Causality and functional relevance of BRCA1 and BRCA2 pathogenic variants in non-high-grade serous ovarian carcinomas.

The identification of causal BRCA1/2 pathogenic variants (PVs) in epithelial ovarian carcinoma (EOC) aids the selection of patients for genetic counselling and treatment decision-making. Current recommendations therefore stress sequencing of all EOCs, regardless of histotype. Although it is recognised that BRCA1/2 PVs cluster in high-grade serous ovarian carcinomas (HGSOC), this view is largely unsubstantiated by detailed analysis. Here, we aimed to analyse the results of BRCA1/2 tumour sequencing in a centrally revised, consecutive, prospective series including all EOC histotypes. Sequencing of n = 946 EOCs revealed BRCA1/2 PVs in 125 samples (13%), only eight of which were found in non-HGSOC histotypes. Specifically, BRCA1/2 PVs were identified in high-grade endometrioid (3/20; 15%), low-grade endometrioid (1/40; 2.5%), low-grade serous (3/67; 4.5%), and clear cell (1/64; 1.6%) EOCs. No PVs were identified in any mucinous ovarian carcinomas tested. By re-evaluation and using loss of heterozygosity and homologous recombination deficiency analyses, we then assessed: (1) whether the eight 'anomalous' cases were potentially histologically misclassified and (2) whether the identified variants were likely causal in carcinogenesis. The first 'anomalous' non-HGSOC with a BRCA1/2 PV proved to be a misdiagnosed HGSOC. Next, germline BRCA2 variants, found in two p53-abnormal high-grade endometrioid tumours, showed substantial evidence supporting causality. One additional, likely causal variant, found in a p53-wildtype low-grade serous ovarian carcinoma, was of somatic origin. The remaining cases showed retention of the BRCA1/2 wildtype allele, suggestive of non-causal secondary passenger variants. We conclude that likely causal BRCA1/2 variants are present in high-grade endometrioid tumours but are absent from the other EOC histotypes tested. Although the findings require validation, these results seem to justify a transition from universal to histotype-directed sequencing. Furthermore, in-depth functional analysis of tumours harbouring BRCA1/2 variants combined with detailed revision of cancer histotypes can serve as a model in other BRCA1/2-related cancers. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

[From gene to disease; hypophosphataemic rickets and the PHEX gene]. / Van gen naar ziekte; hypofosfatemische rachitis en het PHEX-gen.

X-linked hypophosphataemic rickets is associated with mutations in the PHEX gene on the short arm of the X chromosome, encoding a membrane-bound endoprotease which is predominantly expressed in osteoblasts. Defective PHEX function leaves phosphaturic peptides such as FGF23 uncleaved, enabling these peptides, known as phosphatonins, to fully exert their phosphaturic potential in the proximal tubule of the kidney. An autosomally inherited form of hypophosphataemic rickets is caused by mutations in the proteolytic processing site of FGF23 itself, while in tumour-induced osteomalacia overproduction of FGF23 and possibly other phosphatonins causes the processing capacity to be exceeded, resulting in phosphaturic hypophosphataemia and osteomalacia.

A homozygous deletion in a small cell lung cancer cell line involving a 3p21 region with a marked instability in yeast artificial chromosomes.

All types of lung carcinoma are characterized by a high frequency of loss of sequences from the short arm of chromosome 3, the smallest region of overlap containing D3F15S2 in band p21. Here we characterize a 440-kilobase segment from this region, which we found homozygously deleted in one of our small cell lung cancer-derived cell lines. The homozygous deletion maps between UBE1L and ZnF16, just centromeric to D3F15S2. Yeast artificial chromosomes with inserts originating from the deleted region are very unstable and readily lose parts of their insert.

[From gene to disease; incontinentia pigmenti and the NEMO-gene]. / Van gen naar ziekte; incontinentia pigmenti en het NEMO-gen.

Incontinentia pigmenti (IP; MIM308310) is a rare neurocutaneous X-dominant inherited disorder. Besides skin and neurological abnormalities, there is also ophthalmologic and dental involvement. The first stage is characterised by inflammation and apoptosis of the skin and central nervous system. The first stage consists of vesicles and the second of verrucous elements; the third stage is characterised by hyperpigmentation while the fourth is characterised by slightly atrophic hypopigmentations. The skin abnormalities follow the lines of Blaschko. The disorder is observed almost exclusively in girls, but diseased boys are more seriously affected. The IP gene is localised on chromosome Xq28. Mutations in the NEMO-gene are responsible for IP. This gene codes for the nuclear factor-KB essential modulator protein (NEMO; synonym: inhibitor kappaB kinase (IKK)y). In the absence of serious neurological symptoms, the prognosis is not poor.

The growth response to GH treatment is greater in patients with SHOX enhancer deletions compared to SHOX defects.

OBJECTIVE: Short stature caused by point mutations or deletions of the short stature homeobox (SHOX) gene (SHOX haploinsufficiency (SHI)) is a registered indication for GH treatment. Patients with a SHOX enhancer deletion (SED) have a similar phenotype, but their response to GH is unknown. It is uncertain if duplications of SHOX or its enhancer (SDUP) cause short stature. This study aimed to describe the clinical characteristics and growth response to GH treatment in patients with aberrations of SHOX and its enhancers. DESIGN: In this retrospective multi-center study (2002-March 2014) clinical information was available from 130 patients (72 SHI, 44 SED, and 14 SDUP) of whom 52 patients were treated with GH. We evaluated height, sitting height (SH), arm span, dysmorphic features and indicators of the growth response to GH (delta height SDS, height velocity, and index of responsiveness). RESULTS: Patients with SEDs showed similar HtSDS to patients with SHI (-2.3 and -2.6, respectively, P=0.2), but they were less disproportionate (SH/height ratio SDS 2.0 vs 3.1 (P<0.01) and extremities/trunk ratio 2.57 vs 2.43 (P=0.03)). The 1st year growth response to GH treatment was significantly greater in prepubertal patients with SEDs than SHI. None of the patients with an SDUP was disproportionate and SDUP cosegregated poorly with short stature; their growth response to GH treatment (n=3) was similar to the other groups. CONCLUSIONS: Patients with SEDs are equally short, but less disproportionate than patients with SHI, and show a greater response to GH.

A BRCA1 founder mutation, identified with haplotype analysis, allowing genotype/phenotype determination and predictive testing.

We searched for a founder mutation in a population from one geographic region of Norway with prevalent breast/ovarian cancer families. We sampled 33 breast/ovarian cancer families and determined haplotypes of four markers linked to the BRCA1 region. Of the affected 33 index women, 13 (39.4%) shared one haplotype. In five (15% of total), an identical mutation was indicated by an abnormal truncated protein test (PTT) of exon 11 and shown to represent a 1675delA mutation. In the other index women, PTT of exon 11 showed no abnormality. No other BRCA1 founder mutation of this prevalence is likely because no other haplotype was more frequent in affecteds than in controls. All families with the 1675delA mutation in this geographic region may be considered as part of one large kindred. This allows a genotype-phenotype correlation to be precisely determined and used in genetic counselling for predictive testing within this kindred. Identification of identical haplotypes between unrelated affected individuals may be used to estimate the extent of founder effects for any mapped disease, without knowledge of the specific founder mutation.

Translocation (11;22)(q24;q12) in a small cell tumor of the thigh in a 2-year-old boy: immunohistology, cytogenetics, molecular genetics, and review of the literature.

A case of a 2-year-old boy with a palpable mass in the left thigh is presented. Incisional biopsy was performed and subsequent histopathological examination revealed an infiltrative tumor composed of relatively large cells. The tumor cells were immunoreactive for vimentin and keratin, but not for desmin or smooth muscle actin. Cytogenetic analysis showed a 46,XY,t(11;22)(q24;q12) karyotype. The translocation (11;22)(q24;q12) is said to be characteristic for the family of Ewing's sarcoma and related tumors. As a result of the t(11;22)(q24;q12) the EWS gene on chromosome 22q12 joins the 3' part of FLI-1 gene on chromosome 11q24, which encodes a member of the ets family of transcriptional regulators. Using reverse transcription polymerase chain reaction (RT-PCR) a corresponding EWS-FLI-1 fusion product was detected. Additional immunohistological staining for p30/p32MIC2, which is suggestive, but not specific for Ewing's sarcoma, appeared to be weakly positive. In the current case a diagnosis of Ewing's sarcoma was considered unlikely, because of the location of the tumor and the immunohistological profile. Nevertheless it was decided to treat the patient according to a Ewing's sarcoma protocol based on the genotype of the tumor. The findings were compared with other extraosseous pediatric small cell tumors showing the t(11;22)(q24;q12) described in the literature.

Localization by in situ hybridization of three 3p probes with respect to the breakpoint in a t(3;8) in hereditary renal cell carcinoma.

Three 3p probes were localized by in situ hybridization on chromosomes from a carrier of a balanced t(3;8) associated with renal cell cancer. For one of the probes (pH3E4/D3S48), a previous localization in 3p21 was confirmed; for a second probe (pHF12-32/D3S2), a broader localization could be confined to 3p21. Both probes appeared to be located distal to the breakpoint in 3p. The third probe (pMS1-37/D3S3) was localized to 3p14, in accordance with a previous localization. This probe, however, hybridized very weakly or not at all to either of the translocation products, although it is known from Southern analysis that the D3S3 sequence is present on one of them. We assume that this probe is located close to the breakpoint on 3p and that distortion of the higher-order chromosomal structure in this region is causing the failure of the in situ hybridization.

Characterization and chromosomal assignment of yeast artificial chromosomes containing human 3p13-p21-specific sequence tagged sites.

Human chromosomal region 3p12-p23 is proposed to harbor at least three tumor suppressor genes involved in the development of lung cancer, renal cell carcinoma, and other neoplasias. In order to identify one of these genes we defined sequence tagged sites (STSs) specific for 3p13-p24.2 by analyzing a chromosome 3p14 microdissection library. STSs were used for isolating yeast artificial chromosome (YAC) clones from the Centre d'Etude du Polymorphisme Humain (CEPH) YAC libraries. Thirty-eight YACs were assembled into a contig approximately 2.5 Mb in size spanning the t(3;8) and t(3;6) translocation breakpoints associated with hereditary renal cell carcinoma and hematologic malignancies, respectively. Chromosomal localization and chimeric status of 126 YACs was analyzed by fluorescence in situ hybridization (FISH). The order of 17 YACs determined by double-color FISH was in agreement with the STS-based arrangement of the YAC-contig.

Direct molecular analysis of a deletion of 3p in tumors from patients with sporadic renal cell carcinoma.

Normal and tumorous nephrectomy specimens from seven renal cell carcinoma patients were subjected to a Southern analysis using chromosome #3-specific polymorphic probes. Three patients were not informative because of homozygosity at all loci studied. One patient showing heterozygosity at 3q in normal tissue had a tumor that remained heterozygous. In three patients the tumor showed loss of heterozygosity for a short arm market at 3p21. In one of them heterozygosity for a second short arm marker was also lost. Another of these three patients retained heterozygosity for this second short arm marker, as well as for a long arm marker, suggesting a chromosomal breakpoint between the loci for the two short arm markers. Our results demonstrate that the known involvement of a short arm region of chromosome #3 in the development of renal cell carcinoma can readily be further evaluated by direct molecular methods.

Localization of amplified c-myc and n-myc in small cell lung cancer cell lines.

In this study 12 small cell lung cancer cell lines were tested for amplification of myc oncogenes, the location of amplified sequences, and the possible correlation between number of dmin and degree of amplification in dmin-containing lines. C-myc appeared to be amplified in four cell lines, and N-myc amplification was detected in two cell lines. No amplification of L-myc was found. The degree of amplification in the different cell lines varied between 20X and 100X. The cell lines with myc amplification appeared to contain numerous dmin, although in one cell line they occurred in only 10% of the cells. The other cells in this line contained a homogeneously staining region (HSR). In situ hybridization was carried out to find the location of the amplification. In four cell llines the amplified myc genes were found to be located on the dmin. In the cell line with the HSR in most cells and dmin in a minority of its cells, amplification was found both at the HSR and on the dmin. In one cell line the myc sequences seemed to be dispersed through the genome. The ratio between the average number of dmin per cell and the degree of amplification did not vary considerably between the cell lines, with one exception. In that cell line the number of dmin exceeded the number of myc sequences by about one order of magnitude. Apparently, the population of dmin in this cell was heterogeneous and amplified myc genes were only present on a subpopulation.

BRCA1 and BRCA2 heterozygosity and repair of X-ray-induced DNA damage.

PURPOSE: Up to 90% of hereditary breast cancer cases are linked to germ-line mutations in one of the two copies of the BRCA1 or BRCA2 genes. Brca1 and Brca2 proteins are both involved in the cellular defence against DNA damage, although the precise function of the proteins is still not known. Some studies on a small number of samples as well as the present pilot study also suggested that BRCA1 heterozygosity may lead to impaired repair of ionizing-radiation-induced DNA double-strand breaks. The purpose of the study was to test in a larger family-matched study whether carriers of BRCA1 or BRCA2 mutations have an increased sensitivity to ionizing radiation. MATERIALS AND METHODS: In a blind study, the effect of different germ-line mutations in one allele of the BRCA1 or BRCA2 gene on the ability to repair X-ray-induced DNA breaks was investigated. Fibroblasts and lymphocytes were taken from heterozygotic individuals (BRCA1+ /- and BRCA2+ /-) with different mutations and from relatives proven to be non-carriers of the BRCA mutations. Rejoining of DNA breaks was analysed by pulsed-field gel electrophoresis (for fibroblasts) or the comet assay (for lymphocytes). RESULTS: Significant interindividual differences were found in the capacities of the fibroblasts and lymphocytes to rejoin DNA breaks induced by X-radiation. However, these differences were not related to heterozygosity in BRCA1 or BRCA2. CONCLUSIONS: Cells from carriers of mutations in one allele of the BRCA1 or BRCA2 genes have no gross defects in their ability to rejoin radiation-induced DNA breaks. Hence, these carriers may not be at risk of developing excess normal tissue reactions after radiotherapy consistent with data from recent clinical studies.

Optimal selection for BRCA1 and BRCA2 mutation testing using a combination of 'easy to apply' probability models.

To establish an efficient, reliable and easy to apply risk assessment tool to select families with breast and/or ovarian cancer patients for BRCA mutation testing, using available probability models. In a retrospective study of 263 families with breast and/or ovarian cancer patients, the utility of the Frank (Myriad), Gilpin (family history assessment tool) and Evans (Manchester) model was analysed, to select 49 BRCA mutation-positive families. For various cutoff levels and combinations, the sensitivity and specificity were calculated and compared. The best combinations were subsequently validated in additional sets of families. Comparable sensitivity and specificity were obtained with the Gilpin and Evans models. They appeared to be complementary to the Frank model. To obtain an optimal sensitivity, five 'additional criteria' were introduced that are specific for the selection of small or uninformative families. The optimal selection is made by the combination 'Frank >or=16% or Evans2 >or=12 or one of five additional criteria'. The efficiency of the selection of families for mutation testing of BRCA1 and BRCA2 can be optimised by using a combination of available easy to apply risk assessment models.

SMN genotypes producing less SMN protein increase susceptibility to and severity of sporadic ALS.

BACKGROUND: ALS is believed to be multifactorial in origin with modifying genes affecting its clinical expression. Childhood-onset spinal muscular atrophy (SMA) is an autosomal recessive disorder of motor neurons, caused by mutations of the survival motor neuron (SMN) gene. The SMN gene exists in two highly homologous variants: SMN1, the causative gene responsible for the production of the majority of functional SMN protein, and SMN2, responsible for the production of less protein but sufficient for modifying the SMA phenotype. OBJECTIVE: To test whether SMN genotypes are associated with susceptibility to and severity of sporadic ALS. METHODS: We performed competitive quantitative PCR analysis for both SMN1 and SMN2 genes in 242 clinically well-defined ALS patients and 175 controls. The combined determination of SMN1 and SMN2 copies also allowed for an estimation of the level of SMN for each patient (estimated SMN protein level = SMN1 copy number + 0.20 x SMN2 copy number). RESULTS: One copy of SMN1 was associated with an increased risk of developing ALS (odds ratio = 4.1, 95% CI = 1.2 to 14.2, p = 0.02) and ALS patients carried fewer SMN2 copy numbers (p < 0.001). Sixty-one percent of patients had an estimated protein SMN level < or = 2.2 vs only 36% of controls (p = 0.0000004). Multivariate Cox regression analyses showed that lower SMN2 copy numbers and lower levels of estimated SMN protein (hazard ratio = 1.3, 95% CI = 1.1 to 1.6, p = 0.03) were associated with an increased mortality rate. CONCLUSIONS: SMN genotypes producing less SMN protein increase susceptibility to and severity of ALS.

Construction of a pulsed-field map around D3S3 using partially demethylated DNA.

Heavy methylation of restriction sites in the relevant chromosomal region can be a major problem in the construction of a long-range restriction map. In the region around the locus D3S3 there appeared to be few accessible restriction sites. Therefore, we cultured cells in the presence of 5-azacytidine and used the partially demethylated DNA to construct a relatively detailed restriction map spanning approximately 1 Mb. Using partially demethylated DNA is a recommendable approach when a genome region appears inaccessible for pulsed-field analysis because excessively long restriction fragments are obtained.

Localization of DNA probes with tight linkage to the cystic fibrosis locus by in situ hybridization using fibroblasts with a 7q22 deletion.

Five DNA probes known to originate from the region 7q22-q31 were sublocalized by in situ hybridization to metaphase preparations of fibroblasts having besides a normal chromosome 7, a homologue 7 with an apparent interstitial deletion of a large part of band q22. A flow cytometric chromosome analysis confirmed a loss of material from one of the homologues of chromosome 7. Four of the probes, B79a, 7C22, metH, and pJ3.11, have been shown to be closely linked to the cystic fibrosis (CF) locus. We localized probes B79a and 7C22 to the part of 7q22 involved in the deletion, whereas metH and pJ3.11 could be assigned to band 7q31. Probe pJu28, for which polymorphisms have not yet been described, also appeared to derive from the latter band. Since pJ3.11 and metH are most tightly linked to the CF locus, this disease locus is indirectly assigned to 7q31. A comparison of our findings with linkage data suggests a discrepancy between genetic and physical distances in the region 7q22-q31.

Genome analysis of small cell lung cancer (SCLC) and clinical significance.

A chromosome analysis of three cell lines derived from SCLC showed deletions of the short arm of chromosome 3 with bands p21-p23 as the shortest region of overlap. Hybridization of a polymorphic 3p21 probe to DNA from leukocytes of seven SCLC patients revealed heterozygosity for two of them. In the tumours of both these patients the probe detected homozygosity. This suggests the presence of a mutant cancer gene in the short arm of chromosome 3 which might express itself and/or activate some oncogene(s) after deletion of a suppressing normal allele. Amplification of the oncogene C-MYC was found in four cell lines including the ones cytogenetically analyzed. Amplification of C-MYC, though to a lesser degree, was also found in an available pleural effusate from which one of these lines had been established. As shown by in situ hybridization, the amplified oncogene was present in double minutes in three of the cell lines. In the remaining line it was in a homogeneously staining chromosome region. All patients from whom cell lines with C-MYC amplification were obtained had a negative response to chemotherapy. The observed correlation between amplification of C-MYC, occurrence of so-called variant type SCLC-derived cell lines, and negative response to chemotherapy indicates that a genome analysis of SCLC might provide further criteria for the characterization and subdivision of this highly malignant cancer and thereby a base for an optimal selection of therapy for distinct cases of SCLC.

The region of common allelic losses in sporadic renal cell carcinoma is bordered by the loci D3S2 and THRB.

Cytogenetic studies and DNA analysis have shown that the short arm of chromosome 3 is the region in the genome that is commonly deleted in renal cell carcinoma. By studying loss of heterozygosity in 41 matched tumor/normal kidney tissue pairs, we could delimit the commonly deleted part of 3p to the region between the loci THRB (in 3p24) and D3S2 (in 3p21). The regions on 3p suggested to be involved in the Von Hippel-Lindau syndrome and in hereditary renal cell carcinoma are both outside this smallest region of overlapping deletions. Consequently, renal cell cancer would be an illustration of the possibility that different genes cause the same type of tumor.