Antisense locked nucleic acids efficiently suppress BCR/ABL and induce cell growth decline and apoptosis in leukemic cells

ASP210: a potent oligonucleotide-based inhibitor effective against TKI-resistant CML cells

Clinical experience with tyrosine kinase inhibitors (TKIs) over the past two decades has shown that, despite the apparent therapeutic benefit, nearly 30% of patients with chronic myelogenous leukemia (CML) display primary resistance or intolerance to TKIs, and approximately 25% of those treated are forced to switch TKIs at least once during therapy due to acquired resistance. Safe and effective treatment modalities targeting leukemic clones that escape TKI therapy could hence be game changers in the professional management of these patients. Here, we aimed to investigate the efficacy of a novel therapeutic oligonucleotide of unconventional design, called ASP210, to reduce BCR-ABL1 mRNA levels in TKI-resistant CML cells, with the assumption of inducing their apoptosis. Imatinib- and dasatinib-resistant sublines of BCR-ABL1-positive MOLM-7 and CML-T1 cells were established and exposed to 0.25 and 2.5 µM ASP210 for 10 days. RT-qPCR showed a remarkable reduction of the target mRNA level by >99% after a single application. Cell viability was monitored daily by trypan blue staining. In response to the lack of driver oncoprotein BCR-ABL1, TKI-resistant CML cells underwent apoptosis regardless of the presence of the clinically relevant T315I mutation by day 5 after redosing with ASP210. The effect was selective for cancer cells, indicating a favorable safety profile for this therapeutic modality. Furthermore, the spontaneous uptake and high intracellular concentrations of ASP210 suggest its potential to be effective at relatively low doses. The present findings suggest that ASP210 is a promising therapeutic avenue for patients with CML who fail to respond to TKI therapy.NEW & NOTEWORTHY Effective treatment modalities targeting leukemic clones that escape tyrosine kinase inhibitor (TKI) therapy could be game changers in the professional management of patients displaying primary resistance, intolerance, or acquired resistance to TKIs. Although delivering authentic innovations today is more complex than ever, we developed a highly potent and safe oligonucleotide-based modality against BCR-ABL1 mRNA named ASP210 that effectively induces cell death in BCR-ABL1-positive TKI-resistant cells while sparing BCR-ABL1-negative healthy cells.

Non-Coding RNAs: Foes or Friends for Targeting Tumor Microenvironment

Non-coding RNAs (ncRNAs) are a group of molecules critical for cell development and growth regulation. They are key regulators of important cellular pathways in the tumor microenvironment. To analyze ncRNAs in the tumor microenvironment, the use of RNA sequencing technology has revolutionized the field. The advancement of this technique has broadened our understanding of the molecular biology of cancer, presenting abundant possibilities for the exploration of novel biomarkers for cancer treatment. In this review, we will summarize recent achievements in understanding the complex role of ncRNA in the tumor microenvironment, we will report the latest studies on the tumor microenvironment using RNA sequencing, and we will discuss the potential use of ncRNAs as therapeutics for the treatment of cancer.

Fluorescent base analogues in gapmers enable stealth labeling of antisense oligonucleotide therapeutics

To expand the antisense oligonucleotide (ASO) fluorescence labeling toolbox beyond covalent conjugation of external dyes (e.g. ATTO-, Alexa Fluor-, or cyanine dyes), we herein explore fluorescent base analogues (FBAs) as a novel approach to endow fluorescent properties to ASOs. Both cytosine and adenine analogues (tC, tC^O, 2CNqA, and pA) were incorporated into a 16mer ASO sequence with a 3-10-3 cEt-DNA-cEt (cEt = constrained ethyl) gapmer design. In addition to a comprehensive photophysical characterization, we assess the label-induced effects on the gapmers' RNA affinities, RNA-hybridized secondary structures, and knockdown efficiencies. Importantly, we find practically no perturbing effects for gapmers with single FBA incorporations in the biologically critical gap region and, except for pA, the FBAs do not affect the knockdown efficiencies. Incorporating two cytosine FBAs in the gap is equally well tolerated, while two adenine analogues give rise to slightly reduced knockdown efficiencies and what could be perturbed secondary structures. We furthermore show that the FBAs can be used to visualize gapmers inside live cells using fluorescence microscopy and flow cytometry, enabling comparative assessment of their uptake. This altogether shows that FBAs are functional ASO probes that provide a minimally perturbing in-sequence labeling option for this highly relevant drug modality.

Chronic myelogenous leukemia on target

Chronic myelogenous leukemia (CML) is commonly treated with tyrosine kinase inhibitors (TKIs) that inhibit the pro-leukemic activity of the BCR-ABL1 oncoprotein. Despite the therapeutic progress mediated by TKI use, off-target effects, treatment-induced drug resistance, and the limited effect of these drugs on CML stem cells (SCs) are major drawbacks frequently resulting in insufficient or unsustainable treatment. Therefore, intense research efforts have focused on development of improved TKIs and alternative treatment strategies to eradicate CML SCs. Alongside efforts to design superior protein inhibitors, the need to overcome the poor therapeutic effect of TKIs on CML SCs has led to a renaissance of antisense strategies, as they are reported as effective in more primitive cell types. Despite the greater drug design flexibility offered by antisense sequence variability and remarkable chemical improvements, antisense drugs exhibit unacceptable levels of off-target effects, precluding them from large-scale clinical testing. Recent advances in antisense drug design have led to a pioneering mRNA recognition concept that may offer a helping hand in eliminating off-target effects, and has potential to bridge the gap between research and clinical practice.

Oridonin Triggers Chaperon-mediated Proteasomal Degradation of BCR-ABL in Leukemia

Inducing degradation of oncoproteins by small molecule compounds has the potential to avoid drug resistance and therefore deserves to be exploited for new therapies. Oridonin is a natural compound with promising antitumor efficacy that can trigger the degradation of oncoproteins; however, the direct cellular targets and underlying mechanisms remain unclear. Here we report that oridonin depletes BCR-ABL through chaperon-mediated proteasomal degradation in leukemia. Mechanistically, oridonin poses oxidative stress in cancer cells and directly binds to cysteines of HSF1, leading to the activation of this master regulator of the chaperone system. The resulting induction of HSP70 and ubiquitin proteins and the enhanced binding to CHIP E3 ligase hence target BCR-ABL for ubiquitin-proteasome degradation. Both wild-type and mutant forms of BCR-ABL can be efficiently degraded by oridonin, supporting its efficacy observed in cultured cells as well as mouse tumor xenograft assays with either imatinib-sensitive or -resistant cells. Collectively, our results identify a novel mechanism by which oridonin induces rapid degradation of BCR-ABL as well as a novel pharmaceutical activator of HSF1 that represents a promising treatment for leukemia.

miR-93 regulates Msk2-mediated chromatin remodelling in diabetic nephropathy

How the kidney responds to the metabolic cues from the environment remains a central question in kidney research. This question is particularly relevant to the pathogenesis of diabetic nephropathy (DN) in which evidence suggests that metabolic events in podocytes regulate chromatin structure. Here, we show that miR-93 is a critical metabolic/epigenetic switch in the diabetic milieu linking the metabolic state to chromatin remodelling. Mice with inducible overexpression of a miR-93 transgene exclusively in podocytes exhibit significant improvements in key features of DN. We identify miR-93 as a regulator of nucleosomal dynamics in podocytes. miR-93 has a critical role in chromatin reorganization and progression of DN by modulating its target Msk2, a histone kinase, and its substrate H3S10. These findings implicate a central role for miR-93 in high glucose-induced chromatin remodelling in the kidney, and provide evidence for a previously unrecognized role for Msk2 as a target for DN therapy.

Podocyte injury is central to kidney dysfunction in diabetic nephropathy. Here the authors show that Msk2 is a target of miR-93 and this interaction mediates pathogenic chromatin remodelling in diabetic nephropathy.

Morpholino Oligo Antisense efficiently suppresses BCR/ABL and cell proliferation in CML: specific inhibition of BCR-ABL gene expression by Morpholino Oligo Antisense in BCR-ABL(+) cells

Chronic myeloid leukemia is a disorder that develops when a hematopoietic stem cell acquires the Philadelphia chromosome carrying the chimeric BCR/ABL oncogene leading to a deregulated cell proliferation and a decreased apoptosis in response to mutagenic stimuli. Therefore, it has been considered that BCR/ABL oncogene is a potential attractive target for anticancer agents. Antisense strategies aiming to suppress the expression of BCR/ABL in chronic myeloid leukemia cells have been studied by several research groups over the last decade. In the present study, the effect of Morpholino Oligo Antisense in BCR/ABL oncogene silencing was evaluated. To examine the hypothesis, K562 was used as a BCR/ABL fusion gene positive cell line using a Jurkat cell line as a control. The capacity of Morpholino Oligo Antisense in inhibiting the translation of p210(bcr-abl) protein by a western blotting technique, inhibition of cell proliferation, and stimulation of apoptosis by flow cytometric analysis after 24 and 48 hours was studied. Prolonged exposure of K562 cell line to Morpholino Oligo Antisense targeted against BCR-ABL showed proliferation inhibition as the main feature. Following western blotting, we found that complete silencing of BCR-ABL had been achieved but flow cytometric analysis showed no significant apoptosis. The results indicate that Morpholino Oligo Antisense was able to inhibit p210(bcr-abl), but did not induce apoptosis due to co-silencing of BCR.

Ras inhibition by FTS attenuates brain tumor growth in mice by direct antitumor activity and enhanced reactivity of cytotoxic lymphocytes

One of the concerns in targeted drug therapy is that the inhibition of receptors and signaling molecules in tumor cells may also affect similar components in the tumor microenvironment or in the immune system, with undefined consequences for inhibition of tumor growth. Thus, in addition to its antitumor activity in mice and humans, the Ras inhibitor salirasib (S-farnesylthiosalicylic acid, FTS) also exhibits anti-inflammatory activity. Here we show three antitumor effects of FTS in immune-competent mice with subcutaneous or intracranial tumors. First, FTS exhibited antitumor activity in immune-competent, intracranial tumor-bearing mice and increased their survival relative to tumor-bearing immune-compromised mice. Second, FTS induced an increase in regulatory T cells in mouse splenocytes, but the inhibitory effects of FTS on tumor growth were not affected by these Foxp3+ T lymphocytes. Third, FTS increased antitumor T-cell reactivity by downregulating Foxp3. This caused TGF-β-dependent sensitization of the tumor to the immune system.

A strand-specific burst in transcription of pericentric satellites is required for chromocenter formation and early mouse development

At the time of fertilization, the paternal genome lacks the typical configuration and marks characteristic of pericentric heterochromatin. It is thus essential to understand the dynamics of this region during early development, its importance during that time period and how a somatic configuration is attained. Here, we show that pericentric satellites undergo a transient peak in expression precisely at the time of chromocenter formation. This transcription is regulated in a strand-specific manner in time and space and is strongly biased by the parental asymmetry. The transcriptional upregulation follows a developmental clock, yet when replication is blocked chromocenter formation is impeded. Furthermore, interference with major satellite transcripts using locked nucleic acid (LNA)-DNA gapmers results in developmental arrest before completion of chromocenter formation. We conclude that the exquisite strand-specific expression dynamics at major satellites during the 2-cell stage, with both up and downregulation, are necessary events for proper chromocenter organization and developmental progression.

Optimizing anti-gene oligonucleotide 'Zorro-LNA' for improved strand invasion into duplex DNA

Zorro-LNA (Zorro) is a newly developed, oligonucleotide (ON)-based, Z-shaped construct with the potential of specific binding to each strand of duplex DNA. The first-generation Zorros are formed by two hybridized LNA/DNA mixmers (2-ON Zorros) and was hypothesized to strand invade. We have now established a method, which conclusively demonstrates that an LNA ON can strand invade into duplex DNA. To make Zorros smaller in size and easier to design, we synthesized 3′–5′–5′–3′ single-stranded Zorro-LNA (ssZorro) by using both 3′- and 5′-phosphoramidites. With ssZorro, a significantly greater extent and rate of double-strand invasion (DSI) was obtained than with conventional 2-ON Zorros. Introducing hydrophilic PEG-linkers connecting the two strands did not significantly change the rate or extent of DSI as compared to ssZorro with a nucleotide-based linker, while the longest alkyl-chain linker tested (36 carbons) resulted in a very slow DSI. The shortest alkyl-chain linker (3 carbons) did not reduce the extent of DSI of ssZorro, but significantly decreased the DSI rate. Collectively, ssZorro is smaller in size, easier to design and more efficient than conventional 2-ON Zorro in inducing DSI. Analysis of the chemical composition of the linker suggests that it could be of importance for future therapeutic considerations.

LNAzyme targeting the HCV internal ribosome entry site inhibits HCV RNA expression in HepG2.9706 cells

AIM: To investigate the inhibitory effects of LNAzyme targeting the hepatitis C virus (HCV) internal ribosome entry site (IRES) on HCV RNA expression in HepG2.9706 cells.

METHODS: The sequences encoding DNAzyme, thiolmodificated DNAzyme and LNAzyme directing against the HBV IRES (located in the 5' non-coding region) were designed and synthesized. The following experimental groups were set up: Lipofectamine-DNAzyme group, Lipofectamine-S-DNAzyme group, Lipofectamine-LNAzyme group, blank control group, empty Lipofectamine group, DNAzyme group, and random DNAzyme group. On days 1, 3, 5 and 7 after transfection, the expression of HCV RNA and luciferase gene in HepG2.9706 cells was detected.

RESULTS: Significant down-regulation of HCV RNA and luciferase gene expression was noted in the Lipofectamine-DNAzyme, Lipofectamine-S-DNAzyme and Lipofectamine-LNAzyme groups when compared with other groups (all P < 0.05). The reduced rates of HCV RNA expression in the above three groups were 28.10%, 35.25% and 44.58%, respectively. The reduced rates of luciferase gene expression were 31.18%, 40.69% and 52.33%, respectively. LNAzyme did not exert cytotoxicity in HepG2.9706 cells.

CONCLUSION: LNAzyme has a significant inhibitory effect on HCV RNA expression in HepG2.9706 cells. The inhibitory effect of LNAzyme on HCV RNA expression is stronger than that of thiolmodificated DNAzyme.

Ion trap collision-induced dissociation of locked nucleic acids

Gas-phase dissociation of model locked nucleic acid (LNA) oligonucleotides and functional LNA-DNA chimeras have been investigated as a function of precursor ion charge state using ion trap collision-induced dissociation (CID). For the model LNA 5 and 8 mer, containing all four LNA monomers in the sequence, cleavage of all backbone bonds, generating a/w-, b/x-, c/y-, and d/z-ions, was observed with no significant preference at lower charge states. Base loss ions, except loss of thymine, from the cleavage of N-glycosidic bonds were also present. In general, complete sequence coverage was achieved in all charge states. For the two LNA-DNA chimeras, however, dramatic differences in the relative contributions of the competing dissociation channels were observed among different precursor ion charge states. At lower charge states, sequence information limited to the a-Base/w-fragment ions from cleavage of the 3'C-O bond of DNA nucleotides, except thymidine (dT), was acquired from CID of both the LNA gapmer and mixmer ions. On the other hand, extensive fragmentation from various dissociation channels was observed from post-ion/ion ion trap CID of the higher charge state ions of both LNA-DNA chimeras. This report demonstrates that tandem mass spectrometry is effective in the sequence characterization of LNA oligonucleotides and LNA-DNA chimeric therapeutics.

Hepatitis B virus preS2 gene-specific locked nucleic acid antisense oligonucleotides significantly inhibit hepatitis B virus replication and expression in HepG2 2.2.15 cells

AIM: To investigate the inhibitory effects of hepatitis B virus (HBV) preS2 gene-specific locked nucleic acid (LNA) antisense oligonucleotides on HBV replication and expression in HepG2 2.2.15 cells.

METHODS: Three LNA antisense oligonucleotides of different lengths that are complementary to the translation initiation region of the HBV preS2 gene were designed, synthesized and introduced into HepG2 2.2.15 cells by cationic liposome-mediated transfection. Hepatitis B surface antigen (HbsAg) and HBV DNA levels in cell supernatant were tested by time-resolved immunofluorescence assay (TRFIA) and fluorescent quantitative-polymerase chain reaction (FQ-PCR). The inhibitory effects of different antisense oligonucleotides on HBV DNA replication and expression were compared. The cell toxicity of LNA antisense oligonucleotides was evaluated by methyl thiazolyl tetrazolium (MTT) assay.

RESULTS: On day 1 after transfection with LNA antisense oligonucleotides, the expression of HBsAg and the replication of HBV DNA were inhibited. On day 7, the reduced rates of HBsAg and HBV DNA levels were 45.79%, 52.92% and 67.21% as well as 35.15%, 40.69% and 52.16% in the non-modified antisense oligonucleotide group, all-phosphorothioate-modified antisense oligonucleotide group and LNA antisense oligonucleotide group, respectively. LNA antisense oligonucleotides showed the strongest inhibitory effects on viral activity and had no impact on cell metabolism. Compared with the control group, the reduced rates of HBsAg and HBV DNA levels achieved in each of the above groups were significantly higher (all P < 0.01). Moreover, the reduced rates of HBsAg and HBV DNA levels in the LNA antisense oligonucleotide group were significantly higher than those in other antisense oligonucleotide groups (all P < 0.05).

CONCLUSION: LNA antisense oligonucleotides targeting the preS2 gene can effectively inhibit the replication and expression of HBV in vitro. The preS2 gene can be used as an effective target for gene therapy of HBV infection.

Antiviral effects of locked nucleic acid antisense oligonucleotides targeting HBV S gene mRNA in HepG2 2.2.15 cells

AIM: To investigate the inhibitory effects of locked nucleic acid (LNA) antisense oligonucleotides targeting hepatitis B virus (HBV) S gene in HepG2 2.2.15 cells, and screen effective LNA antisense oligonucleotides.

METHODS: Four LNA antisense oligonucleotides of different lengths that are complementary to the translation initiation region of HBV S gene were designed, synthesized, and introduced into HepG2 2.2.15 cells by cationic liposome-mediated transfection. Hepatitis B surface antigen (HBsAg) and HBV DNA levels in cell supernatant were tested by enzyme-linked immunosorbent assay (ELISA) and fluorescent quantitative-polymerase chain reaction (FQ-PCR) 24, 48 and 72 h after transfection. The cell toxicity of LNA antisense oligonucleotides was detected by methyl thiazolyl tetrazolium (MTT) assay.

RESULTS: All four LNA antisense oligonucleotides (10, 15, 20 and 25 base, respectively) could inhibit the expression of HBsAg and the replication of HBV DNA. Seventy-two hours after transfection, the reduced rates of HBsAg and HBV DNA levels were 46.58%, 54.38%, 72.43% and 69.92% as well as 27.09%, 28.77%, 34.71% and 32.68%, respectively. No obvious cell toxicity of LNA antisense oligonucleotides was noted.

CONCLUSION: LNA antisense oligonucleotides targeting HBV S gene show strong inhibitory effects on HBV replication in vitro. The optimal length of LNA antisense oligonucleotides ranges from 15 to 25 base. LNA antisense oligonucleotides targeting HBV S gene have a therapeutic potential in patients infected with HBV.

HBV S gene-specific antisense locked nucleic acid significantly inhibits HBV replication and expression in HBV transgenic mice

AIM: To investigate the inhibitory effects of hepatitis B virus (HBV) S gene-specific antisense locked nucleic acid (LNA) on HBV replication and expression.

METHODS: Thirty HBV transgenic mice were randomly divided into five groups (n = 6): glucose (5% GLU solution) control group, empty liposome control group, LNA group, S-ASODN-liposome group and LNA-liposome group. Antisense LNA was injected into mice via the tail vein. Serum HBsAg was quantified by ELISA. Serum HBV DNA was quantified by PCR. The expression of HBsAg in the liver was detected by immunohistochemistry. Serum ALB, ALT, BUN, CR, ApoA1 and ApoB were measured using an automatic biochemical analyzer. The effects of antisense LNA on mouse organs were investigated by HE staining of mouse liver and kidney sections.

RESULTS: On days 1, 3, 7 and 14 after LNA injection, serum HBsAg levels in the LNA-liposome group were reduced by 41.7%, 52.8%, 57.8% and 30.5%, respectively, while serum HBV DNA expression levels were decreased by 18.5%, 36.1%, 52.9% and 32.7%, respectively. These values were significantly higher than those in the control groups (all P < 0.05). No significant differences were noted in serum ALB, ALT, BUN, CR, ApoA1 and ApoB between the experiment group and the control groups (all P > 0.05). The expression level of HBsAg in the liver in the LNA-liposome group was significantly lower than those in the control groups. No significant histological abnormalities were found in the liver in all groups.

CONCLUSION: HBV S gene-specific antisense LNA can significantly inhibit the replication and expression of HBV.