This study explores the roles of genome copy number abnormalities (CNAs) in breast cancer pathophysiology by identifying associations between recurrent CNAs, gene expression, and clinical outcome in ...a set of aggressively treated early-stage breast tumors. It shows that the recurrent CNAs differ between tumor subtypes defined by expression pattern and that stratification of patients according to outcome can be improved by measuring both expression and copy number, especially high-level amplification. Sixty-six genes deregulated by the high-level amplifications are potential therapeutic targets. Nine of these (
FGFR1,
IKBKB,
ERBB2,
PROCC,
ADAM9,
FNTA,
ACACA,
PNMT, and
NR1D1) are considered druggable. Low-level CNAs appear to contribute to cancer progression by altering RNA and cellular metabolism.
Recent studies suggest that thousands of genes may contribute to breast cancer pathophysiologies when deregulated by genomic or epigenomic events. Here, we describe a model “system” to appraise the ...functional contributions of these genes to breast cancer subsets. In general, the recurrent genomic and transcriptional characteristics of 51 breast cancer cell lines mirror those of 145 primary breast tumors, although some significant differences are documented. The cell lines that comprise the system also exhibit the substantial genomic, transcriptional, and biological heterogeneity found in primary tumors. We show, using Trastuzumab (Herceptin) monotherapy as an example, that the system can be used to identify molecular features that predict or indicate response to targeted therapies or other physiological perturbations.
Models of bladder tumor progression have suggested that genetic alterations may determine both phenotype and clinical course.
We have applied expression microarray analysis to a divergent set of ...bladder tumors to further elucidate the course of disease
progression and to classify tumors into more homogeneous and clinically relevant subgroups. cDNA microarrays containing 10,368
human gene elements were used to characterize the global gene expression patterns in 80 bladder tumors, 9 bladder cancer cell
lines, and 3 normal bladder samples. Robust statistical approaches accounting for the multiple testing problem were used to
identify differentially expressed genes. Unsupervised hierarchical clustering successfully separated the samples into two
subgroups containing superficial (pT a and pT 1 ) versus muscle-invasive (pT 2 -pT 4 ) tumors. Supervised classification had a 90.5% success rate separating superficial from muscle-invasive tumors based on a
limited subset of genes. Tumors could also be classified into transitional versus squamous subtypes (89% success rate) and
good versus bad prognosis (78% success rate). The performance of our stage classifiers was confirmed in silico using data from an independent tumor set. Validation of differential expression was done using immunohistochemistry on tissue
microarrays for cathepsin E, cyclin A2, and parathyroid hormone–related protein. Genes driving the separation between tumor
subsets may prove to be important biomarkers for bladder cancer development and progression and eventually candidates for
therapeutic targeting.
Liposarcoma represents a unique model insofar as some well-differentiated liposarcomas progress to non-lipogenic, so-called 'dedifferentiated,' forms. The well-differentiated and dedifferentiated ...family of liposarcomas demonstrates amplification of the chromosome subregion 12q13-q15 with resultant amplification of the MDM2 and CDK4 genes. However, the specific genetic changes that distinguish between well-differentiated and dedifferentiated liposarcomas are less well understood. To study the genetic changes in dedifferentiated liposarcomas, paired well-differentiated and dedifferentiated components of 29 tumors were analyzed separately by array-based comparative genomic hybridization. A bacterial artificial chromosome array at approximately 1-Mb resolution was used. The genetic changes were compared with clinical presentation, grade of the dedifferentiated component and overexpression of MDM2 and CDK4. Most tumors (n=21, 72%) were retroperitoneal, with both components present at initial diagnosis (n=25, 86%). Eight tumors (28%) were classified as low-grade dedifferentiation. In four cases (14%), a well-differentiated liposarcoma preceded the presentation of the dedifferentiated tumor by 1-5 years. 12q13-q15 was amplified in all tumors. Using unsupervised hierarchical clustering of copy-number changes, all but two tumors showed close similarities between well-differentiated and dedifferentiated components, and segregated as pairs. Dedifferentiated components had more total amplifications (P=0.008) and a trend for gain at 19q13.2, but no genetic changes were significant in distinguishing between the two components. High-level amplifications of 1p21-32 (n=7, 24%), 1q21-23 (n=9, 31%), 6q23-24 (n=6, 21%) and 12q24 (n=3, 10%) were common, but none significantly correlated with differentiation. Presentation and grade correlated with the frequency of changes at a number of genetic loci (P<0.001), whereas CDK4 immunostaining showed negative correlation with 12q13.13 amplification. The genotypic similarity, at the limit of the array's resolution, between components implies that most genetic changes precede phenotypic 'progression,' early in tumorigenesis. The relationship between genetic changes and presentation or grade may reflect differences in factors that control genomic instability or the background genotype of the tumor.
Purpose: Bladder carcinogenesis is believed to follow alternative pathways of disease progression driven by an accumulation of genetic
alterations. The purpose of this study was to evaluate ...associations between measures of genomic instability and bladder cancer
clinical phenotype.
Experimental Design: Genome-wide copy number profiles were obtained for 98 bladder tumors of diverse stages (29 pT a , 14 pT 1 , 55 pT 2-4 ) and grades (21 low-grade and 8 high-grade superficial tumors) by array-based comparative genomic hybridization (CGH). Each
array contained 2,464 bacterial artificial chromosome and P1 clones, providing an average resolution of 1.5 Mb across the
genome. A total of 54 muscle-invasive cases had follow-up information available. Overall outcome analysis was done for patients
with muscle-invasive tumors having “good” (alive >2 years) versus “bad” (dead in <2 years) prognosis.
Results: Array CGH analysis showed significant increases in copy number alterations and genomic instability with increasing stage
and with outcome. The fraction of genome altered (FGA) was significantly different between tumors of different stages (pT a versus pT 1 , P = 0.0003; pT a versus pT 2-4 , P = 0.02; and pT 1 versus pT 2-4 , P = 0.03). Individual clones that differed significantly between different tumor stages were identified after adjustment for
multiple comparisons (false discovery rate < 0.05). For muscle-invasive tumors, the FGA was associated with patient outcome
(bad versus good prognosis patients, P = 0.002) and was identified as the only independent predictor of overall outcome based on a multivariate Cox proportional
hazards method. Unsupervised hierarchical clustering separated “good” and “bad” prognosis muscle-invasive tumors into clusters
that showed significant association with FGA and survival (Kaplan-Meier, P = 0.019). Supervised tumor classification (prediction analysis for microarrays) had a 71% classification success rate based
on 102 unique clones.
Conclusions: Array-based CGH identified quantitative and qualitative differences in DNA copy number alterations at high resolution according
to tumor stage and grade. Fraction genome altered was associated with worse outcome in muscle-invasive tumors, independent
of other clinicopathologic parameters. Measures of genomic instability add independent power to outcome prediction of bladder
tumors.
Genomic DNA copy number aberrations are frequent in solid tumors, although the underlying causes of chromosomal instability in tumors remain obscure. Genes likely to have genomic instability ...phenotypes when mutated (e.g. those involved in mitosis, replication, repair, and telomeres) are rarely mutated in chromosomally unstable sporadic tumors, even though such mutations are associated with some heritable cancer prone syndromes.
We applied array comparative genomic hybridization (CGH) to the analysis of breast tumors. The variation in the levels of genomic instability amongst tumors prompted us to investigate whether alterations in processes/genes involved in maintenance and/or manipulation of the genome were associated with particular types of genomic instability.
We discriminated three breast tumor subtypes based on genomic DNA copy number alterations. The subtypes varied with respect to level of genomic instability. We find that shorter telomeres and altered telomere related gene expression are associated with amplification, implicating telomere attrition as a promoter of this type of aberration in breast cancer. On the other hand, the numbers of chromosomal alterations, particularly low level changes, are associated with altered expression of genes in other functional classes (mitosis, cell cycle, DNA replication and repair). Further, although loss of function instability phenotypes have been demonstrated for many of the genes in model systems, we observed enhanced expression of most genes in tumors, indicating that over expression, rather than deficiency underlies instability.
Many of the genes associated with higher frequency of copy number aberrations are direct targets of E2F, supporting the hypothesis that deregulation of the Rb pathway is a major contributor to chromosomal instability in breast tumors. These observations are consistent with failure to find mutations in sporadic tumors in genes that have roles in maintenance or manipulation of the genome.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Purpose: Ductal carcinoma in situ (DCIS) is thought to be a nonobligate precursor of invasive cancer. Genomic changes specific to pure DCIS versus invasive cancer, as well as alterations unique to ...individual DCIS subtypes, have not been fully defined.
Experimental Design: Chromosomal copy number alterations were examined by comparative genomic hybridization in 34 cases of pure DCIS and compared
with 12 cases of paired synchronous DCIS and invasive ductal cancer, as well as to 146 additional cases of invasive breast
cancer of ductal or lobular histology. Genomic differences between high-grade and low/intermediate-grade DCIS, as well as
between pure DCIS and invasive cancer, were identified.
Results: Pure DCIS showed almost the same degree of chromosomal instability as invasive ductal cancers. A higher proportion of low/intermediate-grade
versus high-grade DCIS had loss of 16q (65 versus 12%, respectively; P = 0.002). When compared with lower grade DCIS, high-grade DCIS exhibited more frequent gain of 17q (65 versus 41%; P = 0.15) and higher frequency loss of 8p (77 versus 41%; P = 0.04). Chromosomal alterations in those cases with synchronous DCIS and invasive ductal cancer showed a high degree of
shared changes within the two components.
Conclusions: DCIS is genetically advanced, showing a similar degree of chromosomal alterations as invasive ductal cancer. The pattern
of alterations differed between high- and low/intermediate-grade DCIS, supporting a model in which different histological
grades of DCIS are associated with distinct genomic changes. These regions of chromosomal alterations may be potential targets
for treatment and/or markers of prognosis.
Endocrine therapy is commonly recommended in the adjuvant setting for patients as treatment for ductal carcinoma in situ (DCIS). However, it is unknown whether a neoadjuvant (preoperative) ...anti-estrogen approach to DCIS results in any biological change. This study was undertaken to investigate the pathologic and biomarker changes in DCIS following neoadjuvant endocrine therapy compared to a group of patients who did not undergo preoperative anti-estrogenic treatment to determine whether such treatment results in detectable histologic alterations.
Patients (n = 23) diagnosed with ER-positive pure DCIS by stereotactic core biopsy were enrolled in a trial of neoadjuvant anti-estrogen therapy followed by definitive excision. Patients on hormone replacement therapy, with palpable masses, or with histologic or clinical suspicion of invasion were excluded. Premenopausal women were treated with tamoxifen and postmenopausal women were treated with letrozole. Pathologic markers of proliferation, inflammation, and apoptosis were evaluated at baseline and at three months.Biomarker changes were compared to a cohort of patients who had not received preoperative treatment.
Median age of the cohort was 53 years (range 38-78); 14 were premenopausal. Following treatment, predominant morphologic changes included increased multinucleated histiocytes and degenerated cells, decreased duct extension, and prominent periductal fibrosis. Two postmenopausal patients had ADH only with no residual DCIS at excision. Postmenopausal women on letrozole had significant reduction of PR, and Ki67 as well as increase in CD68-positive cells. For premenopausal women on tamoxifen treatment, the only significant change was increase in CD68. No change in cleaved caspase 3 was found. Two patients had invasive cancer at surgery.
Preoperative therapy for DCIS is associated with significant pathologic alterations. These changes may be clinically significant. Further work is needed to identify which women may be the best candidates for such treatment for DCIS, and whether best responders may safely avoid surgical intervention.
ClinicalTrials.gov NCT00290745.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Purpose: Breast cancer is thought to develop from noninvasive precursor lesions, although the earliest steps of neoplastic transformation
are still undefined. Usual ductal hyperplasia (UDH) is ...considered to represent a benign proliferation of ductal epithelial
cells, whereas atypical ductal hyperplasia (ADH) may represent the first clonal neoplastic expansion of these cells. The aim
of this study was to examine genetic alterations in UDH and ADH and to determine the relationship between these lesions in
the same breast biopsy.
Experimental Design: Comparative genomic hybridization analysis was used to define copy number alterations in DNA extracted from archival sections
of 18 patients. Nine patients showed ADH with adjacent UDH, and nine showed pure UDH. None showed evidence of invasive cancer
or ductal carcinoma in situ .
Results: Five of the nine ADH lesions showed chromosome copy number alterations. 16q loss (five cases) and 17p loss (two cases) were
the most frequent changes. The associated UDH lesions in these five patients also showed copy number alterations, always a
subset of the changes present in the paired ADH. In one other patient, the UDH showed eight chromosomal alterations, whereas
the paired ADH showed no changes. Only one of nine cases with pure UDH showed comparative genomic hybridization abnormalities.
Conclusions: These data support the likelihood that UDH is a precursor of ADH, at least in some cases representing neoplastic growth.
The frequencies of 16q and 17p losses suggest that alterations of candidate genes located in these chromosomal regions may
play a role early in breast carcinogenesis.
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