MutAid: Sanger and NGS Based Integrated Pipeline for Mutation Identification, Validation and Annotation in Human Molecular Genetics

Blockade of neutral sphingomyelinase 2 exerts antitumor effect on metastatic castration resistant prostate cancer cells and promotes tumor regression when combined with Enzalutamide

Prostate cancer (PCa) is the second leading cause of cancer-related deaths among American men. The development of metastatic castration resistant PCa (mCRPC) is the current clinical challenge. Antiandrogens such as Enzalutamide (ENZ) are commonly used for CRPC treatment. However, patients with androgen receptor (AR)-negative tumors do not respond to ENZ, while AR-positive tumors frequently develop resistance, limiting the long-term efficacy of this therapy. This study investigates the efficacy of neutral sphingomyelinase 2 (n-SMase2) inhibition by DPTIP, both alone and in combination with ENZ, as a therapeutic strategy for mCRPC. In vitro assays were conducted to determine the half-maximal inhibitory concentration (IC50) of DPTIP and ENZ in mCRPC cells. The effect of these treatments on cell proliferation, migration, and colony formation was assessed. The antitumor effect of DPTIP was also evaluated in a preclinical PCa mouse model. Elevated n-SMase2 expression was observed in PCa patients compared to normal subjects at both mRNA and protein levels. In CWR-R1ca and PC-3 cells, DPTIP had IC50 values of 10.31 and 14.57 µM, while ENZ had IC50 values of 33.7 and 81 µM, respectively. Combined treatment significantly suppressed cell proliferation, colony formation, and migration of mCRPC cells. Mechanistically, the ERK1/2 activity and the expression of nSMase2 and NF-kB p65 were inhibited by DPTIP. The in vivo combination of DPTIP and ENZ reduced tumor size and weight more effectively than either drug alone, without significant changes in body weight. This study highlights the therapeutic potential of targeting n-SMase2 for mCRPC. Inhibition of n-SMase2 using DPTIP, both as a standalone treatment and in combination with ENZ, effectively suppressed the growth and migration of mCRPC cells. These findings suggest a promising novel approach to treating mCRPC and warrant further investigation in clinical settings.

Next-Generation Sequencing Markup Language (NGSML): A Medium for the Representation and Exchange of NGS Data

With the increasing demand for low-cost high-throughput sequencing of large genomes, next-generation sequencing (NGS) technology has developed rapidly. NGS can not only be used in basic scientific research but also in clinical diagnostics and healthcare. Numerous software systems and tools have been developed to analyze NGS data, and various data formats have been produced to accommodate different sequencing equipment providers or analytical software. However, the data interoperability between these tools brings great challenges to researchers. A generic format that could be shared by most of the software and tools in the NGS field would make data interoperability and sharing easier. In this paper, we defined a general XML-based NGS markup language (NGSML) format for the representation and exchange of NGS data. We also developed a user-friendly GUI tool, NGSMLEditor, for presenting, creating, editing, and converting NGSML files. By using NGSML, various types of NGS data can be saved in one unified format. Compared with the unstructured plain text file, a structured data format based on XML technology solves the incompatibility of various NGS data formats. The NGSML specifications are freely available from http://www.sysbio.org.cn/NGSML. NGSMLEditor is open source under GNU GPL and can be downloaded from the website.

Breaking Proportional Recovery After Stroke

People with hemiparesis after stroke appear to recover 70% to 80% of the difference between their baseline and the maximum upper extremity Fugl-Meyer (UEFM) score, a phenomenon called proportional recovery (PR). Two recent commentaries explained that PR should be expected because of mathematical coupling between the baseline and change score. Here we ask, If mathematical coupling encourages PR, why do a fraction of stroke patients (the "nonfitters") not exhibit PR? At the neuroanatomical level of analysis, this question was answered by Byblow et al-nonfitters lack corticospinal tract (CST) integrity at baseline-but here we address the mathematical and behavioral causes. We first derive a new interpretation of the slope of PR: It is the average probability of scoring across remaining scale items at follow-up. PR therefore breaks when enough test items are discretely more difficult for a patient at follow-up, flattening the slope of recovery. For the UEFM, we show that nonfitters are most unlikely to recover the ability to score on the test items related to wrist/hand dexterity, shoulder flexion without bending the elbow, and finger-to-nose movement, supporting the finding that nonfitters lack CST integrity. However, we also show that a subset of nonfitters respond better to robotic movement training in the chronic phase of stroke. These persons are just able to move the arm out of the flexion synergy and pick up small blocks, both markers of CST integrity. Nonfitters therefore raise interesting questions about CST function and the basis for response to intensive movement training.

KIT exon 11 and PDGFRA exon 18 gene mutations in gastric GIST: proposal of a short panel for predicting therapeutic response

Background

GIST is the most common mesenchymal tumor of gastrointestinal tract and is more frequent in stomach. Its main mutations affect KIT and PDGFRA genes. Full genetic analysis panels are currently used to study mutations in GIST and other tumors. Considering that in gastric GIST KIT gene mutations in exon 11 are sensitive to IM whereas PDGFRΑ gene mutations in exon 18 (D842V) are resistant to the same drug, the aim of this study is to focus on these two molecular targets as a short alternative panel for predicting therapeutic response in gastric GIST which might optimize resources.

Methods

The genotypes of 38 cases of primary GIST were determined by performing bidirectional DNA sequencing.

Results

Exon 11 of KIT gene showed mutations in 65.3% and the exon 18 of PDGFRA gene showed 9% of cases. So it was possible to determine a subgroup of tumors which presented mutations in KIT exon 11 and PDGFRA exon 18.

Conclusion

Considering all of the foregoing analyzed globally, the application of short panel has impact on the cost and time of release of results to the physician, allowing a rapid approach to patients eligible for treatment with the target therapy.

Application of a molecular diagnostic algorithm for haemophilia A and B using next-generation sequencing of entire F8, F9 and VWF genes

Currently, molecular diagnosis of haemophilia A and B (HA and HB) highlights the excess risk-inhibitor development associated with specific mutations, and enables carrier testing of female relatives and prenatal or preimplantation genetic diagnosis. Molecular testing for HA also helps distinguish it from von Willebrand disease (VWD). Next-generation sequencing (NGS) allows simultaneous investigation of several complete genes, even though they may span very extensive regions. This study aimed to evaluate the usefulness of a molecular algorithm employing an NGS approach for sequencing the complete F8, F9 and VWF genes. The proposed algorithm includes the detection of inversions of introns 1 and 22, an NGS custom panel (the entire F8, F9 and VWF genes), and multiplex ligation-dependent probe amplification (MLPA) analysis. A total of 102 samples (97 FVIII- and FIX-deficient patients, and five female carriers) were studied. IVS-22 screening identified 11 out of 20 severe HA patients and one female carrier. IVS-1 analysis did not reveal any alterations. The NGS approach gave positive results in 88 cases, allowing the differential diagnosis of mild/moderate HA and VWD in eight cases. MLPA confirmed one large exon deletion. Only one case did have no pathogenic variants. The proposed algorithm had an overall success rate of 99 %. In conclusion, our evaluation demonstrates that this algorithm can reliably identify pathogenic variants and diagnose patients with HA, HB or VWD.

Supplementary Material to this article is available online at www.thrombosis-online.com.