An Automated High-Throughput Screening (HTS) Spotter for 3D Tumor Spheroid Formation.

Three-dimensional (3D) culture platforms have been adopted in a high-throughput screening (HTS) system to mimic in vivo physiological microenvironments. The automated dispenser has been established commercially to enable spotting or distributing non-viscous or viscous biomaterials onto microplates. However, there are still challenges to the precise and accurate dispensation of cells embedded in hydrogels such as Alginate- and Matrigel-extracellular matrices. We developed and improved an automated contact-free dispensing machine, the ASFA SPOTTER (V5 and V6), which is compatible with 96- and 384-pillar/well plates and 330- and 532-micropillar/well chips for the support of 3D spheroid/organoid models using bioprinting techniques. This enables the distribution of non-viscous and viscous biosamples, including chemical drugs and cancer cells, for large-scale drug screening at high speed and small volumes (20 to 4000 nanoliters) with no damage to cells. The ASFA SPOTTER (V5 and V6) utilizes a contact-free method that minimizes cross-contamination for the dispensation of encapsulated tissue cells with highly viscous scaffolds (over 70%). In particular, the SPOTTER V6 does not require a washing process and offers the advantage of almost no dead volume (defined as additional required sample volume, including a pre-shot and flushing shot for dispensing). It can be successfully applied for the achievement of an organoid culture in automation, with rapid and easy operation, as well as miniaturization for high-throughput screening. In this study, we report the advantages of the ASFA SPOTTER, which distributes standard-sized cell spots with hydrogels onto a 384-pillar/well plate with a fast dispensing speed, small-scale volume, accuracy, and precision.

Methylation-sensitive high-resolution melting analysis of the USP44 promoter can detect early-stage hepatocellular carcinoma in blood samples.

Hepatocellular carcinoma (HCC) is dangerous cancer that often evades early detection because it is asymptomatic and an effective detection method is lacking. For people with chronic liver inflammation who are at high risk of developing HCC, a sensitive detection method for HCC is needed. In a meta-analysis of The Cancer Genome Atlas pan-cancer methylation database, we identified a CpG island in the USP44 promoter that is methylated specifically in HCC. We developed methylation-sensitive high-resolution melting (MS-HRM) analysis to measure the methylation levels of the USP promoter in cell-free DNA isolated from patients. Our MS-HRM assay correctly identified 40% of patients with early-stage HCC, whereas the α-fetoprotein test, which is currently used to detect HCC, correctly identified only 25% of early-stage HCC patients. These results demonstrate that USP44 MS-HRM analysis is suitable for HCC surveillance. [BMB Reports 2022; 55(11): 553-558].

Predicting Pharmacodynamic Drug-Drug Interactions through Signaling Propagation Interference on Protein-Protein Interaction Networks.

As pharmacodynamic drug-drug interactions (PD DDIs) could lead to severe adverse effects in patients, it is important to identify potential PD DDIs in drug development. The signaling starting from drug targets is propagated through protein-protein interaction (PPI) networks. PD DDIs could occur by close interference on the same targets or within the same pathways as well as distant interference through cross-talking pathways. However, most of the previous approaches have considered only close interference by measuring distances between drug targets or comparing target neighbors. We have applied a random walk with restart algorithm to simulate signaling propagation from drug targets in order to capture the possibility of their distant interference. Cross validation with DrugBank and Kyoto Encyclopedia of Genes and Genomes DRUG shows that the proposed method outperforms the previous methods significantly. We also provide a web service with which PD DDIs for drug pairs can be analyzed at http://biosoft.kaist.ac.kr/targetrw.

Context-based resolution of semantic conflicts in biological pathways.

BACKGROUND: Interactions between biological entities such as genes, proteins and metabolites, so called pathways, are key features to understand molecular mechanisms of life. As pathway information is being accumulated rapidly through various knowledge resources, there are growing interests in maintaining the integrity of the heterogeneous databases. METHODS: Here, we defined conflict as a status where two contradictory pieces of evidence (i.e. 'A increases B' and 'A decreases B') coexist in a same pathway. This conflict damages unity so that inference of simulation on the integrated pathway network might be unreliable. We defined rule and rule group. A rule consists of interaction of two entities, meta-relation (increase or decrease), and contexts terms about tissue specificity or environmental conditions. The rules, which have the same interaction, are grouped into a rule group. If the rules don't have a unanimous meta-relation, the rule group and the rules are judged as being conflicting. RESULTS: This analysis revealed that almost 20% of known interactions suffer from conflicting information and conflicting information occurred much more frequently in the literature than the public database. CONCLUSIONS: By identifying and resolving the conflicts, we expect that pathway databases can be cleaned and used for better secondary analyses such as gene/protein annotation, network dynamics and qualitative/quantitative simulation.

Incidence of venous thromboembolism using 64 channel multidetector row computed tomography-indirect venography and anti-coagulation therapy after total knee arthroplasty in Korea.

PURPOSE: This study evaluated the incidence of a venous thromboembolism (VTE) after total knee arthroplasty (TKA) using multidetector row computed tomography-indirect venography (MDCT-indirect venography) and assessed the efficacy of anti-coagulation therapy. MATERIALS AND METHODS: We enrolled 118 patients with 126 cases of TKA. The average age of the patients was 68.4 years. We used 64 channel MDCT-indirect venography for the detection of VTE. We treated selectively proximal deep vein thrombosis (DVT) or pulmonary thromboembolism (PTE) cases according to the results of MDCT-indirect venography. We re-evaluated the change in VTE using follow-up MDCT-indirect venography after 3 months. RESULTS: We identified VTE in 35.7%. DVT only was identified in 22.2% including 8 cases of proximal DVT and 20 cases of distal DVT. PTE without DVT was identified in 4.8%, and combined DVT and PTE in 8.7%. All patients with PTE were asymptomatic, but 4 DVT patients had signs of leg swelling. After anti-coagulation therapy, 20 patients showed complete resolution in 16 cases, improvement in 3 cases and one case showed a new distal DVT. CONCLUSIONS: The incidence of VTE after primary TKA was 35.7% in Korea. Furthermore, anti-coagulation therapy for proximal DVT and PTE patients may be a useful method for preventing the occurrence of a fatal PTE.

Discovering context-specific relationships from biological literature by using multi-level context terms.

BACKGROUND: The Swanson's ABC model is powerful to infer hidden relationships buried in biological literature. However, the model is inadequate to infer relations with context information. In addition, the model generates a very large amount of candidates from biological text, and it is a semi-automatic, labor-intensive technique requiring human expert's manual input. To tackle these problems, we incorporate context terms to infer relations between AB interactions and BC interactions. METHODS: We propose 3 steps to discover meaningful hidden relationships between drugs and diseases: 1) multi-level (gene, drug, disease, symptom) entity recognition, 2) interaction extraction (drug-gene, gene-disease) from literature, 3) context vector based similarity score calculation. Subsequently, we evaluate our hypothesis with the datasets of the "Alzheimer's disease" related 77,711 PubMed abstracts. As golden standards, PharmGKB and CTD databases are used. Evaluation is conducted in 2 ways: first, comparing precision of the proposed method and the previous method and second, analysing top 10 ranked results to examine whether highly ranked interactions are truly meaningful or not. RESULTS: The results indicate that context-based relation inference achieved better precision than the previous ABC model approach. The literature analysis also shows that interactions inferred by the context-based approach are more meaningful than interactions by the previous ABC model. CONCLUSIONS: We propose a novel interaction inference technique that incorporates context term vectors into the ABC model to discover meaningful hidden relationships. By utilizing multi-level context terms, our model shows better performance than the previous ABC model.

Intramedullary nailing versus submuscular plating in adolescent femoral fracture.

BACKGROUND: Femoral fractures in adolescents usually need operative treatment, but the optimal method is unclear. The purpose of this study is to compare intramedullary nailing (IN) and submuscular plating (SP) in adolescent femoral fractures. MATERIALS AND METHODS: We performed the prospective, comparison study of IN and SP in adolescent femoral shaft fractures at a mean age of 13.9 years (11-17.4). Twenty-two cases of IN and 23 cases of SP were followed for a minimum of 1 year. We compared radiological and clinical results, surgical parameters, and complications of two techniques. RESULTS: Bony union was achieved in all cases except one case of IN. Time to union was similar in both groups. None showed mal-union over 10° or limb length discrepancy over 1 cm. None of SP group and 2 in IN group experienced re-operation; one patient had deep infection with nonunion. The other patient sustained mal-rotation. Both patients healed after revision procedure. All patients showed excellent or satisfactory results of Flynn's criteria. The time to full-weight bearing was shorter in IN (IN: 57.3 days, SP: 89.2 days, p<0.05). In surgical parameters, operative time seemed shorter in IN (IN: 94.7 min, SP: 104 min, p=0.095), and fluoroscopy time was shorter in IN (IN: 58s, SP: 109s, p<0.05) than SP group. CONCLUSION: Although both IN and SP yield good results and minimal complication in adolescent femoral fractures, IN may be advantageous in less need of fluoroscopy, technical easiness in reduction and early weight bearing.