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LAMIN B1; LMNB1

LAMIN B1; LMNB1

Alternative titles; symbolsLMNBHGNC Approved Gene Symbol: LMNB1Cytogenetic location: 5q23.2 Genomic coordinates (GRCh38): 5:126,776,622-126,837,019 (from NCB...

Alternative titles; symbols

  • LMNB

HGNC Approved Gene Symbol: LMNB1

Cytogenetic location: 5q23.2 Genomic coordinates (GRCh38): 5:126,776,622-126,837,019 (from NCBI)

▼ Description
Lamins are the major components of the nuclear lamina which underlies the nuclear envelope of eukaryotic cells (see lamin A, 150330). Maeno et al. (1995) noted that lamins are members of the intermediate filament protein family. Vertebrate lamins are classified into 2 types, A and B, and mammalian somatic cells show 2 species of each type: lamins A and C for the A type and B1 and B2 for the B type. In addition, germ-cell-specific lamins have been reported for both types (Furukawa and Hotta, 1993 and Furukawa et al., 1994). Whereas A-type lamins are expressed in a developmentally controlled manner, B-type lamins are expressed in all kinds of cells.

▼ Cloning and Expression
Pollard et al. (1990) cloned a lamin B cDNA from the human T-cell line MOLT-4. LMNB1 encodes a deduced 586-amino acid protein with a calculated molecular mass of 66,334 Da. The LMNB1 protein shares approximately 72% sequence similarity with lamin A/C (150330).

▼ Gene Function
Lamin B, a component of the interphase nuclear lamina, is required to maintain nuclear shape and mechanical integrity (Goldman et al., 2002).

Tsai et al. (2006) reported that lamin B has a role in spindle assembly. Lamin B assembled into a matrix-like network in mitosis through a process that depended on the presence of the GTP-bound form of the small guanosine triphosphatase (GTPase) Ran (601179). Depletion of lamin B resulted in defects in spindle assembly. Dominant-negative mutant lamin B proteins that disrupt lamin B assembly in interphase nuclei also disrupted spindle assembly in mitosis. Furthermore, lamin B was essential for the formation of the mitotic matrix that tethers a number of spindle assembly factors. Tsai et al. (2006) proposed that lamin B is a structural component of the long-sought-after spindle matrix that promotes microtubule assembly and organization in mitosis.

Kim et al. (2011) found that mouse embryonic stem cells do not need any lamins for self-renewal and pluripotency. Although genomewide lamin-B binding profiles correlate with reduced gene expression, such binding is not directly required for gene silencing in embryonic stem cells or trophectoderm cells. However, B-type lamins are required for proper organogenesis. Defects in spindle orientation in neural progenitor cells and migration of neurons probably cause brain disorganizations found in lamin-B-null mice. Kim et al. (2011) concluded that their studies not only disprove several prevailing views of lamin-Bs but also establish a foundation for redefining the function of the nuclear lamina in the context of tissue building and homeostasis.

Dou et al. (2015) reported that the autophagy machinery mediates degradation of nuclear lamina components in mammals. The autophagy protein LC3/Atg8 (601242), which is involved in autophagy membrane trafficking and substrate delivery, is present in the nucleus and directly interacts with the nuclear lamina protein lamin B1, and binds to lamin-associated domains on chromatin. This LC3-lamin B1 interaction does not downregulate lamin B1 during starvation, but mediates its degradation upon oncogenic insults, such as by activated RAS (see 190020). Lamin B1 degradation is achieved by nucleus-to-cytoplasm transport that delivers lamin B1 to the lysosome. Inhibiting autophagy or the LC3-lamin B1 interaction prevented activated RAS-induced lamin B1 loss and attenuated oncogene-induced senescence in primary human cells. Dou et al. (2015) concluded that this function of autophagy acts as a guarding mechanism protecting cells from tumorigenesis.

▼ Gene Structure
Lin and Worman (1995) determined that the human LMNB1 gene contains 11 exons. The transcription unit spans more than 45 kb and the transcription start site is 348 nucleotides upstream from the translation initiation codon. Exon 1 codes for the N-terminal head domain and the first portion of the central rod domain, exons 2 through 6 the central rod domain, and exons 7 through 11 the C-terminal tail domain. Intron positions are conserved in other lamin genes from frogs, mice, and humans but different in lamin genes from Drosophila and C. elegans.

Maeno et al. (1995) demonstrated that the mouse lamin B1 gene spans about 43 kb of the genome and contains 11 exons, Exon/intron structure of the B1 gene clearly showed the conserved organization among the intermediate filament protein family genes. The presumptive promoter region has high GC content and contains a CAAT box and multiple Sp1 sites but no classical TATA box, suggesting to the authors that the lamin B1 gene has a typical housekeeping gene promoter with a CpG island.

▼ Mapping
The lamin B gene in the mouse is located on chromosome 18 (Justice et al., 1992) in a region of linkage homology to the long arm of human chromosome 5. Wydner et al. (1996) mapped the human LMNB1 gene to 5q23.3-q31.1 by fluorescence in situ hybridization.

▼ Molecular Genetics
Autosomal Dominant Adult-Onset Leukodystrophy

Padiath et al. (2006) identified a tandem genomic duplication resulting in an extra copy of the LMNB1 gene (150340.0001) as the cause of adult-onset autosomal dominant leukodystrophy (ADLD; 169500), a slowly progressive neurologic disorder characterized by symmetric widespread myelin loss in the central nervous system. The duplication was identified by sequencing genomic DNA from affected individuals and also from mouse-human hybrid cell lines derived from cells of affected individuals. The hybrid cell lines enabled Padiath et al. (2006) to separate chromosomes derived from each of the 2 parents of an individual and to assign phase unambiguously when identifying sequencing variants. They constructed a haplotype map of the chromosome carrying the disease-causing mutation and observed a large shared haplotype block in the critical region, suggesting that the 2 families arose from a common founder. Increased expression of lamin B1 in Drosophila melanogaster resulted in a degenerative phenotype. In addition, an abnormal nuclear morphology was apparent when cultured cells overexpressed this protein. Padiath et al. (2006) stated that ADLD was the first human disease attributable to mutations in the gene encoding lamin in the LMNB1 gene. Antibodies to lamin B are found in individuals with autoimmune diseases, and it is also an antigen recognized by a monoclonal antibody raised against plaques from brains of individuals with multiple sclerosis (126200). This raised the possibility that lamin B may be a link to the autoimmune attack that occurs in multiple sclerosis.

Brussino et al. (2009) found a 140- to 190-kb duplication of 5q including the entire LMNB1 gene, the AX748201 transcript, and the 3-prime end of the MARCH3 gene (613333) in 1 of 8 Italian probands with adult-onset leukoencephalopathy. The patient's affected cousin also carried the duplication, and there was a family history of a similar disorder. Lamin B1 expression was increased in lymphoblasts from one of the patients with the duplication.

In affected members of 4 unrelated families with ADLD, Schuster et al. (2011) found duplication of the LMNB1 gene. All 4 duplications were of different sizes, ranging from 107 to 218 kb, supporting independent events. Five patients from 2 families had about a 2-fold increased level of LMNB1 protein in white blood cells, and LMNB1 mRNA was also increased compared to controls. Each duplication extended over part of the MARCH3 gene, but MARCH3 mRNA was not increased in patient leukocytes. Schuster et al. (2011) concluded that an accurate molecular diagnosis of the disorder could be made by direct analysis of LMNB1 in peripheral leukocytes.

In a 42-year-old woman of Italian ancestry, who was born in Brazil, with clinical features of ADLD, Pedroso et al. (2017) identified a heterozygous missense variant in the LMNB1 gene (R29W). The variant, which was found by whole-exome sequencing, was not present in several public databases, including the Exome Sequencing Project and ExAC. Patient-derived cells showed increased expression of variant LMNB1 mRNA, as well as nuclear structural abnormalities. Functional studies demonstrated an impaired response to DNA damage, suggesting genomic instability. The patient presented at 23 years of age with progressive cerebellar atrophy and cognitive impairment. Brain imaging showed white matter abnormalities in the cerebellum, as well as atrophy of the corpus callosum, brainstem, and spinal cord. In in vitro studies, Cristofoli et al. (2020) demonstrated that the R29W variant was present in the nuclear extract, suggesting that it did not disrupt nuclear lamina localization of LMNB1.

Autosomal Dominant Primary Microcephaly 26

In 7 patients from 5 unrelated families with autosomal dominant primary microcephaly-26 (MCPH26; 619179), Cristofoli et al. (2020) identified heterozygous mutations in the LMNB1 gene (150340.0002-150340.0006). The mutations were found by whole-exome sequencing or microarray analysis and confirmed by Sanger sequencing. The mutations occurred de novo in 3 patients, whereas 1 was inherited from a mildly affected mother, and in 3 sibs were inherited from an unaffected father who was mosaic for the mutation. There was 1 intragenic deletion, 1 splice site mutation, and 3 missense variants affecting highly conserved residues. In vitro functional expression studies of the 3 missense variants showed that they caused variable abnormalities of the nuclear lamina and misshapen nuclei. One was associated with decreased protein expression, and the others caused mislocalization of LMNB1 to the cytoplasm. However, mitotic spindle formation and mitotic segregation did not appear to be affected. The authors postulated a dominant-negative effect.

In 7 unrelated patients (P1-P3, P9-P11, P13) with MCPH26, Parry et al. (2021) identified heterozygous mutations in the LMNB1 gene (see, e.g., 150340.0004 and 150340.0007). There were 2 recurrent missense mutations and an in-frame deletion; none were present in the gnomAD database. The mutations occurred de novo in all patients for whom parental material was available. The location of the mutations predicted interference with dimer or filament assembly, and in vitro functional expression studies in cells transfected with the mutations showed that they caused abnormal LMNB1 nuclear aggregates and an altered nuclear shape. Parry et al. (2021) postulated that the mutations may alter the properties of lamin filaments, resulting in fragile nuclei that are susceptible to the mechanical stresses of nuclear and neuronal migration, leading to increased cell death during brain development.

▼ Animal Model
Mutations affecting A-type lamins have been associated with a variety of human diseases, including muscular dystrophy (e.g., 181350), cardiomyopathy (e.g., 115200), lipodystrophy (e.g., 151660), and progeria (176670), but mutations in B-type lamins had not been identified in humans or in experimental animals. To investigate the in vivo function of lamin B1, Vergnes et al. (2004) generated mice with an insertional mutation in Lmnb1. The mutation resulted in the synthesis of a mutant lamin B1 protein lacking several key functional domains, including a portion of the rod domain, the nuclear localization signal, and the CAAX motif (the C-terminal signal for farnesylation). Homozygous Lmnb1 mutant mice survived embryonic development but died at birth with defects in lung and bone. Fibroblasts from mutant embryos grew under standard cell culture conditions but displayed grossly misshapen nuclei, impaired differentiation, increased polyploidy, and premature senescence. Thus, the lamin B1 mutant mice provided evidence for a broad and nonredundant function of lamin B1 in mammalian development.

▼ ALLELIC VARIANTS ( 7 Selected Examples):

.0001 LEUKODYSTROPHY, ADULT-ONSET, AUTOSOMAL DOMINANT
LMNB1, DUP, CHR5:126,102,443-126,199,753 SRO, GRCh37
In 2 families of Irish American descent and in 2 other families with autosomal dominant adult-onset leukodystrophy (169500), Padiath et al. (2006) found a duplication of the LMNB1 gene and part of the MARCH3 gene (613333). Haplotype analysis suggested that the 2 Irish American families arose through a common founder.

In affected members of 4 unrelated families with ADLD, Schuster et al. (2011) found duplication of the LMNB1 gene and part of the MARCH3 gene. All 4 duplications were of different sizes, ranging from 107 to 218 kb, supporting independent events. Five patients from 2 families had about a 2-fold increased level of LMNB1 protein in white blood cells, and LMNB1 mRNA was also increased compared to controls. MARCH3 mRNA was not increased in patient leukocytes. Schuster et al. (2011) concluded that an accurate molecular diagnosis of the disorder could be made by direct analysis of LMNB1 in peripheral leukocytes.

In a symptomatic man with ADLD and his asymptomatic sister who had leukodystrophy on brain imaging, Dos Santos et al. (2012) identified a 148-kb duplication on chromosome 5q23.2 including the LMNB1 gene, but not the MARCH3 gene. The findings confirmed the central role of the LMNB1 gene in ADLD.

Using a custom array, Giorgio et al. (2013) performed detailed breakpoint junction sequence analysis of the duplicated 5q23 region containing the LMNB1 gene in 20 independent families with ADLD in whom genomic LMNB1 duplication was initially identified by aCGH, QT-PCR, or MLPA. Seven families had previously been reported (Brussino et al., 2009; Schuster et al., 2011; Dos Santos et al., 2012). There were a total of 16 unique rearrangements. Three of the duplications were shared by more than 1 family: 1 was found in 3 families and the other 2 duplications were found in 2 families each. Individuals with identical junctions shared the same haplotype, consistent with a founder effect. Duplication sizes ranged from about 128 kb to 475 kb. The largest duplication also included the PHAX (604924), ALDH7A1 (107323), and GRAMD3 genes. Comparison of all the samples identified a 72-kb minimal critical duplicated region required for ADLD that contained only the LMNB1 gene. All but 1 of the duplications were in the direct tandem orientation; the remaining duplication was inverted. Characterization of the junction sequences showed that most (11 of 15) showed short stretches of microhomology overlap ranging from 1 to 6 nucleotides, whereas the others showed small insertions at the breakpoints. All duplications resulted from intrachromosomal rearrangements. Analysis of the genomic architecture suggested several potential mechanisms for the duplications, including nonhomologous end joining (NHEJ) or fork stalling and template switching/microhomology-mediated break-induced repair (FoSTeS/MMBIR). The enrichment of Alu repetitive elements at the centromeric breakpoints (found in 4 cases), higher GC content, and high frequency of repetitive sequences at breakpoints likely also played a role in mediating ADLD duplications. RT-PCR of patients fibroblasts or blood showed increased LMNB1 expression (2.1- to 4.8-fold compared to controls), as well as increased protein levels (1.6- to 3.2-fold compared to controls). There was no apparent difference in phenotype according to duplication size, with the exception of the 1 family with a large inverted duplication affecting multiple genes.

.0002 MICROCEPHALY 26, PRIMARY, AUTOSOMAL DOMINANT
LMNB1, ALA152GLY
In a 10-year-old boy (P1), born of unrelated Belgian parents, with autosomal dominant primary microcephaly-26 (MCPH26; 619179), Cristofoli et al. (2020) identified a de novo heterozygous c.455C-G transversion (c.455C-G, NM_005573.3) in exon 2 of the LMNB1 gene, resulting in an ala152-to-gly (A152G) substitution at a highly conserved residue in the coil 1B domain. The mutation, which was found by trio-based whole-exome sequencing and confirmed by Sanger sequencing, was not present in public databases, including gnomAD. Patient cells showed decreased levels of the mutant protein. Transfection of the mutant protein into LMNB1-null HeLa cells also resulted in reduced protein levels, suggesting possible instability of the mutant protein, although further studies did not show increased turnover of the A152G protein compared to controls. The A152G variant caused abnormalities in the nuclear lamina, including abnormal and irregular ruffling, suggesting global disruption of the nuclear envelope. There was an increase in the percentage of cells with condensed nuclei, which may have been a result of overexpression.

.0003 MICROCEPHALY 26, PRIMARY, AUTOSOMAL DOMINANT
LMNB1, EX6-8 DEL
In a 9-year-old Belgian girl (P2) with autosomal dominant primary microcephaly-26 (MCPH26; 619179), Cristofoli et al. (2020) identified a heterozygous in-frame deletion in the LMNB1 gene, causing the deletion of exons 6-8 (Ser314_Thr497del). The deletion, which was found by microarray analysis, was inherited from the similarly affected mother in whom it occurred de novo. The deletion was predicted to result in a shortened protein lacking the nuclear localization signal. The authors postulated that the mutation results in insufficient protein abundance in the nucleus to form a stable laminar network and acts in a dominant-negative manner. However, functional studies of the variant and studies of patient cells were not performed. These patients had a milder phenotype than the others: the proband had a head circumference (HC) of -3.6 SD, whereas her mother had a HC of -2.5 SD and had learning difficulties.

.0004 MICROCEPHALY 26, PRIMARY, AUTOSOMAL DOMINANT
LMNB1, LYS33GLU
In a 6-year-old Italian girl (P3) with autosomal dominant primary microcephaly-26 (MCPH26; 619179), Cristofoli et al. (2020) identified a de novo heterozygous c.97A-G transition (c.97A-G, NM_005573.3) in exon 1 of the LMNB1 gene, resulting in a lys33-to-glu (K33E) substitution at a highly conserved residue in the coil 1A domain near the head of the protein. The mutation, which was found by trio-based whole-exome sequencing and confirmed by Sanger sequencing, was not present in public databases, including gnomAD. Transfection of the mutant protein into LMNB1-null HeLa cells resulted in abnormal morphology of the nuclear lamina, which appeared diffuse, poorly formed, and with no discrete boundary. There was an increase in multilobed nuclei, which was also observed in patient-derived cells. Mutant LMNB1 was dispersed throughout the cell in the cytoplasm, indicating failure to incorporate into the laminar network; LMNB1 aggregates were often observed.

In 3 unrelated patients (P1, P9, and P11) with MCPH26, Parry et al. (2021) identified a de novo heterozygous K33E mutation in the LMNB1 gene. The location of the mutation was predicted to interfere with dimer or filament assembly, and in vitro functional expression studies in cells transfected with the mutant protein showed that it caused abnormal LMNB1 nuclear aggregates and an altered nuclear shape.

.0005 MICROCEPHALY 26, PRIMARY, AUTOSOMAL DOMINANT
LMNB1, ARG42TRP
In a 2-year-old girl (P4) with autosomal dominant primary microcephaly-26 (MCPH26; 619179), Cristofoli et al. (2020) identified a de novo heterozygous c.124C-T transition (c.124C-T, NM_005573.3) in exon 1 of the LMNB1 gene, resulting in an arg42-to-trp (R42W) substitution at a highly conserved residue in the coil 1A domain near the head of the protein. The mutation, which was found by trio-based whole-exome sequencing and confirmed by Sanger sequencing, was not present in public databases, including gnomAD. Transfection of the mutant protein into LMNB1-null HeLa cells resulted in abnormal morphology of the nuclear lamina, which appeared diffuse, poorly formed, and with no discrete boundary. There was an increase in multilobed nuclei, which was also observed in patient-derived cells. Mutant LMNB1 was dispersed throughout the cell in the cytoplasm, indicating failure to incorporate into the laminar network; LMNB1 aggregates were often observed.

.0006 MICROCEPHALY 26, PRIMARY, AUTOSOMAL DOMINANT
LMNB1, IVS5DS, G-A, +1
In 3 sibs (P5-P7), born of unrelated Arab parents, with autosomal dominant primary microcephaly-26 (MCPH26; 619179), Cristofoli et al. (2020) identified a heterozygous G-to-A transition in intron 5 of the LMNB1 gene (c.939+1G-A, NM_005573.3). The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was inherited from an unaffected father who was mosaic for the mutation (15% mosaicism). The mutation was predicted to result in a splicing defect, but patient cells were not available for confirmation.

.0007 MICROCEPHALY 26, PRIMARY, AUTOSOMAL DOMINANT
LMNB1, ARG90PRO
In 2 unrelated patients (P10 and P13) with autosomal dominant primary microcephaly-26 (MCPH26; 619179), Parry et al. (2021) identified a heterozygous c.269G-C transversion (c.269G-C, NM_005573.4) in the LMNB1 gene, resulting in an arg90-to-pro (R90P) substitution at a highly conserved residue at the interdimer interface of the coil 1B domain. The mutation occurred de novo in P10, whereas parental data was not available for P13. The mutation, which was found by exome sequencing, was not present in the gnomAD database. The location of the mutation was predicted to interfere with dimer or filament assembly, and in vitro functional expression studies in cells transfected with the mutation showed that it caused abnormal LMNB1 nuclear aggregates and an altered nuclear shape.

Tags: 5q23.2

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