Identification of patient samples
In the validation phase, we identified potential markers and targets in patient samples by next generation sequencing, G-banding, and flow cytometry, and the results are shown in Table I.
Tab. I
Cell surface markers, chromosome characteristics, and genetic analysis in patients

Engraftment of AML and ALL PDOX model evaluated by fluorescence-activated cell sorting (FACS)
Patient characteristics, diagnosis, and treatment history, are shown in Table II. Xenograft models of AML and ALL were prepared by intrafemoral injection of fresh blasts from the peripheral blood (PB) or bone marrow (BM) of leukemia patients into NCG mice and screened for their potential to initiate leukemia in the mouse models. The frequency of CD45+CD33+ cells or CD45+ cells in mouse peripheral blood was monitored weekly by FACS beginning 3–4 weeks after transplantation. To confirm the engraftment of human AML/ALL in the mouse models. P0 indicates the primary passage of patient cell suspension prepared from patient blood or bone marrow samples. When the percentage of positive cells reached 10%, single cell suspensions prepared from the mouse spleen were inoculated intrafemorally into naïve NCG mice (P1), or cryopreserved in liquid nitrogen until inoculation (FP0+1). The percentages of leukemia cells at P0, P1, and FP0+1 in 12 representative PDOX models are shown in Figure 2. Successfully engraftment of PDOX models was defined as 10% CD45+CD33+ or CD45+ at P1. Successfully established PDOX required stable morphologic and molecular characteristics for at least two passages.
Tab. II
Patient characterization
Summarized clinical data of patients at the time of sample withdrawal. All samples used in this study were from patients with AML/ALL.

Cell suspensions prepared from patient samples were injected intrafemorally into NCG mice to generate the PDOX models. The frequency and percentage of CD45+ or CD45+CD33+ cells in mouse peripheral blood were determined by FACS at P0 (black lines), P1 (red lines), and FP0+1 (blue lines) of established PDOX models. Individual mice are shown as point values. Group results are shown with bars that give the standard deviation.
Cell suspensions prepared from patient samples were injected intrafemorally into NCG mice to generate the PDOX models. The frequency and percentage of CD45+ or CD45+CD33+ cells in mouse peripheral blood were determined by FACS at P0 (black lines), P1 (red lines), and FP0+1 (blue lines) of established PDOX models. Individual mice are shown as point values. Group results are shown with bars that give the standard deviation.
Consistency of cell surface markers in patient samples and PDOX models
FACS analysis of cell surface markers in peripheral blood of patient samples and the PDOX models established using the samples are shown in Table III. CD19 was positive in both patient samples and all four of the corresponding PDOX ALL models. The ALL were B cell-derived phenotypes. All four were CD10+ and CD38+, suggesting that CD19+CD10+CD38+ cell populations might be a useful as a panel to determine the establishment of PDOX in this type of B-ALL. The series of ALL-associated antigens revealed that the immunophenotype of PDOX cells was consistent with the primary specimens for most antigens tested and that they preserved the disease characteristics of the patients that they originated from.
Tab. III
Consistency of partial PDOX with the clinical: FACS analysis
Model ID
|
Clinical
|
PDOX FACS
|
Immunophenotype
|
Result
|
Immunophenotype
|
Result
|
LD1-0041-362073
|
abnormal cells
|
69.44%
|
abnormal cells
|
86.77%
|
CD34
|
+
|
CD34
|
+
|
HLA-DR
|
+
|
HLA-DR
|
No detection
|
CD33
|
+
|
CD33
|
No detection
|
CD123
|
+
|
CD123
|
+
|
CD9
|
+
|
CD9
|
No detection
|
CD19
|
+
|
CD19
|
+
|
CD10
|
+
|
CD10
|
+
|
cCD79a
|
+
|
cCD79a
|
No detection
|
TDT
|
+
|
TDT
|
+
|
CD13
|
+
|
CD13
|
No detection
|
CD22
|
+
|
CD22
|
No detection
|
|
|
CD24
|
+
|
|
|
CD81dim
|
+
|
|
|
CD73
|
+
|
CD20
|
-
|
CD20
|
-
|
CD38
|
-
|
CD38
|
-
|
LD1-1041-362519
|
abnormal cells
|
90.83%
|
abnormal cells
|
94.74%
|
CD38
|
+
|
CD38
|
+
|
HLA-DR
|
+
|
HLA-DR
|
No detection
|
CD22
|
+
|
CD22
|
No detection
|
CD19
|
+
|
CD19
|
+
|
CD10
|
+
|
CD10
|
+
|
CD9
|
+
|
CD9
|
No detection
|
cCD79a
|
+
|
cCD79a
|
No detection
|
CD34
|
+/-
|
CD34
|
-
|
TDT
|
+/-
|
TDT
|
No detection
|
|
|
CD81
|
+
|
CD20
|
-
|
CD20
|
-
|
CD123
|
-
|
CD123
|
-
|
LD1-0041-362021
|
abnormal cells
|
94.40%
|
abnormal cells
|
80.25%
|
CD19
|
+
|
CD19
|
+
|
CD22
|
+
|
CD22
|
No detection
|
CD34
|
+
|
CD34
|
+
|
CD38
|
+
|
CD38
|
+
|
cCD79a
|
+
|
cCD79a
|
No detection
|
CD10
|
-
|
CD10dim
|
+
|
cIgM
|
-
|
cIgM
|
No detection
|
|
|
CD24
|
+
|
|
|
CD81dim
|
+
|
|
|
CD123
|
+
|
CD20
|
-
|
CD20
|
-
|
|
|
CD73
|
-
|
LD1-0041-362478
|
abnormal cells
|
84.98%
|
abnormal cells
|
98.44%
|
CD19
|
+
|
CD19
|
+
|
CD10
|
+
|
CD10
|
+
|
CD34
|
+
|
CD34
|
-
|
HLA-DR
|
+
|
HLA-DR
|
No detection
|
CD9
|
+
|
CD9
|
No detection
|
CD24
|
+
|
CD24
|
No detection
|
CD58
|
+
|
CD58
|
No detection
|
CD38
|
+
|
CD38
|
+
|
cκdim
|
+
|
cκdim
|
No detection
|
|
|
CD81
|
+
|
|
|
CD20
|
-
|
|
|
CD123
|
-
|
Note:”+” means positive, ”-” means negative.
Chromosome analysis of clinical samples and PDOX cells
G-banding karyotype analysis showed normal karyotypes and revealed that the karyotype of PDX cells was similar to that of patient specimens. (Table IV, Figure 3)
Tab. IV
Consistency of partial PDX/PDOX with the clinical: Chromosomal analysis
Model ID
|
Tissue type
|
Clinical result
|
PDOX result
|
LD1-0041-362073
|
peripheral blood
|
+5
|
|
t(9;22)(q34;q11.2)[18]/51
|
t(9;22)(q34;q11.2)
|
+der(22)t(9;22)(q34;q11.2)[1]/48
|
der(22)t(9;22)[cp14]/46
|
LD1-1041-362519
|
Bone marrow
|
del(9)(p13)
|
Normalization
|
der(9)[18]/46
|
-9
|
add(9)(p13)
|
del(9)(p22)
|
del(1)(q21)
|
Normalization
|
del(18)(q21)
|
Normalization
|
LD1-0041-362021
|
Bone marrow
|
Normalization
|
Normalization
|
Normalization
|
del(9)(p12p21)
|
del(9)(p21)[20]
|
i(17)(q10)[20]
|
PDOX and the parental clinical sample have similar genetic profiles
An AML patient (LD1-0040-361280) had a mutation on exon 12 of NPM1, a typical hot-spot alteration seen in AML patients without chromosome abnormalities [13]. As shown in Table V, an NPM1exon12A mutation was found in the PDOX model by either RNAseq or whole exon sequencing. Other mutations such as c-kit/D816V, CEBPA, or FLT3/ITD that are often found in AML were not present in either the PDOX model or the original patient sample. The result indicates consistency in the genetic profiles of the patient and the PDOX model.
Tab. V
Consistency of partial PDX/PDOX with the clinical: Genetic alteration
Model ID
|
Gene
|
Clinical result
|
PDOX result
|
WES_Mut(AF)
|
RNA_Mut(AF)
|
RNA_TPM
|
RNA_TPM_zscore_GTEx
|
RNA_TPM_zscore_TCGA
|
LD1-0040-361280
|
c-kit/D816V
|
-
|
-
|
-
|
12.5
|
4.200862
|
-1.08643
|
CEBPA
|
-
|
-
|
-
|
117.22
|
1.922675
|
0.460406
|
NPM1exon12A
|
+
|
Trp288fs(0.312)
|
Trp288fs(0.355)
|
1558.02
|
4.793047
|
3.388323
|
FLT3/ITD
|
-
|
-
|
-
|
146.78
|
2.790451
|
0.758332
|
Standard of care validation with therapeutic regimens used in clinical practice
Validation using the same treatments that were administered to patient was performed in five of the established PDOXs. Cytarabine, which is commonly given to AML/ALL, patents had antitumor activity in both the AML and the ALL PDOXs (Figure 4B–E). In the AML PDOX, cladribine completely eliminated the tumor (Figure 4A). Epirubicin and vincristine, which are components in CEOP treatment [14] had good anti-tumor activity in three of the four ALL PDOX models (Figure 4C–E), but not in the LD1-0040-362519 model (Figure 4F). Imatinib and ibrutinib, two small molecules that target BCR-Abl and BTK, respectively, were not effective in all the PDOX models (Figure 4C and F). As shown in Table II, response or nonresponse of the PDOX models was consistent with the clinical outcomes that occurred in response to those agents by the corresponding patients. The patient responses to treatment were maintained in the PDOX mouse models.