APC loss induces Warburg effect via increased PKM2 transcription in colorectal cancer.

BACKGROUND: Most cancer cells employ the Warburg effect to support anabolic growth and tumorigenesis. Here, we discovered a key link between Warburg effect and aberrantly activated Wnt/ß-catenin signalling, especially by pathologically significant APC loss, in CRC. METHODS: Proteomic analyses were performed to evaluate the global effects of KYA1797K, Wnt/ß-catenin signalling inhibitor, on cellular proteins in CRC. The effects of APC-loss or Wnt ligand on the identified enzymes, PKM2 and LDHA, as well as Warburg effects were investigated. A linkage between activation of Wnt/ß-catenin signalling and cancer metabolism was analysed in tumour of Apcmin/+ mice and CRC patients. The roles of PKM2 in cancer metabolism, which depends on Wnt/ß-catenin signalling, were assessed in xenograft-tumours. RESULTS: By proteomic analysis, PKM2 and LDHA were identified as key molecules regulated by Wnt/ß-catenin signalling. APC-loss caused the increased expression of metabolic genes including PKM2 and LDHA, and increased glucose consumption and lactate secretion. Pathological significance of this linkage was indicated by increased expression of glycolytic genes with Wnt target genes in tumour of Apcmin/+ mice and CRC patients. Warburg effect and growth of xenografted tumours-induced by APC-mutated-CRC cells were suppressed by PKM2-depletion. CONCLUSIONS: The ß-catenin-PKM2 regulatory axis induced by APC loss activates the Warburg effect in CRC.

Probing the Neuraminidase Activity of Influenza Virus Using a Cytolysin A Protein Nanopore.

Neuraminidase (NA), one of the major surface glycoproteins of influenza A virus (IAV), is an important diagnostic biomarker and antiviral therapeutic target. Cytolysin A (ClyA) is a nanopore sensor with an internal constriction of 3.3 nm, enabling the detection of protein conformations at the single-molecule level. In this study, a nanopore-based approach is developed for analysis of the enzymatic activity of NA, which facilitates rapid and highly sensitive diagnosis of IAV. Current blockade analysis of the d-glucose/d-galactose-binding protein (GBP) trapped within a type I ClyA-AS (ClyA mutant) nanopore reveals that galactose cleaved from sialyl-galactose by NA of the influenza virus can be detected in real time and at the single-molecule level. Our results show that this nanopore sensor can quantitatively measure the activity of NA with 40-80-fold higher sensitivity than those previously reported. Furthermore, the inhibition of NA is monitored using small-molecule antiviral drugs, such as zanamivir. Taken together, our results reveal that the ClyA protein nanopore can be a valuable platform for the rapid and sensitive point-of-care diagnosis of influenza and for drug screening against the NA target.

Small molecule-induced simultaneous destabilization of ß-catenin and RAS is an effective molecular strategy to suppress stemness of colorectal cancer cells.

BACKGROUND: Cancer stem cells (CSCs), the major driver of tumorigenesis, is a sub-population of tumor cells responsible for poor clinical outcomes. However, molecular mechanism to identify targets for controlling CSCs is poorly understood. METHODS: Gene Set Enrichment Analyses (GSEA) of Wnt/ß-catenin and RAS signaling pathways in stem-like subtype of colorectal cancer (CRC) patients were performed using two gene expression data set. The therapeutic effects of destabilization of ß-catenin and RAS were tested by treatment of small molecule KYA1797K using CRC patient derived cells. RESULTS: Treatment with KYA1797K, a small molecule that destabilizes both ß-catenin and RAS via Axin binding, effectively suppresses the stemness of CSCs as shown in CRC spheroids and small intestinal tumors of ApcMin/+/K-RasG12DLA2 mice. Moreover, KYA1797K also suppresses the stemness of cells in CRC patient avatar model systems, such as patient-derived tumor organoids (PDTOs) and patient-derived tumor xenograft (PDTX). CONCLUSION: Our results suggest that destabilization of both ß-catenin and RAS is a potential therapeutic strategy for controlling stemness of CRC cells. Video abstract.

Probing the Small-Molecule Inhibition of an Anticancer Therapeutic Protein-Protein Interaction Using a Solid-State Nanopore.

Nanopore sensing is an emerging technology for the single-molecule-based detection of various biomolecules. In this study, we probed the anticancer therapeutic p53 transactivation domain (p53TAD)/MDM2 interaction and its inhibition with a small-molecule MDM2 antagonist, Nutlin-3, using low-noise solid-state nanopores. Although the translocation of positively charged MDM2 through a nanopore was detected at the applied negative voltage, this MDM2 translocation was almost completely blocked upon formation of the MDM2/GST-p53TAD complex owing to charge conversion. In combination with NMR data, the nanopore measurements showed that the addition of Nutlin-3 rescued MDM2 translocation, indicating that Nutlin-3 disrupted the MDM2/GST-p53TAD complex, thereby releasing MDM2. Taken together, our results reveal that solid-state nanopores can be a valuable platform for the ultrasensitive, picomole-scale screening of small-molecule drugs against protein-protein interaction (PPI) targets.

Nanopore Analysis on the Drug-Induced Conformation Change of a p53-Linker-Mouse Double Minute 2 Protein Complex.

Detection of conformational changes in proteins by protein-protein interaction (PPI) is a key issue in developing drug screening platforms. In order to effectively investigate the conformational change in a protein at a single-molecule level, we propose the use of nanopore detection to identify protein conformational changes resulting from protein-protein interactions and their inhibition by Nutlin-3. We designed a protein complex comprising a p53 peptide and a mouse double minute 2 (MDM2) linked by 6 amino acids, transforming its shape from globular to dumbbell structure by inhibition of interaction between p53 peptide and MDM2. In the NMR experiment, no distinguished crosspeaks were observed upon Nutlin-3 addition. However, the nanopore experiment clearly showed double-peak signals with the addition of Nutlin-3. The observed fraction of the double-peak among single-peak signals increased from 8.77% to 22.03% with a concurrent increase in the Nutlin-3 concentration from a molar ratio of 1 to 10-fold. From the nanopore data, we estimated the dwell time for the elongated form of Nutlin-3-bound protein, which traverses for a longer duration (∼2 times) than the globular form. Finally, the hydrodynamic diameter of the local peak of the double-peak signal was calculated and compared with the X-ray crystallography results. This approach shows feasibility of the nanopore detection to verify the protein conformational change by inhibition of protein-protein interaction at a single-molecule level.

Translocation of DNA and protein through a sequentially polymerized polyurea nanopore.

Here, we investigated the translocation of biomolecules, such as DNA and protein, through a sequentially polymerized polyurea nanopore, with a thin (<10 nm) polymer membrane of uniform thickness. The polyurea membrane was synthesized by molecular layer deposition using p-phenylenediisocyanate (PDI) and p-phenylenediamine (PDA) as sequential precursors. The membrane exhibited a hydrophobic surface with a highly negative surface charge density (-51 mC m-2 at pH 8). It was particularly noted that the high surface charge density of the membrane resulted in a highly developed electro-osmotic flow which, in turn, strongly influenced the capture probability of biomolecules, depending on the balance between the electro-osmotic and electrophoretic forces. For instance, the capture frequency of negatively charged DNA was demonstrated to be quite low, since these two forces more or less cancelled each other, whereas that of positively charged MDM2 was much higher, since these two forces were additive. We also identified that the mean translocation time of MDM2 through the polyurea nanopore was 26.1 ± 3.7 µs while that of the SiN nanopore was 14.2 ± 2.0 µs, hence suggesting that the enhanced electrostatic interaction between positively charged MDM2 and the negatively charged pore surface affects the translocation speed.

Solid-state nanopore analysis on conformation change of p53TAD-MDM2 fusion protein induced by protein-protein interaction.

Although protein-protein interactions (PPIs) are emerging therapeutic targets for human diseases, development of high-throughput screening (HTS) technologies against PPI targets remains challenging. In this study, we propose a protein complex structure to effectively detect conformational changes of protein resulting from PPI using solid-state nanopore for a novel, widely-applicable drug screening method against various PPI targets. To effectively detect conformational changes resulting from PPI, we designed a fusion protein MLP (MDM2-linker-p53TAD), where p53TAD and MDM2 are connected by a 16 amino acid linker. The globular conformation of MLP exhibited a single-peak translocation event, whereas the dumbbell-like conformation of nutlin-3-bound MLP revealed as a double-peak signal. The proportion of double-peak to single-peak signals increased from 9.3% to 23.0% as nutlin-3 concentration increased. The translocation kinetics of the two different MLP conformations with varied applied voltage were analyzed. Further, the fractional current of the intra-peak of the double-peak signal was analyzed, probing the structure of our designed protein complex. This approach of nanopore sensing may be extendedly employed in screening of PPI inhibitors and protein conformation studies.

Correction: Solid-state nanopore analysis on conformation change of p53TAD-MDM2 fusion protein induced by protein-protein interaction.

Correction for 'Solid-state nanopore analysis on conformation change of p53TAD-MDM2 fusion protein induced by protein-protein interaction' by Hongsik Chae et al., Nanoscale, 2018, DOI: 10.1039/c8nr06423g.