Differential pathogenesis of lung adenocarcinoma subtypes involving sequence mutations, copy number, chromosomal instability, and methylation

BACKGROUND: Lung adenocarcinoma (LAD) has extreme genetic variation among patients, which is currently not well understood, limiting progress in therapy development and research. LAD intrinsic molecular subtypes are a validated stratification of naturally-occurring gene expression patterns and encompass different functional pathways and patient outcomes. Patients may have incurred different mutations and alterations that led to the different subtypes. We hypothesized that the LAD molecular subtypes co-occur with distinct mutations and alterations in patient tumors. METHODOLOGY/PRINCIPAL FINDINGS: The LAD molecular subtypes (Bronchioid, Magnoid, and Squamoid) were tested for association with gene mutations and DNA copy number alterations using statistical methods and published cohorts (n = 504). A novel validation (n = 116) cohort was assayed and interrogated to confirm subtype-alteration associations. Gene mutation rates (EGFR, KRAS, STK11, TP53), chromosomal instability, regional copy number, and genomewide DNA methylation were significantly different among tumors of the molecular subtypes. Secondary analyses compared subtypes by integrated alterations and patient outcomes. Tumors having integrated alterations in the same gene associated with the subtypes, e.g. mutation, deletion and underexpression of STK11 with Magnoid, and mutation, amplification, and overexpression of EGFR with Bronchioid. The subtypes also associated with tumors having concurrent mutant genes, such as KRAS-STK11 with Magnoid. Patient overall survival, cisplatin plus vinorelbine therapy response and predicted gefitinib sensitivity were significantly different among the subtypes. CONCLUSIONS/ SIGNIFICANCE: The lung adenocarcinoma intrinsic molecular subtypes co-occur with grossly distinct genomic alterations and with patient therapy response. These results advance the understanding of lung adenocarcinoma etiology and nominate patient subgroups for future evaluation of treatment response.     

Mosaiktrisomie 8p11.21q11.21 als Pr?disposition für myeloische Leuk?mien

Juvenile myelomonocytic leukemia (JMML) is a unique myeloproliferative disorder of early childhood in which mutations in NRAS, KRAS, PTPN11, NF1 and CBL are frequently found. Using high-resolution oligo array-based comparative genomic hybridization (aCGH), 20 JMML samples were investigated for submicroscopic genomic copy number alterations. Besides known cytogenetic aberrations, ten samples displayed additional submicroscopic alterations. Interestingly, an almost identical gain of chromosome 8 was identified in two patients. Subsequently, fluorescence in situ hybridization indicated a constitutional partial trisomy 8 mosaic (cT8M) in both patients. A survey on 27 cT8M patients with reported malignancies showed a predominance of myeloid malignancies including JMML. Our results dramatically reduce the critical region on chromosome 8 to 8p11.21q11.21. To determine how constitutional partial trisomy 8 mosaicisms may contribute to leukemogenesis in different mutational subtypes of JMML and other myeloid malignancies, further investigations are required.     

All roads lead to IKKepsilon

Extensive genetic alterations have been found in many epithelial malignancies. Using three complementary genetic approaches, Boehm et al. (2007) identify IKBKE--which encodes IKKepsilon, a component of the NF-kappaB pathway--as a breast cancer oncogene.     

FISH in der Diagnostik hämatologischer Neoplasien

All hematological malignancies are characterized by considerable clinical heterogeneity. The diverse entities can be subdivided into a variety of prognosis-defining subtypes on the basis of cytogenetic aberrations and molecular mutations. To adapt the intensity of treatment to the patient’s individual risk profile, an exact classification of the subtypes on the basis of genetic markers is essential. Diverse fluorescent in situ hybridization (FISH) techniques thereby play a central role in interaction with classic chromosome banding analyses for clarifying findings of chromosome analyses, such as in the acute leukemias, or for classifying the diverse subtypes, as in the non-Hodgkin’s lymphomas. Depending on the disease, the clinical impact of FISH varies. It is used as the method of choice for genetic characterization (e.g., in multiple myeloma) or is used in combination with chromosome banding analysis. Furthermore, interphase FISH is essential when rapid confirmation of the diagnosis is needed, as in acute promyelocytic leukemia with the t(15;17)/PML-RARA rearrangement, for which therapy with all-trans retinoic acid (ATRA) should be immediately started.     

Oncogene alterations in primary,recurrent, and metastatic human bone tumors

We investigated the structure and the expression of various oncogenes in three of the most common human bone tumors—osteosarcoma (36 samples from 34 patients), giant cell tumor (10 patients), and chondrosarcoma (18 patients)—in an attempt to identify the genetic alterations associated with these malignancies. Alterations of RB and p53 were detected only in osteosarcomas. Alterations of c-myc, N-myc, and c-fos were detected in osteosarcomas and giant cell tumors. Ras alterations (H-ras, Ki-ras, N-ras) were rare. Chondrosarcomas did not contain any detectable genetic alterations. Our results suggest that alterations of c-myc, N-myc, and c-fos oncogenes occur in osteosarcomas, in addition to those previously described for the tumor suppressor genes RB and p53. Moreover, statistical analyses indicate that c-fos alterations occur more frequently in osteosarcoma patients with recurrent or metastatic disease. © 1996 Wiley-Liss, Inc.     

Cancer type‐dependent genetic interactions between cancer driver alterations indicate plasticity of epistasis across cell types

Cancers, like many diseases, are normally caused by combinations of genetic alterations rather than by changes affecting single genes. It is well established that the genetic alterations that drive cancer often interact epistatically, having greater or weaker consequences in combination than expected from their individual effects. In a stringent statistical analysis of data from > 3,000 tumors, we find that the co‐occurrence and mutual exclusivity relationships between cancer driver alterations change quite extensively in different types of cancer. This cannot be accounted for by variation in tumor heterogeneity or unrecognized cancer subtypes. Rather, it suggests that how genomic alterations interact cooperatively or partially redundantly to driver cancer changes in different types of cancers. This re‐wiring of epistasis across cell types is likely to be a basic feature of genetic architecture, with important implications for understanding the evolution of multicellularity and human genetic diseases. In addition, if this plasticity of epistasis across cell types is also true for synthetic lethal interactions, a synthetic lethal strategy to kill cancer cells may frequently work in one type of cancer but prove ineffective in another.     

Glioma models

Gliomas are primary central nervous system tumors that arise from astrocytes, oligodendrocytes or their precursors. Gliomas can be classified into several groups according to their histologic characteristics, the most malignant of the gliomas is glioblastoma multiforme. In contrast to the long-standing and well-defined histopathology, the underlying molecular and genetic bases for gliomas are only just emerging. Many genetic alterations have been identified in human gliomas, however, establishing unequivocal correlation between these genetic alterations and gliomagenesis requires accurate animal models for this disease. Here we are reviewing the existing animal models for gliomas with different strategies and our current knowledge on the important issues about this disease, such as activation of signal transduction pathways, disruption of cell cycle arrest pathways, cell-of-origin of gliomas, and therapeutic strategies.     

Glioma models.

Gliomas are primary central nervous system tumors that arise from astrocytes, oligodendrocytes or their precursors. Gliomas can be classified into several groups according to their histologic characteristics, the most malignant of the gliomas is glioblastoma multiforme. In contrast to the long-standing and well-defined histopathology, the underlying molecular and genetic bases for gliomas are only just emerging. Many genetic alterations have been identified in human gliomas, however, establishing unequivocal correlation between these genetic alterations and gliomagenesis requires accurate animal models for this disease. Here we are reviewing the existing animal models for gliomas with different strategies and our current knowledge on the important issues about this disease, such as activation of signal transduction pathways, disruption of cell cycle arrest pathways, cell-of-origin of gliomas, and therapeutic strategies.     

Age dependent association of endometrial polyps with increased risk of cancer involvement

BACKGROUND: Endometrial polyps (EMPs) are commonly encountered in routine surgical pathology practice, but opinions differ on whether they are intrinsically a marker for concurrent or subsequent malignancy. The objectives of the present study are 1) to investigate the age-group in which EMP are most commonly encountered 2) to document the age-group in which EMP are most commonly associated with malignancies 3) To investigate whether the age of diagnosis of the various carcinoma subtypes in EMPs is congruent with published data on similar malignancies arising in non-polypoid endometrium and 4) To investigate whether the histologic subtype distribution of malignancies associated with EMPs are similar or different from the distribution of malignancies arising from non-polypoid endometrium based on published data. PATIENTS AND METHODS: All cases of EMPs were retrieved from the files of Yale-New Haven Hospital for the period 1986-1995. The patients were divided into 5 age groups: Each group was further subclassified based on an association (or lack thereof) of EMPs with endometrial carcinoma. Chi-square test was used to compare the proportion of malignancy associated EMPs between the age groups. RESULTS: We identified 513 EMPs, of which 209 (41%) were from biopsy specimens and 304 (59%) from hysterectomy specimens. Sixty six (13%) of all EMPs were malignant. The 66 malignant EMPs included 58 endometrioid, 6 serous, 1 carcinosarcoma, and 1 clear cell carcinoma. In age group >35, only 1(2.5%) of 40 EMPs was associated with endometrial malignancy. In contrast, 37(32%) of 115 EMPs were associated with malignancy in the age group > 65. The frequency of malignant EMPs increased with age and reached statistical significance in the age group >65 (p < 0.001). The most common histologic type of malignancy was endometrioid adenocarcinoma. CONCLUSIONS: EMPs show statistically significant age dependent association with malignant tumor involvement. Careful search for malignancy, particularly in women with multiple risk factors is advised in daily practice. Additional studies are needed to address the histological features and immunohistochemical profiles in the context of association between endometrioid and high-grade endometrial carcinoma and endometrial polyps.     

Histone deacetylases: a new class of efficient anti-tumor drugs

Circa twenty-five years ago, cancer research was dominated by the concept that the origin of cancer was genetic. Thousands of genetic alterations have indeed been identified involving more than hundred different genes in cancer development. Today, the model has evolved: it has been demonstrated that malignancies can be initiated not only through genetic alterations but also through epigenetic deregulations. By altering the expression of gene involved in cell regulation, epigenetic alterations, such as histone acetylation, play a key role in the initiation and progression of neoplasm. It has been shown that an imbalance between the acelylated and deacetylated status of chromatin is significantly involved in the acquisition of a malignant phenotype. Thus, the modulation of the histone acetylation level by histone deacetylase (HDAC) inhibitors could lead to a genetic re-programmation in cancer cells that would favor apoptosis and prevent proliferation. The potential therapeutic value of several HDAC inhibitors for cancer patients has been evaluated in clinical assays with very promising outcome. Indeed, the first inhibitors available for patients has been recently approved for cancer patients tracing the way for a new class of promising anti-cancer therapy modalities.     

Epigenetic and genetic burden measures are associated with tumor characteristics in invasive breast carcinoma

The development and progression of invasive breast cancer is characterized by alterations to the genome and epigenome. However, the relationship between breast tumor characteristics, disease subtypes, and patient outcomes with the cumulative burden of these molecular alterations are not well characterized. We determined the average departure of tumor DNA methylation from adjacent normal breast DNA methylation using Illumina 450K methylation data from 700 invasive breast tumors and 90 adjacent normal breast tissues in The Cancer Genome Atlas. From this we generated a novel summary measure of altered DNA methylation, the DNA methylation dysregulation index (MDI), and examined the relation of MDI with tumor characteristics and summary measures that quantify cumulative burden of genetic mutation and copy number alterations. Our analysis revealed that MDI was significantly associated with tumor stage (P = 0.017). Across invasive breast tumor subtypes we observed significant differences in genome-wide DNA MDIs (P = 4.9E–09) and in a fraction of the genome with copy number alterations (FGA) (P = 4.6E–03). Results from a linear regression adjusted for subject age, tumor stage, and estimated tumor purity indicated a positive significant association of MDI with both MCB and FGA (P = 0.036 and P < 2.2E–16). A recursively partitioned mixture model of all 3 somatic alteration burden measures resulted in classes of tumors whose epigenetic and genetic burden profile were associated with the PAM50 subtype and mutations in TP53, PIK3CA, and CDH1. Together, our work presents a novel framework for characterizing the epigenetic burden and adds to the understanding of the aggregate impact of epigenetic and genetic alterations in breast cancer.     

Cytology of peritoneal washings in gynecologic patients. Diagnostic criteria and pitfalls

A total of 226 peritoneal washing specimens obtained from gynecologic patients over a three-year period was reviewed. The diagnostic problems encountered were: differentiating reactive mesothelium from low-grade malignancies; distinguishing between benign ovarian tumors, ovarian tumors of borderline malignancy and low-grade ovarian malignancies; and potential false-positive diagnoses in endometriosis. Low-grade malignancies could be distinguished from reactive mesothelium by evaluating subtle cytologic criteria and by comparing the cells to those of the tumor on histologic section. The differentiation of low-grade epithelial malignancies from benign epithelial lesions caused difficulties that could only be resolved by evaluating the histologic material. Positive peritoneal washings increased the stage in 8 of 110 patients undergoing initial surgery for gynecologic malignancy. Two of 76 patients undergoing a second-look laparotomy had positive washings without histologic evidence of tumor. These ten patients did less well than did those with similar histology but negative washing cytology, despite receiving additional therapy because of the cytologic findings.     

A mathematical methodology for determining the temporal order of pathway alterations arising during gliomagenesis

Human cancer is caused by the accumulation of genetic alterations in cells. Of special importance are changes that occur early during malignant transformation because they may result in oncogene addiction and thus represent promising targets for therapeutic intervention. We have previously described a computational approach, called Retracing the Evolutionary Steps in Cancer (RESIC), to determine the temporal sequence of genetic alterations during tumorigenesis from cross-sectional genomic data of tumors at their fully transformed stage. Since alterations within a set of genes belonging to a particular signaling pathway may have similar or equivalent effects, we applied a pathway-based systems biology approach to the RESIC methodology. This method was used to determine whether alterations of specific pathways develop early or late during malignant transformation. When applied to primary glioblastoma (GBM) copy number data from The Cancer Genome Atlas (TCGA) project, RESIC identified a temporal order of pathway alterations consistent with the order of events in secondary GBMs. We then further subdivided the samples into the four main GBM subtypes and determined the relative contributions of each subtype to the overall results: we found that the overall ordering applied for the proneural subtype but differed for mesenchymal samples. The temporal sequence of events could not be identified for neural and classical subtypes, possibly due to a limited number of samples. Moreover, for samples of the proneural subtype, we detected two distinct temporal sequences of events: (i) RAS pathway activation was followed by TP53 inactivation and finally PI3K2 activation, and (ii) RAS activation preceded only AKT activation. This extension of the RESIC methodology provides an evolutionary mathematical approach to identify the temporal sequence of pathway changes driving tumorigenesis and may be useful in guiding the understanding of signaling rearrangements in cancer development.     

Glioblastoma models reveal the connection between adult glial progenitors and the proneural phenotype

Background

Tumor heterogeneity is a major obstacle for finding effective treatment of Glioblastoma (GBM). Based on global expression analysis, GBM can be classified into distinct subtypes: Proneural, Neural, Classical and Mesenchymal. The signatures of these different tumor subtypes may reflect the phenotypes of cells giving rise to them. However, the experimental evidence connecting any specific subtype of GBM to particular cells of origin is lacking. In addition, it is unclear how different genetic alterations interact with cells of origin in determining tumor heterogeneity. This issue cannot be addressed by studying end-stage human tumors.

Methodology/Principal Findings

To address this issue, we used retroviruses to deliver transforming genetic lesions to glial progenitors in adult mouse brain. We compared the resulting tumors to human GBM. We found that different initiating genetic lesions gave rise to tumors with different growth rates. However all mouse tumors closely resembled the human Proneural GBM. Comparative analysis of these mouse tumors allowed us to identify a set of genes whose expression in humans with Proneural GBM correlates with survival.

Conclusions/Significance

This study offers insights into the relationship between adult glial progenitors and Proneural GBM, and allows us to identify molecular alterations that lead to more aggressive tumor growth. In addition, we present a new preclinical model that can be used to test treatments directed at a specific type of GBM in future studies.     

The choice of allogeneic or autologous hematopoietic transplantation for NHL

NHL constitutes the sixth most common malignancy diagnosed in the USA every year, accounting for approximately 24,400 deaths. Although a subset of patients can be cured with chemotherapy or radiation therapy, the outlook is generally poor for patients with refractory or recurrent disease. High-dose therapy supported by both autologous and allogeneic transplantation has been widely studied in this group of patients. Autologous transplantation may be considered standard therapy for patients with diffuse large-cell NHL in chemotherapy-sensitive relapse. Selected categories of patients with other histologic subtypes may also benefit from this strategy. Allogeneic transplantation using high-dose myeloablative conditioning regimen is an effective, yet hazardous approach. A GvL effect leads to a lower rate of disease recurrence than occurs with autologous transplants, but this benefit is offset by higher risk of treatment related mortality. The recent use of less toxic non-myeloablative conditioning regimens for allogeneic transplantation has reduced the risk of transplant-related mortality, allowing this approach even in older or medically infirm patients. Nonablative allogeneic transplants are a promising strategy, particularly for patients with indolent lymphoid malignancies.     

Penile squamous cell carcinoma: anatomic, pathologic and viral studies in Paraguay (1993-2007)

In developed countries, penile squamous cell carcinoma (SCC) account for < 1% of all malignancies in men. It is more frequent in rural populations of Africa, Asia and Latin America, where it may constitute nearly 10% of all carcinomas. In Paraguay, approximately 30-40 new cases are diagnosed per year. Different subtypes of penile carcinomas have been described. Most SCCs are of the usual type (60%). Less frequent variants include basaloid (10%), warty (10%), papillary (15%), verrucous (3%), sarcomatoid (4%) and adenosquamous (1%). Mixed forms also exist. Because there is a correlation between histologic subtype and biologic behavior, accurate subtyping is important. The prevalence of human papillomavirus (HPV) in invasive SCC is approximately 42%, with a strong association of HPV and basaloid and warty variants. Among the most important prognostic factors are histologic grade and depth of invasion. It is important for surgical pathologists to know the anatomy of the penis and possible routes of tumor spread because negative resection margins are crucial to avoid local recurrences. The most frequently involved margins are the urethra and periurethral tissues, including Buck's fascia. Probable precursor lesions of penile carcinoma include squamous hyperplasia, low and high grade squamous intraepithelial neoplasia and lichen sclerosus.     

Cooperativity of Rb,Brca1, and p53 in Malignant Breast Cancer Evolution

Breast cancers that are “triple-negative” for the clinical markers ESR1, PGR, and HER2 typically belong to the Basal-like molecular subtype. Defective Rb, p53, and Brca1 pathways are each associated with triple-negative and Basal-like subtypes. Our mouse genetic studies demonstrate that the combined inactivation of Rb and p53 pathways is sufficient to suppress the physiological cell death of mammary involution. Furthermore, concomitant inactivation of all three pathways in mammary epithelium has an additive effect on tumor latency and predisposes highly penetrant, metastatic adenocarcinomas. The tumors are poorly differentiated and have histologic features that are common among human Brca1-mutated tumors, including heterogeneous morphology, metaplasia, and necrosis. Gene expression analyses demonstrate that the tumors share attributes of both Basal-like and Claudin-low signatures, two molecular subtypes encompassed by the broader, triple-negative class defined by clinical markers.