SPSNet: subpopulation-sensitive network-based analysis of heterogeneous gene expression data

Local injection therapy for carpal tunnel syndrome: a network meta-analysis of randomized controlled trial

Objective: Clinical research has shown that local injections for carpal tunnel syndrome reduce the symptoms of patients and enhance their quality of life considerably. However, there are several therapy options, and the optimal choice of regimen remains uncertain. Therefore, we comprehensively evaluated the variations in clinical efficacy and safety of several medications for treating carpal tunnel syndrome. Methods: Computer searches of Embase, PubMed, Cochrane Library, and Web of Science databases were used to collect articles of randomized controlled trials on local injections for treating carpal tunnel syndrome from database creation till 10 June 2023. Two researchers independently screened the literature, extracted information, evaluated the risk of bias in the included studies, and performed network Meta-analysis using Stata 17.0 software. Drug efficacy was assessed using symptom severity/function and pain intensity. Surface under the cumulative ranking curve (SUCRA) ranking was used to determine the advantage of each therapy. Results: We included 26 randomized controlled trials with 1896 wrists involving 12 interventions, such as local injections of corticosteroids, platelet-rich plasma, 5% dextrose, progesterone, and hyaluronidase. The results of the network meta-analysis showed the following: (i) symptom severity: at the 3-month follow-up, D5W combined with splinting (SUCRA = 95%) ranked first, and hyaluronidase (SUCRA = 89.6%) at 6 months; (ii) functional severity: either at the 3-month follow-up (SUCRA = 89.5%) or 6 months (SUCRA = 83.6%), iii) pain intensity: 5% dextrose in water combined with splinting was the most effective at the 3-month (SUCRA = 85%) and 6-month (SUCRA = 87.6%) follow-up. Conclusion: Considering the combination of symptoms/function and pain intensity, combining 5% dextrose in water with splinting is probably the treatment of choice for patients with carpal tunnel syndrome. It is more effective than glucocorticoids and no adverse effects have been observed. Systematic Review Registration: https://www.crd.york.ac.uk/PROSPERO/, identifier CRD42022370525.

Acupuncture and other traditional Chinese medicine therapies in the treatment of children's tic syndrome: A network meta-analysis

BACKGROUND

Tic disorders (TD) are a kind of neuropsychiatric disease that frequently occur among preschool and school-age children, mainly characterized by motor tics or sometimes accompanied by vocal tics, and its pathogenesis is still unclear. The clinical manifestations are mainly characterized by chronic multiple movements, rapid muscle twitching, involuntary occurrence, and language disorder. Acupuncture, tuina, traditional Chinese medicine, and other methods are commonly used in clinical treatments, which have unique therapeutic advantages but have not been recognized and accepted by the international community. This study conducted a quality evaluation and meta-analysis of the currently published randomized controlled trials (RCTs) of acupuncture for TD in children in order to provide reliable evidence-based medical evidence for acupuncture for TD.

METHODS

All the randomized controlled trials (RCTs) using the intervention methods acupuncture + traditional Chinese medical herbs, acupuncture + tuina, and acupuncture, and the control group using Western medicine were included in the analysis. The main outcomes were obtained by using the Yale Global Tic Severity Scale (YGTSS), the Traditional Chinese medicine (TCM) syndrome score scale, and clinical treatment efficiency. Secondary outcomes included adverse events. The risk of bias in the included studies was assessed according to the tool recommended by Cochrane 5.3. The risk of bias assessment chart, risk of bias summary chart, and evidence chart in this study will be produced using R and Stata software.

RESULTS

There were 39 studies that met the inclusion criteria, including 3,038 patients. In terms of YGTSS, the TCM syndrome score scale changes and shows a clinically effective rate, and we found that acupuncture combined with Chinese medicine is the best treatment.

CONCLUSION

Acupuncture + traditional Chinese medical herbs may be the best therapy to improve TD in children. At the same time, compared with Western medicine commonly used in clinical practice, acupuncture and acupuncture combined with tuina therapy have better effects on improving TD in children.

LncTx: A network-based method to repurpose drugs acting on the survival-related lncRNAs in lung cancer

Despite the fact that an increased amount of survival-related lncRNAs have been found in cancer, few drugs that target lncRNAs are approved for treatment. Here, we developed a network-based algorithm, LncTx, to repurpose the medications that potentially act on survival-related lncRNAs in lung cancer. We used eight survival-related lncRNAs derived from our previous study to test the efficacy of this method. LncTx calculates the shortest path length (proximity) between the drug targets and the lncRNA-correlated proteins in the protein-protein interaction network (interactome). LncTx contains seven different proximity measures, which are calculated in the unweighted or weighted interactome. First, to test the performance of LncTx in predicting correct indication of drugs, we benchmarked the proximity measures based on the accuracy of differentiating anticancer drugs from non-anticancer drugs. The closest proximity weighted by clustering coefficient (closestCC) has the best performance (AUC around 0.8) compared to other proximity measures across all survival-related lncRNAs. The majority of the other six proximity measures have decent performance as well, with AUC greater than 0.7. Second, to evaluate whether LncTx can repurpose the drugs effectively acting on the lncRNAs, we clustered the drugs according to their proximities by hierarchical clustering. The drugs with smaller proximity (proximal drugs) were proved to be more effective than the drugs with larger proximity (distal drugs). In conclusion, LncTx enables us to accurately identify anticancer drugs and can potentially be an index to repurpose effective agents acting on survival-related lncRNAs in lung cancer.

Measuring consistency among gene set analysis methods: A systematic study

Gene set analysis is a quantitative approach for generating biological insight from gene expression datasets. The abundance of gene set analysis methods speaks to their popularity, but raises the question of the extent to which results are affected by the choice of method. Our systematic analysis of 13 popular methods using 6 different datasets, from both DNA microarray and RNA-Seq origin, shows that this choice matters a great deal. We observed that the overall number of gene sets reported by each method differed by up to 2 orders of magnitude, and there was a bias toward reporting large gene sets with some methods. Furthermore, there was substantial disagreement between the 20 most statistically significant gene sets reported by the methods. This was also observed when expanding to the 100 most statistically significant reported gene sets. For different datasets of the same phenotype/condition, the top 20 and top 100 most significant results also showed little to no agreement even when using the same method. GAGE, PAGE, and ORA were the only methods able to achieve relatively high reproducibility when comparing the 20 and 100 most statistically significant gene sets. Biological validation on a juvenile idiopathic arthritis (JIA) dataset showed wide variation in terms of the relevance of the top 20 and top 100 most significant gene sets to known biology of the disease, where GAGE predicted the most relevant gene sets, followed by GSEA, ORA, and PAGE.