Classification of DBS microelectrode recordings using a residual neural network with attention in the temporal domain

During the Deep Brain Stimulation (DBS) surgery for Parkinson's disease (PD), the main goal is to place the permanent stimulating electrode into an area of the brain that becomes pathologically hyperactive. This area, called Subthalamic Nucleus (STN), is small and located deep within the brain. Therefore, the main challenge is the precise localization of the STN region, considering various measurement errors and artifacts. In this paper, we have designed and developed a computer-aided decision support system for neurosurgical DBS surgery. The implementation of this system provides a novel method for calculating the expected position of the stimulating electrode based on the recordings of the electrical activity of brain tissue. The artificial neural network with attention is used to classify the microelectrode recordings and determine the final position of the stimulating electrode within the STN area. Experiments have verified the utility and efficiency of our system. The tests were carried out on many recordings collected during DBS surgeries, giving encouraging results. The experimental results demonstrate that deep learning methods extended with self-attention blocks compete with the other solutions. They provide significant robustness to recording artifacts and improve the accuracy of the stimulating electrode placement.

Spinal tumours: recommendations of the Polish Society of Spine Surgery, the Polish Society of Oncology, the Polish Society of Neurosurgeons, the Polish Society of Oncologic Surgery, the Polish Society of Oncologic Radiotherapy, and the Polish Society of Orthopaedics and Traumatology

PURPOSE

The purpose of these recommendations is to spread the available evidence for evaluating and managing spinal tumours among clinicians who encounter such entities.

METHODS

The recommendations were developed by members of the Development Recommendations Group representing seven stakeholder scientific societies and organizations of specialists involved in various forms of care for patients with spinal tumours in Poland. The recommendations are based on data yielded from systematic reviews of the literature identified through electronic database searches. The strength of the recommendations was graded according to the North American Spine Society's grades of recommendation for summaries or reviews of studies.

RESULTS

The recommendation group developed 89 level A-C recommendations and a supplementary list of institutions able to manage primary malignant spinal tumours, namely, spinal sarcomas, at the expert level. This list, further called an appendix, helps clinicians who encounter spinal tumours refer patients with suspected spinal sarcoma or chordoma for pathological diagnosis, surgery and radiosurgery. The list constitutes a basis of the network of expertise for the management of primary malignant spinal tumours and should be understood as a communication network of specialists involved in the care of primary spinal malignancies.

CONCLUSION

The developed recommendations together with the national network of expertise should optimize the management of patients with spinal tumours, especially rare malignancies, and optimize their referral and allocation within the Polish national health service system.

Aberrant DNA methylation of alternative promoter of DLC1 isoform 1 in meningiomas

DLC1 encodes GTPase-activating protein with a well-documented tumor suppressor activity. This gene is downregulated in various tumors through aberrant promoter hypermethylation. Five different DLC1 isoforms can be transcribed from alternative promoters. Tumor-related DNA methylation of the DLC1 isoform 1 alternative promoter was identified as being hypermethylated in meningiomas in genome-wide DNA methylation profiling. We determined the methylation pattern of this region in 50 meningioma FFPE samples and sections of 6 normal meninges, with targeted bisulfite sequencing. All histopathological subtypes of meningiomas showed similar and significant increase of DNA methylation levels. High DNA methylation was associated with lack of DLC1 protein expression in meningiomas as determined by immunohistochemistry. mRNA expression levels of 5 isoforms of DLC1 transcript were measured in an additional series of meningiomas and normal meninges. The DLC1 isoform 1 was found as the most expressed in normal control tissue and was significantly downregulated in meningiomas. Transfection of KT21 meningioma cell line with shRNA targeting DLC1 isoform 1 resulted in increased activation of RHO-GTPases assessed with pull-down assay, enhanced cell migration observed in scratch assay as well as slight increase of cell metabolism determind by MTT test. Results indicate that isoform 1 represents the main pool of DLC1 protein in meninges and its downregulation in meningiomas is associated with hypermethylation of CpG dinucleotides within the corresponding promoter region. This isoform is functional GAP protein and tumor suppressor and targeting of its expression results in the increase of DLC1 related cell processes: RHO activation and cell migration.

Abstract P6-11-07: Quantitative p95HER2 levels in primary breast cancers and in matched brain metastases

Background: Patients with HER2-positive breast cancer are at high risk for brain metastases. A large number of HER2-positive tumors also express p95HER2 (p95), a truncated form of HER2 that lacks the trastuzumab binding site but retains kinase activity. Although p95 expression in primary breast tumors is well studied, the prevalence and significance of p95 expression in brain metastases is unknown. In the current study we examined expression of p95 in brain metastases and in matched primary breast tumors.

Methods: Seventy-five pairs of formalin-fixed paraffin-embedded samples from matched primary breast cancers and brain metastases were assayed for quantitative p95 protein expression using the p95 VeraTag® assay (Clin Cancer Res, 16:4226, 2010) specific for the M611 form of p95. Sufficient material to obtain p95 data in both primary and matched brain metastasis samples was available in 52 cases. In the remaining 23 cases, a p95 measurement was obtained in either the primary or brain metastasis sample. Estrogen (ER) and progesterone (PR) receptor status were scored using immunohistochemistry. Hormone receptor positivity was defined as either ER or PR positive. Quantitative HER2 protein expression was measured using the HERmark® assay. Both the p95 VeraTag assay and the HERmark assay measure tumor-averaged protein expression in units of relative fluorescence per mm2 tumor (RF/mm2). Measurements of p95 > 2.8 RF/mm2 and HER2 > 17.8 RF/mm2 were considered as positive results.

Results: There was a net increase in p95 expression in brain metastases relative to the matched primary tumor with a median increase of 1.5-fold (p = 0.001, range 0.2-fold to 35-fold). The increase in p95 expression was only weakly correlated with the increase in quantitative HER2 expression (R2 = 0.18; p = 0.0018). Cases with HERmark-positive tumors were more likely to have the largest (≥ 5-fold) increase in p95 expression compared to those with lower HER2 expression (odds ratio = 6.3; p = 0.018). Changes in p95 levels from primary to brain metastasis were unrelated to hormone receptor status (p = 0.59). P95 positivity in the primary tumor correlated with time from breast cancer diagnosis to first progression (HR = 2.2; p = 0.012) when stratified by hormone receptor status and tumor grade. Although there was a trend towards correlation of p95 positivity in the brain metastasis with time from diagnosis to brain metastasis (HR = 1.7; p = 0.058, stratified as above), p95 positivity did not correlate with overall survival from the time of brain metastasis diagnosis (HR = 1.3; p = 0.42, stratified as above).

Conclusions: This is the first study of quantitative p95 expression in matched primary tumors and brain metastases. Brain metastases of breast cancer show significant increases in p95 protein expression compared to matched primary tumors. These data provide a rationale for future correlative studies on p95 levels in brain metastases.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P6-11-07.

Molecular characteristics of matched brain metastasis (BM) versus the primary breast cancer (PBC)

Abstract #2028

Background: Brain is increasingly a site of relapse in breast cancer patients, however the molecular patho-physiology of this process is not well understood. Using a novel assay allowing high-throughput analysis of gene expression from formalin-fixed paraffin-embedded (FFPET) tumor samples, we compared molecular characteristics of BM with those of the PBC in a series of breast cancer patients who underwent excision of brain metastasis.
 Methods: In each patient we performed molecular analysis of paired archived FFPET specimens from both the PBC and excised BM. Of the 37 pairs of PBC/BM samples, 24 pairs had sufficient pathology material for molecular analysis. Patient characteristics: mean age at PBC diagnosis was 46.7 years (range 27-67 years); 7 (29%) ER+, 17 (71%) ER-, 12 (50%) HER2-positive(3+). We performed cDNA-mediated annealing, selection, extension and ligation (DASL) assay (Illumina Corp) for expression of 502 known cancer genes, using 200 ng RNA. Statistical analysis for microarrays (SAM) accounting for the pairing of the primary and metastasized tumors was used to identify differentially expressed genes while controlling the false discovery rate (FDR <0.01). BeadStudio™ Absolute correlation clustering was used to cluster samples based on their expression profiles.
 Results: In only 7 (29%) cases matched PBC and BM pair clustered together on unsupervised hierarchical clustering, the pairs in remaining cases clustered apart. Comparison of the two groups (PBC and BM) showed that 41 genes were up regulated in BM, including proliferation genes (CDC2, CDC25a, CCNA2 and E2F family), anti-apoptotic (BIRC5), DNA repair (RAD51, -54b, XRCC2, BRCA2, BARD1, TOP1), angiogenesis (VEGF), and development of drug resistance (ABCB1, -G2). In contrast, the 43 genes that were down regulated in BM included those associated with invasion (MMP2, -3, -14), cellular motility, and epithelial to mesenchymal transformation (CDH11). Additional analysis to validate these trends and to identify potential therapeutic targets is underway.
 Conclusions: Although some BM retain remarkable similarity to the PBC, majority exhibit considerable deviation in their gene expression profile. These “adaptive” changes include greater resistance to drug therapy, increased DNA repair, a reversal back to the epithelial phenotype and decreased capacity for cell motility and invasion.

Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 2028.

Tract identification by novel MRI signal changes following stereotactic anterior capsulotomy

BACKGROUND

Five patients underwent magnetic resonance imaging (MRI) following MRI-guided stereotactic bilateral anterior capsulotomy to detect lesion-related anatomic changes.

METHODS

Five disabled and treatment-resistant patients with major depression (n = 4) and obsessive-compulsive disorder (n = 1) underwent stereotactic bilateral anterior capsulotomy. All patients had postoperative MRI at 2 months and at 1-4 years after surgery. An additional patient who had a pure motor deficit following a spontaneous basal ganglia hemorrhagic stroke was imaged as a comparator.

RESULTS

The 2-month postcapsulotomy MRI showed a previously undescribed increase in T1-weighted signal within similar neural pathways for each patient. These pathways showed no changes in T2-weighted or fluid-attenuated inversion recovery sequences. The signal changes are different from the expected changes associated with anterograde Wallerian degeneration and identify retrograde changes in the proximal segment of the interrupted axon.

CONCLUSION

Previously undescribed T1-weighted signal alterations following stereotactic surgery identify retrograde non-Wallerian changes in interrupted axons and provide a new method in identifying and tracing lesioned pathways.