Sam Ng

Breast cancers are comprised of molecularly distinct subtypes that may respond differently to pathway-targeted therapies now under development. Collections of breast cancer cell lines mirror many of the molecular subtypes and pathways found in tumors, suggesting that treatment of cell lines with candidate therapeutic compounds can guide identification of associations between molecular subtypes, pathways, and drug response. In a test of 77 therapeutic compounds, nearly all drugs showed differential responses across these cell lines, and approximately one third showed subtype-, pathway-, and/or genomic aberration-specific responses. These observations suggest mechanisms of response and resistance and may inform efforts to develop molecular assays that predict clinical response.

BACKGROUND: Chronic subdural hematoma (CSDH) is a common condition requiring surgical treatment; however, recurrence occurs in 15% of cases at 1 year. Middle meningeal artery (MMA) embolization has recently emerged as a promising treatment to prevent CSDH recurrence. OBJECTIVE: To investigate the effect of MMA embolization on hematoma volume resorption (HVR) after surgery in symptomatic patients. METHODS: From April 2018 to October 2018, participants with CSDH requiring surgery were prospectively randomized in a pilot study, and received either surgical treatment alone (ST group) or surgery and adjuvant MMA embolization (ST+MMAE group). The primary outcome was HVR measured on the 3 month CT scan compared with the immediate pre-embolization CT scan. Secondary outcomes were clinical recurrence of CSDH and safety measures. RESULTS: 46 patients were randomized and 41 of these achieved a 3 month follow-up . Twenty-one patients received MMA embolization. At 3 months, the HVR from postsurgical level was higher in the ST+MMAE group (mean difference 17.5 mL, 95% CI 3.87 to 31.16 mL; p=0.015). Two participants presented a CSDH recurrence (one in each group). One patient died (ST group). No MMA embolization-related adverse events were reported. CONCLUSION: The addition of MMA embolization to surgery led to an increase in CSDH resorption at 3 months. One recurrence of CSDH was reported in each group, and there were no treatment-related complications.

MOTIVATION: A current challenge in understanding cancer processes is to pinpoint which mutations influence the onset and progression of disease. Toward this goal, we describe a method called PARADIGM-SHIFT that can predict whether a mutational event is neutral, gain-or loss-of-function in a tumor sample. The method uses a belief-propagation algorithm to infer gene activity from gene expression and copy number data in the context of a set of pathway interactions. RESULTS: The method was found to be both sensitive and specific on a set of positive and negative controls for multiple cancers for which pathway information was available. Application to the Cancer Genome Atlas glioblastoma, ovarian and lung squamous cancer datasets revealed several novel mutations with predicted high impact including several genes mutated at low frequency suggesting the approach will be complementary to current approaches that rely on the prevalence of events to reach statistical significance. AVAILABILITY: All source code is available at the github repository http:github.org/paradigmshift. CONTACT: jstuart@soe.ucsc.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.