Methods and compositions for perturbing gene expression in hematopoietic stem cell lineages in vivo

1. A method of generating transduced resting cells of the hematopoietic stem cell lineage that are differentiated in vivo and inducibly express an RNA encoded by an exogenous DNA integrated into the genome of the cells by at least one viral vector, comprising:

a) obtaining cells of the hematopoietic stem cell lineage;

b) transducing the cells with at least one viral vector, wherein each viral vector integrates an exogenous DNA into the genome of the cell and the integrated exogenous DNA inducibly expresses an RNA encoded by the exogenous DNA; bb

c) transplanting the transduced cells to an immunocompromised incubator animal, wherein the transplanted transduced cells reconstitute the immunocompromised incubator animal immune system;

d) selecting populations of resting reconstituted immune cells of interest from the incubator animal; and

e) transplanting the resting reconstituted immune cells of interest from the incubator animal transduced resting cells of the hematopoietic stem cell lineage that are differentiated in vivo into an experimental animal, wherein the experimental animal expresses an inducer of the inducible RNA expression before transplantation, and monitoring the transplanted cells in response to exogenous perturbation,

thereby generating transduced resting cells of the hematopoietic stem cell lineage that are differentiated in vivo and inducibly express an RNA encoded by an exogenous DNA integrated into the genome of the cells by at least one viral vector.

2. The method of claim 1 , wherein the cells of the hematopoietic stem cell lineage are murine or human.

3. The method of claim 1 , wherein the cells of the hematopoietic stem cell lineage are selected from the group consisting of hematopoietic stem cells (HSC), common myeloid progenitor cells (CMP), common lymphoid progenitor cells (CLP), committed lymphoid progenitor cells, granulocyte/macrophage progenitor cells (GMP), megakaryocyte/erythroid progenitor cells (MEP), granulocyte progenitor cells, macrophage progenitor cells, erythroid progenitor cells, megakaryocyte progenitor cells (MKP), NK cell progenitor cells (NKP), B cell progenitor cells (BCP), and T cell progenitor cells (TCP), optionbally wherein the cells of the hematopoietic stem cell lineage

i) are not terminally differentiated or post-mitotic;

ii) are not thymocytes or are not derived from the thymus; and/or

iii) are obtained from a biological source selected from the group consisting of bone marrow, umbilical cord blood, amniotic fluid, peripheral blood, and fetal liver.

4. The method of claim 1 , wherein the cells are transduced with a single viral vector.

5. The method of claim 1 , wherein the viral vector is a lentiviral vector.

6. The method of claim 1 , wherein the inducible expression is regulated using lactose operon operator (LacO) and lactose operon repressor (LacI) sequences.

7. The method of claim 1 , wherein the RNA

i) is selected from the group consisting of mRNA, antisense RNA, shRNA, siRNA, microRNA, PiwiRNA, and combinations thereof;

ii) is an shRNA; and/or

iii) is an engineered, non-naturally occurring Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) guide RNA that hybridizes with a target nucleic acid sequence of interest.

8. The method of claim 1 , wherein the viral vector further comprises a nucleic acid encoding a reporter or a nucleotide sequence encoding a Type II Cas9 protein.

9. The method of claim 8 , wherein the reporter is a fluorescent protein.

10. The method of claim 1 , wherein the incubator animal

i) is immunocompromised using lethal irradiation or chemotherapy; and/or

ii) is immunodeficient.

11. The method of claim 1 , wherein the immunocompromised incubator animal and the animal from which the cells of step a) were obtained are congenic.

12. The method of claim 1 , wherein transplantation of the transduced cells to the immunocompromised incubator animal is autologous, syngeneic, allogeneic, or xenogeneic.

13. The method of claim 1 , wherein the resting reconstituted immune cells of interest selected in step d)

i) are selected from the group consisting of terminally differentiated cells, post-mitotic cells, and/or unactivated cells;

ii) have not been exogenously stimulated to divide;

iii) are resting T cells or resting B cells; and/or

iv) are isolated.

14. The method of claim 1 , further comprising a step f) of culturing the selected cells in vitro and monitoring the selected cells in response to exogenous perturbation.

15. The method of claim 14 , wherein the exogenous perturbation is the application of an assay for testing autoimmune, allergic, vaccination, immunotolerance, cancer immunotherapy, immune exhaustion, immunological memory, immunological epitope, stem cell, hematopoietic stem cell, or immune disease responses.

16. Exogenously perturbed transduced resting cells of the hematopoietic stem cell lineage that are differentiated in vivo produced according to claim 1 .

17. Non-human animals comprising exogenously perturbed transduced resting cells of the hematopoietic stem cell lineage that are differentiated in vivo produced according to claim 1 .

18. The method of claim 1 , wherein the exogenous perturbation is the application of an assay for testing autoimmune, allergic, vaccination, immunotolerance, cancer immunotherapy, immune exhaustion, immunological memory, immunological epitope, stem cell, hematopoietic stem cell, or immune disease responses.