JP2021514624A - 前立腺癌の検出および治療方法 - Google Patents
前立腺癌の検出および治療方法 Download PDFInfo
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Abstract
Description
本出願は、2018年2月22日出願の米国仮出願第62/633,675号への優先権および利益を主張し、その全内容が参照により本明細書に援用される。
本出願は、EFS-Web経由でASCII形式で提出された配列表を含み、その全体が参照により本明細書に組み込まれる。2019年2月19日に作成された上記ASCIIコピーの名称は
「LBIO-005_001WO_SeqList.txt」であり、サイズは299 KBである。
本発明は前立腺癌の検出に関する。
冠詞「a」および「an」は、その冠詞の文法上の目的語の1または複数(すなわち、少なくとも1つ)を指すために本明細書で使用される。例として、「1つの要素(an element)」は、1つの要素または2つ以上の要素を意味する。
均等物
Claims (33)
- 必要とする対象において前立腺癌を検出する方法であって、
試験サンプルを、少なくとも38個のバイオマーカーの発現の検出に特異的な複数の剤と接触させることにより、対象の試験サンプルからの少なくとも38個のバイオマーカーの発現レベルを決定し、ここで前記少なくとも38個のバイオマーカーはAAMP、ANO7、AR、AR-V7、C16orf89、CHTOP、COL1A1、EDC4、FGFR2、FXYD7、FYCO1、HNRNPU、HPN、KRT15、KRT23、MAN2B2、MAX、MRPS25、NDUFS2、PPARGC1A、PPRC1、RAD23A、REPIN1、SDR39U1、SETBP1、SLC14A1、SLC18A2、SMC4、SPARC、SQLE、STRIP1、STX12、TMPRSS2_1、TMPRSS2_2、TRIM29、UNC45A、XPCおよびハウスキーピング遺伝子を含み;
前記ハウスキーピング遺伝子の発現レベルに対してAAMP、ANO7、AR、AR-V7、C16orf89、CHTOP、COL1A1、EDC4、FGFR2、FXYD7、FYCO1、HNRNPU、HPN、KRT15、KRT23、MAN2B2、MAX、MRPS25、NDUFS2、PPARGC1A、PPRC1、RAD23A、REPIN1、SDR39U1、SETBP1、SLC14A1、SLC18A2、SMC4、SPARC、SQLE、STRIP1、STX12、TMPRSS2_1、TMPRSS2_2、TRIM29、UNC45A、およびXPCの各々の発現レベルを正規化し、それによりAAMP、ANO7、AR、AR-V7、C16orf89、CHTOP、COL1A1、EDC4、FGFR2、FXYD7、FYCO1、HNRNPU、HPN、KRT15、KRT23、MAN2B2、MAX、MRPS25、NDUFS2、PPARGC1A、PPRC1、RAD23A、REPIN1、SDR39U1、SETBP1、SLC14A1、SLC18A2、SMC4、SPARC、SQLE、STRIP1、STX12、TMPRSS2_1、TMPRSS2_2、TRIM29、UNC45A、およびXPCの各々の正規化発現レベルを取得し;
前記各々の正規化発現レベルをアルゴリズムに入力してスコアを生成し;
そのスコアを第一の所定のカットオフ値と比較し;そして
前記スコアが第一の所定のカットオフ値以上である場合、対象において前立腺癌の存在を確定し、または前記スコアが第一の所定のカットオフ値未満である場合、対象において前立腺癌の非存在を確定することを含む方法。 - 対象において前立腺癌が安定であるか進行性であるかを判定する方法であって、
試験サンプルを、少なくとも38個のバイオマーカーの発現の検出に特異的な複数の剤と接触させることにより、対象の試験サンプルからの少なくとも38個のバイオマーカーの発現レベルを決定し、ここで前記少なくとも38個のバイオマーカーはAAMP、ANO7、AR、AR-V7、C16orf89、CHTOP、COL1A1、EDC4、FGFR2、FXYD7、FYCO1、HNRNPU、HPN、KRT15、KRT23、MAN2B2、MAX、MRPS25、NDUFS2、PPARGC1A、PPRC1、RAD23A、REPIN1、SDR39U1、SETBP1、SLC14A1、SLC18A2、SMC4、SPARC、SQLE、STRIP1、STX12、TMPRSS2_1、TMPRSS2_2、TRIM29、UNC45A、XPC、およびハウスキーピング遺伝子を含み;
前記ハウスキーピング遺伝子の発現レベルに対してAAMP、ANO7、AR、AR-V7、C16orf89、CHTOP、COL1A1、EDC4、FGFR2、FXYD7、FYCO1、HNRNPU、HPN、KRT15、KRT23、MAN2B2、MAX、MRPS25、NDUFS2、PPARGC1A、PPRC1、RAD23A、REPIN1、SDR39U1、SETBP1、SLC14A1、SLC18A2、SMC4、SPARC、SQLE、STRIP1、STX12、TMPRSS2_1、TMPRSS2_2、TRIM29、UNC45A、およびXPCの各々の発現レベルを正規化し、それによりAAMP、ANO7、AR、AR-V7、C16orf89、CHTOP、COL1A1、EDC4、FGFR2、FXYD7、FYCO1、HNRNPU、HPN、KRT15、KRT23、MAN2B2、MAX、MRPS25、NDUFS2、PPARGC1A、PPRC1、RAD23A、REPIN1、SDR39U1、SETBP1、SLC14A1、SLC18A2、SMC4、SPARC、SQLE、STRIP1、STX12、TMPRSS2_1、TMPRSS2_2、TRIM29、UNC45A、およびXPCの各々の正規化発現レベルを取得し;
前記各々の正規化発現レベルをアルゴリズムに入力してスコアを生成し;
そのスコアを第一の所定のカットオフ値と比較し;そして
前記スコアが第一の所定のカットオフ値以上である場合、前立腺癌が進行性であると判定し、前記スコアが第一の所定のカットオフ値未満である場合、前立腺癌が安定であると判定することを含む方法。 - 対象において前立腺癌が低悪性度であるか高悪性度であるかを判定する方法であって、
試験サンプルを少なくとも38個のバイオマーカーの発現の検出に特異的な複数の薬剤と接触させることにより、対象の試験サンプルからの少なくとも38個のバイオマーカーの発現レベルを決定し、ここで前記少なくとも38個のバイオマーカーはAAMP、ANO7、AR、AR-V7、C16orf89、CHTOP、COL1A1、EDC4、FGFR2、FXYD7、FYCO1、HNRNPU、HPN、KRT15、KRT23、MAN2B2、MAX、MRPS25、NDUFS2、PPARGC1A、PPRC1、RAD23A、REPIN1、SDR39U1、SETBP1、SLC14A1、SLC18A2、SMC4、SPARC、SQLE、STRIP1、STX12、TMPRSS2_1、TMPRSS2_2、TRIM29、UNC45A、XPC およびハウスキーピング遺伝子を含み;
前記ハウスキーピング遺伝子の発現レベルに対してAAMP、ANO7、AR、AR-V7、C16orf89、CHTOP、COL1A1、EDC4、FGFR2、FXYD7、FYCO1、HNRNPU、HPN、KRT15、KRT23、MAN2B2、MAX、MRPS25、NDUFS2、PPARGC1A、PPRC1、RAD23A、REPIN1、SDR39U1、SETBP1、SLC14A1、SLC18A2、SMC4、SPARC、SQLE、STRIP1、STX12、TMPRSS2_1、TMPRSS2_2、TRIM29、UNC45AおよびXPCの各々の発現レベルを正規化し、それによりAAMP、ANO7、AR、AR-V7、C16orf89、CHTOP、COL1A1、EDC4、FGFR2、FXYD7、FYCO1、HNRNPU、HPN、KRT15、KRT23、MAN2B2、MAX、MRPS25、NDUFS2、PPARGC1A、PPRC1、RAD23A、REP1、REPIN1 、SETBP1、SLC14A1、SLC18A2、SMC4、SPARC、SQLE、STRIP1、STX12、TMPRSS2_1、TMPRSS2_2、TRIM29、UNC45AおよびXPCの各々の正規化発現レベルを取得し;
前記各々の正規化発現レベルをアルゴリズムに入力してスコアを生成し;
そのスコアを第一の所定のカットオフ値と比較し;そして
前記スコアが第一の所定のカットオフ値以上である場合、前立腺癌が高悪性度であると判定し、または前記スコアが第一の所定のカットオフ値未満である場合、前立腺癌が低悪性度であると判定することを含む方法。 - 前立腺癌を有する対象において手術の完全性を決定する方法であって、
試験サンプルを、少なくとも38個のバイオマーカーの発現の検出に特異的な複数の薬剤と接触させることにより、対象の試験サンプルからの少なくとも38個のバイオマーカーの発現レベルを決定し、ここで前記少なくとも38個のバイオマーカーはAAMP、ANO7、AR、AR-V7、C16orf89、CHTOP、COL1A1、EDC4、FGFR2、FXYD7、FYCO1、HNRNPU、HPN、KRT15、KRT23、MAN2B2、MAX、MRPS25、NDUFS2、PPARGC1A、PPRC1、RAD23A、REPIN1、SDR39U1、SETBP1、SLC14A1、SLC18A2、SMC4、SPARC、SQLE、STRIP1、STX12、TMPRSS2_1、TMPRSS2_2、TRIM29、UNC45A、XPC およびハウスキーピング遺伝子を含み;
前記ハウスキーピング遺伝子の発現レベルに対してAAMP、ANO7、AR、AR-V7、C16orf89、CHTOP、COL1A1、EDC4、FGFR2、FXYD7、FYCO1、HNRNPU、HPN、KRT15、KRT23、MAN2B2、MAX、MRPS25、NDUFS2、PPARGC1A、PPRC1、RAD23A、REPIN1、SDR39U1、SETBP1、SLC14A1、SLC18A2、SMC4、SPARC、SQLE、STRIP1、STX12、TMPRSS2_1、TMPRSS2_2、TRIM29、UNC45AおよびXPCの各々の発現レベルを正規化し、それによりAAMP、ANO7、AR、AR-V7、C16orf89、CHTOP、COL1A1、EDC4、FGFR2、FXYD7、FYCO1、HNRNPU、HPN、KRT15、KRT23、MAN2B2、MAX、MRPS25、NDUFS2、PPARGC1A、PPRC1、RAD23A、REP1、REPIN1 、SETBP1、SLC14A1、SLC18A2、SMC4、SPARC、SQLE、STRIP1、STX12、TMPRSS2_1、TMPRSS2_2、TRIM29、UNC45AおよびXPCの各々の正規化発現レベルを取得し;
前記各々の正規化発現レベルをアルゴリズムに入力してスコアを生成し;
そのスコアを第一の所定のカットオフ値と比較し;そして
前記スコアが第一の所定のカットオフ値以上である場合、前立腺癌が完全に除去されていないと判定し、または前記スコアが第一の所定のカットオフ値未満である場合、前立腺癌が完全に除去されていると判定することを含む方法。 - 前立腺肥大を有する対象において良性前立腺肥大を前立腺癌から区別する方法であって、
試験サンプルを、少なくとも38個のバイオマーカーの発現の検出に特異的な複数の薬剤と接触させることにより、対象の試験サンプルからの少なくとも38個のバイオマーカーの発現レベルを決定し、ここで前記少なくとも38個のバイオマーカーはAAMP、ANO7、AR、AR-V7、C16orf89、CHTOP、COL1A1、EDC4、FGFR2、FXYD7、FYCO1、HNRNPU、HPN、KRT15、KRT23、MAN2B2、MAX、MRPS25、NDUFS2、PPARGC1A、PPRC1、RAD23A、REPIN1、SDR39U1、SETBP1、SLC14A1、SLC18A2、SMC4、SPARC、SQLE、STRIP1、STX12、TMPRSS2_1、TMPRSS2_2、TRIM29、UNC45A、XPC およびハウスキーピング遺伝子を含み;
前記ハウスキーピング遺伝子の発現レベルに対してAAMP、ANO7、AR、AR-V7、C16orf89、CHTOP、COL1A1、EDC4、FGFR2、FXYD7、FYCO1、HNRNPU、HPN、KRT15、KRT23、MAN2B2、MAX、MRPS25、NDUFS2、PPARGC1A、PPRC1、RAD23A、REPIN1、SDR39U1、SETBP1、SLC14A1、SLC18A2、SMC4、SPARC、SQLE、STRIP1、STX12、TMPRSS2_1、TMPRSS2_2、TRIM29、UNC45AおよびXPCの各々の発現レベルを正規化し、それによりAAMP、ANO7、AR、AR-V7、C16orf89、CHTOP、COL1A1、EDC4、FGFR2、FXYD7、FYCO1、HNRNPU、HPN、KRT15、KRT23、MAN2B2、MAX、MRPS25、NDUFS2、PPARGC1A、PPRC1、RAD23A、REP1、REPIN1 、SETBP1、SLC14A1、SLC18A2、SMC4、SPARC、SQLE、STRIP1、STX12、TMPRSS2_1、TMPRSS2_2、TRIM29、UNC45AおよびXPCの各々の正規化発現レベルを取得し;
前記各々の正規化発現レベルをアルゴリズムに入力してスコアを生成し;
そのスコアを第一の所定のカットオフ値と比較し;そして
前記スコアが第一の所定のカットオフ値以上である場合、対象における前立腺癌の存在を確定し、または前記スコアが第一の所定のカットオフ値未満である場合、対象における良性前立腺肥大の存在を確定することを含む方法。 - 前立腺癌を有する対象の一次療法に対する反応を評価する方法であって、
(1) 第一の時点で:
(a) 試験サンプルを、少なくとも38個のバイオマーカーの発現の検出に特異的な複数の薬剤と接触させることにより対象の試験サンプルからの少なくとも38個のバイオマーカーの発現レベルを決定し、ここで少なくとも38個のバイオマーカーはAAMP、ANO7、AR、AR-V7、C16orf89、CHTOP、COL1A1、EDC4、FGFR2、FXYD7、FYCO1を含むHNRNPU、HPN、KRT15、KRT23、MAN2B2、MAX、MRPS25、NDUFS2、PPARGC1A、PPRC1、RAD23A、REPIN1、SDR39U1、SETBP1、SLC14A1、SLC18A2、SMC4、SPARC、SQLE、STRIP1、STX12、TMPRSS2_2、TRPR2、TMPRSS2 XPC、およびハウスキーピング遺伝子を含み;
(b) 前記ハウスキーピング遺伝子の発現レベルに対してAAMP、ANO7、AR、AR-V7、C16orf89、CHTOP、COL1A1、EDC4、FGFR2、FXYD7、FYCO1、HNRNPU、HPN、KRT15、KRT23、MAN2B2、MAX、MRPS25、NDUFS2、PPARGC1A、PPRC1、RAD23A、REPIN1、SDR39U1、SETBP1、SLC14A1、SLC18A2、SMC4、SPARC、SQLE、STRIP1、STX12、TMPRSS2_1、TMPRSS2_2、TRIM29、UNC45A、およびXPCの各々の発現レベルを正規化することにより、AAMP、ANO7、AR、AR-V7、C16orf89、CHTOP、COL1A1、EDC4、FGFR2、FXYD7、FYCO1、HNRNPU、HPN、KRT15、KRT23、MAN2B2、MAX、MRPS25、NDUFS2、PPARGC1A、PPRC1、RAD23A、REP1、REPIN1 、SETBP1、SLC14A1、SLC18A2、SMC4、SPARC、SQLE、STRIP1、STX12、TMPRSS2_1、TMPRSS2_2、TRIM29、UNC45A、およびXPCの各々の正規化発現レベルを取得し;
(c) 前記各々の正規化発現レベルをアルゴリズムに入力して第一のスコアを生成し;
(2) 第二の時点であって、第一の時点の後でありそして対象に第一の治療法を施した後である第二の時点で:
(d) 少なくとも38個のバイオマーカーの発現レベルの検出に特異的な複数の剤と試験サンプルとを接触させることにより、対象の試験サンプルからの少なくとも38個のバイオマーカーの発現レベルを決定し;
(e) 前記ハウスキーピング遺伝子の発現レベルに対してAAMP、ANO7、AR、AR-V7、C16orf89、CHTOP、COL1A1、EDC4、FGFR2、FXYD7、FYCO1、HNRNPU、HPN、KRT15、KRT23、MAN2B2、MAX、MRPS25、NDUFS2、PPARGC1A、PPRC1、RAD23A、REPIN1、SDR39U1、SETBP1、SLC14A1、SLC18A2、SMC4、SPARC、SQLE、STRIP1、STX12、TMPRSS2_1、TMPRSS2_2、TRIM29、UNC45AおよびXPCの各々の発現レベルを正規化し、それによりAAMP、ANO7、AR、AR-V7、C16orf89、CHTOP、COL1A1、EDC4、FGFR2、FXYD7、FYCO1、HNRNPU、HPN、KRT15、KRT23、MAN2B2、MAX、MRPS25、NDUFS2、PPARGC1A、PPRC1、RAD23A、REPIN1、SDR39U1、SETBP1、SLC14A1、SLC18A2、SMC4、SPARC、SQLE、STRIP1、STX12、TMPRSS2_1、TMPRSS2_2、TRIM29、UNC45A、およびXPCの各々の正規化発現レベルを取得し;
(f) 前記各々の正規化発現レベルをアルゴリズムに入力して第二のスコアを生成し;
(3) 第一のスコアを第二のスコアと比較し;そして
(4) 第二のスコアが第一のスコアと比較して有意に減少している場合に対象を一次療法に反応すると判定し、第二のスコアが第一のスコアと比較して有意には減少しない場合に対象を一次療法に反応しないと判定することを含む方法。 - 必要とする対象において前立腺癌を治療する方法であって、
試験サンプルを、少なくとも38個のバイオマーカーの発現の検出に特異的な複数の剤と接触させることにより、対象の試験サンプルからの少なくとも38個のバイオマーカーの発現レベルを測定し、ここで少なくとも38個のバイオマーカーはAAMP、ANO7、AR、AR-V7、C16orf89、CHTOP、COL1A1、EDC4、FGFR2、FXYD7、FYCO1、HNRNPU、HPN、KRT15、KRT23、MAN2B2、MAX、MRPS25、NDUFS2、PPARGC1A、PPRC1、RAD23A、REPIN1、SDR39U1、SETBP1、SLC14A1、SLC18A2、SMC4、SPARC、SQLE、STRIP1、STX12、TMPRSS2_1、TMPRSS2_2、TRIM29、UNC45A、XPCおよびハウスキーピング遺伝子を含み;
前記ハウスキーピング遺伝子の発現レベルに対してAAMP、ANO7、AR、AR-V7、C16orf89、CHTOP、COL1A1、EDC4、FGFR2、FXYD7、FYCO1、HNRNPU、HPN、KRT15、KRT23、MAN2B2、MAX、MRPS25、NDUFS2、PPARGC1A、PPRC1、RAD23A、REPIN1、SDR39U1、SETBP1、SLC14A1、SLC18A2、SMC4、SPARC、SQLE、STRIP1、STX12、TMPRSS2_1、TMPRSS2_2、TRIM29、UNC45AおよびXPC の各々の発現レベルを正規化し、それによりAAMP、ANO7、AR、AR-V7、C16orf89、CHTOP、COL1A1、EDC4、FGFR2、FXYD7、FYCO1、HNRNPU、HPN、KRT15、KRT23、MAN2B2、MAX、MRPS25、NDUFS2、PPARGC1A、PPRC1、RAD23A、REPIN1、SDR39U1、SETBP1、SLC14A1、SLC18A2、SMC4、SPARC、SQLE、STRIP1、STX12、TMPRSS2_1、TMPRSS2_2、TRIM29、UNC45AおよびXPC の各々の正規化発現レベルを取得し;
前記各々の正規化発現レベルをアルゴリズムに入力してスコアを生成し;
そのスコアを第一の所定のカットオフ値と比較し;そして
前記スコアが第一の所定のカットオフ値以上である場合、対象に少なくとも一次療法を施し、または前記スコアが第一の所定のカットオフ値未満である場合、対象において前立腺癌の不在を確定することを含む方法。 - 前記ハウスキーピング遺伝子が、ALG9、SEPN、YWHAQ、VPS37A、PRRC2B、DOPEY2、NDUFB11、ND4、MRPL19、PSMC4、SF3A1、PUM1、ACTB、GAPD、GUSB、RPLP0、TFRC、MORF4L1、18S、PPIA、PGK1、RPL13A、B2M、YWHAZ、SDHA、HPRT1、TOX4、およびTPT1から成る群より選択される、請求項1に記載の方法。
- 前記ハウスキーピング遺伝子がTOX4である、請求項8に記載の方法。
- 前記第一の所定のカットオフ値が0〜100%のスケールで少なくとも33%である、請求項1〜5または7のいずれか一項に記載の方法。
- 前記第一の所定のカットオフ値が0〜100%のスケールで少なくとも50%である、請求項10に記載の方法。
- 少なくとも92%の感度を有する、請求項1〜7のいずれか一項に記載の方法。
- 少なくとも95%の特異度を有する、請求項1〜7のいずれか一項に記載の方法。
- 前記少なくとも38個のバイオマーカーの少なくとも1つがRNA、cDNAまたはタンパク質である、請求項1〜13のいずれか一項に記載の方法。
- 前記バイオマーカーがRNAであり、該RNAが逆転写されてcDNAを産生し、産生されたcDNAの発現レベルが検出される、請求項14に記載の方法。
- 前記バイオマーカーの発現レベルが、該バイオマーカーと標識プローブまたはプライマーとの間で複合体を形成させることによって検出される、請求項14に記載の方法。
- 前記第一の所定のカットオフ値が、腫瘍性疾患をもたないかまたは腫瘍性疾患と診断されていない対象から得られた複数の参照サンプルから導出される、請求項1〜16のいずれか一項に記載の方法。
- 前記腫瘍性疾患が前立腺癌である、請求項17に記載の方法。
- 前記試験サンプルが血液、血清、血漿または腫瘍性組織である、請求項1〜16のいずれか一項に記載の方法。
- 各参照サンプルが血液、血清、血漿または非腫瘍性組織である、請求項17に記載の方法。
- 前立腺癌を有すると判定された対象を、少なくとも1つの治療法を施すことによって治療することを更に含み、ここで前記少なくとも1つの治療法が積極的監視、手術、放射線療法、凍結療法、ホルモン療法、化学療法、ワクチン療法、骨転移治療、またはその組み合わせを含む、請求項1〜5のいずれか一項に記載の方法。
- 前記少なくとも1つの治療法がホルモン療法を含む場合、そのホルモン療法がアンドロゲン抑制療法を含む、請求項21に記載の方法。
- 前記少なくとも1つの治療法が化学療法を含む場合、その化学療法がドセタキセル、カバジタキセル、ミトキサントロン、エストラムスチンまたはその組み合わせを含む、請求項21に記載の方法。
- 前記少なくとも1つの治療法がワクチン療法を含む場合、そのワクチン療法がシプロイセルTを含む、請求項21に記載の方法。
- 前記少なくとも1つの治療法が骨転移治療を含む場合、その骨転移治療がビスホスホネート、デノスマブ、コルチコステロイドまたはその組み合わせを含む、請求項21に記載の方法。
- 前記アルゴリズムがXGB、RF、glmnet、cforest、CART、treebag、knn、nnet、SVM-ラジアル、SVM-線形、NBまたはmlpである、請求項1〜25のいずれか一項に記載の方法。
- 前記アルゴリズムがXGBである、請求項26に記載の方法。
- 前記第一の時点が対象への一次療法の施行前である、請求項6に記載の方法。
- 前記第一の時点が対象への一次療法の施行後である、請求項6に記載の方法。
- 前記第二のスコアが第一のスコアより少なくとも25%低い場合に、第二のスコアが第一のスコアと比較して有意に減少している、請求項6に記載の方法。
- 前記第二のスコアが第一のスコアに比較して有意に減少している場合、対象に一次療法の施行を続けることを更に含む、請求項6または28〜30のいずれか一項に記載の方法。
- 前記第二のスコアが第一のスコアに比較して有意に減少していない場合、対象への一次療法の施行を中止することを更に含む、請求項6または28〜30のいずれか一項に記載の方法。
- 前記第二のスコアが第一のスコアに比較して有意に減少していない場合、対象に二次療法を施すことを更に含む、請求項6、30または32のいずれか一項に記載の方法。
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