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High frequency of LOH at chromosome 18q in human breast cancer: Association with high S-phase fraction and low progesterone receptor content
Abstract
Human primary breast cancers were analysed for somatic loss of heterozygosity (LOH) at chromosome 18 with 15 polymorphic microsatellite markers. LOH was observed in 148 of the 228 cases analyzed, (65%). Three smallest common deletion regions (SCDR) were detected on the long arm of chromosome 18. The marker D18S51 at the region 18q22 showed the highest LOH (42%). Tumors with and without LOH at 18q were tested for association with clinico-pathological features of the tumors, such as estrogen and progesterone receptor content, age at diagnosis, tumor size, node status, histological type, S-phase fraction, DNA ploidy and LOH at other chromosomal regions. A significant association was found between LOH at 18q and high S-phase fraction (99.9% confidence interval) and low progesterone receptor content (99% confidence interval). Furthermore, an association was found between LOH at 18q and LOH at 1p, 7q, 9p, 13q and 17q. We conclude that there are three separate LOH target regions at chromosome 18q, and that inactivation of one or more genes at these regions might be important for human breast carcinogenesis.
... Chromosome 18 carries both known and candidate tumor suppressor genes like the well-characterized DCC [Deleted in Colon Cancer Gene], SMAD2, and SMAD4 (Nguyen & Duong, 2018). Loss of heterozygosity (LOH) at the long arm of this chromosome (18q) can occur in colon (Ogunbiyi et al, 1998;Sheffer et al, 2009), pancreatic (Sunamura et al, 2004), lung (Takei et al, 1998), prostate (Kluth et al, 2016), and breast cancers (Huiping et al, 1998), as well as head and neck squamous cell carcinoma (Takebayashi et al, 2000). One gene localized on 18q is VPS4B (Vacuolar Protein Sorting 4 Homolog B). ...
Somatic copy number alterations play a critical role in oncogenesis. Loss of chromosomal regions containing tumor suppressors can lead to collateral deletion of passenger genes. This can be exploited therapeutically if synthetic lethal partners of such passenger genes are known and represent druggable targets. Here, we report that VPS4B gene, encoding an ATPase involved in ESCRT-dependent membrane remodeling, is such a passenger gene frequently deleted in many cancer types, notably in colorectal cancer (CRC). We observed downregulation of VPS4B mRNA and protein levels from CRC patient samples. We identified VPS4A paralog as a synthetic lethal interactor for VPS4B in vitro and in mouse xenografts. Depleting both proteins profoundly altered the cellular transcriptome and induced cell death accompanied by the release of immunomodulatory molecules that mediate inflammatory and anti-tumor responses. Our results identify a pair of novel druggable targets for personalized oncology and provide a rationale to develop VPS4 inhibitors for precision therapy of VPS4B-deficient cancers.
... Huiping et al., 1999 ;Driouch et al., 1998 16q23-q24 -DCIS, bessere Prognose Hansen et al., 1998;Chen et al., 1996 17p13.1-p13.3 TP53 höheres Rezidivrisiko, ER-negativ Hirano et al., 2001;Schmutzler et al., 1997 17q21-q24 BRCA1 höheres Grading, ER-negativ Phelan et al., 1998;Plummer et al., 1997 18q21-q22 DCC PR-negativ Huiping et al., 1998;Yokota et al., 1997 22q13 NF2 höheres Rezidivrisiko Hirano et al., 2001;Iida et al., 1998 Amplifikation Kandidatengene Histologie und Progression Literatur 1q31-q32 ELF3, MDM - Tirkkonen et al., 1998 ;Benitez et al., 1997 8p11-p12 FGFR1 ILC, ER-positiv Courjal et al., 1997;Dib et al., 1995 8q24 MYC IDC, ER-negativ, schlechte Prognose Hermsen et al., 1998;Courjal et al., 1997 11q13 CCND1, FGF3 ILC, ER-positiv, schlechte Prognose Hermsen et al., 1998;Courjal et al., 1997 12q13-q15 MDM2 - Aubele et al., 1999;Bueso-Ramos et al., 1996 17q11-q12 ERBB2/ HER-2 IDC, ER-negativ; schlechte Prognose Hermsen et al., 1998;Courjal et al., 1997 20q13 -schlechte Prognose Hermsen et al., 1998;Tanner et al., 1996 Tab. 28: Auswahl an Referenzen für Aberrationen (LOH, Amplifikation) in Ovarialtumoren und endometrialen Tumoren mit Angabe von Kandidatengenen und Assoziationen bestimmter Aberrationen zur Histologie und Progression der Tumore. ...
Brust- und Ovarialkarzinome gehören zu den häufigsten sporadischen Tumorerkrankungen bei der Frau. Die Progression von benignen Neoplasien zu malignen Karzinomen werden von spezifischen Veränderungen der Genexpression begleitet. Durch die bioinformatische Auswertung von vier Millionen ESTs aus cDNA-Bibliotheken von Normalgeweben und der korrespondierenden Tumore wurden Hunderte von differenziell exprimierten Genen selektiert. Nach der chromosomalen Kartierung der Kandidatengene erfolgten weitere Untersuchungen für Gene aus den chromosomalen Regionen 1q32-q41 und 11q12-q23, die häufig in Brust- und Ovarialkarzinomen als aberrant beschrieben wurden. Die Validierung der in-silico Expressionsdaten erfolgte über Northernblot- und cDNA-Array-Analysen von unselektierten und mikrodissezierten Tumorproben. Es konnte für einige der Gene die differenzielle Expression in Brusttumoren bestätigt und dadurch neue Kandidatengene für die untersuchten Genloci identifiziert werden. Das Expressionsmuster einer Acyltransferase in 11q13 als potenzielles Tumorsuppressorgen erbrachte den Hinweis auf eine mögliche Involvierung in den Retinol-Metabolismus und könnte auf einen Mechanismus der Inhibierung der Karzinogenese im Brustepithel hindeuten.
The genome of breast tumour cells is considered to be unstable, as reflected by multiple chromosomal and gene abnormalities. The molecular mechanism of genomic instability progression in breast cancer is poorly understood, but recent data suggest that mutated or overexpressed proteins affect the genome in several ways, including an abnormal number of centrosomes, inefficient DNA repair and unwanted telomere maintenance. Among these proteins are p53, Brca1, Brca2, Aurora kinase A, Myc and telomerase. The involved molecular networks include co-regulation with cell cycle checkpoints. p53 has been relatively well studied and is considered to be a guardian of the genome integrity. Myc seems to affect tumour pathogenesis in several ways, including increased proliferation and immortalisation of the cancer cells and induction of genomic instability. Aurora kinase A has been shown to control the centrosome number of cells and the segregation of the correct chromosomes to the daughter cells during mitosis. Genomic instability is high in some hereditary breast cancer, particularly in tumours of Brca1- and Brca2-mutation carriers, a finding that is in line with their role in DNA repair.
Gene and chromosome changes in breast cancer have been analysed using molecular and cytological methods. No single gene alterations are frequent in breast cancer, but several alterations have been detected, in line with multigenetic disease, although malignant progression in relation to gene changes is poorly documented. The most common tumour suppressor gene mutations, detected in about ¼ of breast tumours are in the TP53 gene, that encodes a transcription factor. Mutations and other alterations in the CDH1 gene, encoding the E-cadherin adhesion protein, in the CHK2 gene, encoding a cell cycle checkpoint kinase, in the BRCA1 and BRCA2 genes, encoding DNA repair proteins and FHIT, encoding a diadenosine hydrolase, will be reviewed. The molecular mechanism behind the frequently detected instability of the genome of breast cancer cells is poorly understood, but some studies have associated it with mutations in the TP53, BRCA1 or BRCA2 genes.
Breast cancer is the most prevalent disease and cause of death among women in Northern Europe and the USA. The incidence rate
is still increasing, and despite early diagnosis and improved treatment, the mortality is still high. Breast cancer is a very
heterogeneous disease and less than 10% of the diagnosed cases are believed to be caused by an inherited factor. The information
on tumor specific genomic alterations has dramatically increased during the past decade, and seen in relation to the effect
on survival and treatment efficiency, these genomic changes may prove to act as prognostic and predictive factors. The introduction
of methods to screen the entire genome for alterations has led to important knowledge of tumor biology, progression and targets
of therapy. This chapter describes the different kinds of genomic alterations found in the tumor, the methods to assess them
and examples of correlations between the changes and prognostic or predictive parameters
Several chromosome regions exhibit loss of heterozygosity (LOH) in human breast carcinoma and are thought to carry tumor suppressor genes. We have analysed human breast tumors with 9 polymorphic microsatellite markers that are specific to chromosome 6q. The mapping of smallest region of overlap (SRO) indicated location of candidate suppressor genes at 6q23 and 6q27. Variations in estrogen receptor (ER) expression were independent of the number of copies of the corresponding gene. Tumors with and without LOH on chromosome 6q were tested for association with clinicopathological factors. A significant association was found between LOH at 6q and the following: high S-phase, aneuploidy, deletions at chromosomes 3p and 9p and lower survival rate. In a multivariate model LOH at 6q is an independent prognostic variable and patients having tumors with LOH have approximately twofold increase in relative risk of death. It can be concluded that the 6q deletions give additional prognostic information that might be useful in breast cancer treatment.
In this study, we report the expression and genomic structure of the gene encoding human suppressor of cytokine signaling 6 (SOCS6), and the characterization of the functional promoter region. The human SOCS6 gene, spanning 40 kb on chromosome 18q22.2, is composed of two exons separated by an intron of 35 kb. Two transcripts are ubiquitously expressed, and both encode the full-length open reading frame of SOCS6. A primer extension assay revealed that the major transcription initiation site is located 469 bp upstream the ATG codon. Luciferase promoter analysis demonstrated that the 5'-flanking region is able to drive transcription, and the CpG-rich sequences near the transcription initiation site are important for the TATA-less SOCS6 promoter activity. Analogous to SOCS1 and SOCS3, which are down-regulated in several human cancers, SOCS6 is expressed at lower levels in carcinomas of stomach and colon. We demonstrated that hypermethylation of the SOCS6 promoter is one of the mechanisms for the epigenetic regulation of SOCS6 expression. Firstly, in vitro methylation of the reporter promoter plasmid significantly suppressed the promoter activity. Secondly, SOCS6 expression in vivo was enhanced by treating cells with a methyltransferase inhibitor. The SOCS6 gene from various species shares significant homology in amino acid sequences, transcription factor binding motifs in promoter regions and the two-exon genomic structure, suggesting that the SOCS6 gene is highly conserved.
Members of the suppressor of cytokine-induced signaling (SOCS) family are negative regulators of cytokine signaling pathways. By mRNA differential display, we showed that SOCS6 was frequently down-regulated in gastric cancer (GC). Our data showed that allelic loss and promoter hypermethylation may account for the major mechanisms leading to SOCS6 inactivation. Ectopic expression of SOCS6 suppressed cell growth and colony formation, in part through eliciting intrinsic apoptotic pathway, accompanied with decreased mitochondrial membrane potential. Taken together, this study provides molecular and functional data supporting the importance of loss-of-function of SOCS6 as a frequent event in gastric tumorigenesis.
Anaplastic thyroid cancer (ATC) is one of the malignant tumors with the poor prognosis that is thought to arise from well-differentiated thyroid cancer (DTC). To investigate the molecular mechanism of ATC, we studied genomic alterations of eight ATC cell lines and three DTC cell lines by means of the comparative genomic hybridization (CGH) method. Loss of 16p was observed in five of eight ATC cell lines (62. 5%), but none of the three DTC cell lines showed loss of this chromosome arm. It is notable that loss of 18q [7/8 of ATC (87.5%), 2/3 of DTC (67%)] and gain of 20q [5/8 of ATC (62.5%), 3/3 of DTC (100%)] were frequently seen in both histologic types. Our results suggest that there is a gene in 16p that is closely associated with transformation from well-differentiated thyroid cancer to anaplastic cancer.
The loss of genetic material from a specific chromosome region in tumors suggests the presence of tumor-suppressor genes. Loss of heterozygosity (LOH) or allelic imbalance (AI) on the long arm of chromosome 16 is a known event in sporadic breast cancer. To locate the commonly deleted regions, and therefore (a) candidate tumor-suppressor gene(s), a deletion map of chromosome 16 was made, using 10 microsatellite markers on 150 sporadic breast tumors. The 3 smallest regions of overlap (SRO) were detected on the long arm of chromosome 16. Allelic imbalance was observed with at least one marker in 67% of the tumors. One marker, D16S421, at the 16q22-23 region, showed the highest allelic imbalance, 58%. Tumors with and without AI on 16q were tested for correlation with clinico-pathological features of the tumors such as estrogen- and progesterone-receptor content (ER and PgR), age at diagnosis, tumor size, node status, histological type, S-phase fraction, AI on chromosome 3p, and ploidy. A correlation was found between AI on 16q and high PgR content, also low S-phase fraction (99% confidence limits). A comparison of tumors with and without AI at the D16S421 marker locus revealed a slight correlation with high PgR content. The survival data showed no difference between patients with AI on 16q and those with a normal allele pattern on the long arm of chromosome 16. © 1995 Wiley-Liss, Inc.
Human breast tumours were analyzed with polymorphic microsatellite markers specific to chromosome 3p. Allelic imbalance (AI) was observed in 34% of the tumours. Microsatellite markers from two regions showed higher percentage of imbalance suggesting the presence of tumour suppressor genes or genes important for malignancy. Microsatellite instability was also found, implying errors in DNA replication. No significant correlation was found between AI and conventional prognostic variables. However, a striking correlation was found between AI and tumour S-phase fraction; AI was also significantly correlated with low steroid receptor content. A multivariate model including prognostic variables, showed that AI was without exception a significant prognostic variable; patients having tumours with AI had approximately a four-fold increase in relative risk of death. We conclude that screening for 3p deletions gives prognostic information and further investigations should reveal whether this finding could assist in treatment of the disease.
Several chromosome regions exhibit loss of heterozygosity (LOH) in human breast carcinoma and are thought to carry tumor suppressor genes. We have analysed human breast tumors with 9 polymorphic microsatellite markers that are specific to chromosome 6q. The mapping of smallest region of overlap (SRO) indicated location of candidate suppressor genes at 6q23 and 6q27. Variations in estrogen receptor (ER) expression were independent of the number of copies of the corresponding gene. Tumors with and without LOH on chromosome 6q were tested for association with clinicopathological factors. A significant association was found between LOH at 6q and the following: high S-phase, aneuploidy, deletions at chromosomes 3p and 9p and lower survival rate. In a multivariate model LOH at 6q is an independent prognostic variable and patients having tumors with LOH have approximately twofold increase in relative risk of death. It can be concluded that the 6q deletions give additional prognostic information that might be useful in breast cancer treatment.
232 human primary invasive breast tumors were analyzed with 13 polymorphic microsatellite markers specific to chromosome 1p. Loss of heterozygosity (LOH) was observed in 126 cases or 54% of the tumors. One marker, D1S496, at the 1p35 region showed the highest LOH, 28%. High frequencies of LOH were also detected by the markers, D1S488, D1S167 and D1S435, at the 1p31 region, 25%, 24% and 26% LOH, respectively. This suggests the presence of tumor suppressor genes at these two regions. Tumors with and without LOH at 1p were tested for association with clinico-pathological features of the tumors such as estrogen- and progesterone-receptor content (ER and PgR), age at diagnosis, tumor size, node status, histological type, S-phase fraction, ploidy, survival and LOH at chromosomes 3p, 6q, 9p, 11p, 11q, 13q, 16q, 17p and 17q. A significant association was found between LOH at chromosome 1p and high S-phase fraction and lower survival rate. Association was also found between LOH at 1p and chromosome regions 3p, 6q, 9p and 17q. A multivariate model including prognostic variables, showed that LOH at 1p is an independent prognostic variable and patients who have breast tumors with LOH at 1p have approximately a two-fold increase in relative risk of death. We conclude that screening for 1p deletions gives additional prognostic information that might be useful in breast cancer treatment.
Allelic deletions involving chromosome 18q occur in more than 70 percent of colorectal cancers. Such deletions are thought to signal the existence of a tumor suppressor gene in the affected region, but until now a candidate suppressor gene on this chromosomal arm had not been identified. A contiguous stretch of DNA comprising 370 kilobase pairs (kb) has now been cloned from a region of chromosome 18q suspected to reside near this gene. Potential exons in the 370-kb region were defined by human-rodent sequence identities, and the expression of potential exons was assessed by an "exon-connection" strategy based on the polymerase chain reaction. Expressed exons were used as probes for cDNA screening to obtain clones that encoded a portion of a gene termed DCC; this cDNA was encoded by at least eight exons within the 370-kb genomic region. The predicted amino acid sequence of the cDNA specified a protein with sequence similarity to neural cell adhesion molecules and other related cell surface glycoproteins. While the DCC gene was expressed in most normal tissues, including colonic mucosa, its expression was greatly reduced or absent in most colorectal carcinomas tested. Somatic mutations within the DCC gene observed in colorectal cancers included a homozygous deletion of the 5' end of the gene, a point mutation within one of the introns, and ten examples of DNA insertions within a 0.17-kb fragment immediately downstream of one of the exons. The DCC gene may play a role in the pathogenesis of human colorectal neoplasia, perhaps through alteration of the normal cell-cell interactions controlling growth.
The development of human breast cancer is characterized by a variety of genetic alterations, and cytogenetic analyses have documented the consistent involvement of both arms of chromosome I. In the present study, molecular markers detecting restriction fragment length polymorphisms were used in pairwise screening of normal and tumor DNA to determine the frequency of allelic imbalance in breast tumors. Loss of heterozygosity (LOH) in the polymorphic epithelial mucin (PEM or MUCI) gene at 1q21 was found in 16% of 89 informative (constitutionally heterozygous) cases, whereas gain in intensity of one allelic band was more frequent (37%), a total of 47% of cases manifesting either allelic loss or gain. Three additional tumors manifested a structural alteration. Allelic loss or gain in the PEM gene was not associated with other prognostic factors, e.g., tumor size, lymph node status, steroid receptors, DNA ploidy, S phase fraction, protooncogene amplification, histological type, or patient age. However, LOH in the PEM gene was significantly correlated with early disease recurrence (P = 0.006). LOH on 1p was found in 27% of 117 informative cases, using probes for either DIS57 or DIZ2 located at 1p33-p35 and 1p36, respectively. Somatic allelic imbalance on 1p and 1q seemed to be independent events and not the effect of loss of a whole chromosome 1. LOH on 1 p was significantly correlated to the presence of lymph node metastasis, to larger tumor size, and to DNA nondiploidy, but no correlation was found to disease outcome at this limited duration of follow-up (median 29 months). ©1992 Wiley-Liss, Inc.
Fifty-nine primary breast carcinomas and 11 metastases were examined to identify genetic alterations in the tumour suppressor gene regions 3p, 11p, 13q, 17p, and 17q. Loss of heterozygosity (LOH) was frequently observed on chromosome arms 17p (p144D6 lost in 75%, pYNZ22.1 in 55%, and TP53 in 48% of the primary tumours), 13q (RBI lost in 40% of the primary tumours), and 17q (pRMU3 lost in 35%, pTHH59 in 29%, and NM23HI in 26% of the primary tumours). Loss of all the markers except p144D6 was observed even more frequently in the metastases. Pairwise comparisons for concordance of allele losses on 17p indicated that there might be two genes on 17p implicated in breast cancer development; the TP53 gene and a gene located close to the p144D6 and pYNZ22.1 markers. LOH of the RBI gene was associated with LOH of pYNZ22.1 and p144D6, but not with LOH of TP53. LOH of RBI and TP53 was associated with occurrence of ductal carcinomas, RBI and p144D6 losses with tumour size, and p144D6 losses with positive node status as well. LOH of TP53 and the three 17q markers NM23HI, pTHH59, and pRMU3 was most frequently observed in tumours from postmenopausal women. p144D6 losses occurred most frequently in progesterone receptor-negative tumours, whereas pTHH59 losses occurred most frequently in oestrogen receptor-negative tumours. LOH of the investigated loci was not associated with ERBB2 protooncogene amplification, with positive family history of breast cancer, or with survival.
All human chromosomes were screened in 52 human breast carcinomas for the occurrence of allele losses, in order to identify genomic alterations involved in initiation and progression of the disease. Loss of chromosome 22 alleles was detected in 6 out of 8 lobular carcinomas, while chromosome 17 losses were most frequent in ductal carcinomas. Furthermore, patients who developed advanced disease after many years of mild clinical course showed significantly higher frequencies of allele losses in their primary tumors, compared to patients with a persistently mild disease course. Finally, in one case, molecular examination suggested a translocation t(10;17) with coamplification of the ERBB2 oncogene and chromosome 10 sequences present in the two tumors from this patient, consistent with one of the tumors being a metastasis originating from a subclone of cells in the other tumor.