ES2580044T3 - Método de incremento de la función de un vector de AAV - Google Patents
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Abstract
Un método de incremento del rendimiento de empaquetamiento, de la eficacia de transducción, y/o de la eficacia de transferencia de gen de un AAV parental, comprendiendo dicho método las etapas de: (a) comparar una secuencia de cápside de AAV parental con una librería de secuencias de cápside de AAV funcional en alineamiento, en la que dicha librería comprende al menos cuatro cápsides de AAV funcional procedentes de al menos dos clados diferentes, y comprende además al menos dos secuencias procedentes de cada clado; (b) identificar al menos un singletón en la cápside de AAV parental, siendo dicho singletón un residuo de aminoácido en una posición en la cápside de AAV parental que difiere del residuo de aminoácido en la posición correspondiente de las secuencias de cápside de AAV funcional alineadas en la librería, todas las cuales tienen el mismo residuo de aminoácido en esa posición; (c) alterar el singletón en la cápside de AAV parental respecto al aminoácido localizado en la posición correspondiente en las secuencias de cápside de AAV funcional en la librería, para proporcionar una secuencia de cápside de AAV modificada, y (d) evaluar el AAV modificado en cuanto a rendimiento de empaquetamiento, eficacia de transducción, y/o eficacia de transferencia de gen incrementados, en comparación con el AAV parental.
Description
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El término “altamente conservado” significa al menos una identidad del 80%, con preferencia una identidad de al menos el 90%, y más preferiblemente, una identidad sobre el 97%. Un experto en la materia determina fácilmente la identidad recurriendo a algoritmos y programas de ordenador conocidos por los expertos en la materia.
El término “serotipo” es una distinción con respecto a un AAV que tiene una cápside que es serológicamente distinta de otros serotipos de AAV. La distintividad serológica se determina en base a la falta de reactividad cruzada entre anticuerpos con el AAV en comparación con otro AAV. La reactividad cruzada se mide típicamente en un ensayo de anticuerpo neutralizante. Para este ensayo, se genera suero policlonal frente a un AAV específico en un conejo y otro modelo de animal adecuado usando los virus adeno-asociados. En este ensayo, el suero generado frente a un AAV específico se prueba a continuación en su capacidad para neutralizar el mismo AAV (homólogo) o bien un AAV heterólogo. La dilución que alcanza una neutralización del 50% se considera el título de anticuerpo neutralizante. Si para dos AAVs, el cociente del título heterólogo dividido por el título homólogo es inferior a 16 de una manera recíproca, esos dos vectores se consideran como el mismo serotipo. A la inversa, si la relación del título heterólogo sobre el título homólogo es de 16 o superior de una manera recíproca, los dos AAVs se consideran serotipos distintos.
En un ejemplo adicional, el método puede ser usado para proporcionar AAV que tenga nuevas cápsides, incluyendo rh.20, rh23/33, rh.39, rh.46, rh.73 y rh.74. Las secuencias de rh.20 tienen la misma secuencia de aminoácido de SEQ ID Núm. 1 o una secuencia de 95 a 99% idéntica sobre la longitud completa de SEQ ID Núm. 1. La cápside de rh.32/33 tiene una secuencia de aminoácido de SEQ ID Núm. 2 o secuencias de 95% a 99% idénticas con la misma sobre la longitud completa de SEQ ID Núm. 2. Esta cápside de rh.39 tiene una secuencia de aminoácido de SEQ ID Núm. 3, o secuencias de 95% a 99% idénticas con la misma sobre la longitud completa de SEQ ID Núm. 3. La cápside de rh.46 tiene una secuencia de aminoácido de SEQ ID Núm. 4, o secuencias de 95% a 99% idénticas con la misma sobre la longitud completa de SEQ ID Núm. 4. La cápside de rh.73 tiene una secuencia de aminoácido de SEQ ID Núm. 5, o secuencias de 95% a 99% idénticas con la misma sobre la longitud completa de SEQ ID Núm. 5. La cápside de rh.74 tiene una secuencia de aminoácido de SEQ ID Núm. 6, o secuencias de 95% a 99% idénticas con la misma sobre la longitud completa de SEQ ID Núm. 6. Con preferencia, la identidad de secuencia de estas nuevas cápsides de AAV es tal que carece de cualquier singletón. Las secuencias del nuevo AAV se proporcionan en el Listado de Secuencia.
En otro ejemplo más, las nuevas secuencias de AAV incluyen las proteínas de cápside de AAV corregidas en singletón y las secuencias que codifican esas proteínas de cápside. Ejemplos de secuencias de AAV adecuadas corregidas en singletón incluyen las AAV6.1, AAV6.2, AAV6.1.2, rh.8R, rh.48.1, rh.48.2, rh.48.1.2, hu.44R1, hu.44R2, hu.44R3, hu.29R, ch.5R1, rh.67, rh.54, hu.48R1, hu.48R2, y hu.48R3. Por ejemplo, la AAV6 corregida en singletón, incluyendo las AAV6.1, AAV6.2 y AAV6.1.2., han mostrado una mejora funcional significativa sobre la secuencia de AAV6 parental.
Las proteínas particularmente deseables incluyen las proteínas de cápside de AAV, las cuales son codificadas por las secuencias de nucleótido identificadas con anterioridad. La cápside de AAV está compuesta por tres proteínas, las vp1, vp2 y vp3, las cuales son variantes de empalme alternativas. Otros fragmentos deseables de la proteína de cápside incluyen las regiones constante y variable, situadas entre regiones hipervariables (HVR). Otros fragmentos deseables de la proteína de cápside incluyen las propias HVR.
Un algoritmo desarrollado para determinar áreas de la divergencia de secuencia en AAV2 ha producido 12 regiones hipervariables (HVR) de las que 5 se superponen o son parte de las cuatro regiones variables descritas con anterioridad. [Chiorini et al., J. Virol. 73: 1309-19 (1999); Rutledge et al., J. Virol, 72: 309-319]. Usando este algoritmo y/o las técnicas de alineamiento descritas en la presente memoria, se determina la HVR de los nuevos serotipos de AAV. Por ejemplo, las HVR se localizan como sigue: HVR1, aa 146-152; HVR2, aa 182-186; HVR3, aa 262-264; HVR4, aa 381-383; HVR5, aa 450-474; HVR6, aa 490-495; HVR7, aa-500-504; HVR8, aa 514-522; HVR9, aa 534-555; HVR10, aa 581-594; HVR11, aa 658-667; y HVR12, aa 705-719 [el sistema de numeración se basa en un alineamiento que usa la vp1 de AAV2 como punto de referencia]. Usando el alineamiento proporcionado en la presente memoria, llevado a cabo usando el programa Clustal X en configuraciones por defecto, o usando otros programas de alineamiento disponibles comercialmente o públicamente en configuraciones por defecto tales como las descritas en la presente memoria, un experto en la materia puede determinar fácilmente fragmentos correspondientes de las nuevas cápsides de AAV.
Adecuadamente, los fragmentos de al menos 8 aminoácidos de longitud. Sin embargo, se pueden utilizar fácilmente fragmentos de otras longitudes deseadas. Tales fragmentos pueden ser producidos recombinantemente o mediante otros medios adecuados, por ejemplo mediante síntesis química.
El método de la invención puede ser usado también para proporcionar otras secuencias de AAV que se identifican usando la información de secuencia proporcionada en la presente memoria. Por ejemplo, dadas las secuencias proporcionadas en la presente memoria, la infecciosa puede ser aislada usando tecnología de genoma andante (Siebert, et al., 1995, Nucleic Acid Research, 23: 1087-1088, Friezner-Degen et al., 1986, J. Biol. Chem. 261: 69726985, BD Biosciences Clontech, Palo Alto, CA). El genoma andante es particularmente adecuado para identificar y aislar las secuencias adyacentes a las nuevas secuencias identificadas conforme al método de la invención. Esta técnica es también útil para aislar repeticiones terminales invertidas (ITRs) del nuevo AAV, en base a las nuevas
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marcadores seleccionables que pueden ser usados para indicar la presencia del vector en células bacterianas, tal como resistencia a ampicilina. Otros componentes del plásmido pueden incluir un origen de replicación y un amplicón, tal como el sistema de amplicón que emplea el antígeno nuclear del virus de Epstein Barr. Este sistema de amplicón, u otros componentes de amplicón similares, permiten una replicación episómica de copia alta en las células. Con preferencia, la molécula que porta el ningún es transfectada en la célula, donde puede existir transitoriamente. Alternativamente, el ningún (que porta la ITR 5’ de AAV – molécula heteróloga – ITR 3’ de AAV), puede estar integrado de forma estable en el genoma de la célula anfitrión, ya sea cromosómicamente o ya sea como episoma. En determinados ejemplos, el ningún puede estar presente en múltiples copias, opcionalmente en concatámeros de cabeza con cabeza, cabeza con cola, o cola con cola. Las técnicas de transfección adecuadas son conocidas y pueden ser fácilmente utilizadas para suministrar el ningún a la célula anfitrión.
En general, cuando se suministra el vector que comprende el ningún mediante transfección, el vector es suministrado en una cantidad que va desde aproximadamente 5 µg a aproximadamente 100 µg de ADN, aproximadamente 10 µg a aproximadamente 50 µg de ADN , aproximadamente 1 x 104 células a aproximadamente 1 x 1013 células, o aproximadamente 1 x 105 células. Sin embargo, las cantidades relativas de ADN de vector en células anfitrión pueden ser ajustadas por experto en la materia, quién puede tener en cuenta factores tales como el vector seleccionado, el método de suministro y las células anfitrión seleccionadas.
B. Secuencias rep y cap
Adicionalmente al ningún, la célula anfitrión contiene las secuencias que activan expresión de una nueva proteína de cápside de AAV (o una proteína de cápside que comprende un fragmento de las mismas) en la célula anfitrión y secuencias rep de la misma fuente que la fuente de las ITRs de AAV encontradas en el ningún, o de una fuente de complementación cruzada. Las secuencias cap y rep de AAV pueden ser obtenidas, de forma independiente, a partir de una fuente de AAV según se ha descrito en lo que antecede, y pueden ser introducidas en la célula anfitrión de cualquier manera conocida por los expertos en la materia, según se ha descrito con anterioridad. Adicionalmente, cuando se seudotipa un vector de AAV, las secuencias que codifican cada una de las proteínas rep esenciales pueden ser suministradas mediante diferentes fuentes de AAV 8por ejemplo, los AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9). Por ejemplo, las secuencias rep78/68 pueden proceder del AAV2, mientras que las secuencias rep52/40 pueden proceder del AAV8.
En un ejemplo, la célula anfitrión contiene de forma estable la proteína de cápside bajo el control de un promotor adecuado, tal como los que se han descrito con anterioridad. Más deseablemente, en este ejemplo, la proteína de cápside se expresa bajo el control de un promotor inducible. En otro ejemplo, la proteína de cápside se suministra a la célula anfitrión en trans. Cuando se suministra a la célula anfitrión en trans, la proteína de cápside puede ser suministrada por medio de un plásmido que contiene las secuencias necesarias para dirigir la expresión de la proteína de cápside seleccionada en la célula anfitrión. Más deseablemente, cuando se suministra a la célula anfitrión en trans, el plásmido que porta la proteína de cápside porta también otras secuencias requeridas para empaquetar el rAAV, por ejemplo las secuencias rep.
En otro ejemplo, la célula anfitrión contiene de forma estable las secuencias rep bajo el control de un promotor adecuado, tal como los que se han descrito en lo que antecede. Más deseablemente, en este ejemplo, las proteínas rep esenciales son expresadas bajo el control de un promotor inducible. En otro ejemplo, las proteínas rep son suministradas a la célula anfitrión en trans. Cuando se suministran a la célula anfitrión en trans, las proteínas rep pueden ser suministradas por medio de un plásmido que contiene las secuencias necesarias para dirigir la expresión de las proteínas rep seleccionadas en la célula anfitrión. Más deseablemente, cuando se suministra a la célula anfitrión en trans, el plásmido que porta la proteína de cápside porta también otras secuencias requeridas para empaquetar el rAAV, por ejemplo, las secuencias rep y cap.
Así, en un ejemplo, las secuencias rep y cap pueden ser transfectadas en la célula anfitrión sobre una molécula simple de ácido nucleico y existir establemente en las células a modo de episoma. En otra realización, las secuencias rep y cap están integradas establemente en el cromosoma de la célula. Otro ejemplo tiene las secuencias rep y cap expresadas transitoriamente en la célula anfitrión. Por ejemplo, una molécula de ácido nucleico útil para tal transfección comprende, desde 5’ hasta 3’, un promotor, un espaciador opcional intercalado entre el promotor y el sitio de inicio de la secuencia de gen rep, una secuencia de gen rep de AAV, y una secuencia de gen cap de AAV.
Opcionalmente, las secuencias rep y/o cap pueden ser suministradas sobre un vector que contiene otras secuencias de ADN que han de ser introducidas en las células anfitrión. Por ejemplo, el vector puede contener la construcción de rAAV que comprende el ningún. El vector puede comprender uno o más de los genes que codifican las funciones auxiliares, por ejemplo las proteínas adenovirales E1, E2a, y E4 ORF6, y el gen para VAI ARN.
Con preferencia, el promotor utilizado en esta construcción puede ser cualquiera de entre los promotores constitutivos, inducibles o naturales conocidos por los expertos en la materia o según se ha discutido en lo que antecede. En un ejemplo, se emplea una secuencia de promotor P5 de AAV. La selección del AAV para proporcionar cualquiera de esas secuencias no constituye una limitación de la invención.
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Véase, por ejemplo, G. Gao, et al., J. Virol. 78(12): 6381-6388 (Junio de 2004) y publicación de Patente Internacional núm. WO 2204/042397 [todas las secuencias citadas en la misma están depositadas en GenBank], y la publicación de Patente Internacional núm. WO 2005/033321, depositada el 30 de Septiembre de 2004.
Por ejemplo, con referencia a la tabla que sigue, la nomenclatura debe ser leída como sigue. Cy5R1 se refiere a la
5 secuencia de aminoácido de SEQ ID núm. 24, la cual ha sido modificada ara que contenga ácido aspártico (D) en la posición 13 de residuo de aminoácido; cy5 tiene una glicina en su secuencia de aminoácido natural en el residuo número 13. Cy5R2 se refiere a la secuencia de aminoácido de SEQ ID núm. 24, la cual ha sido modificada para contener un ácido aspártico en la posición 13 de aminoácido (glicina en la secuencia natural) y una asparagina en la posición 403 de residuo de aminoácido (ácido aspártico en la secuencia natural). Cy5R3 tiene la secuencia de
10 aminoácido de SEQ ID núm. 24, la cual ha sido modificada para tener las mismas modificaciones que la Cy5R2 y, adicionalmente, una lisina en la posición 158 (de forma natural, una asparagina) y una glutamina en la posición 161 (de forma natural, una prolina). Dada esta información, un experto en la material podría estar fácilmente capacitado para determinar las otras modificaciones de singletón que se citan en la tabla que sigue.
- Nombre
- SEQ ID No. (AAV Parental) Sitios Mutados Clado
- cy5
- 24
- Cy5R1
- G13D D
- Cy5R2
- G13D D403N D
- Cy5R3
- G13D D403N R51K D
- Cy5R4
- G13D D403N R51K N158K + P161Q D
- rh.13
- 26 D
- Rh.13R
- E538K D
- Rh37
- 40 D
- Rh37R2
- E634K T207M D
- Rh.2
- 39 E
- rh.2R
- V6511 E
- rh.8
- 41
- rh.8R
- D531E
- Rh.48
- 44
- Rh.48.1
- K217E B
- Rh.48.2
- S304N B
- Rh.48.1.2
- K217E S304N B
- Hu.44
- 45 A
- Hu.44R1
- E137K A
- Hu.44R2
- E137K P446L A
- Hu.44R3
- E137K P446L G609D A
- Rh32/33
- 2
- Hu.29
- 42 B
- Hu.29R
- G396E B
- Ch.5
- 46
- Ch.5R1
- T611I
- rh.67
- 47 D
- rh.58
- 48 S653N E
- Rh.64
- 43 E
- Rh64R1
- R697W E
- Rh64R2
- R697W V686E E
- AAV6
- 29 A
- AAV6.2
- F129L A
- AAV6.1
- K531E A
- AAV6.12
- F129L K531E A
21
Claims (1)
-
imagen1
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ES10184600.4T Active ES2525143T3 (es) | 2005-04-07 | 2006-04-07 | Cápsides de AAVrh.64 modificado, composiciones que las contienen y usos de las mismas |
ES10179330T Active ES2428218T3 (es) | 2005-04-07 | 2006-04-07 | Cápsides de AAV rh48 modificadas, composiciones que las contienen y usos de las mismas |
ES10179534.2T Active ES2525067T3 (es) | 2005-04-07 | 2006-04-07 | Método de incremento de la función de un vector de AAV |
ES10179347T Active ES2426245T3 (es) | 2005-04-07 | 2006-04-07 | Método para incrementar la funcionalidad de un vector de AAV |
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ES10179330T Active ES2428218T3 (es) | 2005-04-07 | 2006-04-07 | Cápsides de AAV rh48 modificadas, composiciones que las contienen y usos de las mismas |
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DK (2) | DK2383346T3 (es) |
ES (6) | ES2580044T3 (es) |
WO (1) | WO2006110689A2 (es) |
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