Concomitant TP53 mutation in early-stage resected EGFR-mutated non-small cell lung cancer: a narrative approach in a genetically admixed Brazilian cohort

TP53 mutations are frequent in non-small cell lung cancer (NSCLC) and have been associated with poor outcome. The prognostic and predictive relevance of EGFR/TP53 co-mutations in NSCLC is controversial. We analyzed lung tissue specimens from 70 patients with NSCLC using next-generation sequencing to determine EGFR and TP53 status and the association between these status with baseline patient and tumor characteristics, adjuvant treatments, relapse, and progression-free (PFS) and overall survival (OS) after surgical resection. We found the EGFR mutation in 32.9% of patients (20% classical mutations and 12.9% uncommon mutations). TP53 missense mutations occurred in 25.7% and TP53/EGFR co-mutations occurred in 43.5% of patients. Stage after surgical resection was significantly associated with OS (P=0.028). We identified an association between progression-free survival and poor outcome in patients with distant metastases (P=0.007). We found a marginally significant difference in OS between genders (P=0.057) and between mutant and wild type TP53 (P=0.079). In univariate analysis, distant metastases (P=0.027), pathological stage (IIIA-IIIB vs I-II; P=0.028), and TP53 status (borderline significance between wild type and mutant; P=0.079) influenced OS. In multivariable analysis, a significant model for high risk of death and poor OS (P=0.029) selected patients in stage IIIA-IIIB, with relapse and distant metastases, non-responsive to platin-based chemotherapy and erlotinib, with tumors harboring EGFR uncommon mutations, with TP53 mutant, and with EGFR/TP53 co-mutations. Our study suggested that TP53 mutation tends to confer poor survival and a potentially negative predictive effect associated with a non-response to platinum-based chemotherapy and erlotinib in early-stage resected EGFR-mutated NSCLC.

237 EXPRESSION OF THE FULL-LENGTH AND ALTERNATIVELY SPLICED BOVINE LH RECEPTOR mRNAs IN GRANULOSA CELLS FROM FOLLICLES ≥ 7 mm IN DIAMETER

The objective of this study was to characterize the pattern of gene expression of LH receptor (LHR) transcripts from bovine antral follicles from 5 to 14 mm in diameter (theca and granulosa cells, TC and GC, respectively) in crossbreed cattle and from cultured GC. From ovaries collected in abattoir (Bos indicus � B. taurus cattle), antral follicles were dissected, and samples of TC and GC were obtained for total RNA extraction (Trizol protocol). Steroid concentrations in the follicular fluid were determined by RIA. Samples of GC cultured for 6 days (obtained from B. taurus follicles), were treated with FSH (0 (control), 1, or 10 ng) and processed for total RNA extraction. Total RNA (1 �g) was utilized in the RT reaction (SuperScript III; Invitrogen, Brasil Ltd., S�o Paulo, Brazil). The PCR conditions were 29 cycles of 95�C, 60�C, and 70�C (1 min each) for denaturation, annealing, and extension (PTC200 thermocycler; MJ Research, Biozym, Landgraaf, The Netherlands). Gene expression of LHR was measured by semiquantitative RT-PCR with specific primers to amplify the fragment from exon 9 to exon 11 (LHRBC; full-length amplicon with 1240 bp). To investigate a putative site of alternative splicing on exon 3 specific primers were utilized to amplify a fragment containing the exons 2 to 9 (LHRA). As an internal control of the PCR, GAPDH expression was used. After sequencing, four isoforms were detected from the LHRBC fragment two with deletion of exon 10 (M2 and M4) and two with deletion of part of exon 11 (M3 and M4) as well as the fragment without deletions (M1). There was no correlation (P > 0.05; Spearman correlation) between LHRBC isoform expression and steroid hormones or follicular diameter (TC). However, estradiol and progesterone concentrations (r > 0.51 and P < 0.01) and follicular diameter (r > 0.82 and P < 0.01) were correlated with expression of the four LHRBC isoforms (GC). Expression of isoforms from fragment LHRBC was observed in GC from follicles with a diameter of 7 mm. In six follicles with a diameter of 7 mm, only one (16.7%) expressed LHR in GC, whereas most of the follicles e 8 mm expressed LHR (87.5%, 21/24). No LHR isoforms were detected in GC from follicles (n = 7) d 6 mm in diameter. From LHRA fragment amplification, an alternative transcript with a deletion of 75 bp, homologous to the rat exon 3, was detected by sequencing. In cultured GC (without FSH treatment), only a weak LHR expression (in vitro control) was observed when compared with the in vivo control (TC sample). The treatment with FSH (1 or 10 ng) was effective to induce LHR expression in cultured GC, however, with a different pattern of expression (lower M1/M2 ratio) when compared to in vivo GC samples (0.8 � 0.14 vs. 3.5 � 0.66; mean � SEM, P < 0.01, unpaired t-test). It is concluded that, in GC from follicles with a diameter e 7 mm, the gene expression of the LHR was positively correlated with follicular diameter and with estradiol and progesterone concentration in the follicular fluid. Treatment with FSH was effective in inducing LHR expression in cultured GC, however, with a different pattern than in the in vivo control. Additionally, sites of alternative splicing were detected in exons 3, 10, and 11 from the bovine LHR gene. This work was supported by a Fellowship from FAPESP.

The contribution of 700,000 ORF sequence tags to the definition of the human transcriptome

Open reading frame expressed sequences tags (ORESTES) differ from conventional ESTs by providing sequence data from the central protein coding portion of transcripts. We generated a total of 696,745 ORESTES sequences from 24 human tissues and used a subset of the data that correspond to a set of 15,095 full-length mRNAs as a means of assessing the efficiency of the strategy and its potential contribution to the definition of the human transcriptome. We estimate that ORESTES sampled over 80% of all highly and moderately expressed, and between 40% and 50% of rarely expressed, human genes. In our most thoroughly sequenced tissue, the breast, the 130,000 ORESTES generated are derived from transcripts from an estimated 70% of all genes expressed in that tissue, with an equally efficient representation of both highly and poorly expressed genes. In this respect, we find that the capacity of the ORESTES strategy both for gene discovery and shotgun transcript sequence generation significantly exceeds that of conventional ESTs. The distribution of ORESTES is such that many human transcripts are now represented by a scaffold of partial sequences distributed along the length of each gene product. The experimental joining of the scaffold components, by reverse transcription-PCR, represents a direct route to transcript finishing that may represent a useful alternative to full-length cDNA cloning.

Loss of imprinting and loss of heterozygosity on 11p15.5 in head and neck squamous cell carcinomas

BACKGROUND

IGF2 and H19 are reciprocal imprinted genes with paternal and maternal monoallelic expression, respectively. This is interesting, because IGF2 is known as a growth factor, and H19 encodes a RNA with putative tumor suppressor action. Furthermore, IGF2 and H19 are linked genes located on chromosome 11p15.5, a common site of loss of heterozygosity in human cancers.

METHODS

We performed an allelic-typing assay using a PCR-RFLP-based method for identification of heterozygous informative cases in head and neck squamous cell carcinomas. Tumoral total RNA was extracted from each of the heterozygotes and further studied by RT-PCR analysis.

RESULTS

We detected the expression of the IGF2 gene in 10 of 10 informative cases. Two cases exhibited LOI of the IGF2 gene as evidenced by biallelic expression, and in another case, LOH was coupled with monoallelic expression of this growth factor. LOI for the H19 gene was observed in 1 of 14 informative samples analyzed. In this case, we also detected parallel monoallelic expression of the IGF2 gene. Down-regulation of the H19 gene was observed in 10 of 14 cases.

CONCLUSION

These findings support the hypothesis that H19 may be a tumor suppressor gene involved in head and neck carcinogenesis. Furthermore, our data showed that genetic and epigenetic changes at 11p15.5 could lead to abnormal expression of imprinted genes in HNSCC.

Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags

Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central coding regions of the resulting transcripts. They are termed ORF expressed sequence tags (ORESTES). The 250,000 ORESTES were assembled into 81,429 contigs. Of these, 1, 181 (1.45%) were found to match sequences in chromosome 22 with at least one ORESTES contig for 162 (65.6%) of the 247 known genes, for 67 (44.6%) of the 150 related genes, and for 45 of the 148 (30.4%) EST-predicted genes on this chromosome. Using a set of stringent criteria to validate our sequences, we identified a further 219 previously unannotated transcribed sequences on chromosome 22. Of these, 171 were in fact also defined by EST or full length cDNA sequences available in GenBank but not utilized in the initial annotation of the first human chromosome sequence. Thus despite representing less than 15% of all expressed human sequences in the public databases at the time of the present analysis, ORESTES sequences defined 48 transcribed sequences on chromosome 22 not defined by other sequences. All of the transcribed sequences defined by ORESTES coincided with DNA regions predicted as encoding exons by genscan. (http://genes.mit.edu/GENSCAN.html).

Expression and imprinting of insulin-like growth factor II (IGF2) and H19 genes in uterine leiomyomas

Genomic imprinting is defined as a gamete of origin-specific epigenetic modification of DNA leading to differential gene expression in the zygote. Several imprinted genes have been identified and some of them are associated with tumor development. We investigated the expression and the imprinting status of IGF2 and H19 genes in 47 uterine leiomyomas. Using allelic transcription assay, we detected the expression of the IGF2 gene in 10 of a total of 15 informative cases. No loss of imprinting, as determined by the finding of biallelic expression, was detected in any case. The expression of H19 gene was detected in 10 of 20 informative cases and the imprinting pattern was also maintained in all of them. Our data suggest that alterations in IGF2 and H19 genes expression by loss of imprinting do not occur in uterine leiomyomas.

Hemangioendothelioma of bone in a patient with a constitutional supernumerary marker

A 13-year old girl was diagnosed as having a bone hemangioendothelioma. Cytogenetic studies identified the presence of a small supernumerary marker chromosome in this patient. Classical cytogenetic methods using G-, C-, Ag-NOR-banding were supplemented by spectral karyotyping (SKY) and fluorescence in situ hybridization to reveal a karyotype 47,XX,+mar.ish der(22)(D22S543+) karyotype in cells derived from the tumor and lymphocytes. These findings suggest that the supernumerary marker chromosome originated from the proximal centromeric region of chromosome 22, and that trisomy of the region 22q11 was not associated with adverse phenotypic effects, but that the presence of trisomy 22q11 may be related to the development of this tumor.

Cytogenetic report of a male breast cancer

The cytogenetic findings on G-banding in an infiltrating ductal breast carcinoma in a 69-year-old man are reported. The main abnormalities observed were trisomy of chromosomes 8 and 9 and structural rearrangement in the long arm of chromosome 17 (add(17)(q25)). Our results confirm the trisomy of chromosome 8 in the characterization of the subtype of ductal breast carcinomas and demonstrate that chromosome 17, which is frequently involved in female breast cancers, is also responsible for the development or progression of primary breast cancers in males.

Chromosomes in the genesis and progression of ependymomas

Cytogenetic analysis was performed on cultures of primary ependymal tumors with different degrees of malignancy (I-IV) obtained from four patients, none of whom had received therapy before karyotypic evaluation. The most common abnormalities were monosomy 17 and 22 in four cases and losses of sex chromosomes in three cases. Structural rearrangements of chromosome 2 were a finding for all cases and involved loss of material at 2q32-34. Other structural chromosome abnormalities detected involved chromosomes 4, 6, 10, 11, 12, and X. We also reviewed data on 22 cases previously reported.

Cytogenetic study of a pineocytoma

The cytogenetic findings based on G-banding in a pineocytoma detected in a 29-year-old woman are reported. The chromosomal study showed numerical alterations involving chromosomes X, 5, 8, 11, 14, and 22, structural alterations of chromosomes 1, 3, 12, and 22, as well as various markers. Tumors of the pineal region are infrequent, and this is the first report of a pineocytoma studied cytogenetically.