Abstract 3363: Spatial and longitudinal tumor heterogeneity in head and neck squamous cell carcinoma patients treated with primary surgery

Introduction: Cell-free tumor DNA (ctDNA) is an emerging biomarker in head and neck squamous cell carcinoma (HNSCC) for disease staging, patients’ recurrence risk stratification and early detection of relapse. We aimed to compare variants identified in ctDNA versus surgical tumor specimen, and to study the evolution of the mutational landscape of ctDNA over time in HNSCC.

Patients and Method: Forty-one HNSCC patients treated with curative-intent primary surgery from SCANDARE cohort (NCT03017573) were evaluated for longitudinal ctDNA-based NGS. Overall, 28 patients were treated with adjuvant (chemo)radiotherapy, and 31 experienced recurrence. Formalin-fixed paraffin-embedded tumor tissues at surgery were available for 41 patients. Serial contributive ctDNA were retrieved from all 41 patients at the date of surgery, 36 patients within 19 weeks after surgery, 20 patients at six months after surgery, and 22 patients at recurrence. Tissue DNA was personalized detected with a custom NGS panel of 571 genes (DRAGON) and ctDNA was sequenced using another personalized dedicated NGS panel including up to 15 genes (OncoFOLLOW).

Results: Most frequently mutated genes in tissue included TP53 (15.9%), FAT1 (6.7%), NOTCH1 (5.5%) and PIK3CA (4.3%) with similar allelic ratio to ctDNA at baseline surgery. Higher prevalence of KRAS and TP53 mutations was found in ctDNA at recurrence in comparison with ctDNA and tissue, respectively, at baseline surgery (KRAS: 6.3% versus 1.6% and 0.6%; TP53: 31.2% versus 21.1% and 15.9%). Additional variants in NRAS, HRAS, TP53, JAK2 and SDHA were detected in 6 patients in ctDNA at surgery and were not found in tissue, suggesting spatial intratumor heterogeneity. Twenty-three/36 patients (64%) had detected ctDNA within 19 weeks after surgery among whom, 17/23 patients (74%) had disease recurrence. Eleven/20 patients (including 10 with adjuvant treatment) had detected ctDNA at six months after surgery among whom 6 patients (55%) had disease recurrence. Fifteen/22 patients (68%) had detected ctDNA at recurrence. Emerging pathogenic variants were found in patients with detected ctDNA after surgery (n=7/23; 30%), at six months after surgery (n=1/11; 9%) and at recurrence (n=4/15; 27%).

Conclusion: Our study suggests spatial and longitudinal tumor heterogeneity and reports emerging mutations in ctDNA over time in HNSCC. Prognostic significance characterization of the ctDNA dominant clone allele frequency is ongoing.

Citation Format: Grégoire Marret, Constance Lamy, Sophie Vacher, Mathieu Séné, Ladidi Ahmanache, Laura Courtois, Zakhia El Beiano, Jerzy Klijanienko, Charlotte Martinat, Nicolas Servant, Choumouss Kamoun, Linda Larbi Chérif, Thierry Bronzini, Cédric Balsat, Jean-François Laes, Aubray Prévot, Sébastien Sauvage, Maxime Lienard, Emmanuel Martin, Bérengère Genin, Nathalie Badois, Maria Lesnik, Antoine Dubray-Vautrin, Olivier Choussy, Wahib Ghanem, Rabah Taouachi, Julien Masliah Planchon, Ivan Bièche, Maud Kamal, Christophe Le Tourneau. Spatial and longitudinal tumor heterogeneity in head and neck squamous cell carcinoma patients treated with primary surgery [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3363.

c-MET as a Potential Resistance Mechanism to Everolimus in Breast Cancer: From a Case Report to Patient Cohort Analysis

BACKGROUND

We describe in a patient with breast cancer the change in c-MET expression during everolimus treatment, opening a better understanding of the resistance to everolimus and a role for cabozantinib.

OBJECTIVE

The objective of this study was to evaluate c-MET as a potential predictive biomarker for everolimus efficacy in breast cancer.

METHODS

We first selected a patient with breast cancer with a long-lasting response to everolimus and retrospectively profiled biopsies that were taken before everolimus initiation (Biopsy 1) and at progression on everolimus (Biopsy 2) using amplicon sequencing and immunohistochemistry. We then retrospectively evaluated c-MET expression in a cohort of patients with breast cancer treated with everolimus.

RESULTS

While not expressed in Biopsy 1, c-MET was highly expressed in Biopsy 2, suggesting a role for c-MET in breast cancer progression. Cabozantinib resulted in a rapid radiological response in this patient. Twenty-nine patients were included (12 c-MET-positive and 17 c-MET-negative patients) in the second part of the study. Baseline c-MET expression was associated with higher tumor grade, higher frequency of visceral metastases, and lower endocrine sensitivity. The c-MET-positive patients presented with a shorter progression-free survival (6.1 vs 10.5 months, respectively; p = 0.002) and a lower response rate (0% vs 12%) to everolimus, compared with c-MET-negative patients.

CONCLUSIONS

c-MET could play a role in the resistance to everolimus and its inhibition should be evaluated in breast cancer.

Abstract LB-221: Circulating tumor DNA detects early response to regorafenib in advanced colorectal cancer

Purpose: To demonstrate that an early increase in ctDNA plasmatic levels after 14 days may identify patients (pts) with advanced chemorefractory colorectal cancer (aCRC) unlikely to benefit from regorafenib. Experimental procedures: The RegARd-C prospective multicentric clinical trial (NCT01929616) collected archival tumor tissue and plasma samples at baseline (BL), 14 days (D14) and every 2 months after treatment initiation in aCRC pts (n=141). A targeted gene sequencing was performed on pts' tumor tissue to identify tumor-specific mutations using a panel of 47 genes commonly mutated in CRC. To monitor circulating tumor DNA (ctDNA) levels in plasma samples collected at BL and D14 via droplet digital PCR (Bio-Rad QX200 ddPCR system), we selected tumor-specific mutations based on their allelic frequency.

Results: As foreseen, in 96 pts the most common mutated genes were APC (73%), TP53 (72%), KRAS (66%), and PI3KCA (23%). Among these pts, 24 (25%), 49 (51%), 18 (19%) and 5 (5%) had respectively one, two, three and four tumor-specific mutations followed via ddPCR. On average 2 (range 1-4) tumor-specific mutations were followed per patient. In total, 65 specific paired PrimePCRTM ddPCRTM Mutation Detection Assays were optimized following digital MIQE guidelines to assess ctDNA levels. As previously described1, ctDNA levels were assessed in terms of absolute values of mutated copies per mL of plasma to avoid bias in the mutated/mutated + wild-type copies ratio. We considered an increase in ctDNA level of at least 12% as significant2. Pts were separated according to the presence (n=53) or absence (n=43) of at least one increasing mutation between BL and D14. An increase of at least one tumor-specific mutation as compared to none is associated with a significantly worse clinical outcome with a median PFS of 1.3 months versus 3.0 months (HR 1.88, P=0.002, 95% CI 1.24-2.85) and a median OS of 3.9 months versus 8.5 months (HR 2.04, P<0.001, 95% CI 1.33-3.12).

Conclusion: Early (14 days) change in ctDNA levels under regorafenib therapy describes adequately the outcome of patients and may be used as a reliable tool for treatment personalization. Additionally, we confirmed the importance of using the absolute value of ctDNA instead of the mutated/total copies ratio usually reported in the literature for monitoring the outcome of a toxic treatment such as regorafenib. 1Kehagias P. et al. Oral presentation. LKI symposium, 2017; Leuven 2Whale AS. et al. Anal Chem. 2017

Citation Format: Pashalina Kehagias, Caroline Vandeputte, Lieveke Ameye, Hakim El Housni, Jean-François Laes, Amélie Deleporte, Karen Geboes, Thierry Delaunoit, Gauthier Demolin, Marc Peeters, Lionel D'Hondt, Jos Janssens, Javier Carrasco, Maria Gomez Galdon, Ghanem Ghanem, Pierre Heimann, Marianne Paesmans, Patrick Flamen, Alain Hendlisz. Circulating tumor DNA detects early response to regorafenib in advanced colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-221.

Circulating tumor DNA in early response assessment and monitoring of advanced colorectal cancer treated with a multi-kinase inhibitor

Predictive biomarkers are eagerly awaited in advanced colorectal cancer (aCRC). Targeted sequencing performed on tumor and baseline plasma samples in 20 patients with aCRC treated with regorafenib identified 89 tumor-specific mutations of which ≥50% are also present in baseline plasma. Droplet digital PCR (ddPCR) assays were optimized to monitor circulating tumor DNA (ctDNA) levels in plasmatic samples collected throughout the treatment course and showed the importance of using the absolute value for ctDNA rather than the mutant/wild type ratio in monitoring the therapy outcome. High baseline cell free DNA (cfDNA) levels are associated with shorter overall survival (OS) (HR 7.38, P=0.001). An early increase (D14) in mutated copies/mL is associated with a significantly worse PFS (HR 6.12, P=0.008) and OS (HR 8.02, P=0.004). These data suggest a high prognostic value for early ctDNA level changes and support the use of blood-born genomic markers as a tool for treatment.

EML4-ALK translocation identification in RNA exosomal cargo (ExoALK) in NSCLC patients: a novel role for liquid biopsy

The introduction of druggable targets has significantly improved the outcomes of non-small cell lung cancer patients (NSCLC). EML4-ALK translocation represents 4–6% of the druggable alterations in NSCLC. With the approval of Crizotinib, first discovered drug for the EML4-ALK translocation, on first line treatment for patients with detected mutation meant a complete change on the treatment landscape. The current standard method for EML4-ALK identification is immunohistochemistry or FISH in a tumor biopsy. However, a big number of NSCLC patients have not tissue available for analysis and others are not suitable for biopsy due to their physical condition or the location of the tumor. Liquid biopsy seems the best alternative for identification in these patients that have no tissue available. Circulating free RNA has not been validated for the identification of this mutation. As a complementary tool, exosomes might represent a good tool for predictive biomarkers study, and due to their stability, they preserve the genetic material contained in them. Our group has described for the first time the translocation EML4-ALK in RNA isolated from exosomes derived from NSCLC patients using next generation sequencing.

Tumor-biopsy stratification based on mTOR-pathway activity and functional mutations in the upstream genes PIK3CA and PTEN

The mechanistic target of the rapamycin (mTOR) pathway is frequently activated in human cancers. Our objective was to evaluate relationships between mTOR-pathway activity and functional mutations in the upstream genes PIK3CA and PTEN in solid-tumor biopsies from a broad selection of cancer types. Formalin-fixed paraffin-embedded (FFPE) tumor samples were analyzed by immunohistochemistry (IHC) and next-generation sequencing (NGS). TOR-pathway activation was identified by expression (by IHC) of the downstream effector p-4E-BP1. Activating PIK3CA mutations and null PTEN mutations were identified by NGS, and for PTEN, confirmed by IHC. Overall, mTOR-pathway activation was identified in 444/538 (83%) samples representing 40 different cancer types. Functional mutations in either or both PIK3CA and PTEN genes were identified in 173/538 (32%) samples. PIK3CA mutations were identified in 60/538 (11%) samples, PTEN mutations were identified in 155/538 (29%) samples and mutations in both PIK3CA and PTEN were identified in 18/538 (3%) samples. Overall, mTOR-pathway activation was not significantly associated with the PIK3CA and PTEN genotypes. However, all 18 samples with both PIK3CA and PTEN mutations also displayed mTOR-pathway activation (χ²p=0.0471). Also, out of a total of 95 breast cancer samples, there were 5 breast-cancer samples which did not have mTOR-pathway activation, and all 5 (100%) of these had PIK3CA and PTEN mutations compared to 51/90 (57%) in the breast-cancer samples with mTOR-pathway activation (χ²p=0.0134). Finally, the percentages of PIK3CA mutations were higher in colorectal-cancer samples which had mTOR-pathway activation (9/27, 33%) than in colorectal-cancer samples without mTOR-pathway activation (6/44; 14%; χ² p=0.0484). Therefore, tumor-biopsy analyses based on combined mTOR-pathway biomarkers (and combined NGS and IHC assessments) could potentially provide treatment-informative stratification for particular cancer types.

A Case Report Demonstrating the Potential Clinical Benefit of Exhaustive Molecular Profiling in an Aggressive Muscle-Invasive High-Grade Metastatic Urothelial Carcinoma

We present a muscle-invasive high-grade metastatic urothelial carcinoma patient, aged 71 years, with rapid progression from the diagnosis and a poor prognosis after 3 lines of treatment. A clinical exhaustive genomic profile was performed with the goal of finding potential actionable molecular alterations. The patient showed significant symptomatic and laboratory improvement with a nonstandard chemotherapy combination treatment identified by the molecular profiling, which would otherwise not have been considered. This approach illustrates the clinical benefit of a comprehensive genomic analysis in an aggressive and refractory urothelial carcinoma.

Abstract 3891: Tackling the obstacles facing the implementation of a molecular screening program in an early drug development unit: The Jules Bordet Institute Program for Molecular Profiling of Metastatic Lesions - feasibility (Precision-f)

Introduction

The identification of pathways involved in carcinogenesis, the emergence of high-throughput technologies enabling tumor molecular analysis and the development of targeted therapies have led to the concept of precision medicine. Higher response rates and longer survivals have been achieved in recent genomic-driven clinical trials. However, genomic-driven cancer medicine is hindered by multiple obstacles. Our aim was to assess the feasibility of incorporating real-time targeted gene sequencing (TGS) of DNA derived from metastatic biopsies into daily clinical practice.

Experimental procedures

Precision-f (NCT01932489) is a pilot trial conducted at the Jules Bordet Institute. Patients with metastatic colorectal cancer (CRC), melanoma or non-small cell lung (NSCLC) cancer were enrolled. Two FFPE blocks and one fresh frozen sample embedded in OCT were collected from newly performed metastatic biopsies as well as one whole blood sample. The FFPE samples were checked for tumor cellularity and 5×5 μm sections were cut and sent to 2 laboratories. Targeted gene sequencing was performed on DNA extracted for the same sample using the Illumina TruSeq Amplicon Cancer Panel performed on a MiSeq Desktop Sequencer, and the Life Technologies Ion AmpliSeq Cancer Hotspot Panel performed on an Ion Personal Genome Machine. Results were reported to the institutional sequencing tumor board for discussion, annotation and treatment assignment. The main objectives were the evaluation of biopsy quality, turnaround time, the presence of “actionable” alterations, technology cross-validity and treatment assignments.

Results

Thirty-four patients were enrolled between December 2013 and August 2014: 13 NSCLC patients, 11 CRC patients, 10 melanoma patients. Successful molecular results were achieved from 32/34 biopsies (94%). The most frequent site of biopsy was the liver (10) followed by the lung (7), the skin (5) and lymph nodes (5). 27/34 (79%) samples had ≥ 20% tumor cells. 31/34 (91%) of samples had > 10 ng of DNA for TGS. The median turnaround time for results reporting was 15 calendar days [8-22]. “Actionable” mutations were found for 66% (21/32) of patients, 76% (16/21) of which were treated with therapy according to the identified molecular alteration. Reasons for non-targeted therapy were: non-eligibility (2), unavailable drugs (2) and patient refusal (1). The results of the comparison of TGS data across the 2 platforms is ongoing and will be presented at the meeting.

Conclusion

The precision-f pilot trial has demonstrated the feasibility and clinical relevance of a molecular screening program in a clinical pharmacology unit. A Belgian national initiative will follow in order to enhance patient participation in genomic-driven clinical trials.

Citation Format: Philippe G. Aftimos, Marion Maetens, Catherine Sibille, Jean-François Laes, Sylvain Brohée, Thierry Berghmans, Joseph Kerger, Alain Hendlisz, Alexandre Irrthum, Olivier De Henau, Amélie Deleporte, Stylianos Drisis, Denis Larsimont, Jalal Vakili, Christos Sotiriou, Martine Piccart, Ahmad Awada. Tackling the obstacles facing the implementation of a molecular screening program in an early drug development unit: The Jules Bordet Institute Program for Molecular Profiling of Metastatic Lesions - feasibility (Precision-f). [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3891. doi:10.1158/1538-7445.AM2015-3891

Abstract PD3-7: Plasma circulating tumor DNA as an alternative to metastatic biopsies for mutational analyses in breast cancer

Background: Molecular screening programs are using next-generation sequencing (NGS) for cancer gene panels in metastatic biopsies. We interrogated whether plasma can be used as an alternative to metastatic biopsies.

Patients and methods: The Ion AmpliSeqTM Cancer Hotspot Panel v2 (Ion Torrent), covering approximately 2,800 COSMIC mutations from 50 cancer genes was used to analyze 70 primary and/or metastases and 29 plasma samples from 17 metastatic breast cancer patients. The targeted coverage for tissue DNA was 1000x and for plasma circulating DNA 25000x. Whole blood normal DNA was used to exclude germline variants. The Illumina technology was used for independent validation.

Results: Twelve patients had estrogen receptor (ER)+/ human epidermal growth factor receptor 2 (HER2)-, 1 ER+/HER2+, 2 ER-/HER2+ and 2 ER-/HER2- tumors. Evaluable NGS results were obtained for 61 primary/metastases and 29 plasma samples from 17 patients. When primary/metastases were analyzed, 12 of 17 patients had at least 1 mutation (median 1 mutation per patient, range 0-2) in either p53, PIK3CA, PTEN, AKT1 or IDH2 gene. When plasma was analyzed, 11 of 17 patients had at least 1 mutation (median 1 mutation per patient, range 0-2) in either p53, PIK3CA, PTEN, AKT1, IDH2 and SMAD4. All primary/metastases/plasma mutations were independently validated using the illumina technology. When we focused on metastases and plasma samples collected at the same time point, we observed that in 4 patients, no mutation was identified in either metastases or plasma, in 9 patients the same mutations were identified in metastases and plasma, in 2 patients a mutation was identified in metastases but not in plasma and in 2 patients a mutation was identified in plasma but not in metastases (Table 1). Thus, in 13 of 17 (76%) patients, metastases and plasma analysis provided concordant results whereas in 4 of 17 (24%) demonstated discordant results providing complementary information (Table 1). Conclusion: Plasma can be tested as an alternative tissue source in molecular screening programs.

Table Mutational status of synchronous metastatic biopsies and plasma samples analysed using the Ion AmpliSeqTM Cancer Hotspot Panel v2Patient IDGeneMutationMetastasis (MAF)Plasma (MAF)3PTENp.Q171EYES (27.5%)YES (25.9%)3SMAD4p.E394*NOYES (10.9%)4NONO6PIK3CAp.H1047RYES (20.5-47.7%)YES (4.6%)7TP53p.V274AYES (35.6-56.1%)YES (20.7%)8IDH2p.R140RYES (28.2)YES (0.5%)10PIK3CAp.H1047RYES (19.7%)NO11PIK3CAp.E453KYES (4.6-17.8%)YES (2.8%)11PIK3CAp.E453KYES (13.1-23%)YES (3.4%)14PIK3CAp.H1047RYES (24.8%)NO14PIK3CAp.H1047RYES (0-13.8%)YES (0.5%)16TP53p.Y103*YES (59.8-86.3%)YES (49%)17NONO19NONO20PIK3CAp.E545KNOYES (14.3%)30TP53p.M237KYES (27.6-50%)YES (51.8%)37TP53p.H193LYES (61.6-82.9%)YES (55.5%)38AKT1p.E17KYES (26-68.2%)YES (10%)38TP53p.R248WYES (23.6-56.8%)YES (5.9%)39TP53p.R136HYES (7.5%)NO40NONOMAF: Mutant allele frequency; For patients with multiple metastases samples at the same time point, the MAF range is provided. Patients 11 & 14 had 2 timepoints with synchronous metastases/plasma samples.

Citation Format: Michail Ignatiadis, Françoise Rothe, Jean-François Laes, Diether Lambrechts, Dominiek Smeets, Delphine Vincent, Marion Maetens, Debora Fumagalli, Stefan Michiels, Stylianos Drisis, Carine Moerman, Jean-Pol Detiffe, Denis Larsimont, Ahmad Awada, Martine Piccart, Christos Sotiriou. Plasma circulating tumor DNA as an alternative to metastatic biopsies for mutational analyses in breast cancer [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr PD3-7.

Multi-factor data normalization enables the detection of copy number aberrations in amplicon sequencing data

Motivation: Because of its low cost, amplicon sequencing, also known as ultra-deep targeted sequencing, is now becoming widely used in oncology for detection of actionable mutations, i.e. mutations influencing cell sensitivity to targeted therapies. Amplicon sequencing is based on the polymerase chain reaction amplification of the regions of interest, a process that considerably distorts the information on copy numbers initially present in the tumor DNA. Therefore, additional experiments such as single nucleotide polymorphism (SNP) or comparative genomic hybridization (CGH) arrays often complement amplicon sequencing in clinics to identify copy number status of genes whose amplification or deletion has direct consequences on the efficacy of a particular cancer treatment. So far, there has been no proven method to extract the information on gene copy number aberrations based solely on amplicon sequencing.

Results: Here we present ONCOCNV, a method that includes a multifactor normalization and annotation technique enabling the detection of large copy number changes from amplicon sequencing data. We validated our approach on high and low amplicon density datasets and demonstrated that ONCOCNV can achieve a precision comparable with that of array CGH techniques in detecting copy number aberrations. Thus, ONCOCNV applied on amplicon sequencing data would make the use of additional array CGH or SNP array experiments unnecessary.

Availability and implementation:http://oncocnv.curie.fr/

Contact:valentina.boeva@curie.fr

Supplementary information:Supplementary data are available at Bioinformatics online.

IL-12 and type I IFN response of neonatal myeloid DC to human CMV infection

Following congenital human CMV (HCMV) infection, 15-20% of infected newborns develop severe health problems whereas infection in immunocompetent adults rarely causes illness. The immaturity of neonatal antigen presenting cells could play a pivotal role in this susceptibility. Neonatal myeloid DC were shown to be deficient in IFN-beta and IL-12 synthesis in response to TLR triggering. We studied the response of cord and adult blood-derived myeloid DC to HCMV infection. Neonatal and adult DC were equally susceptible to in vitro HCMV infection. Among immunomodulatory cytokines, IL-12, IFN-beta and IFN-lambda1 were produced at lower levels by neonatal as compared with adult DC. In contrast, neonatal and adult DC produced similar levels of IFN-alpha and IFN-inducible genes. Microarray analysis indicated that among the more than thousand genes up- or down-regulated by HCMV infection of myeloid DC, 88 were differently regulated between adult and neonatal DC. We conclude that neonatal and adult DC trigger a partly different response to HCMV infection. The deficient IL-12 and mature IFN-alpha production by neonatal DC exposed to HCMV are likely to influence the quality of the T lymphocyte response to HCMV infection in early life.

Evolution of microRNA expression during human bronchial squamous carcinogenesis

MicroRNAs, negative post-transcriptional regulators of gene expression, are involved in cancer. Their role in early bronchial carcinogenesis was analysed in 60 biopsies obtained by fluorescence bronchoscopy (six per stage: normal tissue of nonsmokers, normal normofluorescent and hypofluorescent bronchial tissue of smokers, hyperplasia, metaplasia, mild, moderate and severe dysplasia, in situ carcinoma and invasive squamous cell carcinoma (SQCC)). In total, 69 microRNAs were found to be differentially expressed in the course of bronchial carcinogenesis. Among them, some microRNAs showed a linear evolution of their expression level, such as miR-32 and miR-34c, whose expression progressively decreased from normal bronchial tissues of nonsmokers to SQCC. Others behaved differently at successive stages, such as miR-142-3p or miR-9, or are only altered from a specific stage, such as miR-199a or miR-139. MicroRNAs globally followed a two-step evolution, first decreasing (a reverse of their increase during embryogenesis) during the earliest morphological modifications of bronchial epithelium, and thereafter increasing at later stages of lung carcinogenesis. Moreover, microRNA expression was very efficient for the prediction of the histological classification between low- and high-grade lesions and between in situ and invasive carcinoma. The present data show, for the first time, that microRNAs are involved in bronchial carcinogenesis from the very early steps of this process and, thus, could provide tools for early detection of lung cancer.

Mutation of a potassium channel-related gene in progressive myoclonic epilepsy

OBJECTIVE

We investigated a large consanguineous Moroccan family with progressive myoclonic epilepsy (PME) consistent with autosomal recessive inheritance, to describe the phenotype and identify the causal gene.

METHODS

We recorded the clinical course of the disease and the response to drug therapy, whereas carefully excluding known causes of progressive myoclonic epilepsy. We then linked the disease by homozygosity mapping using microsatellite markers and single nucleotide polymorphism microarrays (11K GeneChip), and studied candidate genes in the critical linkage region.

RESULTS

Epilepsy started between 16 and 24 months of age after normal initial development. Seizures were multifocal myoclonus aggravated by movements, and generalized tonic-clonic seizures were experienced by two patients. Electroencephalogram showed slow dysrhythmia, multifocal and occasionally generalized epileptiform discharges, and photosensitivity. Brain magnetic resonance images were normal. All patients were demented. Two had refractory epilepsy and a severe course. Seizures were controlled in the third patient, whose disease course was less severe. Linkage analyses identified a new locus on 7q11.2, with a maximum multipoint logarithm of odds of 4.0 at D7S663. In the critical linkage region, we found a C to T mutation in exon 2 of the potassium channel tetramerization domain containing 7 gene (KCTD7). The mutation affected a highly conserved segment of the predicted protein, changing an arginine codon into a stop codon (R99X).

INTERPRETATION

Neurodegeneration in progressive myoclonic epilepsy presented by our patients paralleled the refractoriness of epilepsy. The disease was transmitted as an autosomal recessive trait linked to a novel locus at 7q11.2, where we identified a mutation in KCTD7.

Isolation of two regions on rat chromosomes 5 and 18 affecting mammary cancer susceptibility

We previously mapped several quantitative trait loci (QTLs) controlling DMBA-induced mammary tumor development in female rats derived from a SPRD-Cu3 (susceptible strain) x WKY (resistant strain) cross. Two of these QTLs were assigned to chromosomes 5 and 18. In the present study, we generated and characterized congenic strains in which a segment of WKY chromosomes 5 or 18 was introduced in the SPRD-Cu3 genetic background, thereby physically demonstrating that each of these two chromosomes controls mammary tumor multiplicity. The chromosome 5 QTL (Mcstm1) accounts for 7 tumors per animal (versus a total of 11 tumors per SPRD-Cu3 rat). The chromosome 18 QTL (Mcstm2) accounts for 3 tumors per animal and is the first chemically-induced mammary cancer susceptibility locus assigned to this chromosome. In addition, the Mcstm1 region was shown to also controls tumor latency. These loci thus play a major role in chemically-induced mammary tumor development. QTLs controlling chemically-induced or estrogen-induced mammary tumor development have independently been identified on chromosomes 5 and 18, using susceptible strains others than SPRD-Cu3. Therefore the haplotype structure of the relevant chromosome regions was analyzed in the different strains. Some chromosome regions were found to be highly mosaic (haplotype blocks < 1 Mb), while one region showed an apparently conserved haplotype block of 7.5 Mb. This analysis points to limited regions that could harbor the causative genes and also indicates that at least Mcstm2 is a novel QTL.

Bortezomib (PS-341, Velcade) increases the efficacy of trastuzumab (Herceptin) in HER-2-positive breast cancer cells in a synergistic manner

BACKGROUND

Preclinical and clinical studies have shown that the proteasome inhibitor bortezomib (PS341, Velcade) is highly effective when combined with chemotherapeutic agents. The value of trastuzumab (Herceptin) in HER-2-positive (3+ score by immunohistochemistry or fluorescence in situ hybridization positive) breast cancer is also known; however, the response rate is <40% for metastatic breast cancer. These two pharmacologic agents prevent nuclear factor-kappaB (NF-kappaB) activation and induce nuclear accumulation of the cyclin-dependent kinase inhibitor p27(kip1), suggesting that combining bortezomib with trastuzumab could increase trastuzumab efficacy.

METHODS

Drug cytotoxicity, both individually and together, and drug effects on p27 localization and NF-kappaB activation were investigated on four breast cancer cell lines: SKBR-3 (HER-2+++), MDA-MB-453 (HER-2++), HER-2-transfected MCF-7 (HER-2+++), and MCF-7 (HER-2-).

RESULTS

Bortezomib induced apoptosis in HER-2-positive and HER-2-negative breast cancer cells in a dose- and time-dependent manner. Together, these drugs induced apoptosis of HER-2++/+++ cells at low concentrations, which had no effect when used alone, indicating there was a synergistic effect. Sequential treatment (trastuzumab then bortezomib) induced either necrosis or apoptosis, depending on the trastuzumab preincubation time. Susceptibility to bortezomib alone and the drug combination correlated with NF-kappaB activity and p27 localization.

CONCLUSIONS

The addition of bortezomib to trastuzumab increases the effect of trastuzumab in HER-2+++/++ cell lines in a synergistic way. This effect likely results from the ability of these two drugs to target the NF-kappaB and p27 pathways. The potential clinical application of this drug combination is under current evaluation by our group in a phase 1 clinical trial.

Alpha-fetoprotein controls female fertility and prenatal development of the gonadotropin-releasing hormone pathway through an antiestrogenic action

It has been shown previously that female mice homozygous for an alpha-fetoprotein (AFP) null allele are sterile as a result of anovulation, probably due to a defect in the hypothalamic-pituitary axis. Here we show that these female mice exhibit specific anomalies in the expression of numerous genes in the pituitary, including genes involved in the gonadotropin-releasing hormone pathway, which are underexpressed. In the hypothalamus, the gonadotropin-releasing hormone gene, Gnrh1, was also found to be down-regulated. However, pituitary gene expression could be normalized and fertility could be rescued by blocking prenatal estrogen synthesis using an aromatase inhibitor. These results show that AFP protects the developing female brain from the adverse effects of prenatal estrogen exposure and clarify a long-running debate on the role of this fetal protein in brain sexual differentiation.

Genetic identification of distinct loci controlling mammary tumor multiplicity, latency, and aggressiveness in the rat

The rat is considered an excellent model for studying human breast cancer. Therefore, understanding the genetic basis of susceptibility to mammary cancer in this species is of great interest. Previous studies based on crosses involving the susceptible strain WF (crossed with the resistant strains COP or WKY) and focusing on tumor multiplicity as the susceptibility phenotype led to the identification of several loci that control chemically induced mammary cancer. The present study was aimed to determine whether other loci can be identified by analyzing crosses derived from another susceptible strain on the one hand, and by including phenotypes other than tumor multiplicity on the other hand. A backcross was generated between the susceptible SPRD-Cu3 strain and the resistant WKY strain. Female progeny were genotyped with microsatellite markers covering all rat autosomes, treated with a single dose of DMBA, and phenotyped with respect to tumor latency, tumor multiplicity, and tumor aggressiveness. Seven loci controlling mammary tumor development were detected. Different loci control tumor multiplicity, latency, and aggressiveness. While some of these loci colocalize with loci identified in crosses involving the susceptible strain WF, new loci have been uncovered, indicating that the use of distinct susceptible and resistant strain pairs will help in establishing a comprehensive inventory of mammary cancer susceptibility loci.

Gene regulation by phorbol 12-myristate 13-acetate in MCF-7 and MDA-MB-231, two breast cancer cell lines exhibiting highly different phenotypes

We have examined the effects of the protein kinase C (PKC)-activator phorbol 12-myristate 13-acetate (PMA) on gene expression in two breast cancer cell (BCC) lines exhibiting highly different phenotypes. These are the estrogen receptor alpha (ERalpha)-positive, weakly invasive, luminal epithelial-like MCF-7 and the ERalpha-negative, highly invasive, fibroblast-like MDA-MB-231. They express constitutively low and high PKC activities, respectively. After a 24-h exposition to 100 nM PMA, the number of genes showing an altered expression at the 2-fold change level was much higher in MCF-7 (n=435) than in MDA-MB-231 (n=18) BCC. Four of these genes, namely CDC2, CENPA, NR4A1 and MMP10, were altered in the same way in both cell lines. Two genes were regulated in an opposite way: ID1 and EVA1. Many of the genes down-regulated in MCF-7 BCC appeared to be preferentially expressed in the G1, S, and/or G2 phases of the cell cycle. The ERalpha gene, ESR1, and other genes associated to the ERalpha-positive, luminal epithelial-like BCC phenotype were down-regulated, while a series of genes related to a more aggressive, fibroblast-like BCC phenotype were up-regulated. Other altered genes were notably linked to cell architecture, supporting profound effects of PMA on cell morphology and motility, as well as on the interactions between BCC and their neighboring proteins. Of note, all the modulated genes involved in proteolysis and its control were up-regulated. In summary, PMA effects suggest that PKC activation may induce, to some extent, a more fibroblast-like phenotype in the ERalpha-positive, luminal epithelial-like MCF-7 BCC, and significantly modulate the interactions of these cells with their environment.

Improved radiation hybrid map of rat chromosome 2: colocalization of the genes encoding corticotropin-releasing hormone and IL6-receptor with quantitative trait loci regulating the inflammatory response

We established a radiation hybrid (RH) map of several genes and anonymous markers in the lower half of rat chromosome 2, a chromosome region that contains quantitative trait loci (QTLs) for blood pressure, diabetes and inflammatory response. Two of the newly localized genes (Crh and Il6r) encode proteins involved in the regulation of inflammatory and immune events. Our data show that they reside within regions that were genetically defined as QTLs controlling the inflammatory response. These genes are thus both functional and positional candidates.

Analysis of candidate genes included in the mammary cancer susceptibility 1 (Mcs1) region

The rat strain COP is resistant to spontaneous and carcinogen-induced mammary cancer, whereas the strain WF is susceptible. Using genetic linkage analysis of (WF x COP) F1 x WF backcrosses, LC Hsu, LA Shepel and co-workers showed that a region at the centromeric end of Chromosome (Chr) 2 (2q1) segregates with the sensitivity to mammary cancer development. The responsible locus was named Mcs1 (for mammary cancer susceptibility 1). We have developed the chromosome map of the 2q1 region by localizing 18 genes, 4 ESTs, and several anonymous markers, using radiation hybrids and fluorescence in situ hybridization. The region containing Mcs1 was delineated to 2q12-q14. Five of the genes (Mef2c, Map1b, Ccnh, Rasa, Rasgrf2) were assigned to this region and were shown to be expressed in the rat mammary glands, while three possible functional candidate genes, Pi3kr1, Rad17, and Naip, were excluded from the critical region. Since cyclin H, encoded by Ccnh, plays an important role in the control of the cell cycle and since the proteins encoded by Rasa and Rasgrf2 control the activity of the RAS oncoprotein, the corresponding genes appeared as both functional and positional Mcs1 candidates. RT-PCR experiments on RNA extracted from mammary glands of the two rat strains (COP, WF) was done. No amino acid sequence difference was found between the two strains. These results argue against the hypothesis that any of these three genes is Mcs1.

Localization of new, microdissection- generated, anonymous markers and of the genes Pcsk1, Dhfr, Ndub13, and Ccnb1 to rat chromosome region 2q1

The centromeric region of rat chromosome 2 (2q1) harbors unidentified quantitative trait loci of genes that control tumor growth or development. To improve the mapping of this chromosome region, we microdissected it and generated 10 new microsatellite markers, which we included in the linkage map and/or radiation hybrid map of 2q1, together with other known markers, including four genes: Pcsk1 (protein convertase 1), Dhfr (dihydrofolate reductase), Ndub13 (NADH ubiquinone oxidoreductase subunit b13), and Ccnb1 (cyclin B1). To generate anchor points between the different maps, the gene Ndub13 and the microsatellite markers D2Ulb25 and D2Mit1 were also localized cytogenetically. The radiation map generated in region 2q1 extends its centromeric end of about 150 cR.