METHODS AND COMPOSITIONS FOR TREATING CANCERS
20230338494 · 2023-10-26
Inventors
- Frank Griscelli (Villejuif, FR)
- Ali Turhan (Villejuif, FR)
- Annelise Bennaceur Griscelli (Villejuif, FR)
- Christophe Desterke (Villejuif, FR)
Cpc classification
A61K39/39
HUMAN NECESSITIES
A61P35/00
HUMAN NECESSITIES
International classification
A61K39/00
HUMAN NECESSITIES
A61P35/00
HUMAN NECESSITIES
Abstract
The inventors provide a new therapeutic strategy to treat cancers expressing embryonic antigens. Accordingly, the present invention relates to a method of treating a subject suffering from a cancer comprising a step of administration simultaneously, separately or sequentially to said subject a therapeutically amount of i) a population of derived engineered fetal stem cells carrying cancer associated fetal neo-antigen and ii) a compound selected from a group which activates immune response, as a combined preparation.
Claims
1. A method for producing a population of inactivated cells, comprising: a. differentiation of a population of pluripotent stem cells towards the lineage pathway pertaining to a specific cancer, wherein the pluripotent stem cells have optionally been expanded in presence of a mutagenic agent or de-differentiation of adult cells, b. expansion of the cells thus differentiated, c. optionally exposition to a mutagenic agent during expansion, to induce mutagenesis of genes in cells of said population, d. verification that at least 70% of the cells of the population express markers that are expressed by fetal cells, and are depleted in markers which are characteristic of pluripotency, e. optionally, verification that the cells of the population express at least one tumor associated antigen (TAA) or neo-antigen that is present in the cancer cells, and f. inactivation of the cells, in order for the cells to lose their ability to divide.
2. The method of claim 1, wherein the mutagenic agent is selected from the group consisting of chemical mutagenic agents and radiation mutagenic agent (X-Ray, UV radiation).
3. The method of claim 1, wherein the mutagenic agent is selected from the group consisting of ENU, reactive oxygen species, deaminating agents, polycyclic aromatic hydrocarbons, aromatic amines and sodium azide.
4. The method of claim 3, wherein the mutagenic agent is ENU.
5. The method of claim 1, wherein the cells are expanded after differentiation in the presence of an agent that improves presentation of antigens through the MHC I pathway.
6. The method of claim 5, wherein the agent that improves presentation of antigens through the MHC I pathway is a histone deacetylase inhibitor (HDACi).
7. The method of claim 6, wherein the HDACi is valproic acid.
8. The method of claim 1, wherein the pluripotent stem cells are induced pluripotent stem cells (iPSCs).
9. The method of claim 1, wherein the cells differentiated and expanded form an organoid.
10. The method of claim 7, wherein the inactivated cells have been obtained by disrupting the 3D structure of the organoid.
11. The method of claim 1, further comprising freezing or lyophilizing the inactivated cells.
Description
FIGURES
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[0422] The affected 123 genes in the “blast crisis in dish” model integrated in AML patient blast transcriptome analysis predict a prognosis discrimination (log rank p value=1E-4).
[0423] Small grey spots : G2 good prognosis AML. Large black spots: G1 bad prognosis AML.
[0424] Abscissa: first dimension, as expressed in arbitrary units of factorial analysis (principal component analysis); Ordinate: second dimension, as expressed in arbitrary units of factorial analysis (principal component analysis).
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[0426] Upper curve: Good prognosis AML (G2). Lower curve: Bad prognosis AML (G1).
[0427] Abscissa: Probability of overall survival; Ordinate: time, as expressed in months.
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[0431] Left panel: Normalization of the RFI MEAN to the DMSO control of iPSC (PB32) treated with 4 different HDACi using a MHC I HLA-ABC monoclonal antibody coupled with APC. Ordinate: RF/MHC1 fold of fluorescence.
[0432] Right panel: % of MHC1 expression normalized to the DMSO control of a CML-derived IPSCs (PB32) exposed to 4 different HDACi. Ordinate: % of positive APC fluorescence normalized to DMSO control.
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[0434] Left panel: Normalization of the RFI MEAN to the DMSO control of IPSC (PB33) treated with 4 different HDACi using a MHC I HLA-ABC monoclonal antibody coupled with APC. Ordinate: RF/MHC1 fold of fluorescence.
[0435] Right panel: % of MHC1 expression normalized to the DMSO control of a IPSCs (PB33) exposed to 4 different HDACi. Ordinate: % of positive APC fluorescence normalized to DMSO control.
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[0437] Abscissa: first dimension, as expressed in arbitrary units of factorial analysis (principal component analysis); Ordinate: second dimension, as expressed in arbitrary units of factorial analysis (principal component analysis).
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[0440] Expression of iPSC-enriched genes by quantitative RT-PCR in EndoPCs in comparison to murine iPSCs and to primary murine C57BL/6 fibroblasts. Seven different factors including OCT4, SOX2, NANOG, LIN28, CMYC, KLF4 and Alkaline phosphatase (ALP) were quantified and subsequently normalized to the mRNA level found in miPSCs (value of 100). Ordinate: relative expression of mRNA, as expressed in arbitrary units. Abscissa, groups of bars from left to right: (i) m Fibroblasts; (ii) EndoPCs; (iii) miPSCs. For each group of bars, from left to right: (i) OCT4, (ii) SOX2, (iii) NANOG, (iv) LIN 28, (v) cMYC, (vi) KLF4, (vii) ALP.
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[0442] Left panel: mESC (CK35); Right panel: EndoPCs. Ordinate: fluorescence signal intensity (log), as expressed in arbitrary units. Abscissa: amplitude of the signal.
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[0444] Pan02 cells were incubated with (raws from left to right) : (i) no IL-6, no Jak inhibitor, (ii) no IL-6, no Jak inhibitor, (iii) IL-6, no Jak inhibitor, (iv) IL-6, no Jak inhibitor, (v) IL-6, Jak inhibitor, (vi) IL-6, Jak inhibitor. Lines, from top to bottom: (i) pStat 3 Y705, (ii) Stat 3, (iii) β-actin.
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[0446] Ordinate: percent survival; Abscissa: time, as expressed in days.
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[0448] Ordinate: Region Of Interest (ROI) surface intensity, as expressed in arbitrary units.
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EXAMPLES
Example 1
Characterization of Fetal Antigens From Derived Renal Oragnoids Carrying c-MET Mutation.
[0450] We have generated an iPSC line with hereditary c-MET mutation by reprogramming blood cells from a donor with type 1 papillary renal carcinoma (PRCC) using Sendai virus-mediated pluripotent gene transfer. We designed a 3D-culture system to induce the differentiation of c-MET iPSC into renal organoids, thus composed of fetal cells. We demonstrated that iPSC-derived renal organoids expressed markers of renal progenitors with glomerular and tubular structures. Transmission electron microscopy analyses confirmed the presence of tight junctions in tubular structures. Gene-array analysis was performed in renal organoids (EB56) and parental pluripotent stem cells (PB56). Supervised analysis by ranking products algorithm between the iPSC with c-met mutation (PB56) and derived fetal renal organoids containing committed nephron progenitors allowed to identify 196 differential expressed gene probes: 148 were found down regulated in EB56, as compared to IPSCs PB56 and a minority of them, 48 were found up regulated in EB56 as compared to IPSCs PB56 (
[0451] Machine learning supervised by c-MET status performed on PRCC RNAseq samples allowed to characterize 1333 predictive genes with a minimum error of misclassification. Meta-analysis between c-MET-mutated IPSCs signature and PRCC signature revealed a significant enrichment of IPSCs profile as predictive of c-MET mutated PRCC tumor status (Fold of enrichment: 5.68; p-value<2.2E-16, (
[0452] These results confirm that fetal renal organoids derived from a c-MET-mutated IPSCs are relevant fetal cells to model papillary renal cell carcinoma expressing at least 77 common cancer associated fetal neo-antigens allowing to prepare cancer cell vaccine product or cell extract for renal carcinoma associated with c-met mutation.
Example 2
Common Mutanome in Derived Fetal Hematopoietic Stem Cells With Acute Myeloid Leukemia (AML).
[0453] We developed an induced pluripotent cell (IPSCs) model of chronic myeloid leukemia to model progression of the disease. BCR-ABL fusion protein expression increases during chronic myeloid leukemia progression and this phenomenon is well known to induce genomic instability and promote apparition of secondary genomic events compatible with blast transformation leading to acute myeloid leukemia.
[0454] Human pluripotent stem cells carrying the Bcr-Abl oncogene were cultured and expanded with mutagen agents (ENU) to induce genomic instability and enhance somatic mutations during the successive divisions. Committed hematopoietic progenitor fetal cells were produced by using the technology of embryonic bodies (EB) in the presence of growth and morphogens. Embryonic bodies (EBs) at day 2-3, corresponding to hemangioblast stage, blastic colonies, and EBs at Day 4- 20 were analyzed. Hematopoietic EBs were characterized for their hematopoietic markers CD34, C43, CD45, by FACS analysis. Hematopoietic potential was confirmed by the colony forming assays by counting the number of CFC and analyzing the type of CFC. We show that ENU can induce genomic instability and allowed to reproduce a blast crisis in the dish, with a renewal blast hematopoietic myeloid progenitors in culture. The presence of VPA in cultured hematopoietic EBs allowed to enhance the amount of CMH Class I and with a lower efficiency for the CMH Class II as described by FACS analysis (
[0455] Gene array, exome and CGH array was performed on derived fetal hematopoietic EBs progenitors at Day 16, obtained from IPSC at early passage (> 20 Passages) and IPSC at late passages (> 100 Passage) after exposing to ENU. Whole exome analysis was performed on DNA of parental IPSCs as compared to differentiated Embryonic Bodies with or without genomic instability, and EBs from IPSC cultured at early and late passages. Next generation sequencing was performed on Illumina Technologies by pair end sequencing and using CASAVA pipeline aligned on HG19 genome version. Genomic variants were selected with a frequency less than 0.01 for the general human population in EXAC database.
[0456] We compared genomic variations in hematopoietic EBs to the parental IPSCs with a difference of allele frequence more 0.10. As shown in
[0457] On the other hand, after exposition to ENU, IPSC (<20 passages and > 100 passages) were differentiated into hematopoietic fetal stem cells (EBs) and mutanome signature was compared with derived EBs from parental IPSC without ENU. ENU has been shown to induce genomic instability in hematopoietic EBs a high number of genomic variations and somatic mutations. Importantly, we found similar mutations in derived hematopoietic EBs from IPSC at early passages and late passages, indicating a stable mutanome during scalable expansion of iPSC (
[0458] A total of 123 genomic variations were found in EBs from IPSCs treated by ENU comprising coding missense and stop gained and frameshift. These genomic variations are commonly expressed and reported in primary acute leukemia with at least: ARHGEF10L:221656_s_at, TRIM66:213748_at, ARHGEF10L:1570511_at, NKAIN3:1553241_at, ITGA7:216331_at, GGT1:211417_x_at, PDZD7:220555_s_at, MUC4:235055_x_at, GGT1:215603_x_at, MUC2:204673_at, NECAB3:210720_s_at, GGT1:208284_x_at, MNT:204206_at, GGT1:207131x _at, ITGA7:209663_s_at, BTNL9:230992_at, FNBP1:230086_at, GLTSCR1:219445_at, NECAB3:223954_x_at, COPZ2:219561_at, ZFP36:201531_at, MIB2:241541_at, ABCC12:1553410_a_at, IGFN1:1563098_at, LRRK2:229584_at, MNT:236749_at, RIN3:220439_at, GGT1:233837_at, KIF5C:1557089_at, ANK2:202921_s _at, HDAC7:236326_at, MUC20:1558220_at, SDCCAG3:230058_at, GGT1:209919_x_at, RIN3:1562005_at, DNAI1:233195_at, DNAI1:220125_at, BTNL9:241496_at, ABTB2:232624_at, MC2R:208568_at, DOCK4:244840_x_at, FSD1L:230904_at, HDAC7:217937s_at, CRP:205753_at, PPP1R3A:206895_at, SLC22A17:221106_at, PITPNM1:203826_s_at, BTBD7:224943_at, MIB2:241377_s_at, A2M:1558450_at, CTDSP2:208735s_at, IFNA14:208182_x_at, KIF5C:203130_s_at, MUC20:243774_at, THNSL2:239949_at, KIF5C:203129_s_at, GTF3C3:1555439_at, NRXN1:1558708_at, MED26:1559593_a_at, FNBP1:230389_at, TMCO3:230317_x_at, PPP1R3A:211169_s_at, ING1:208415_x_at, ZNF292:1562991_at, RBL1:1555004_a_at, CD109:239719_at, CD109:229900_at, FOXRED2:233250_x_at, PLIN2:209122_at, ZNF85:1554445_at, SESN1:218346_s_at, TMCO3:220240_s_at, MED26:231724_at, CD109:226545_at, CENPE:205046_at, ING1:210350_x_at, TMCO3:226050_at, FOXRED2:220707_s_at, GTF3C3:222604_at, BTBD7:224945_at, CDC27:217881_s_at, STOM:201061_s_at, CDC27:217880_at, ZNF317:1555337_a_at, TET1:228906_at, LRBA:214109_at, MED4:217843_s_at, CDC27:217879_at, ZNF317:225296_at, ZNF292:212366_at, MED4:222438_at, BCR:226602_s_at, STOM:201060_x_at, BCR:202315_s_at, ZNF85:206572 _x_at, BCR:217223_s_at, HPRT1:202854_at, LRBA:212692_s_at, GTF3C3:218343_s_at, NASP:201969_at, NASP:201970_s_at, MSH2:209421_at.
[0459] These affected 123 genes in the “blast crisis in dish” model integrated in AML patient blast transcriptome analysis predict a prognosis discrimination (p-value=0.00000187,
[0460] These results confirm that neo-antigens affected by genomic variations in IPSCs-derived hematopoietic EBs reproduce similar fetal neo-antigens expressed in AML. Vaccine products such as irradiated cells or cell extract (AND, ARN, Proteins), or neo-epitope and peptides preparation can thus be produced from this modified engineered fetal hematopoietic cells. This relevant fetal hematopoietic cell can thus be used to stimulate the immune response against acute leukemia by the vaccination treatment strategy.
TABLE-US-00001 IPSCs BCR-ABL EB in Hematopoieti c differentiatio n EB in Hematopoietic differentiation early passage with genetic instability EB in Hematopoietic differentiation late passage with genetic instability stop gained 0 4 3 missense 9 77 88 frameshift 5 5 5 SUM of alterations 14 86 96 number of genes affected 14 84 92 total affected genes n =123
[0461] Table 1: Summary of genomic modifications detected by exome sequencing as compared to the parental BCR-ABL Positive IPSCs: by row numbers of different types of genomics variations were described for each process samples (hematopoietic EB : embyonic bodies) as compared to the genome of the parental IPSCs from which they were derived.
Example 3
Common Gene Expression in Derived Fetal Lung Organoid With Lung Cancer
[0462] We investigated a transcriptome analysis of lung organoid derived from IPSCs (and thus composed of fetal cells) in order to predict lung cancer signature: LIMMA algorithm after multi-testing correction by False discovery rate (FDR) identified 8372 variables genes between sorted cells and cell culture from passages 0 to 5. Conjointly SAM algorithm found 5619 differential expressed genes between lung tumors and normal lung tissue (FDR<0.05, n=246 samples). Nested analysis on intersection between alveolar organoid and lung cancer signature was tuned with machine learning leave one out algorithm from Stanford identified. A common signature of 19 predictive genes was found with a minimum of misclassification error less than 9% (
Example 4
HDAC Inhibitors Increase the Immunogenicity of the Vaccine
[0463] Higher expression of MHC I in cells used as a vaccine will allow to enhance the presentation of neo-antigens associated with MHC- I to APC/ Dendritic cells to induce TH1 immune response. For this purpose we tested four different HDACi to check their capacity to increase the expression of MHC 1 on two independent iPSCs. One iPSCs having no genetic alterations (PB33) and one iPSCS caring a fusion product of BCR-ABL that was produced from a patient with a CML disease (PB32).
[0464] Four HDACi were tested including verinostat, Entinestat, Leviteracetam and Valproic acid at a dose of 1 to 1.5 .Math.M (
Example 5
Vaccination With Autologous Endodermal Progenitor Cells in Combination With Valproic Acid (VPA) Generates an Anti-Tumoral Response Against Ductal Pancreatic Adenocarcinoma (PDAC).
[0465] We have produced endodermal progenitor cells (EndoPCs) from murine tail fibroblasts-derived iPSCs and from murine differentiated hepatocytes by using viral vector expressing Oct4/Sox2/cMyc/Kfl4 transcriptional factors. These progenitors are fetal cells. In order to highlight pancreatic tumor expression profile of EndoPCs, its transcriptome was associated with a Pan02 cells that were engrafted into syngeneic C57BL/6 mice as compared to stem cell expression profile of iIPSCs derived from tail murine fibroblast associated to murine embryonic stem cell (D3). On combined and cross batch normalized transcriptome matrix, a supervised ANOVA between the 4 sample groups was performed with a p-value threshold less than 10.sup.-4 and implementation of 500 permutations between groups. A list of 3230 gene identifiers was found significantly variable between the 4 experimental conditions (data not shown). In a second time, on these variable expression profile SAM supervised algorithm was employed to found significant differential expressed genes between following groups: (EndoPCs + Pan02 in vivo) versus (D3-ES + murine _iPSCs) with a FDR less than 1 percent. With these analyses, a pancreatic tumor gene expression profile of EndoPCs was found comprising 359 gene identifiers which allowed to significantly individualized experimental groups (P-value=1.138249e-10) by unsupervised principal component analysis (
[0466] We also demonstrated that EndoPCs processing a unique molecular signature were dissimilar to murine iPSCs and were found to be negative by quantitative RT-PCR for gene implicated in the pluripotent maintenance such as OCT4, SOX2, NANOG, LIN28, CMYC, KLF4 and Alkaline phosphatase (ALP) (
[0467] The activation of this pathway in both cell lines was correlated with a phosphorylation of STAT3 on tyrosine 705 in response to IL-6 (
[0468] We then investigated whether vaccination with irradiated EndoPCs in combination with VPA was effective against pancreas cancer in a syngeneic PDAC mice model. The vaccination consisted in injecting by sub cutaneous route two suspensions of 2×10.sup.6 EndoPCS that were irradiated with a dose of 80 greys.
[0469] The cells were injected 7 and 14 days before the orthotropic injection into the tail part of the pancreas of 2×10.sup.6 Pan02Luc cells expressing the luciferase gene. The mice (n=8) receiving the 2 boosts of vaccine received the day of challenge VPA at the dose of 0.40 mM in drinking water. At the same time, unvaccinated mice received the same number of cancer Pan02Luc cells without VPA. We discovered that in contrast to the none-vaccinated mice, a significant improvement of survival rate following the beforehand injection of mice’s with irradiated EndoPCs (
[0470] Throughout this application, various references describe the state of the art to which this invention pertains. The disclosures of these references are hereby incorporated by reference into the present disclosure.
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