Exome sequence comparison of seventy-seven multiple myeloma cases identifies potential risk alleles

honors thesisCollege of EngineeringBiomedical EngineeringNicola J. CampMultiple Myeloma (MM) is a heritable cancer of plasma cells with poor prognosis. Although a few genomic risk-loci have been identified for MM, no risk variants have been published that explain MM heritability. We hypothesize MM heritability is due to rare germ-line variants that can be discovered through sequence comparison in high-risk MM cases. To uncover these rare risk-variants we sequenced the exomes (all protein-coding regions) of seventy-seven cases in high-risk pedigrees or diagnosed younger than usual. Alleles variant from a reference genome were prioritized based on sharing between cases and rarity in unaffected controls. Initial prioritization resulted in 7,344 variants which were further prioritized based on proximity to GWAS loci and effect on protein function. Six variants were within a thousand base pairs from a published GWAS locus. Of the six, an intronic SNP in CCND1 is of special interest as CCND1 is somatically altered in the tumors of 30% of MM cases and important in cell cycle progression. One hundred-nine variants were predicted to have high impact on protein function. Four of these variants were seen in additional samples including a frame-shift deletion in HAUS3. This variant is of special interest as HAUS3 regulates cell cycle progression in hematopoietic stem and progenitor cells. The potential risk-variants identified in this study demonstrate rare, genomic variants likely contribute to MM risk and can be identified through sequence comparison. These rare risk-variants could shed light on the genetic factors effecting MM and lead to eventual improved early detection and personalized treatment

Adequacy of the gamma distribution.

<p>The gamma distribution provides an adequate fit for multiple types of pedigrees. For example, HRP UT-549917 has <i>k</i> = 4.4 and <i>σ</i> = 3.6 with good visual density (a) and CDF (b) fit, with <i>λ</i> = 0.9. (Goodness of fit was estimated with <i>λ</i>, the median of empirical chi-squared distribution divided by the median of the expected chi-squared distribution.) HRP UT-34955 has <i>k</i> = 2.8 and <i>σ</i> = 2.9 with good visual density (c) and CDF (d) fit, with <i>λ</i> = 1.0.</p

Germline Lysine-Specific Demethylase 1 ( LSD1/KDM1A ) Mutations Confer Susceptibility to Multiple Myeloma

Given the frequent and largely incurable occurrence of multiple myeloma, identification of germline genetic mutations that predispose cells to multiple myeloma may provide insight into disease etiology and the developmental mechanisms of its cell of origin, the plasma cell (PC). Here, we identified familial and early-onset multiple myeloma kindreds with truncating mutations in lysine-specific demethylase 1 (LSD1/KDM1A), an epigenetic transcriptional repressor that primarily demethylates histone H3 on lysine 4 and regulates hematopoietic stem cell self-renewal. In addition, we found higher rates of germline truncating and predicted deleterious missense KDM1A mutations in patients with multiple myeloma unselected for family history compared with controls. Both monoclonal gammopathy of undetermined significance (MGUS) and multiple myeloma cells have significantly lower KDM1A transcript levels compared with normal PCs. Transcriptome analysis of multiple myeloma cells from KDM1A mutation carriers shows enrichment of pathways and MYC target genes previously associated with myeloma pathogenesis. In mice, antigen challenge followed by pharmacologic inhibition of KDM1A promoted PC expansion, enhanced secondary immune response, elicited appearance of serum paraprotein, and mediated upregulation of MYC transcriptional targets. These changes are consistent with the development of MGUS. Collectively, our findings show that KDM1A is the first autosomal-dominant multiple myeloma germline predisposition gene providing new insights into its mechanistic roles as a tumor suppressor during post-germinal center B-cell differentiation. KDM1A is the first germline autosomal dominant predisposition gene identified in multiple myeloma and provides new insights into multiple myeloma etiology and the mechanistic role of KDM1A as a tumor suppressor during post-germinal center B-cell differentiation.

Adequacy of the gamma distribution.

<p>The gamma distribution provides an adequate fit for multiple types of pedigrees. For example, HRP UT-549917 has <i>k</i> = 4.4 and <i>σ</i> = 3.6 with good visual density (a) and CDF (b) fit, with <i>λ</i> = 0.9. (Goodness of fit was estimated with <i>λ</i>, the median of empirical chi-squared distribution divided by the median of the expected chi-squared distribution.) HRP UT-34955 has <i>k</i> = 2.8 and <i>σ</i> = 2.9 with good visual density (c) and CDF (d) fit, with <i>λ</i> = 1.0.</p

Significant SGS, pedigrees, and segregating SNVs.

<p>In pedigrees, MM cases are fully shaded and MGUS cases are half shaded. Numbers indicate multiple individuals. a) Utah pedigree, 571744, sharing the genome-wide significant SGS. The pedigree is trimmed to allow for viewing (37 MM confirmed cases are known in this pedigree, 3 were ascertained and genotyped). + indicates the genotyped MM cases that are SGS carriers, − indicates genotyped and non-carriers, no carrier status indicates not genotyped. Note–the genealogy extends beyond SEER cancer registry data. MGUS status is unknown in this pedigree. b) Genomic region of significant SGS. c) INSERM pedigree carrying the stop gain SNV marked by “c” in box e. 1 MM and 2 MGUSs carry the SNV. d) Mayo Clinic pedigree carrying the missense SNV marked by “d” in box e. 1 MM and 1 MGUS carry the SNV, but 2 unaffected siblings do not carry the SNV. e) Risk candidate gene, <i>USP45</i>, has 2 segregating SNVs in the ubiquitin C-terminal hydrolase 2 (UCH) domain.</p

SGS with multiple lines of evidence.

<p>a/b) Utah pedigrees carrying the overlapping SGSs on chr1p36.11-p35.1. + indicates the genotyped MM cases that are SGS carriers, − indicates genotyped and non-carriers, no carrier status indicates not genotyped. c) Weill Cornell pedigree with a segregating, missense SNV in <i>ARID1A</i> indicated by “c” in box e. d) Genomic region of overlapping SGS. Dark black genes fall in both regions. e) 2 rare and segregating, missense SNVs were observed in whole-exome sequencing. SNV “b” is carried by the cases indicated with + in box b. SNV “c” in carried by the cases in box c.</p

Significant or overlapping SGSs and segregating SNVs.

<p>Significant or overlapping SGSs and segregating SNVs.</p