Different Effects of sgRNA Length on CRISPR-mediated Gene Knockout Efficiency.

CRISPR-Cas9 is a powerful genome editing technology, yet with off-target effects. Truncated sgRNAs (17nt) have been found to decrease off-target cleavage without affecting on-target disruption in 293T cells. However, the potency of 17nt sgRNAs relative to the full-length 20nt sgRNAs in stem cells, such as human mesenchymal stem cells (MSCs) and induced pluripotent stem cells (iPSCs), has not been assessed. Using a GFP reporter system, we found that both 17nt and 20nt sgRNAs expressed by lentiviral vectors induce ~95% knockout (KO) in 293T cells, whereas the KO efficiencies are significantly lower in iPSCs (60-70%) and MSCs (65-75%). Furthermore, we observed a decrease of 10-20 percentage points in KO efficiency with 17nt sgRNAs compared to full-length sgRNAs in both iPSCs and MSCs. Off-target cleavage was observed in 17nt sgRNAs with 1-2nt but not 3-4nt mismatches; whereas 20nt sgRNAs with up to 5nt mismatches can still induce off-target mutations. Of interest, we occasionally observed off-target effects induced by the 17nt but not the 20nt sgRNAs. These results indicate the importance of balancing on-target gene cleavage potency with off-target effects: when efficacy is a major concern such as genome editing in stem cells, the use of 20nt sgRNAs is preferable.

[Effects of catalase on the engraftment of human hematopoietic stem cells in NOD/SCID mice].

OBJECTIVE: To investigate the effect of catalase (CAT) on engraftment of human hematopoietic stem cells (HSC) by co-transplanting umbilical cord-derived mesenchymal stem cells (UC-MSC) with over-expressed CAT and human HSC into NOD/SCID mice. METHODS: The UC-MSC cultured in vitro were transfected by the retrovirus containing green fluorescent protein (GFP) and GFP-CAT genes respectively. MSC-GFP and MSC-GFP-CAT cell lines were sorted by flow cytometry. Co-culture and co-transplant experiments were performed to detect the effects of CAT on expansion and engraftment of human HSC. RESULTS: The percentage of GFP(+) cells were approximately 97.6% and 96.8% after sorting. The mRNA expression of CAT in MSC-GFP-CAT was 23.9-fold higher than that in UC-MSC. The activity of CAT in UC-MSC, MSC-GFP, MSC-GFP-CAT cells were 19.5, 20.3 and 74.1 Unit respectively. There was no significant differences in the percentage of CD34(+) cells between 3 groups in co-culture experiment. And the percentage of human CD45(+) cells in NOD/SCID mice were (3.22 ± 3.1)%, (4.26 ± 3.56)% and (7.37 ± 4.51)% respectively. CONCLUSION: MSC-GFP-CAT significantly improves the engraftment of human HSC in NOD/SCID mice, whereas co-culture with the MSC-GFP-CAT can not promote the expansion of HSC in vitro.

[Detection of heterogeneity and evolution of subclones in t(8;21) AML by QM-FISH].

OBJECTIVE: To explore the heterogeneous subclones in acute myeloid leukemia (AML) with t(8;21) by quantitative multicolor- fluorescence in situ hybridization (QM-FISH), and to figure out whether there is putative ancestral relationship among different subclones. METHODS: Bacterial artificial chromosomes (BAC) clones that contain the targeted genes including AML1, ETO, WT1, p27 and c-kit were searched in the data base UCSC Genome Bioinformatics. Multicolor FISH probes were prepared by linking fluorescein labeled dUTP or dCTP to targeted genes by nick translation. Bone marrow mononuclear cells from t (8;21) AML patients are dropped on to the wet surface of glass slides after hypotonic treatment and fixation. After hybridization, the fluorescence signals were captured by Zeiss fluorescence microscope. The copy number of AML1, ETO, WT1, p27, c- kit and the AML1-ETO fusion gene in AML1-ETO positive cells was counted. The cells with same signals were defined as a subclone. Various subclones were recorded and their proportions were calculated, and their evolutionary relationship was deduced. The subclones in matched primary and relapsed samples were compared, the evolution of dominant clones were figured out and the genomic abnormality that is associated with relapse and drug resistance were speculated. RESULTS: In this study, 36 primary AML with t(8;21) cases and 1 relapsed case paired with the primary case were detected. In these 36 primary cases, 4 cases (11.1%) acquired additional AML1-ETO fusion signal, 3(8.3%) had additional AML1 signal, 4(11.1%) had additional ETO signal, 20(55.6%) had additional WT1 signal, 15(41.7%) had additional p27 signal and 14(38.9%) had additional c-kit signal. In addition, 10(27.8%) displayed AML1 signal deletion, and such an aberration represents statistic significance in male patients. It seems that male patients usually accompany AML1 signal deletion. Of 36 cases, 28(77.8 %) harbored at least 2 subclones (ranged from 2 to 10). According to the genetic signature of subclones, we can assemble a putative ancestral tree, and the genetic architecture is linear or branching. In particular, the clonal architecture of the relapsed sample exhibited significant clonal evolution compared to its paired sample at diagnosis, including proportion changes in dominant clone, subclone disappearance and appearance of new dominant clones. CONCLUSION: Genomic abnormality is very diverse in t(8;21) AML. Subclones have linear or complex branching evolutionary histories, and clonal architecture is dynamic.

[The prognostic impact of 1p21 deletion on newly diagnosed multiple myeloma patients receiving thalidomide-based first-line treatment].

OBJECTIVE: To explore the deletion rate, clinical correlation and prognostic significance of 1p21 deletion, a novel genetic prognostic index, in patients with multiple myeloma (MM). METHODS: The interphase fluorescence in situ hybridization (I-FISH) was performed on purified CD138⁺ plasma cells from 78 newly diagnosed patients from Sep 2007 to Sep 2012 receiving thalidomide-based chemotherapy by using BAC probe covered 1p21.2 region that contains the human cell division cycle 14A (HCDC14A) gene. Deletion rate, the cell percentage of deletion, clinical relevance and prognostic significance were analyzed in myeloma patients. RESULTS: Among 78 patients, there were 51 males and 27 females, the median age was 59(42-81). The deletion rate of 1p21.2 was 23.1%. Some patients had amplification (amp) of 1p with amp rate of 5.1% in 1p21.2, the amp rate was significantly lower than the deletion rate (P=0.001). 1p21.2 deletion was positively correlated with renal lesion (Cr≥177 µmol/L), high percentage of plasma cells in bone marrow, high LDH (≥220 U/L) and high ß2-MG (P=0.014, 0.000, 0.010 and 0.022, respectively). With a median follow-up time of 15.0(1.0-53.5) months, the estimated median progressionfree survival (PFS) and overall survival (OS) time for patients with 1p21 deletion was (12.0±2.7) and (14.0±3.4) months, however those were (30.0±8.0) and (38.5±1.8) months in patients without 1p21 deletion, respectively (P=0.000). On multivariate analysis, which included complex karyotype, LDH≥220 U/L, renal lesion and del(17p13), 1p21 deletion remained as an independent risk factor for PFS (HR: 3.312, 95% CI: 1.095-10.017, P=0.034) and OS (HR: 4.961, 95% CI: 1.487-16.552, P=0.009). CONCLUSION: 1p21 deletion is an important genetic prognosis indicator in multiple myeloma patients.

[Cytogenetic abnormality of chromosome 13q14 in 112 patients with multiple myeloma detected by using LSI-RB1 and LSI-D13S319 probes].

Chromosome 13q14 deletion is one of the most common cytogenetic abnormalities in multiple myeloma (MM). LSI (locus-specific identification)-RB1 (13q14.1-14.2 region) and LSI-D13S319 (13q14.3 region) probes are usually used to detect 13q14 deletion. The aims of this study was to compare the incidence of chromosome 13q14.1-14.2 and 13q14.3 deletion and to detect 13q14 deletion size and number of involved cells in MM patients. The chromosome 13q14 region was detected by fluorescence in situ hybridization using probes LSI-RB1 and LSI-D13S319 in plasma cells of 112 MM patients. The results showed that 47.3% (53 out of 112) MM patients had both LSI-RB1 and LSI-D13S319 13q14 deletion (cut-off value: 7%), and the deletion rates detected by probes LSI-RB1 and LSI-D13S319 were accordant. The positive rates of 13q14 deletion were 46.4% and 47.3% respectively when the cut-off level was increased to 20%, and the corresponding rate was 98%. MM patients carrying 13q14 deletion showed 18% - 98% (median value: 72.5%) and 22% - 98.5% (median value: 76.5%) of deleted nuclei involving the RB1 and the D13S319 locus (P = 0.38). There were 67.9% (36 out of 53) and 66% (35 out of 53) cases carrying > 65% of 13q14.1-14.2 and 13q14.3 deleted nuclei as high proportion deletion patients, respectively (P = 0.188). The positive rate of the high proportion deletion patients had still no difference between LSI-RB1 and LSI-D13S319 groups when the cut-off value was defined as 85% (P = 0.439). In conclusion, in this cohort of 112 MM patients, there was no significant difference between the LSI-RB1and LSI-D13S319 probes to detect 13q14 deletion. Both LSI-RB1 and LSI-D13S319 probes can be selected to detect 13q14 deletion in MM patients. All the 53 MM patients with 13q14 deletion had deletions of 13q14.1-14.2 and 13q14.3 regions, which is a large deletion as one of the important characters in MM patients with 13q14 deletion.

[An improved protocol of preparing bone marrow cells for fluorescence in situ hybridization].

This study was aimed to establish a smear protocol for preparing bone marrow cells and investigate its effect on fluorescence in situ hybridization (FISH) signal. Probe DNA (C-myc, MDM2, STK6) was labeled with Spectrum Green, PromoFluor-555 and PromoFluor-415 by nick translation. Five bone marrow samples were tested by two methods separately. Traditional method: after removing the erythrocytes by hypoosmotic solution, the bone marrow cells were fixed in methanol/acetic acid (3:1). Improved method: erythrocytes were removed using density gradient centrifugation and fixed in methanol. The samples were then fixed again in 2 formaldehyde for 5 min. The FISH signal was assessed by comparing the relative signal intensity of each fluorophore with the autofluorescence background. The results indicated that improved method greatly increased the ratio of fluorescence signal intensity in the Spectrum Green, PromoFluor-555 and PromoFluor-415 channel (traditional method: 4.3 ± 0.19, 3.52 ± 0.04, 3.07 ± 0.08; improved method: 9.89 ± 0.41, 7.55 ± 0.5, 5.67 ± 0.18, n = 5, P < 0.01) respectively. The signal intensity increased 2.32, 2.14 and 1.85-fold in the Spectrum Green, PromoFluor-555 and PromoFluor-415 channel respectively. In addition, the improved method decreased the split signals [traditional method: (15.8 ± 1.74), (20.42 ± 2.88), (23.2 ± 3.02); improved method: (8.6 ± 1.2), (12.28 ± 1.33), (12.6 ± 2.56), n = 5, P < 0.05]. It is concluded that the improved optimal procedure which facilitates FISH intensity on bone marrow cells is developed, showing potential for wide application in the diagnosis of hematologic diseases.

[Effects of catalase on human umbilical cord mesenchymal stem cells].

This study was aimed to investigate the growth and multiple differentiation potential of human umbilical cord tissue derived mesenchymal stem cells (UC-MSCs) transfected by a retroviral vector with catalase (CAT) gene. The UC-MSCs cultured in vitro were transfected by using pMSCV carrying GFP (pMSCV-GFP) and pMSCV carrying CAT (pMSCV-GFP-CAT) respectively, then the MSC-GFP cell line and MSC-GFP-CAT cell line were obtained by sorting of flow cytometry. The GFP expression was observed by a fluorescent microscopy at 48 hours after CAT gene transfection. The GFP+ cells were sorted by flow cytometry. The activity of CAT in GFP+ cells was detected by catalase assay kit. The proliferative capacity of transfected UC-MSCs was determined by cell counting kit-8. The differentiation ability of gene-transfected GFP+ cells into osteogenesis and adipogenesis was observed by von Kossa and oil red O staining. The results indicated that green fluorescence in UC-MSCs was observed at 48 hours after transfection, and the fluorescence gradually enhanced to a steady level on day 3. The percentage of MSCs-GFP was (25.54+/-8.65)%, while the percentage of MSCs-GFP-CAT was (35.4+/-18.57)%. The activity of catalase in UC-MSCs, MSCs-GFP, MSCs-GFP-CAT cells were 19.5, 20.3, 67.2 U, respectively. The transfected MSCs-GFP-CAT could be induced into osteoblasts and adipocytes. After 21 days, von Kossa staining showed induced osteoblasts. Many lipid droplets with high refractivity occurred in cytoplasm of the transfected UC-MSCs, and showed red fat granules in oil red O staining cells. There were no significant differences between transfected and non-transfected UC-MSCs cells (p>0.05). It is concluded that UC-MSCs are successfully transfected by retrovirus carrying GFP or CAT gene, the activity of catalase increased by 3.4-fold. The transfected UC-MSCs maintain proliferation potential and ability of differentiation into osteoblasts and adipocytes.