Maria Martinez-Garcia

A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples.

The molecular classification of glioblastoma (GBM) based on gene expression might better explain outcome and response to treatment than clinical factors. Whole transcriptome sequencing using next-generation sequencing platforms is rapidly becoming accepted as a tool for measuring gene expression for both research and clinical use. Fresh frozen (FF) tissue specimens of GBM are difficult to obtain since tumor tissue obtained at surgery is often scarce and necrotic and diagnosis is prioritized over freezing. After diagnosis, leftover tissue is usually stored as formalin-fixed paraffin-embedded (FFPE) tissue. However, RNA from FFPE tissues is usually degraded, which could hamper gene expression analysis. We compared RNA-Seq data obtained from matched pairs of FF and FFPE GBM specimens. Only three FFPE out of eleven FFPE-FF matched samples yielded informative results. Several quality-control measurements showed that RNA from FFPE samples was highly degraded but maintained transcriptomic similarities to RNA from FF samples. Certain issues regarding mutation analysis and subtype prediction were detected. Nevertheless, our results suggest that RNA-Seq of FFPE GBM specimens provides reliable gene expression data that can be used in molecular studies of GBM if the RNA is sufficiently preserved.

Defective Cyclin B1 Induction in Trastuzumab-emtansine (T-DM1) Acquired Resistance in HER2-positive Breast Cancer.

Purpose: Trastuzumab-emtansine (T-DM1) is a standard treatment in advanced HER2-positive breast cancer. However, resistance inevitably occurs. We aimed to identify mechanisms of acquired T-DM1 resistance. Experimental Design: HER2-positive breast cancer cells (HCC1954, HCC1419, SKBR3, and BT474) were treated in a pulse-fashion with T-DM1 to induce a resistant phenotype. Cellular and molecular effects of T-DM1 in parental versus resistant cells were compared. CDK1 kinase activity and cyclin B1 expression were assayed under various conditions. Genetic modifications to up- or downregulate cyclin B1 were conducted. Effects of T-DM1 on cyclin B1 levels, proliferation, and apoptosis were assayed in human HER2-positive breast cancer explants. Results: We obtained three cell lines with different levels of acquired T-DM1 resistance (HCC1954/TDR, HCC1419/TDR, and SKBR3/TDR cells). HER2 remained amplified in the resistant cells. Binding to HER2 and intracellular uptake of T-DM1 were maintained in resistant cells. T-DM1 induced cyclin B1 accumulation in sensitive but not resistant cells. Cyclin B1 knockdown by siRNA in parental cells induced T-DM1 resistance, while increased levels of cyclin B1 by silencing cdc20 partially sensitized resistant cells. In a series of 18 HER2-positive breast cancer fresh explants, T-DM1 effects on proliferation and apoptosis paralleled cyclin B1 accumulation. Conclusions: Defective cyclin B1 induction by T-DM1 mediates acquired resistance in HER2-positive breast cancer cells. These results support the testing of cyclin B1 induction upon T-DM1 treatment as a pharmacodynamic predictor in HER2-positive breast cancer. Clin Cancer Res; 23(22); 7006–19. ©2017 AACR.

Phase II trial of dacomitinib, a pan–human EGFR tyrosine kinase inhibitor, in recurrent glioblastoma patients with EGFR amplification

Background We conducted a multicenter, 2-stage, open-label, phase II trial to assess the efficacy and safety of dacomitinib in adult patients with recurrent glioblastoma (GB) and epidermal growth factor receptor gene (EGFR) amplification with or without variant III (EGFRvIII) deletion. Methods Patients with first recurrence were enrolled in 2 cohorts. Cohort A included patients with EGFR gene amplification without EGFRvIII mutation. Cohort B included patients with EGFR gene amplification and EGFRvIII mutation. Dacomitinib was administered (45 mg/day) until disease progression/unacceptable adverse events (AEs). Primary endpoint was progression-free survival (PFS; RANO criteria) at 6 months (PFS6). Results Thirty patients in Cohort A and 19 in Cohort B were enrolled. Median age was 59 years (range 39-81), 65.3% were male, and Eastern Cooperative Oncology Group Performance Status 0/1/2 were 10.2%/65.3%/24.5%, respectively. PFS6 was 10.6% (Cohort A: 13.3%; Cohort B: 5.9%) with a median PFS of 2.7 months (Cohort A: 2.7 mo; Cohort B: 2.6 mo). Four patients were progression free at 6 months and 3 patients were so at 12 months. Median overall survival was 7.4 months (Cohort A: 7.8 mo; Cohort B: 6.7 mo). The best overall response included 1 complete response and 2 partial responses (4.1%). Stable disease was observed in 12 patients (24.5%: eight in Cohort A and four in Cohort B). Diarrhea and rash were the most common AEs; 20 (40.8%) patients experienced grade 3-4 drug-related AEs. Conclusions Dacomitinib has a limited single-agent activity in recurrent GB with EGFR amplification. The detailed molecular characterization of the 4 patients with response in this trial can be useful to select patients who could benefit from dacomitinib.

Pseudoprogression as an adverse event of glioblastoma therapy

We explored predictive factors of pseudoprogression (PsP) and its impact on prognosis in a retrospective series of uniformly treated glioblastoma patients. Patients were classified as having PsP, early progression (eP) or neither (nP). We examined potential associations with clinical, molecular, and basal imaging characteristics and compared overall survival (OS), progression‐free survival (PFS), post‐progression survival (PPS) as well as the relationship between PFS and PPS in the three groups. Of the 256 patients studied, 56 (21.9%) were classified as PsP, 70 (27.3%) as eP, and 130 (50.8%) as nP. Only MGMT methylation status was associated to PsP. MGMT methylated patients had a 3.5‐fold greater possibility of having PsP than eP (OR: 3.48; 95% CI: 1.606–7.564; P = 0.002). OS was longer for PsP than eP patients (18.9 vs. 12.3 months; P = 0.0001) but was similar for PsP and nP patients (P = 0.91). OS was shorter–though not significantly so—for PsP than nP patients (OS: 19.5 vs. 27.9 months; P = 0.63) in methylated patients. PPS was similar for patients having PsP, eP or nP (PPS: 7.2 vs. 5.4 vs. 6.7; P = 0.43). Neurological deterioration occurred in 64.3% of cases at the time they were classified as PsP and in 72.8% of cases of eP (P = 0.14). PsP confounds the evaluation of disease and does not confer a survival advantage in glioblastoma.

Dissociating morphological and form priming with novel complex word primes: Evidence from masked priming, overt priming, and event-related potentials

Recent research suggests that visually-presented words are initially morphologically segmented whenever the letter-string can be exhaustively assigned to existing morphological representations, but not when an exhaustive parse is unavailable; e.g., priming is observed for both hunter→HUNT and brother →BROTH, but not for brothel→BROTH. Few studies have investigated whether this pattern extends to novel complex words, and the results to date (all from novel suffixed words) are mixed. In the current study, we examine whether novel compounds (drugrack→RACK) yield morphological priming which is dissociable from that in novel pseudoembedded words (slegrack→RACK). Using masked priming, we find significant and comparable priming in reaction times for word-final elements of both novel compounds and novel pseudoembedded words. Using overt priming, however, we find greater priming effects (in both reaction times and N400 amplitudes) for novel compounds compared to novel pseudoembedded words. These results are consistent with models assuming across-the-board activation of putative constituents, while also suggesting that morpheme activation may persevere despite the lack of an exhaustive morpheme-based parse when an exhaustive monomorphemic analysis is also unavailable. These findings highlight the critical role of the lexical status of the pseudoembedded prime in dissociating morphological and orthographic priming.

Experience with a second language affects the use of fundamental frequency in speech segmentation

This study investigates whether listeners’ experience with a second language learned later in life affects their use of fundamental frequency (F0) as a cue to word boundaries in the segmentation of an artificial language (AL), particularly when the cues to word boundaries conflict between the first language (L1) and second language (L2). F0 signals phrase-final (and thus word-final) boundaries in French but word-initial boundaries in English. Participants were functionally monolingual French listeners, functionally monolingual English listeners, bilingual L1-English L2-French listeners, and bilingual L1-French L2-English listeners. They completed the AL-segmentation task with F0 signaling word-final boundaries or without prosodic cues to word boundaries (monolingual groups only). After listening to the AL, participants completed a forced-choice word-identification task in which the foils were either non-words or part-words. The results show that the monolingual French listeners, but not the monolingual English listeners, performed better in the presence of F0 cues than in the absence of such cues. Moreover, bilingual status modulated listeners’ use of F0 cues to word-final boundaries, with bilingual French listeners performing less accurately than monolingual French listeners on both word types but with bilingual English listeners performing more accurately than monolingual English listeners on non-words. These findings not only confirm that speech segmentation is modulated by the L1, but also newly demonstrate that listeners’ experience with the L2 (French or English) affects their use of F0 cues in speech segmentation. This suggests that listeners’ use of prosodic cues to word boundaries is adaptive and non-selective, and can change as a function of language experience.

Effects of native language on the use of segmental and suprasegmental cues to stress in English word recognition: An eye-tracking study

This study investigates whether the presence of lexical stress in the native language (L1) determines second-language (L2) learners’ ability to use stress in L2 lexical access. It focuses on (standard Mandarin) Chinese and (Seoul) Korean listeners’ (and native English listeners’) use of segmental and suprasegmental cues to stress in English word recognition. Stress placement in English is signaled by segmental (vowel reduction) and suprasegmental (fundamental frequency, duration, and intensity) cues. Chinese has full-full and full-reduced words that differ in stress placement, with segmental and suprasegmental cues signaling stress. By contrast, Korean does not have lexical stress. Participants completed an eye-tracking experiment. They heard stimuli containing a target word with initial stress (parrot), and saw four orthographic words in the display, including the target and one of two competitors (stress match: parish; stress mismatch: parade). The first syllable of the target and stress-mismatch compet...

Effects of language bias and proficiency on cross-language activation: Evidence from eye-tracking

Language bias and proficiency have been proposed to modulate cross-language activation, but it is unclear how they operate and whether they interact. This study sheds further light on this by investigating whether stress differences between Spanish-English cognates (material, final-syllable stress in Spanish) affect how native-English second-language-Spanish bilinguals recognize Spanish words (materia “subject/matter,” second-syllable stress in Spanish). In a Spanish-English eye-tracking experiment, participants heard trisyllabic Spanish targets with second-syllable stress (materia) and saw four orthographic words, including the target and a Spanish-English cognate competitor. Cross-language activation was examined by manipulating the stress of the cognate in English; English cognates with the same stress as the Spanish target (target: materia, competitor: material) were predicted to cause more cross-language interference than English cognates with a different stress (target: litera “bunk bed,” competitor...

Perception of epenthetic vowels in English /s/-initial clusters by Spanish-speaking second language learners of English

Second language learners’ (L2ers’) perception and production of consonant clusters is influenced by the syllable structure of the native language (L1). This study investigates whether the perception of epenthetic vowels is partially responsible for why Spanish speakers have difficulty producing /s/ + Consonant (“sC”) clusters in English, and whether it affects word recognition in continuous speech. Spanish, German L2ers of English, and native English speakers completed: (i) an AXB task with (/ə/)sC-initial nonce words (e.g., [əsman]-[sman]); (ii) a word monitoring task with (/ə/)sC-initial words in semantically ambiguous sentences (e.g., I have lived in that (e)state for a long time); and (iii) a production task with the same sentences as in (i). L2ers also took a word-familiarity rating task and a cloze test to assess their proficiency. For (i) and (ii), accuracy rates were recorded, and response times were measured from target onset. For (iii), acoustic analyses showed whether the L2ers’ productions of ...