EBI accession No . GSP : ASS06881 ; Database
`Accession No . ASS06881 , 2003 .
`Apr . 23 , 2014 Office Action issued in U . S . Appl . No . 13 / 712 , 340 .
`Apr . 17 , 2012 Office Action issued in U . S . Appl . No . 12 / 452 , 038 .
`May 18 , 2012 Office Action issued in U . S . Appl . No . 12 / 452 , 034 .
`
`Geneoscopy Exhibit 1048, Page 3
`
`
`
`US 9 , 891 , 223 B2
`Page 4
`
`( 56 )
`
`References Cited
`OTHER PUBLICATIONS
`Jun . 12 , 2012 Office Action issued in U . S . Appl . No . 12 / 452 , 042 .
`Jun . 18 , 2012 Office Action issued in U . S . Appl . No . 12 / 452 , 047 .
`Davies et al . , “ Loss of Cellular Distribution of Ezrin in Human
`Colon Cancer ” , ASCO 2006 , Gastrointestinal Cancers Symposium ,
`2006 Abstract 322
`Mahipal et al . , “ Epidermal Growth Factor Receptor Overexpression
`in Resected Pancreatic Cancer ” , J Clinical Oncology , 2011 , 29 :
`suppl 4 ; Abstract 317 .
`Brattstrom et al . , “ HER - 2 overexpression in patients with esopha
`geal carcinoma correlates with poorer survival ” , ASCO 2005 Gas
`trointestinal Cancers Symposium , 2005 , Abstract 63 .
`Kavanagh et al . , “ Is overexpression of HER - 2 a predictor of
`prognosis in colorectal cancer ? " BMC Cancer , Jan . 1 , 2009 , 9 : 1 - 6 .
`Jun . 18 , 2013 Office Action issued in U . S . Appl . No . 12 / 452 , 037 .
`Jul . 31 , 2012 Office Action issued in U . S . Appl . No . 12 / 452 , 048 .
`Jul . 24 , 2012 Restriction Requirement issued in U . S . Appl . No .
`12 / 999 , 242 .
`Aug . 3 , 2012 Office Action issued in U . S . Appl . No . 12 / 452 , 037 .
`Dec . 28 , 2012 Office Action issued in U . S . Appl . No . 12 / 452 , 037 .
`Jan . 30 , 2014 Office Action issued in U . S . Appl . No . 12 / 452 , 034 .
`Sep . 30 , 2013 Office Action issued in U . S . Appl . No . 12 / 452 , 034 .
`Oct . 15 , 2013 Office Action issued in U . S . Appl . No . 12 / 452 , 037 .
`Sep . 10 , 2014 Office Action issued in U . S . Appl . No . 13 / 732 , 521 .
`Sep . 19 , 2014 Office Action issued in U . S . Appl . No . 13 / 712 , 340 .
`Aug . 1 , 2014 Office Action issued in U . S . Appl . No . 12 / 452 , 034 .
`Jeck et al . , “ Local Ischemia Causes Carcinoma - Like Changes of the
`Rectum ” , Dis Colon Rectum . , 1996 , vol . 39 , No . 9 , pp . 1026 - 1030
`( abstract only ) .
`Jul . 24 , 2014 Office Action issued in U . S . Appl . No . 12 / 452 , 047 .
`Kozak et al . , “ Characterization of Serum Biomarkers for Detection
`of Early Stage Ovarian Cancer ” , Proteomics , 2005 , vol . 5 , pp .
`4589 - 4596 .
`Bury et al . , " Quantification of Human Serum Apolipoprotein Al by
`Enzyme Immunoassay " , Clinical Chemistry , 1985 , vol . 31 , No . 2 ,
`pp . 247 - 251 .
`Laine , Anne , “ Rocket Immunoelectrophoresis Technique or
`Electroimmunodiffusion ” , Methods in Molecular Biology , 1992 ,
`vol . 10 , pp . 201 - 205 .
`Apr . 9 , 2015 Office Action issued in U . S . Appl . No . 13 / 732 , 521 .
`Mar . 6 , 2015 Office Action issued in U . S . Appl . No . 12 / 452 , 034 .
`Feb . 23 , 2015 Office Action issued in U . S . Appl . No . 12 / 452 , 047 .
`Majander - Nordenswan et al . , “ Genomic Structure of the Human
`Ezrin Gene , ” Human Genetics , vol . 103 , 1998 , pp . 662 - 665 .
`Sep . 8 , 2015 Office Action issued in U . S . Appl . No . 14 / 701 , 002 .
`Dec . 3 , 2015 Office Action issued in U . S . Appl . No . 12 / 452 , 034 .
`Intestinal Ischemia Causes , Mayo Clinic , http : / / www . mayoclinic .
`org / diseases - conditions / intestinal - ischemia / basics / causes / con
`20023818 , accessed Nov . 9 , 2015 .
`
`Dec . 31 , 2015 Office Action issued in U . S . Appl . No . 13 / 732 , 521 .
`Abaza et al . , “ Effects of Amino Acid Substitutions Outside an
`Antigenic Site on Protein Binding to Monoclonal Antibodies of
`Predetermined Specificity Obtained by Peptide Immunization :
`Demonstration with Region 94 - 100 ( Antigenic Site 3 ) of
`Myoglobin , ” Journal of Protein Chemistry , vol . 11 , No . 5 , 1992 , pp .
`433 - 444 .
`Harig et al . , “ Induction of Cytotoxic T - cell Responses Against
`Immunoglobulin V region - Derived Peptides Modified at Human
`Leukocyte Antigen - A2 Binding Residues , ” Blood , vol . 98 , pp .
`2999 - 3005 , 2001 .
`Jan . 11 , 2016 Office Action issued in U . S . Appl . No . 13 / 712 , 340 .
`Jul . 15 , 2015 Office Action issued in U . S . Appl . No . 13 / 712 , 340 .
`Guo et al . “ Combined Use of Positive and Negative
`Immunomagnetic Isolation Followed By Real - Time RT - PCR for
`Detection of the Circulating Tumor Cells in Patients with Colorectal
`Cancers . ” J Mol . Med . , 2004 , 82 : 768 - 774 .
`Aug . 5 , 2015 Office Action issued in U . S . Appl . No . 12 / 452 , 047 .
`Mar . 24 , 2016 Office Action Issued in U . S . Appl . No . 14 / 701 , 002 .
`Mar . 3 , 2016 Office Action issued in U . S . Appl . No . 12 / 452 , 047 .
`May 25 , 2016 Office Action issued in U . S . Appl . No . 12 / 452 , 034 .
`Jul . 25 , 2016 Office Action issued in U . S . Appl . No . 13 / 712 , 340 .
`Sep . 21 , 2016 Office Action Issued in U . S . Appl . No . 14 / 701 , 002 .
`Sep . 20 , 2016 Office Action issued in U . S . Appl . No . 12 / 452 , 047 .
`Hogle , Doreen M . et al . “ Quantitation of Plasma Apolipoprotein
`A — I Using Two Monoclonal Antibodies in an Enzyme - Linked
`Immunosorbent Assay . ” Journal of Lipid Research , vol . 29 , pp .
`1221 - 1229 , 1988 .
`Mar . 15 , 2017 Office Action issued in U . S . Appl . No . 13 / 712 , 340 .
`The 1000 Genomes Project Consortium . “ A Map of Human
`Genome Variation from Population - Scale Sequencing . ” Nature ,
`2010 , vol . 467 , pp . 1061 - 1073 .
`Apr . 4 , 2017 Office Action issued in U . S . Appl . No . 12 / 452 , 047 .
`Shin et al . , “ Global Profiling of the Cell Surface Proteome of Cancer
`Cells Uncovers an Abundance of Proteins with Chaperone Func
`tion ; " The Journal of Biological Chemistry ; Feb . 28 , 2003 ; pp .
`7607 - 7616 ; vol . 278 , No . 9 ; The American Society for Biochemistry
`and Molecular Biology , Inc . ; U . S . A .
`Tomonaga et al . ; “ Identification of Altered Protein Expression and
`Post - Translational Modifications in Primary Colorectal Cancer by
`Using Agarose Two - Dimensional Gel Electrophoresis ; " Clinical
`Cancer Research ; vol . 10 , Mar . 15 , 2005 ; pp . 2007 - 2014 .
`Stierum et al . , Proteome analysis reveals novel proteins associated
`with proliferation and differentiation of colorectal cancer cell line
`Caco - 2 ; Biochemica et Biophysica Acta ; 2003 , pp . 73 - 91 ; vol . 1650 ,
`No . 1 - 2 ; Elsevier Publishing “ Human PDIA1 tryptic peptide — SEQ
`ID 33 ; " Retrieved from EBI accession No . GSP : ASS06881 ; Data
`base Accession No . ASS06881 , 2003 .
`* cited by examiner
`
`Geneoscopy Exhibit 1048, Page 4
`
`
`
`U . S . Patent
`
`Feb . 13 , 2018
`
`Sheet 1 of 12
`
`US 9 , 891 , 223 B2
`
`Serum LEI assay
`
`w
`
`CRC +
`
`s
`
`tor
`CRC
`Figure 1
`
`Serum ezrin assay
`
`45007
`4000
`3500
`3000
`52500
`LEI ( ng / ml ) . 20004
`1500
`1000
`500
`
`Ezrin ( ng / ml )
`
`CRC +
`
`CRC
`Figure 2
`
`Geneoscopy Exhibit 1048, Page 5
`
`
`
`U . S . Patent
`
`Feb . 13 , 2018
`
`Sheet 2 of 12
`
`US 9 , 891 , 223 B2
`
`Serum aminoacylase assay
`.
`
`Aminoacylase ( ng / ml )
`
`.
`
`CRC +
`
`CRC
`Figure 3
`
`Serum L - FABP assay
`:
`
`L - FABP ( ng / mi )
`f * * * * *
`
`që
`
`XLV
`
`CRC +
`
`Figure 4
`
`CRC
`
`Geneoscopy Exhibit 1048, Page 6
`
`
`
`U . S . Patent
`
`Feb . 13 , 2018
`
`Sheet 3 of 12
`
`US 9 , 891 , 223 B2
`
`Serum I - FABP assay
`
`1 - FABP ( pg / ml )
`
`CRC +
`
`Figure 5
`
`CRC
`
`Geneoscopy Exhibit 1048, Page 7
`
`
`
`U . S . Patent
`
`Feb . 13 , 2018
`
`Sheet 4 of 12
`
`US 9 , 891 , 223 B2
`
`Serum apoprotein Al assay
`( microplate ELISA )
`
`Apo A1 ( ug / ml )
`
`CRC +
`
`CRC
`
`Serum apoprotein Al assay
`( Lincoplex kit )
`15004
`
`še
`Apo A1 ( ng / ml )
`
`še
`
`e
`
`CRC +
`
`CRC
`
`Figure 6
`
`Geneoscopy Exhibit 1048, Page 8
`
`
`
`U . S . Patent
`
`Feb . 13 , 2018
`
`Sheet 5 of 12
`
`US 9 , 891 , 223 B2
`
`Serum apolipoprotein A2 assay
`
`Apo A2 ( wg / ml )
`
`* : * * * *
`
`CRC +
`Figure 7
`
`CRC
`
`Serum I - plastin assay
`
`1 - Plastin ( RFV )
`
`CRC
`
`CRC +
`
`CRC +
`Figure 8
`
`Geneoscopy Exhibit 1048, Page 9
`
`
`
`U . S . Patent
`
`Feb . 13 , 2018
`
`Sheet 6 of 12
`
`US 9 , 891 , 223 B2
`
`Serum B2 - microglobulin assay
`
`B2 - Microglobulin ( ng / ml )
`
`CRC +
`Figure 9
`
`CRC
`
`1000
`
`Serum CEA assay
`
`CEA ( ng / ml ) P? CRC +
`
`Figure 10
`
`CRC
`
`Geneoscopy Exhibit 1048, Page 10
`
`
`
`U . S . Patent
`
`Feb . 13 , 2018
`
`Sheet 7 of 12
`
`US 9 , 891 , 223 B2
`
`1000 ,
`
`CA 19 - 9 ( U / ml )
`
`PS
`
`Testosterone ( ng / ml )
`
`2 1 P
`
`Serum CA 19 - 9 assay
`
`CRC +
`Figure 11
`
`CRC
`
`Serum testosterone assay
`
`???
`CRC +
`Figure 12
`
`CRC
`
`Geneoscopy Exhibit 1048, Page 11
`
`
`
`U . S . Patent
`
`Feb . 13 , 2018
`
`Sheet 8 of 12
`
`US 9 , 891 , 223 B2
`
`Serum E - cadherin assay
`90009 . 8000
`7000 E - Cadherin ( ng / ml )
`60001
`50004
`40004
`3000
`2000
`1000
`
`CRC +
`Figure 13
`
`CRC
`
`Serum PAPI assay
`. .
`
`Ï
`
`PAP1 ( ng / ml )
`
`Ï
`
`. . .
`
`CRC +
`
`CRC
`
`Figure 14
`
`Geneoscopy Exhibit 1048, Page 12
`
`
`
`U . S . Patent
`
`Feb . 13 , 2018
`
`Sheet 9 of 12
`
`US 9 , 891 , 223 B2
`
`Serum galectin - 3 assay
`
`140007
`Galectin - 3 ( RFV )
`12000
`8000 Y . . . .
`10000
`
`CRC
`
`CRC +
`Figure 15
`
`CRC CRC
`
`Serum LDH assay
`
`2250
`2000
`1750
`1500
`LDH ( ng / ml )
`
`750
`500
`250
`
`:
`
`promet
`
`i potencia
`
`CRC +
`Figure 16
`
`CRC
`
`Geneoscopy Exhibit 1048, Page 13
`
`
`
`U . S . Patent
`
`Feb . 13 , 2018
`
`Sheet 10 of 12
`
`US 9 , 891 , 223 B2
`
`Serum Proteasome 205 assay
`100009
`
`Proteasome 205 ( ng / ml ) AO 1000
`
`CRC +
`Figure 17
`
`CRC
`
`Fecal aminoacylase assay
`
`Aminoacylase ( ng / ml )
`
`0 . 125
`
`0 . 0625
`
`Ley
`
`CRC +
`Figure 18
`
`CRC
`
`Geneoscopy Exhibit 1048, Page 14
`
`
`
`U . S . Patent
`
`Feb . 13 , 2018
`
`Sheet 11 of 12
`
`US 9 , 891 , 223 B2
`
`Fecal galectin - 3 assay
`
`=
`CRC
`CRC +
`Figure 19
`
`Fecal proteasome 205 assay
`
`Galectin - 3 ( RFV )
`
`
`
`Proteasome 205 ( RFV )
`
`CRC +
`Figure 20
`
`CRC
`
`Geneoscopy Exhibit 1048, Page 15
`
`
`
`U . S . Patent
`
`Feb . 13 , 2018
`
`Sheet 12 of 12
`
`US 9 , 891 , 223 B2
`
`12 000
`? ?
`10 000
`
`
`
`?i
`8 000
`
`6 000
`
`
`
`Tumor marker secretion by cancer cells
`60 000
`
`Caco - 2
`HT - 29
`HT29 - 16
`
`50 000
`
`40 000
`
`30 000
`
`20 000
`
`10 000
`
`-
`
`- -
`
`. .
`
`.
`
`-
`
`-
`
`. .
`
`: : . . .
`
`.
`
`! ! .
`
`.
`
`' .
`
`. . .
`
`. .
`
`.
`
`.
`
`.
`
`Gal - 3
`
`
`
`Spots per 109 cells ?i
`
`?i
`4 000
`
`j
`2 000
`
`.
`h
`
`Ezrin
`
`Figure 21
`
`Geneoscopy Exhibit 1048, Page 16
`
`
`
`US 9 , 891 , 223 B2
`
`nificant risk ( 0 . 1 % ) of perforation and bleeding of the colon
`METHOD OF ASSAYING LEUKOCYTE
`and of death ( 1 / 10000 ) , and it is also very expensive for
`ELASTASE INHIBITOR FOR THE IN VITRO
`public health . Furthermore , colonoscopy requires a very
`DIAGNOSIS OF COLORECTAL CANCER
`restrictive prior colonic preparation , which in large part
`The present invention relates to the cancerology field . 5 explains the poor compliance .
`Tumor markers that can be assayed by immunoassays
`More particularly , the subject of the present invention is a
`method for the in vitro diagnosis of colorectal cancer in a
`have for a long time been described in the context of
`human patient , by determining the presence of the Leuko
`colorectal cancer . They are in particular the carcinoembry
`cyte Elastase Inhibitor ( LEI ) in a biological sample taken
`onic antigen ( CEA ) and CA19 - 9 .
`from this patient , it being possi