Profiles of mathematical deficits in children with dyslexia

Despite a high rate of concurrent mathematical difficulties among children with dyslexia, we still have limited information regarding the prevalence and severity of mathematical deficits in this population. To address this gap, we developed a comprehensive battery of cognitive tests, known as the UCSF Mathematical Cognition Battery (MCB), with the aim of identifying deficits in four distinct mathematical domains: number processing, arithmetical procedures, arithmetic facts retrieval, and geometrical abilities. The mathematical abilities of a cohort of 75 children referred to the UCSF Dyslexia Center with a diagnosis of dyslexia, along with 18 typically developing controls aged 7 to 16, were initially evaluated using a behavioral neurology approach. A team of professional clinicians classified the 75 children with dyslexia into five groups, based on parents' and teachers' reported symptoms and clinical history. These groups included children with no mathematical deficits and children with mathematical deficits in number processing, arithmetical procedures, arithmetic facts retrieval, or geometrical abilities. Subsequently, the children underwent evaluation using the MCB to determine concordance with the clinicians' impressions. Additionally, neuropsychological and cognitive standardized tests were administered. Our study reveals that within a cohort of children with dyslexia, 66% exhibit mathematical deficits, and among those with mathematical deficits, there is heterogeneity in the nature of these deficits. If these findings are confirmed in larger samples, they can potentially pave the way for new diagnostic approaches, consistent subtype classification, and, ultimately personalized interventions.

Culture shock: microglial heterogeneity, activation, and disrupted single-cell microglial networks in vitro

BACKGROUND

Microglia, the resident immune cells of the brain, play a critical role in numerous diseases, but are a minority cell type and difficult to genetically manipulate in vivo with viral vectors and other approaches. Primary cultures allow a more controlled setting to investigate these cells, but morphological and transcriptional changes upon removal from their normal brain environment raise many caveats from in vitro studies.

METHODS

To investigate whether cultured microglia recapitulate in vivo microglial signatures, we used single-cell RNA sequencing (scRNAseq) to compare microglia freshly isolated from the brain to primary microglial cultures. We performed cell population discovery, differential expression analysis, and gene co-expression module analysis to compare signatures between in vitro and in vivo microglia. We constructed causal predictive network models of transcriptional regulators from the scRNAseq data and identified a set of potential key drivers of the cultured phenotype. To validate this network analysis, we knocked down two of these key drivers, C1qc and Prdx1, in primary cultured microglia and quantified changes in microglial activation markers.

RESULTS

We found that, although often assumed to be a relatively homogenous population of cells in culture, in vitro microglia are a highly heterogeneous population consisting of distinct subpopulations of cells with transcriptional profiles reminiscent of macrophages and monocytes, and are marked by transcriptional programs active in neurodegeneration and other disease states. We found that microglia in vitro presented transcriptional activation of a set of "culture shock genes" not found in freshly isolated microglia, characterized by strong upregulation of disease-associated genes including Apoe, Lyz2, and Spp1, and downregulation of homeostatic microglial markers, including Cx3cr1, P2ry12, and Tmem119. Finally, we found that cultured microglia prominently alter their transcriptional machinery modulated by key drivers from the homeostatic to activated phenotype. Knockdown of one of these drivers, C1qc, resulted in downregulation of microglial activation genes Lpl, Lyz2, and Ccl4.

CONCLUSIONS

Overall, our data suggest that when removed from their in vivo home environment, microglia suffer a severe case of "culture shock", drastically modulating their transcriptional regulatory network state from homeostatic to activated through upregulation of modules of culture-specific genes. Consequently, cultured microglia behave as a disparate cell type that does not recapitulate the homeostatic signatures of microglia in vivo. Finally, our predictive network model discovered potential key drivers that may convert activated microglia back to their homeostatic state, allowing for more accurate representation of in vivo states in culture. Knockdown of key driver C1qc partially attenuated microglial activation in vitro, despite C1qc being only weakly upregulated in culture. This suggests that even genes that are not strongly differentially expressed across treatments or preparations may drive downstream transcriptional changes in culture.

A phase II study of UCN-01 in combination with irinotecan in patients with metastatic triple negative breast cancer

Mutations in TP53 lead to a defective G1 checkpoint and the dependence on checkpoint kinase 1 (Chk1) for G2 or S phase arrest in response to DNA damage. In preclinical studies, Chk1 inhibition resulted in enhanced cytotoxicity of several chemotherapeutic agents. The high frequency of TP53 mutations in triple negative breast cancer (TNBC: negative for estrogen receptor, progesterone receptor, and HER2) make Chk1 an attractive therapeutic target. UCN-01, a non-selective Chk1 inhibitor, combined with irinotecan demonstrated activity in advanced TNBC in our Phase I study. The goal of this trial was to further evaluate this treatment in women with TNBC. Patients with metastatic TNBC previously treated with anthracyclines and taxanes received irinotecan (100–125 mg/m² IV days 1, 8, 15, 22) and UCN-01 (70 mg/m² IV day 2, 35 mg/m² day 23 and subsequent doses) every 42-day cycle. Peripheral blood mononuclear cells (PBMC) and tumor specimens were collected. Twenty five patients were enrolled. The overall response (complete response (CR) + partial response (PR)) rate was 4 %. The clinical benefit rate (CR + PR + stable disease ≥6 months) was 12 %. Since UCN-01 inhibits PDK1, phosphorylated ribosomal protein S6 (pS6) in PBMC was assessed. Although reduced 24 h post UCN-01, pS6 levels rose to baseline by day 8, indicating loss of UCN-01 bioavailability. Immunostains of γH2AX and pChk1^S296 on serial tumor biopsies from four patients demonstrated an induction of DNA damage and Chk1 activation following irinotecan. However, Chk1 inhibition by UCN-01 was not observed in all tumors. Most tumors were basal-like (69 %), and carried mutations in TP53 (53 %). Median overall survival in patients with TP53 mutant tumors was poor compared to wild type (5.5 vs. 20.3 months, p = 0.004). This regimen had limited activity in TNBC. Inconsistent Chk1 inhibition was likely due to the pharmacokinetics of UCN-01. TP53 mutations were associated with a poor prognosis in metastatic TNBC.

Abstract 1670: Molecular subtypes from PAM50 in a breast cancer cohort: differences by patient characteristic, reproducibility

BACKGROUND Gene expression profiling has been shown to improve prognostication in clinical trials, but data are lacking on expression-based molecular subtypes in context of variables of interest for epidemiology. We provide interim data on the distribution of subtypes determined by PAM50 assay in relation to standard immunohistochemical (IHC) markers and to subject characteristics in a breast cancer cohort. METHODS The study population combines women from the Life After Cancer Epidemiology (LACE) study with invasive breast cancer stages I (>=1 cm), II, or IIIA, diagnosed in 1997-2000 and the Pathways Study with invasive breast cancer at any stage (>= 0.5 cm) diagnosed in 2006-2008. IHC results for estrogen and progesterone receptors (ER, PR) and her2-neu (HER2) were obtained from records. Race, ethnicity, and breast cancer risk factors were from self-report. For a stratified sample of cases, 1 mm punches were obtained from areas of representative tumor in formalin-fixed, paraffin-embedded tissue blocks. Expression of the PAM50 genes was determined by RT-PCR of extracted RNA. Random blind duplicate tissue punches were assayed. A published centroid-based algorithm (Parker, J Clin Oncol 2009;27:1160-7) was used to generate, for each sample, five continuous-scale normalized subtype scores and a predicted subtype classification. We estimated sample-weighted subtype distributions, Pearson correlations among subtype scores, and age-adjusted odds ratios (OR). RESULTS PAM50 subtype predictions for 702 breast tumors from a community cohort were 55% Luminal (Lum) A, 19% LumB, 11% HER2-enriched, 10% Basal-like, and 5% Normal-like. Among the 72% of tumors categorized as ER+ or PR+, HER2- by IHC, PAM50 subtypes were: 72% LumA, 20% LumB, 2% HER2-enriched, 1% Basal-like, and 5% Normal-like. Continuous-scale LumA, LumB, HER2-enriched, and Normal-like scores were mutually positively correlated. Basal-like score was inversely correlated with other subtypes. 32 of 34 (94%) blind duplicate pairs were concordant for subtype. Compared to non-Hispanic whites, African-American women were less likely to have LumB subtype, OR 0.1 (95% CI 0.03 - 0.4), and somewhat more likely to have Basal-like subtype, OR 2.6 (95% CI 0.8-8.5) and Hispanics more often had non-LumA subtypes. Women with a family history of breast cancer had a lower frequency of HER2-enriched tumors, OR 0.3 (95% CI 0.2-0.7). DISCUSSION Molecular subtyping by PAM50 shifted 23% of tumors from the low-risk IHC-based ER+ or PR+, HER2- category to predicted higher-risk subtypes. Correlations among subtype scores and (infrequent) discordance of duplicate tissue punches may be accounted for by borderline phenotypes and/or heterogeneous cancers. Interim results showing PAM50 subtype differences by race and ethnicity and by breast cancer risk factors indicate that molecular subtyping is a promising tool for describing etiologic heterogeneity.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1670. doi:1538-7445.AM2012-1670

A comparison of PAM50 intrinsic subtyping with immunohistochemistry and clinical prognostic factors in tamoxifen-treated estrogen receptor-positive breast cancer

PURPOSE

To compare clinical, immunohistochemical (IHC), and gene expression models of prognosis applicable to formalin-fixed, paraffin-embedded blocks in a large series of estrogen receptor (ER)-positive breast cancers from patients uniformly treated with adjuvant tamoxifen.

EXPERIMENTAL DESIGN

Quantitative real-time reverse transcription-PCR (qRT-PCR) assays for 50 genes identifying intrinsic breast cancer subtypes were completed on 786 specimens linked to clinical (median follow-up, 11.7 years) and IHC [ER, progesterone receptor (PR), HER2, and Ki67] data. Performance of predefined intrinsic subtype and risk-of-relapse scores was assessed using multivariable Cox models and Kaplan-Meier analysis. Harrell's C-index was used to compare fixed models trained in independent data sets, including proliferation signatures.

RESULTS

Despite clinical ER positivity, 10% of cases were assigned to nonluminal subtypes. qRT-PCR signatures for proliferation genes gave more prognostic information than clinical assays for hormone receptors or Ki67. In Cox models incorporating standard prognostic variables, hazard ratios for breast cancer disease-specific survival over the first 5 years of follow-up, relative to the most common luminal A subtype, are 1.99 [95% confidence interval (CI), 1.09-3.64] for luminal B, 3.65 (95% CI, 1.64-8.16) for HER2-enriched subtype, and 17.71 (95% CI, 1.71-183.33) for the basal-like subtype. For node-negative disease, PAM50 qRT-PCR-based risk assignment weighted for tumor size and proliferation identifies a group with >95% 10-year survival without chemotherapy. In node-positive disease, PAM50-based prognostic models were also superior.

CONCLUSION

The PAM50 gene expression test for intrinsic biological subtype can be applied to large series of formalin-fixed, paraffin-embedded breast cancers, and gives more prognostic information than clinical factors and IHC using standard cut points.

DNA reference alignment benchmarks based on tertiary structure of encoded proteins

MOTIVATION

Multiple sequence alignments (MSAs) are at the heart of bioinformatics analysis. Recently, a number of multiple protein sequence alignment benchmarks (i.e. BAliBASE, OXBench, PREFAB and SMART) have been released to evaluate new and existing MSA applications. These databases have been well received by researchers and help to quantitatively evaluate MSA programs on protein sequences. Unfortunately, analogous DNA benchmarks are not available, making evaluation of MSA programs difficult for DNA sequences.

RESULTS

This work presents the first known multiple DNA sequence alignment benchmarks that are (1) comprised of protein-coding portions of DNA (2) based on biological features such as the tertiary structure of encoded proteins. These reference DNA databases contain a total of 3545 alignments, comprising of 68 581 sequences. Two versions of the database are available: mdsa_100s and mdsa_all. The mdsa_100s version contains the alignments of the data sets that TBLASTN found 100% sequence identity for each sequence. The mdsa_all version includes all hits with an E-value score above the threshold of 0.001. A primary use of these databases is to benchmark the performance of MSA applications on DNA data sets. The first such case study is included in the Supplementary Material.