mRNA Quantification of NIPBL Isoforms A and B in Adult and Fetal Human Tissues, and a Potentially Pathological Variant Affecting Only Isoform A in Two Patients with Cornelia de Lange Syndrome.

Cornelia de Lange syndrome (CdLS) is a congenital developmental disorder characterized by craniofacial dysmorphia, growth retardation, limb malformations, and intellectual disability. Approximately 60% of patients with CdLS carry a recognizable pathological variant in the NIPBL gene, of which two isoforms, A and B, have been identified, and which only differ in the C-terminal segment. In this work, we describe the distribution pattern of the isoforms A and B mRNAs in tissues of adult and fetal origin, by qPCR (quantitative polymerase chain reaction). Our results show a higher gene expression of the isoform A, even though both seem to have the same tissue distribution. Interestingly, the expression in fetal tissues is higher than that of adults, especially in brain and skeletal muscle. Curiously, the study of fibroblasts of two siblings with a mild CdLS phenotype and a pathological variant specific of the isoform A of NIPBL (c.8387A > G; P.Tyr2796Cys), showed a similar reduction in both isoforms, and a normal sensitivity to DNA damage. Overall, these results suggest that the position of the pathological variant at the 3´ end of the NIPBL gene affecting only isoform A, is likely to be the cause of the atypical mild phenotype of the two brothers.

De novo heterozygous mutations in SMC3 cause a range of Cornelia de Lange syndrome-overlapping phenotypes.

Cornelia de Lange syndrome (CdLS) is characterized by facial dysmorphism, growth failure, intellectual disability, limb malformations, and multiple organ involvement. Mutations in five genes, encoding subunits of the cohesin complex (SMC1A, SMC3, RAD21) and its regulators (NIPBL, HDAC8), account for at least 70% of patients with CdLS or CdLS-like phenotypes. To date, only the clinical features from a single CdLS patient with SMC3 mutation has been published. Here, we report the efforts of an international research and clinical collaboration to provide clinical comparison of 16 patients with CdLS-like features caused by mutations in SMC3. Modeling of the mutation effects on protein structure suggests a dominant-negative effect on the multimeric cohesin complex. When compared with typical CdLS, many SMC3-associated phenotypes are also characterized by postnatal microcephaly but with a less distinctive craniofacial appearance, a milder prenatal growth retardation that worsens in childhood, few congenital heart defects, and an absence of limb deficiencies. While most mutations are unique, two unrelated affected individuals shared the same mutation but presented with different phenotypes. This work confirms that de novo SMC3 mutations account for ∼ 1%-2% of CdLS-like phenotypes.

RAD21 mutations cause a human cohesinopathy.

The evolutionarily conserved cohesin complex was originally described for its role in regulating sister-chromatid cohesion during mitosis and meiosis. Cohesin and its regulatory proteins have been implicated in several human developmental disorders, including Cornelia de Lange (CdLS) and Roberts syndromes. Here we show that human mutations in the integral cohesin structural protein RAD21 result in a congenital phenotype consistent with a "cohesinopathy." Children with RAD21 mutations display growth retardation, minor skeletal anomalies, and facial features that overlap findings in individuals with CdLS. Notably, unlike children with mutations in NIPBL, SMC1A, or SMC3, these individuals have much milder cognitive impairment than those with classical CdLS. Mechanistically, these mutations act at the RAD21 interface with the other cohesin proteins STAG2 and SMC1A, impair cellular DNA damage response, and disrupt transcription in a zebrafish model. Our data suggest that, compared to loss-of-function mutations, dominant missense mutations result in more severe functional defects and cause worse structural and cognitive clinical findings. These results underscore the essential role of RAD21 in eukaryotes and emphasize the need for further understanding of the role of cohesin in human development.

Analysis of aberrant splicing and nonsense-mediated decay of the stop codon mutations c.109G>T and c.504_505delCT in 7 patients with HMG-CoA lyase deficiency.

Eukaryotic cells can be protected against mutations that generate stop codons by nonsense-mediated mRNA decay (NMD) and/or nonsense-associated altered splicing (NAS). However, the processes are only partially understood and do not always occur. In this work, we study these phenomena in the stop codon mutations c.109G>T (p.Glu37*) and c.504_505delCT; the second and third most frequent mutations in HMG-CoA lyase deficiency (MIM #246450). The deficiency affects the synthesis of ketone bodies and produces severe disorders during early childhood. We used a minigene approach, real-time quantitative PCR and the inhibition of NMD by puromycin treatment, to study the effect of stop codons on splicing (NAS) and NMD in seven patients. Surprisingly, none of the stop codons studied appears to be the direct cause of aberrant splicing. In the mutation c.109G>T, the splicing is due to the base change G>T at position 109, which is critical and cannot be explained by disruption of exonic splicing enhancer (ESE) elements, by the appearance of exonic splicing silencer (ESS) elements which were predicted by bioinformatic tools or by the stop codons. Moreover, the mutation c.504_505delCT produces two mRNA transcripts both with stop codons that generate simultaneous NMD phenomena. The effects of the mutations studied on splicing seemed to be similar in all the patients. Furthermore, we report a Spanish patient with 3-hydroxy-3-methylglutaric aciduria and a novel missense mutation: c.825C>G (p.Asn275Lys).

Cornelia de Lange syndrome with NIPBL mutation and mosaic Turner syndrome in the same individual.

BACKGROUND: Cornelia de Lange syndrome (CdLS) is a dominantly inherited disorder characterized by facial dysmorphism, growth and cognitive impairment, limb malformations and multiple organ involvement. Mutations in NIPBL gene account for about 60% of patients with CdLS. This gene encodes a key regulator of the Cohesin complex, which controls sister chromatid segregation during both mitosis and meiosis. Turner syndrome (TS) results from the partial or complete absence of one of the X chromosomes, usually associated with congenital lymphedema, short stature, and gonadal dysgenesis. CASE PRESENTATION: Here we report a four-year-old female with CdLS due to a frameshift mutation in the NIPBL gene (c.1445_1448delGAGA), who also had a tissue-specific mosaic 45,X/46,XX karyotype. The patient showed a severe form of CdLS with craniofacial dysmorphism, pre- and post-natal growth delay, cardiovascular abnormalities, hirsutism and severe psychomotor retardation with behavioural problems. She also presented with minor clinical features consistent with TS, including peripheral lymphedema and webbed neck. The NIPBL mutation was present in the two tissues analysed from different embryonic origins (peripheral blood lymphocytes and oral mucosa epithelial cells). However, the percentage of cells with monosomy X was low and variable in tissues. These findings indicate that, ontogenically, the NIPBL mutation may have appeared before the mosaic monosomy X. CONCLUSIONS: The coexistence in several patients of these two rare disorders raises the issue of whether there is indeed a cause-effect association. The detailed clinical descriptions indicate predominant CdLS phenotype, although additional TS manifestations may appear in adolescence.

Characterization of splice variants of the genes encoding human mitochondrial HMG-CoA lyase and HMG-CoA synthase, the main enzymes of the ketogenesis pathway.

The genes HMGCS2 and HMGCL encode the two main enzymes for ketone-body synthesis, mitochondrial HMG-CoA synthase and HMG-CoA lyase. Here, we identify and describe possible splice variants of these genes in human tissues. We detected an alternative transcript of HMGCS2 carrying a deletion of exon 4, and two alternative transcripts of HMGCL with deletions of exons 5 and 6, and exons 5, 6 and 7, respectively. All splice variants maintained the reading frame. However, Western blot studies and overexpression measurements in eukaryotic or prokaryotic cell models did not reveal HL or mHS protein variants. Both genes showed a similar distribution of the inactive variants in different tissues. Surprisingly, the highest percentages were found in tissues where almost no ketone bodies are synthesized: heart, skeletal muscle and brain. Our results suggest that alternative splicing might coordinately block the two main enzymes of ketogenesis in specific human tissues.

Mutations and variants in the cohesion factor genes NIPBL, SMC1A, and SMC3 in a cohort of 30 unrelated patients with Cornelia de Lange syndrome.

Cornelia de Lange syndrome (CdLS) manifests facial dysmorphic features, growth and cognitive impairment, and limb malformations. Mutations in three genes (NIPBL, SMC1A, and SMC3) of the cohesin complex and its regulators have been found in affected patients. Here, we present clinical and molecular characterization of 30 unrelated patients with CdLS. Eleven patients had mutations in NIPBL (37%) and three patients had mutations in SMC1A (10%), giving an overall rate of mutations of 47%. Several patients shared the same mutation in NIPBL (p.R827GfsX2) but had variable phenotypes, indicating the influence of modifiers in CdLS. Patients with NIPBL mutations had a more severe phenotype than those with mutations in SMC1A or those without identified mutations. However, a high incidence of palate defects was noted in patients with SMC1A mutations. In addition, we observed a similar phenotype in both male and female patients with SMC1A mutations. Finally, we report the first patient with an SMC1A mutation and the Sandifer complex.

Comparison of several Real-Time PCR Kits versus a Culture-dependent Algorithm to Identify Enteropathogens in Stool Samples.

This study aims to validate the current diagnostic method for the clinical detection of gastroenteritis. We analyzed 400 stool samples to detect three of the most common enteropathogens: Salmonella spp., Campylobacter spp., and Yersinia enterocolitica. All specimens were tested with a routine clinical diagnosis algorithm and with five real-time PCR assays. A total of 98 specimens (24.5%) were positive for enteropathogens. We found 24 samples positive for Salmonella enterica, 71 positive for Campylobacter spp., and 4 positive for Yersinia enterocolitica. All evaluated methods exhibited a good performance in identifying Salmonella and Yersinia enterocolitica, being the highest positive percent agreement (PPA) value of 95.8% and 100%, respectively. The clinical algorithm showed the highest PPA value identifying Salmonella, due to the enrichment in selenite broth. However, the evaluated methods showed notable differences in the identification of Campylobacter species, obtaining a wide range of PPA values: 59.2%-100%. The clinical algorithm showed the lowest PPA value since it was only able to detect Campylobacter jejuni and Campylobacter coli species. This study revealed the importance of implementing the real-time PCR technique in a clinical algorithm: it improved the accuracy of the diagnosis and provided results in a shorter time compared to routine clinical methods.

Two-step ATP-driven opening of cohesin head.

The cohesin ring is a protein complex composed of four core subunits: Smc1A, Smc3, Rad21 and Stag1/2. It is involved in chromosome segregation, DNA repair, chromatin organization and transcription regulation. Opening of the ring occurs at the "head" structure, formed of the ATPase domains of Smc1A and Smc3 and Rad21. We investigate the mechanisms of the cohesin ring opening using techniques of free molecular dynamics (MD), steered MD and quantum mechanics/molecular mechanics MD (QM/MM MD). The study allows the thorough analysis of the opening events at the atomic scale: i) ATP hydrolysis at the Smc1A site, evaluating the role of the carboxy-terminal domain of Rad21 in the process; ii) the activation of the Smc3 site potentially mediated by the movement of specific amino acids; and iii) opening of the head domains after the two ATP hydrolysis events. Our study suggests that the cohesin ring opening is triggered by a sequential activation of the ATP sites in which ATP hydrolysis at the Smc1A site induces ATPase activity at the Smc3 site. Our analysis also provides an explanation for the effect of pathogenic variants related to cohesinopathies and cancer.

Severe ipsilateral musculoskeletal involvement in a Cornelia de Lange patient with a novel NIPBL mutation.

Cornelia de Lange Syndrome (CdLS) is a congenital autosomal dominant (NIPBL, SMC3 and RAD21) or X-linked (SMC1A and HDAC8) disorder characterized by facial dysmorphism, pre and postnatal growth retardation, developmental delay and/or intellectual disability, and multiorgan involvement. Musculoskeletal malformations are usually bilateral and affect mainly the upper limbs; the range goes from brachyclinodactyly to severe reduction defects. Instead lower extremities are usually less and mildly involved. Here, we report on a 3-year-old Senegalese boy with typical craniofacial CdLS features, pre and postnatal growth retardation, atrial septal defect, developmental delay and right ipsilateral limb malformations, consistent with oligodactyly of the 3rd and 4th fingers, tibial agenesis and fibula hypoplasia. Exome sequencing and Sanger sequencing showed a novel missense mutation in NIPBL gene (c.6647A>G; p.(Tyr2216Cys)), which affects a conserved residue located within NIPBL HEAT repeat elements. Pyrosequencing analysis of NIPBL gene, disclosed similar levels of wild-type and mutated alleles in DNA and RNA samples from all tissues analyzed (oral mucosa epithelial cells, peripheral blood leukocytes and fibroblasts). These findings indicated the absence of somatic mosaicism, despite of the segmental asymmetry of the limbs, and confirmed biallelic expression for NIPBL transcripts, respectively. Additionally, conditions like Split-hand/foot malformation with long-bone deficiency secondary to duplication of BHLHA9 gene have been ruled out by the array-CGH and MLPA analysis. To our knowledge, this is the first CdLS patient described with major ipsilateral malformations of both the upper and lower extremities, that even though this finding could be due to a random event, expands the spectrum of limb reduction defects in CdLS.

New case of mitochondrial HMG-CoA synthase deficiency. Functional analysis of eight mutations.

Mitochondrial HMG-CoA synthase deficiency is a rare inherited metabolic disorder that affects ketone-body synthesis. Acute episodes include vomiting, lethargy, hepatomegaly, hypoglycaemia, dicarboxylic aciduria, and in severe cases, coma. This deficiency may have been under-diagnosed owing to the absence of specific clinical and biochemical markers, limitations in liver biopsy and the lack of an effective method of expression and enzyme assay for verifying the mutations found. To date, eight patients have been reported with nine allelic variants of the HMGCS2 gene. We present a new method of enzyme expression and a modification of the activity assay that allows, for first time, the functional study of missense mutations found in patients with this deficiency. Four of the missense mutations (p.V54M, p.R188H, p.G212R and p.G388R) did not produce proteins that could have been detected in soluble form by western blot; three produced a total loss of activity (p.Y167C, p.M307T and p.R500H) and one, variant p.F174L, gave an enzyme with a catalytic efficiency of 11.5%. This indicates that the deficiency may occur with partial loss of activity of enzyme. In addition, we describe a new patient with this deficiency, in which we detected the missense allelic variant, c.1162G>A (p.G388R) and the nonsense variant c.1270C>T (p.R424X).

Isolated NIBPL missense mutations that cause Cornelia de Lange syndrome alter MAU2 interaction.

Cornelia de Lange syndrome (CdLS; or Brachmann-de Lange syndrome) is a dominantly inherited congenital malformation disorder with features that include characteristic facies, cognitive delays, growth retardation and limb anomalies. Mutations in nearly 60% of CdLS patients have been identified in NIPBL, which encodes a regulator of the sister chromatid cohesion complex. NIPBL, also known as delangin, is a homolog of yeast and amphibian Scc2 and C. elegans PQN-85. Although the exact mechanism of NIPBL function in sister chromatid cohesion is unclear, in vivo yeast and C. elegans experiments and in vitro vertebrate cell experiments have demonstrated that NIPBL/Scc2 functionally interacts with the MAU2/Scc4 protein to initiate loading of cohesin onto chromatin. To test the significance of this model in the clinical setting of CdLS, we fine-mapped the NIBPL-MAU2 interaction domain and tested the functional significance of missense mutations and variants in NIPBL and MAU2 identified in these minimal domains in a cohort of patients with CdLS. We demonstrate that specific novel mutations at the N-terminus of the MAU2-interacting domain of NIBPL result in markedly reduced MAU2 binding, although we appreciate no consistent clinical difference in the small group of patients with these mutations. These data suggest that factors in addition to MAU2 are essential in determining the clinical features and severity of CdLS.

Asesoramiento genético en enfermedades con herencia mendeliana / Genetic counseling in mendelian inherited diseases

El asesoramiento genético es el proceso de comunicación por el que un profesional con preparación adecuada (genetista) informa al paciente (familia) sobre un diagnóstico genético y sus repercusiones físicas y psíquicas en el individuo y sus familiares, incluyendo el riesgo de recurrencia, opciones reproductivas, posibilidades de tratamiento y/o prevención y apoyo en la toma de decisiones. El cálculo del riesgo reproductivo se basa principalmente en el tipo de herencia de la enfermedad y en el caso de las enfermedades mendelianas suele ser de gran fiabilidad si el estudio genético ha confirmado el diagnóstico de sospecha (AU)

Genetic counselling is a communication process in which a profesional with the required competences (geneticist) explains the genetic condition to the patient, its physical and physiological consequences, the recurrence risk, the reproductive options and the therapeutic and preventive possibilities available, helping the consultant thorough the decision-taking-process. Recurrence risk calculation depends mainly on the mode of inheritance of the disease and, in the case of mendelian conditions is highly reliable if the diagnosis has been confirmed by the genetic test (AU)

Complejo Sandifer en un paciente con Síndrome Cornelia de Lange y mutación en el gen SMC1A / Sandifer Complex in a patient with Cornelia de Lange Syndrome and mutation in the gene SMC1A

El síndrome Cornelia de Lange es un trastorno del desarrollo hereditario de transmisión dominante que se caracteriza por un fenotipo facial distintivo, anomalías en las extremidades superiores y retraso de crecimiento y psicomotor. Clínicamente se distinguen tres fenotipos: grave, moderado y leve. En la actualidad se conocen tres genes causales del síndrome: NIPBL, SMC1A y SMC3 que codifican proteínas relacionadas con el complejo de cohesinas. Las manifestaciones clínicas más graves suele asociarse a mutaciones en el gen NIPBL, mientras que las mutaciones en los genes SMC1A y SMC3 cursan con cuadros leves y predominio de retraso mental. En este trabajo se describe un paciente con SCdL y mutación en el gen SMC1A que cursa con un fenotipo grave en el que destaca la presencia de un complejo Sandifer y la ausencia de habla (AU)

Cornelia de Lange Syndrome is a dominant inherited developmental disorder characterized by distinctive dysmorphic craniofacial features, limb malformations and growth and cognitive impairment. Clinically, three phenotypes can be distinguished: severe, moderate, and mild. To date, three genes are associated to the disease: NIPBL, SMC1A and SMC3, which encode proteins related with the cohesion complex. The more severe clinical manifestations are seen in patients with mutations in the gene NIPBL, whereas mutations in the genes SMC1A or SMC3 cause mild phenotypes although with cognitive impairment. In this work we reported a patient with mild physical phenotype of CdLS who carries a mutation in SMC1A and has severe clinical manifestations including the Sandifer complex and absence of speech (AU)

Mutaciones de Splicing / Splicing Mutations

El splicing o maduración del pre-mRNA es un mecanismo que está adquiriendo gran relevancia no sólo por las posibilidades que ofrece de expansión del proteoma, sino también por su implicación en la patofisiología de las enfermedades humanas. Las mutaciones de splicing alteran el procesamiento del mRNA al afectar a las secuencias del pre-mRNA (mutaciones en cis) o a las proteínas que intervienen en el splicing (mutaciones en trans). Las secuencias que pueden verse alteradas son: las limitantes de exones e intrones, la zona de ramificación, la zona rica en pirimidinas y también otros elementos reguladores que incrementan o suprimen la selección de un exón. La comprensión en profundidad del efecto de las mutaciones sobre el splicing puede abrir la puerta a su tratamiento mediante terapia moléculas (AU)

Splicing or maturation of pre-mRNA is a mechanism that is becoming more relevant not only for its potential expansion of the proteome, but also for its involvement in the physiopathology of human diseases. Splicing mutations after the processing of mRNA by affecting pre-mRNA sequences (mutations in cis) or proteins involved in splicing (mutations in trans). The sequences that can be altered are: the limiting areas between exons and interns, the branch site, the polypirimidine tract and, finally, other regulatory elements that enhance or suppress the selection of an exon. The whole understanding of the effect of mutations on the splicing processes will help to design molecular therapy targets to correct these defects (AU)

Síndrome X Frágil / Fragile X Syndrome

El Síndrome X Frágil (SXF) es la principal causa de retraso mental hereditario, con una incidencia aproximada de ¼.000 varones y 1/8.000 mujeres en la población general. Se hereda de forma dominante ligada al sexo. Clínicamente se caracteriza por retrasomental, fenotipo peculiar con cara alargada y pabellones auriculares grandes y despegados, hiperlaxitud articular y macroorquidismo tras la pubertad. En las mujeres afectadas las manifestaciones clínicas suelen ser menos evidentes. El mecanismo etiológico es una expansión excesiva (>200) del trinucleótido CGG en el extremo 5´ del gen FMR1, que además está metilado, dando lugar a la ausencia de la proteína FMRP (AU)

Fragile X syndrome (FXS) is considered the most common known cause of inherited mental retardation, with a frequency of approximately 1:4.000 males and 1:8.000 females in the general population. It is an X-linked dominant disorder. Characteristic clinical features included mental retardation, distinctive phenotype with long face and large prominent ears, joint laxity and macroorchidism after puberty. Affected females usually show a less severe phenotype. In the vast majority of the cases, FXS is caused by an abnormal expansion (>200) of a CGG trinucleotide repeat in the 5´- untranslated region of the FMR1 gene, which is methylated, leading to the absence of the FMRP protein (AU)

Bases Moleculares del syndrome Cornelia de Lange / Molecular Basis of Cornelia de Lange Syndrome

El Síndrome de Cornelia de Lange (SCdL) es un trastorno del desarrollo hereditario caracterizado por un fenotipo facial distintivo, malformaciones en extremidades superiores y retrasado de crecimiento y psicomotor. La prevalencia oscila entre 1:45.000 y 1:62.000 nacimientos. Hasta la fecha, se han encontrado mutaciones en tres genes que codifican subunidades reguladoras o estructurales del Complejo de Cohesinas: NIPBL (5p13), SMC1A (Xp11) y SMC3 (10q25), y que afectan alrededor de un 55% de los pacientes. Clínicamente se distinguen tres fenotipos: grave, moderado y leve. El fenotipo grave sólo ha sido descrito en pacientes con mutaciones del gen NIPBL. Las bases patogénicas del síndrome no están aún aclaradas, pero parecen relacionarse con problemas de regulación de la expresión génico y/o de la cohesión cromosómica (AU)

Cornelia de Lange Syndorme (CDLS) is a congenital hereditary developmental disorder characterized by a distinctive craniofacial phenotype, upper limb malformations, and growth and developmental delay. The estimated prevalence range from 1:45.000 to 1:62.000 livebirths. Up to date, there genes that encode structural or regulator subunits of Cohesin Complex: NIPBL (5p13), SMC1A (Xp11), and SMC3 (10q25), have been found to bear mutations in approximately 55% of affected patients. Three phenotypes can be distinguished clinically: severe, moderate and mild. The severe one has been only seen in patients carrying mutations in the NIPBL gene. Although the pathogenic bases of the syndrome remain unclear, it has been hypothesized that CdLS is related to anomalies in gene expression regulations and /or chromosome cohesion (AU)