Neoadjuvant paclitaxel/olaparib in comparison to paclitaxel/carboplatinum in patients with HER2-negative breast cancer and homologous recombination deficiency (GeparOLA study)

BACKGROUND

The efficacy and toxicity of olaparib as combination therapy in early breast cancer (BC) patients with homologous recombinant deficiency (HRD) [score high and/or germline (g) or tumour (t) BRCA1/2 mutation] is not well described. GeparOLA (ClinicalTrials.gov, NCT02789332) investigated olaparib in combination with paclitaxel in HER2-negative early BC with HRD.

PATIENTS AND METHODS

Patients with untreated primary HER2-negative cT2-cT4a-d or cT1c with either cN+ or pNSLN+ or cT1c and triple-negative breast cancer (TNBC) or cT1c and Ki-67>20% BC with HRD were randomised either to paclitaxel (P) 80 mg/m² weekly plus olaparib (O) 100 mg twice daily for 12 weeks or P plus carboplatinum (Cb) area under the curve 2 weekly for 12 weeks, both followed by epirubicin/cyclophosphamide (EC). Stratification factors were hormone receptor (HR) status (HR+ versus HR-) and age (<40 versus ≥40 years). The primary endpoint was pathological complete response (pCR; ypT0/is ypN0). A two-sided one-group χ²-test was planned to exclude a pCR rate of ≤55% in the PO-EC arm. Secondary end points were other pCR definitions, breast conservation rate, clinical/imaging response, tolerability and safety.

RESULTS

A total of 107 patients were randomised between September 2016 and July 2018; 106 (PO N = 69; PCb N = 37) started treatment. Median age was 47.0 years (range 25.0-71.0); 36.2% had cT1, 61.0% cT2, 2.9% cT3, and 31.8% cN-positive tumours; grade 3 tumours: 86.8%; Ki-67>20%: 89.6%; TNBC: 72.6%; confirmed gBRCA1/2 mutation: 56.2%. The pCR rate with PO was 55.1% [90% confidence interval (CI) 44.5% to 65.3%] versus PCb 48.6% (90% CI 34.3% to 63.2%). Analysis for the stratified subgroups showed higher pCR rates with PO in the cohorts of patients <40 years and HR+ patients.

CONCLUSION

GeparOLA could not exclude a pCR rate of ≤55% in the PO arm. PO was significantly better tolerated and the combination merits further evaluation.

Survival analysis of carboplatin added to an anthracycline/taxane-based neoadjuvant chemotherapy and HRD score as predictor of response-final results from GeparSixto

Background

In the neoadjuvant GeparSixto study, adding carboplatin to taxane- and anthracycline-based chemotherapy improved pathological complete response (pCR) rates in patients with triple-negative breast cancer (TNBC). Here, we present survival data and the potential prognostic and predictive role of homologous recombination deficiency (HRD).

Patients and methods

Patients were randomized to paclitaxel plus nonpegylated liposomal doxorubicin (Myocet®) (PM) or PM plus carboplatin (PMCb). The secondary study end points disease-free survival (DFS) and overall survival (OS) were analyzed. Median follow-up was 47.3 months. HRD was among the exploratory analyses in GeparSixto and was successfully measured in formalin-fixed, paraffin-embedded tumor samples of 193/315 (61.3%) participants with TNBC. Homologous recombination (HR) deficiency was defined as HRD score ≥42 and/or presence of tumor BRCA mutations (tmBRCA).

Results

A significantly better DFS (hazard ratio 0.56, 95% CI 0.34-0.93; P = 0.022) was observed in patients with TNBC when treated with PMCb. The improvement of OS with PMCb was not statistically significant. Additional carboplatin did not improve DFS or OS in patients with HER2-positive tumors. HR deficiency was detected in 136 (70.5%) of 193 triple-negative tumors, of which 82 (60.3%) showed high HRD score without tmBRCA. HR deficiency independently predicted pCR (ypT0 ypN0) [odds ratio (OR) 2.60, 95% CI 1.26-5.37, P = 0.008]. Adding carboplatin to PM significantly increased the pCR rate from 33.9% to 63.5% in HR deficient tumors (P = 0.001), but only marginally in HR nondeficient tumors (from 20.0% to 29.6%, P = 0.540; test for interaction P = 0.327). pCR rates with carboplatin were also higher (63.2%) than without carboplatin (31.7%; OR 3.69, 1.46-9.37, P = 0.005) in patients with high HRD score but no tmBRCA. DFS rates were improved with addition of carboplatin, both in HR nondeficient (hazard ratio 0.44, 0.17-1.17, P = 0.086) and HR deficient tumors (hazard ratio 0.49, 0.23-1.04, P = 0.059).

Conclusions

The addition of carboplatin to neoadjuvant PM improved DFS significantly in TNBC. Long-term survival analyses support the neoadjuvant use of carboplatin in TNBC. HR deficiency in TNBC and HRD score in non-tmBRCA TNBC are predictors of response. HRD does not predict for carboplatin benefit.

Abstract P3-09-04: Beyond CHEK2 in breast cancer: Search for additional moderately penetrant risk gene variants by analyzing the oligogenic disease course in CHEK2 mutation carriers

This abstract was not presented at the symposium.

Abstract P3-09-03: Low-level gonosomal mosaicism of a de novo BRCA1 gene mutation – The origin of a constitutional mutation in a breast cancer family

Mosaicisms arise when specific cells within a developing organism mutate to result in two or more cell populations with distinct genotypes. In cases of gonosomal mosaicism a genetic variation is present in both somatic and germline cells.

Here, we describe a large Turkish breast cancer family with four affected individuals. In the Index patient (II-1; age of onset 45 years), a heterozygous deleterious frameshift mutation, c.1310dupA, p.His437Glnfs*2 in BRCA1 was identified using the TruRisk® gene panel designed by the German Consortium for Hereditary Breast and Ovarian Cancer (GC-HBOC). Predictive genetic testing showed heterozygous carrier status in the daughter (III-1).

The mutation was also analyzed in peripheral blood of the affected mother (I-1; age of onset 45 years) of the index patient by Sanger Sequencing. Interestingly, Sanger sequence did demonstrate the presence of remarkable small peaks presenting the frameshift mutation similar to a mosaic pattern. A second and third independent blood draw within a time frame of four month was tested and a mosaic signal of approximately 10 % was reproducibly detected.

In order to exclude a potential allelic drop out, independent sequencing experiments via next generation sequencing (NGS; TruRisk® gene panel) were performed. Again, the mutation was present with an allele read frequency of 12 %. No other pathogenic mutations were detected in any of the other tested breast cancer susceptibility genes.

To further examine and underscore the presence of gonosomal mosaicism different tissues should be analyzed. As no tumor material or surrounding normal breast tissue was available primary skin fibroblasts were isolated from skin biopsy. Sequencing of cultured primary fibroblasts demonstrated the absence of the familial BRCA1 mutation. With NGS-based CNV analysis as well as MLPA analysis we excluded aberrant copy numbers of BRCA1 in blood and fibroblasts.

In conclusion, our data provide striking evidence for a BRCA1 mosaicism, which is not detectable in all body cells. Due to the inheritance of the BRCA1 mutation to the next generations (II-1 and III-1), we assume the presence of a gonosomal mosaicism in the affected mother (I-1).

Additionally, the history of breast cancer onset in the family indicates that the BRCA1 mosaic mutation carrier do not necessarily have a milder phenotype compared to full heterozygotes. In this context our results implicate the importance of using highly sensitive sequencing platforms in routine diagnostics to ensure the detection of disease causing low-level mosaic mutations.Mosaicisms arise when specific cells within a developing organism mutate to result in two or more cell populations with distinct genotypes. In cases of gonosomal mosaicism a genetic variation is present in both somatic and germline cells.

Here, we describe a large Turkish breast cancer family with four affected individuals. In the Index patient (II-1; age of onset 45 years), a heterozygous deleterious frameshift mutation, c.1310dupA, p.His437Glnfs*2 in BRCA1 was identified using the TruRisk® gene panel designed by the German Consortium for Hereditary Breast and Ovarian Cancer (GC-HBOC). Predictive genetic testing showed heterozygous carrier status in the daughter (III-1).

The mutation was also analyzed in peripheral blood of the affected mother (I-1; age of onset 45 years) of the index patient by Sanger Sequencing. Interestingly, Sanger sequence did demonstrate the presence of remarkable small peaks presenting the frameshift mutation similar to a mosaic pattern. A second and third independent blood draw within a time frame of four month was tested and a mosaic signal of approximately 10 % was reproducibly detected.

In order to exclude a potential allelic drop out, independent sequencing experiments via next generation sequencing (NGS; TruRisk® gene panel) were performed. Again, the mutation was present with an allele read frequency of 12 %. No other pathogenic mutations were detected in any of the other tested breast cancer susceptibility genes.

To further examine and underscore the presence of gonosomal mosaicism different tissues should be analyzed. As no tumor material or surrounding normal breast tissue was available primary skin fibroblasts were isolated from skin biopsy. Sequencing of cultured primary fibroblasts demonstrated the absence of the familial BRCA1 mutation. With NGS-based CNV analysis as well as MLPA analysis we excluded aberrant copy numbers of BRCA1 in blood and fibroblasts.

In conclusion, our data provide striking evidence for a BRCA1 mosaicism, which is not detectable in all body cells. Due to the inheritance of the BRCA1 mutation to the next generations (II-1 and III-1), we assume the presence of a gonosomal mosaicism in the affected mother (I-1).

Additionally, the history of breast cancer onset in the family indicates that the BRCA1 mosaic mutation carrier do not necessarily have a milder phenotype compared to full heterozygotes. In this context our results implicate the importance of using highly sensitive sequencing platforms in routine diagnostics to ensure the detection of disease causing low-level mosaic mutations.

Citation Format: Bülow L, Keupp K, Richters L, Pohl E, Wappenschmidt B, Zarghooni V, Reichstein-Gnielinski S, Maringa M, Giesecke J, Rhiem K, Hahnen E, Schmutzler R. Low-level gonosomal mosaicism of a de novo BRCA1 gene mutation – The origin of a constitutional mutation in a breast cancer family [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P3-09-03.

Abstract P3-08-01: TruRisk® based next-generation sequencing in BRCA1/2-negative breast and ovarian cancer families reveal high mutation prevalence in additional risk genes

Background: 24% of familial breast cancer (BC) and/or ovarian cancer (OC) cases analyzed within the framework of the German Consortium for Hereditary Breast and Ovarian Cancer (GC-HBOC) are due to pathogenic BRCA1/2 mutations. However, the mutation prevalence of non-BRCA1/2 genes associated with familial BC and/or BC/OC is largely unknown. Methods: Here, we present the first NGS data generated using the GC-HBOC-designed TruRisk® gene panel. In this study a cohort of 2028 BRCA1/2 and CHEK2 c.1100delC negative index cases was analyzed which comprises consecutive patients from BC families and BC/OC families complying the inclusion criteria of the GC-HBOC. Sequencing was performed on MiSeq, NextSeq, or HiSeq devices (Illumina) using customized SureSelect XT enrichment (Agilent). Data analysis was carried out using the SeqPilot software (version 4.2.2), SophiaDDM (Version 3.5.0.12-p5.0.0) as well as an in house bioinformatics pipeline (Cologne Center for Genomics, varpipe_v2.X). The analysis of copy number variations (CNV) based on NGS-data is currently in process and not yet included in the present mutation prevalence. Results: By focusing on 22 BC/OC associated genes (ATM, BARD1, BRIP1, CDH1, CHEK2, FAM175A, FANCM, MLH1, MRE11A, MSH2, MSH6, NBN, PALB2, PMS2, PTEN, RAD50, RAD51C, RAD51D, RINT1, STK11, TP53, XRCC2), we identified 71 different deleterious variants in 104 unrelated mutation carriers derived from 2028 BC and BC/OC families (8%). Interestingly, we identified a high prevalence of ATM mutations (n=29, 1.4%) in the familial cases. Additionally mutations in PALB2 (n=27), NBN (n=9), CHEK2 (n=14), BARD1 (n=9), BRIP1 (n=10), RAD51C (n=11) were frequently observed and we confirmed FANCM (n=17) as a novel BC predisposing gene. No mutations in MLH1, MRE11A, PTEN, RAD51D, STK11 and XRCC2 were identified in our collective. Conclusions: Due to the unexpectedly high mutation prevalence in familial cases, our study highlights the importance of these genes to be included in BC/OC routine diagnostics. In contrast we found low occurrence or absence of mutations for a subset of our gene selection which requires further investigation to optimize the gene panel for diagnostic purposes. Nevertheless this approach confirms the TruRisk® gene panel as a reliable tool for this comprehensive analysis.

Citation Format: Keupp K, Richters L, Bülow L, Kröber S, Ernst C, Blümcke B, Versmold B, Waha A, Driesen J, Baasner A, Altmüller J, Thiele H, Nuernberg P, Wappenschmidt B, Neidhardt G, Rhiem K, Schmutzler R, Hahnen E, Hauke J. TruRisk® based next-generation sequencing in BRCA1/2-negative breast and ovarian cancer families reveal high mutation prevalence in additional risk genes [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P3-08-01.

Abstract P1-09-02: Homologous repair deficiency (HRD) as measure to predict the effect of carboplatin on survival in the neoadjuvant phase II trial GeparSixto in triple-negative early breast cancer

Introduction

Addition of carboplatin to anthracycline/taxane-based neoadjuvant chemotherapy has shown to improve pathological complete response (pCR; ypT0 ypN0) rates in patients with triple-negative breast cancer (TNBC) in two large phase II studies (GeparSixto: von Minckwitz et al, Lancet Oncol 2014, CALGB 40603: Sikov WM, J Clin Oncol 2015). Participants of the GeparSixto study showed an improvement of pCR rate from 36.9 to 53.2% (p=0.005) and DFS by absolute 9% (HR 0.56 95% CI 0.33-0.96] p=0.035) with the addition of carboplatin in the TNBC subgroup. No effect was observed in the HER2-positive subgroup. We here report results on homologous repair deficiency (HRD) status in relation to pCR and DFS in the TNBC subgroup.

Patients and Methods

In the GeparSixto trial (NCT01426880), patients were treated for 18 weeks with paclitaxel 80mg/m2 q1w and non-pegylated-liposomal doxorubicin (NPLD) 20mg/m2 q1w. Patients with TNBC (N=315) received concurrently bevacizumab 15mg/kg i.v. q2w until surgery. All patients were randomized 1:1 to receive concurrently carboplatin AUC 1.5-2 q1w vs no carboplatin. Carboplatin dose was reduced from AUC 2.0 to 1.5 by an amendment after 330 patients. Primary objective is pCR rate (ypT0 ypN0). Event free survival (EFS), and overall survival (OS) were secondary objectives. HR Deficiency status was assessed on FFPE material from pretherapeutic core biopsies. HR Deficiency was defined as either HRD score high or a BRCA mutation.

Results

HRD status was measurable in 193 of 315 TNBC patients. 101 patients of them were randomly assigned to receive carboplatin and 92 to no additional carboplatin. After median follow-up of 34.3 months 43 event free survival (EFS) events have been reported.

HR deficiency was detected in 136 (70.5%) tumors of which 79 (58.1%) showed high HRD score with intact tBRCA. HR deficiency independently predicted pCR (ypT0is ypN0) (odds ratio (OR) 2.506, CI 1.243-5.051, p=0.009). Adding carboplatin to PM significantly increased the pCR rate from 36.6% to 63.2% in HR deficient tumors with intact tBRCA (p=0.018), only marginally from 61.9% to 72.7% in BRCA mutated tumors (p=0.406), and moderately from 20.0% to 40.7% in HR non-deficient tumors (p=0.086). In general, patients with HRD deficient tumors had a better ESF than non HRD deficient ones (HR 1.805 (0.985-3.309); p=0.0526). Patients with high HRD score had an insignificant trend towards an improved EFS compared to those with low HRD score (HR 1.546 (0.764-3.127) p=0.2223). HRD deficiency did not predict carboplatin effect in patients without BRCA mutation (HR 0.8617). In multivariable analysis, only therapy, clinical nodal status before treatment, and lymphocyte predominant breast cancer were significant prognostic on EFS.

Conclusion

Within the GeparSixto study HR deficiency (either HRD score high or BRCA mutation) was associated with a higher pCR in general and an improved EFS. The effect of carboplatin could not be predicted by HR deficiency in this relatively small study. However, the results will help to understand the role of HR deficiency and the value of the HRD score in TNBC especially in patients without BRCA mutation.

Citation Format: von Minckwitz G, Timms K, Untch M, Elkin EP, Hahnen E, Fasching PA, Schneeweiss A, Salat CT, Rezai M, Blohmer J-U, Zahm D-M, Jackisch C, Gerber B, Klare P, Kümmel S, Paepke S, Schmutzler R, Chau S, Reid J, Hartman A-R, Nekljudova V, Weber KE, Loibl S. Homologous repair deficiency (HRD) as measure to predict the effect of carboplatin on survival in the neoadjuvant phase II trial GeparSixto in triple-negative early breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-09-02.

Klinik und Genetik des familiären Brust- und Eierstockkrebses

Während mit der Entdeckung der Hochrisikogene „breast cancer 1“ (BRCA1) und „breast cancer 2“ (BRCA2) in den Jahren 1994/1995 die Erforschung des hereditären Mamma- und Ovarialkarzinoms zunächst beendet schien, belegen neuere Ergebnisse, dass das hereditäre Mamma- und Ovarialkarzinom eine extreme genetische Heterogenität aufweist. Die genetisch definierten Subtypen zeigen außerdem eine unterschiedliche phänotypische Ausprägung hinsichtlich der histopathologischen Charakteristika, des Krankheitsverlaufs und des Therapieansprechens. Dies erfordert eine Einbettung der Gendiagnostik in ein strukturiertes und standardisiertes Betreuungskonzept, das es erlaubt prospektive Daten zur Tumorinzidenz und zum Verlauf zu erfassen sowie in prospektiven Studien die Wertigkeit der verschiedenen diagnostischen, präventiven und neuen therapeutischen Optionen zu validieren. Das deutsche Konsortium widmet sich dieser Aufgabenstellung, um den betreffenden Familien effiziente Präventions- und Interventionsstrategien anbieten zu können. Dabei kommt der Zusammenarbeit mit der Selbsthilfe (http://www.BRCA-Netzwerk.de) mittlerweile eine große Bedeutung zu, die uns immer wieder vor Augen hält, wie wichtig es ist, den in diesem Artikel aufgeworfenen Fragestellungen nachzugehen.

Valproic acid increases the SMN2 protein level: a well-known drug as a potential therapy for spinal muscular atrophy

Proximal spinal muscular atrophy (SMA) is a common neuromuscular disorder causing infant death in half of all patients. Homozygous absence of the survival motor neuron gene (SMN1) is the primary cause of SMA, while SMA severity is mainly determined by the number of SMN2 copies. One SMN2 copy produces only about 10% of full-length protein identical to SMN1, whereas the majority of SMN2 transcripts is aberrantly spliced due to a silent mutation within an exonic splicing enhancer in exon 7. However, correct splicing can be restored by over-expression of the SR-like splicing factor Htra2-beta 1. We show that in fibroblast cultures derived from SMA patients treated with therapeutic doses (0.5-500 microM) of valproic acid (VPA), the level of full-length SMN2 mRNA/protein increased 2- to 4-fold. Importantly, this up-regulation of SMN could be most likely attributed to increased levels of Htra2-beta 1 which facilitates the correct splicing of SMN2 RNA as well as to an SMN gene transcription activation. Especially at low VPA concentrations, the restored SMN level depended on the number of SMN2 copies. Moreover, VPA was able to increase SMN protein levels through transcription activation in organotypic hippocampal brain slices from rats. Finally, VPA also increased the expression of further SR proteins, which may have important implications for other disorders affected by alternative splicing. Since VPA is a drug highly successfully used in long-term epilepsy therapy, our findings open the exciting perspective for a first causal therapy of an inherited disease by elevating the SMN2 transcription level and restoring its correct splicing.

Analysis of the SMN and NAIP genes in slovak spinal muscular atrophy patients

We identified homozygous absence of exon 7 of the telomeric copy of the survival motor neuron gene (telSMN) in 88.4% (38/43) of spinal muscular atrophy (SMA) patients from Slovakia. Additional deletions within the neuronal apoptosis inhibitory protein (NAIP) gene were found in 38.5% of type I, 12.5% of type II and never in type III SMA patients. Neither the SMN nor the NAIP gene was deleted in 81 healthy relatives and 25 controls tested. In one family, pseudodominant inheritance was identified. Both the type III SMA father and type II SMA son carried the homozygous deletion of the telSMN gene. One SMA I patient showed an SMN hybrid gene, probably created by intrachromosomal deletion. In two haploidentical type II SMA sibs, the telSMN exon 7 was absent on one chromosome, while the other carried an A-->G transition 96 bp upstream of exon 7 of the telSMN gene, a potential disease-causing mutation in these patients.

A novel secreted ribonuclease from Bacillus intermedius: gene structure and regulatory control

A second secreted ribonuclease, designated binase II, has been detected in Bacillus intermedius 7P, and its structural gene was cloned and sequenced. Unlike the well-known binase I, a 109-amino acid guanyl-specific enzyme, the 292-residue binase II is closely related to the B. subtilis nuclease Bsn, in structure and in its enzymatic properties. Binase II is also insensitive to inactivation by barstar, an inhibitor protein that is specific for guanyl-specific ribonucleases. While both B. intermedius enzymes are induced upon phosphate starvation, only the gene for binase I belongs to the pho regulon system and carries pho-box elements adjacent to its promoter sequence. The gene for binase II is similar to that for Bsn in lacking such elements. The birB gene coding for binase II appears to be located next to the 3'-end of a ferric ion transport operon, with which it convergently overlaps. This would allow attenuator control over binase II expression under conditions of starvation for ferric ions.

A single nucleotide in the SMN gene regulates splicing and is responsible for spinal muscular atrophy

SMN1 and SMN2 (survival motor neuron) encode identical proteins. A critical question is why only the homozygous loss of SMN1, and not SMN2, results in spinal muscular atrophy (SMA). Analysis of transcripts from SMN1/SMN2 hybrid genes and a new SMN1 mutation showed a direct relationship between presence of disease and exon 7 skipping. We have reported previously that the exon-skipped product SMNDelta7 is partially defective for self-association and SMN self-oligomerization correlated with clinical severity. To evaluate systematically which of the five nucleotides that differ between SMN1 and SMN2 effect alternative splicing of exon 7, a series of SMN minigenes was engineered and transfected into cultured cells, and their transcripts were characterized. Of these nucleotide differences, the exon 7 C-to-T transition at codon 280, a translationally silent variance, was necessary and sufficient to dictate exon 7 alternative splicing. Thus, the failure of SMN2 to fully compensate for SMN1 and protect from SMA is due to a nucleotide exchange (C/T) that attenuates activity of an exonic enhancer. These findings demonstrate the molecular genetic basis for the nature and pathogenesis of SMA and illustrate a novel disease mechanism. Because individuals with SMA retain the SMN2 allele, therapy targeted at preventing exon 7 skipping could modify clinical outcome.

Quantitative analysis of survival motor neuron copies: identification of subtle SMN1 mutations in patients with spinal muscular atrophy, genotype-phenotype correlation, and implications for genetic counseling

Problems with diagnosis and genetic counseling occur for patients with autosomal recessive proximal spinal muscular atrophy (SMA) who do not show the most common mutation: homozygous absence of at least exon 7 of the telomeric survival motor neuron gene (SMN1). Here we present molecular genetic data for 42 independent nondeleted SMA patients. A nonradioactive quantitative PCR test showed one SMN1 copy in 19 patients (45%). By sequencing cloned reverse-transcription (RT) PCR products or genomic fragments of SMN1, we identified nine different mutations in 18 of the 19 patients, six described for the first time: three missense mutations (Y272C, T274I, S262I), three frameshift mutations in exons 2a, 2b, and 4 (124insT, 241-242ins4, 591delA), one nonsense mutation in exon 1 (Q15X), one Alu-mediated deletion from intron 4 to intron 6, and one donor splice site mutation in intron 7 (c.922+6T-->G). The most frequent mutation, Y272C, was found in 6 (33%) of 18 patients. Each intragenic mutation found in at least two patients occurred on the same haplotype background, indicating founder mutations. Genotype-phenotype correlation allowed inference of the effect of each mutation on the function of the SMN1 protein and the role of the SMN2 copy number in modulating the SMA phenotype. In 14 of 23 SMA patients with two SMN1 copies, at least one intact SMN1 copy was sequenced, which excludes a 5q-SMA and suggests the existence of further gene(s) responsible for approximately 4%-5% of phenotypes indistinguishable from SMA. We determined the validity of the test, and we discuss its practical implications and limitations.

SMN oligomerization defect correlates with spinal muscular atrophy severity

Spinal muscular atrophy (SMA) is a motor-neuron disorder resulting from anterior-horn-cell death. The autosomal recessive form has a carrier frequency of 1 in 50 and is the most common genetic cause of infant death. SMA is categorized as types I-III, ranging from severe to mild, based upon age of onset and clinical course. Two closely flanking copies of the survival motor neuron (SMN) gene are on chromosome 5q13 (ref. 1). The telomeric SMN (SMN1) copy is homozygously deleted or converted in >95% of SMA patients, while a small number of SMA disease alleles contain missense mutations within the carboxy terminus. We have identified a modular oligomerization domain within exon 6 of SMN1. All previously identified missense mutations map within or immediately adjacent to this domain. Comparison of wild-type to mutant SMN proteins of type I, II and III SMA patients showed a direct correlation between oligomerization and clinical type. Moreover, the most abundant centromeric SMN product, which encodes exons 1-6 but not 7, demonstrated reduced self-association. These findings identify decreased SMN self-association as a biochemical defect in SMA, and imply that disease severity is proportional to the intracellular concentration of oligomerization-competent SMN proteins.

De novo rearrangements found in 2% of index patients with spinal muscular atrophy: mutational mechanisms, parental origin, mutation rate, and implications for genetic counseling

Spinal muscular atrophy (SMA) is a relatively common autosomal recessive neuromuscular disorder. We have identified de novo rearrangements in 7 (approximately 2%) index patients from 340 informative SMA families. In each, the rearrangements resulted in the absence of the telomeric copy of the survival motor neuron (SMN) gene (telSMN), in two cases accompanied by the loss of the neuronal apoptosis-inhibitory protein gene . Haplotype analysis revealed unequal recombination in four cases, with loss of markers Ag1-CA and C212, which are near the 5' ends of the SMN genes. In one case, an interchromosomal rearrangement involving both the SMN genes and a regrouping of Ag1-CA and C212 alleles must have occurred, suggesting either interchromosomal gene conversion or double recombination. In two cases, no such rearrangement was observed, but loss of telSMN plus Ag1-CA and C212 alleles in one case suggested intrachromosomal deletion or gene conversion. In six of the seven cases, the de novo rearrangement had occurred during paternal meiosis. Direct detection of de novo SMA mutations by molecular genetic means has allowed us to estimate for the first time the mutation rate for a recessive disorder in humans. The sex-averaged rate of 1.1 x 10(-4), arrived at in a proband-based approach, compares well with the rate of 0.9 x 10(-4) expected under a mutation-selection equilibrium for SMA. These findings have important implications for genetic counseling and prenatal diagnosis in that they emphasize the relevance of indirect genotype analysis in combination with direct SMN-gene deletion testing in SMA families.

Different entities of proximal spinal muscular atrophy within one family

The molecular analysis of the survival motor neuron (SMN) gene and several closely flanking polymorphic markers in an atypical pedigree with four patients suffering from spinal muscular atrophy (SMA) over two generations has raised new aspects concerning the etiology and the molecular spectrum of autosomal recessive SMA. Three patients in two generations show homozygous deletions of exons 7 and 8 of the telomeric copy of SMN (telSMN), thus confirming the presence of autosomal recessive SMA, with localisation on chromosome 5q12. The fourth SMA patient with mild neurogenic atrophy (confirmed by muscle biopsy and electromyography) shows no homozygous deletion of telSMN but carries a heterozygous deletion of telSMN, as can be deduced from her two affected homozygously deleted children. No intragenic mutation has been identified in the remaining telSMN. In addition, she shares only one SMA chromosome with her affected brother, is haploidentical with two healthy brothers, and has a 31-year-old healthy son, who has inherited an SMN-deleted paternal chromosome and the SMN non-deleted maternal chromosome. These results suggest that this patient either has a neurogenic atrophy of a different origin or exhibits an unusual heterozygous manifestation of SMA 5q12. Interestingly, the two haploidentical telSMN-deleted affected sibs in the second generation show a strikingly discordant clinical picture indicating that, in addition to telSMN mutations, other factors influence the phenotype of SMA in the reported pedigree.

Missense mutations in exon 6 of the survival motor neuron gene in patients with spinal muscular atrophy (SMA)

Spinal muscular atrophy (SMA) is a frequent autosomal recessive neurodegenerative disorder leading to weakness and atrophy of voluntary muscles. The survival motor neuron gene (SMN) is a strong candidate for SMA and present in two highly homologous copies (telSMN and cenSMN) within the SMA region (5q11.2-q13.3). More than 90% of SMA patients show homozygous deletions of at least exon 7 of telSMN, whereas absence of cenSMN seems to have no clinical consequences. In 23 non-deleted SMA patients, we searched for intragenic mutations of the SMN genes in exons 1-7 and the promotor region by single strand conformation analysis. We identified two different missense mutations, S2621 and T2741, in exon 6 of telSMN in three independent SMA families, providing further evidence for the telSMN gene as a SMA determining gene. Both mutations, as well as two previously described mutations (Y272C and G279V) are located within a highly conserved interval from codon 258 to codon 279 which seems to be an important functional domain of the telSMN protein. Recently, this region has been shown to contain a tyrosine/glycine-rich motif, which is also present in various RNA binding proteins, suggesting a potential role of SMN in RNA metabolism. Missense mutations might be useful for in vivo and transgenic experiments and further investigations on understanding the function of the telSMN protein.

Hybrid survival motor neuron genes in patients with autosomal recessive spinal muscular atrophy: new insights into molecular mechanisms responsible for the disease

Spinal muscular atrophy (SMA) is a frequent autosomal recessive neurodegenerative disorder leading to weakness and atrophy of voluntary muscles. The survival motor-neuron gene (SMN), a strong candidate for SMA, is present in two highly homologous copies (telSMN and cenSMN) within the SMA region. Only five nucleotide differences within the region between intron 6 and exon 8 distinguish these homologues. Independent of the severity of the disease, 90%-98% of all SMA patients carry homozygous deletions in telSMN, affecting either exon 7 or both exons 7 and 8. We present the molecular analysis of 42 SMA patients who carry homozygous deletions of telSMN exon 7 but not of exon 8. The question arises whether in these cases the telSMN is truncated upstream of exon 8 or whether hybrid SMN genes exist that are composed of centromeric and telomeric sequences. By a simple PCR-based assay we demonstrate that in each case the remaining telSMN exon 8 is part of a hybrid SMN gene. Sequencing of cloned hybrid SMN genes from seven patients, as well as direct sequencing and single-strand conformation analysis of all patients, revealed the same composition in all but two patients: the base-pair differences in introns 6 and 7 and exon 7 are of centromeric origin whereas exon 8 is of telomeric origin. Nonetheless, haplotype analysis with polymorphic multicopy markers, Ag1-CA and C212, localized at the 5' end of the SMN genes suggests different mechanisms of occurrence, unequal rearrangements, and gene conversion involving both copies of the SMN genes. In approximately half of all patients, we identified a consensus haplotype, suggesting a common origin. Interestingly, we identified a putative recombination hot spot represented by recombination-stimulating elements (TGGGG and TGAGGT) in exon 8 that is homologous to the human deletion-hot spot consensus sequence in the immunoglobulin switch region, the alpha-globin cluster, and the polymerase alpha arrest sites. This may explain why independent hybrid SMN genes show identical sequences.

Clinical spectrum and diagnostic criteria of infantile spinal muscular atrophy: further delineation on the basis of SMN gene deletion findings

With the evidence of deletions in the region responsible for autosomal recessive spinal muscular atrophy (SMA) on chromosome 5, it is now possible to further clarify the clinical and diagnostic findings in proximal SMA. Homozygous deletions of the survival motor neuron (SMN) gene can be detected in about 95% of patients with early onset SMA. In a series of more than 200 patients, we tested 31 patients with atypical features of SMA who fulfilled at least one exclusion criterion according to the diagnostic criteria of the International SMA Consortium for the presence of SMN gene deletions. The patients were subdivided into two groups: 1. Seven index patients being not deleted for the SMN gene who belonged to a well-defined SMA plus variant that has already been shown to be unlinked with chromosome 5q markers: diaphragmatic SMA, SMA plus olivopontocerebellar hypoplasia, SMA with congenital arthrogryposis and bone fractures. 2. Twenty-four patients with clinical signs of SMA and neurogenic findings in EMG/muscle biopsy who had unusual features or other organ involvement. In order to structure this heterogeneous group, each patient was assigned to a subgroup according to the leading atypical feature. In 5 out of 8 unrelated patients with a history of preterm birth and/or perinatal asphyxia leading to a picture of severe SMA in combination with respiratory distress and/or cerebral palsy, no deletion of the SMN gene could be detected. There were five unrelated patients with extended central nervous system involvement (cerebral atrophy, EEG abnormalities, pyramidal tract signs, evidence of cerebellar involvement). Most of these patients (4/5) proved to belong to SMA 5q on the basis of SMN gene deletion findings. The same applied to a group of three patients with classical SMA in association with congenital malformations (mainly heart defect). A fourth group of three patients was characterized mainly by an unusual improvement of the condition; in these patients no SMN gene deletions were present. In three index patients a more complex syndrome of the CNS and other organs was suggested, but the detection of SMN gene deletions in two of them made a coincidence of features more likely. In addition, SMN gene deletions were found in two patients with evidence of congenital fibre type dysproportion in one and extremely raised CK activity ( > 10fold) in the other. While the confirmation of SMN gene deletions is very useful in cases with diagnostic doubts, caution is required when offering prenatal prediction with regard to SMA 5q in families with atypical features. There is strong evidence that there are clinical entities resembling SMA which most likely have another pathogenetic background.

Molecular analysis of candidate genes on chromosome 5q13 in autosomal recessive spinal muscular atrophy: evidence of homozygous deletions of the SMN gene in unaffected individuals

Proximal spinal muscular atrophy (SMA) is a common autosomal recessive neuromuscular disorder characterized by degeneration of anterior horn cells in the spinal cord leading to weakness and wasting of voluntary muscles. Here we present the molecular analysis of both SMA candidate genes, the survival motor neuron gene (SMN; exons 7 and 8) and the neuronal apoptosis inhibitory protein gene (NAIP; exons 5, 6 and 13), in 195 patients and 348 parents of SMA families mainly of German origin. The SMN gene is homozygously deleted for both exons 7 and 8 or exon 7 only in 96% of type I SMA, 94% of type II SMA and 82% of type III SMA as well as in 0.3% of SMA parents. The NAIP gene is homozygously deleted in 46% of type I SMA, 17% of type II SMA, 7% of type III SMA and 2% of SMA parents. The frequencies of deletions in patients for both genes, SMN and NAIP, correspond to those for the NAIP gene only. SMA patients of this series who did not show deletions were clinically indistinguishable from deleted patients. In addition to one unaffected mother of a type II SMA patient, we found homozygous deletions of the SMN gene exons 7 and 8 in six further unaffected individuals, all sibs of type II and III patients. These belonged to four families with affected and unaffected sibs who showed identical haplotypes for all SMA flanking markers; therefore, we had regarded these families as chromosome 5 unlinked. All seven unaffected individuals in whom we detected SMA deletions do not show any signs of muscle weakness and are physically inconspicuous. The largest divergence between age at onset of an affected subject and the present age of unaffected deleted sibs is four decades now. The occurrence of SMN deletions in unaffected individuals suggests that other genes or mechanisms may be necessary to produce the SMA phenotype.

Allelic association and deletions in autosomal recessive proximal spinal muscular atrophy: association of marker genotype with disease severity and candidate cDNAs

The candidate region for spinal muscular atrophy (SMA) has been defined as a 750 kb interval on 5q13. In this study, we performed allelic association studies in 154 German SMA families with the multicopy markers Ag1-CA (D5S1556); C212 (D5F149S1/S2) and correlated genotype data with deletion of candidate genes. Both multicopy markers recognize 0-3 alleles pro chromosome. Deletions were detected for all copies of the markers Ag1-CA (C272) and C212 in 13 of 88 (15%) type I SMA patients and three of 48 (6%) type II patients. In all informative cases, the deletion was inherited from one parent. In two further cases (one type I and one type III SMA), de novo deletions of only one copy of Ag1-CA and C212 were found. In both cases the patients were homozygously deleted for the survival motor neuron (SMN) gene (exons 7 and 8) but only the type I SMA patient was deleted for the neuronal apoptosis inhibitory protein (NAIP) gene (exons 5 and 6). A third case (type II SMA) showed de novo deletion of SMN, but not of Ag1-CA, C212 and NAIP. Specific alleles of Ag1-CA and C212 showed significant association with SMA, particularly in type I SMA. When the number of marker copies defines genotypes, 1,1 (one allele on each chromosome) is found to be increased in type I SMA (50%) and 1,2 (one allele on one chromosome and two alleles on the other one) in type II SMA (60%). The 2,2 genotype (two alleles on each chromosome) was found in 4% of type I and II patients. By comparison, pooled normal genotype frequencies were 20, 44 and 36%, respectively. These results suggest a strong correlation between genotype and severity of disease. Based on these data we propose a model which indicates that type I SMA patients are composed of two severe alleles, type II of a mild and a severe, and type III of two mild alleles. Correlation of Ag1-CA genotype with deletion of the XS2G3/NAIP genes indicates that most patients with a deletion have a 1,1 genotype. Owing to the physical proximity of these markers, we propose that a large deletion occurs on type I SMA chromosomes that removes DNA between C212 and XS2G3/NAIP and that type II SMA results from compound heterozygosity for mild (small deletion) and severe mutations.

Prenatal prediction in families with autosomal recessive proximal spinal muscular atrophy (5q11.2-q13.3): molecular genetics and clinical experience in 109 cases

Prenatal prediction in families at risk for autosomal recessive proximal spinal muscular atrophy (SMA) mainly of type I is often requested due to the high incidence and the fetal outcome of the disease. So far, only indirect genotype analysis can be performed in SMA families, since the gene has not yet been identified. We present our experience of 109 prenatal diagnoses obtained in 91 families by use of single- and multi-locus polymorphic microsatellites of the region 5q11.2-q13.3. The marker combinations and specific features of the closest microsatellites are described in detail. From 137 requests for prenatal prediction of SMA between October 1991 and August 1994, 28 families were excluded, mostly because the clinical diagnosis was uncertain or doubtful. Others had to be classified as 'SMA-variants' or showed autosomal dominant transmission of SMA. Of the 109 prenatal diagnoses performed, 29 fetuses were diagnosed to be at high risk (> 99 per cent) of developing the disease, while in seven additional pregnancies no exact prediction could be made due to a recombination event in one parental haplotype. Altogether, recombinations between closely flanking markers were observed in 14 cases. In 35 cases, the parents decided to terminate the pregnancy. Of the remaining pregnancies, 32 could be followed beyond term. All infants were reported to develop normally without signs of SMA. Two children were born with transverse reduction defects of one hand, which was most likely related to early chorionic villus sampling at 9 and 10 weeks' gestation. No further abnormalities could be detected. The limits of indirect genotype analysis and the problems of diagnostic accuracy and heterogeneity of proximal SMA are discussed.