Biology subjects

Balas, M. M.

Publications and source records attributed to Balas, M. M..

3 recordsLinked to original sources

bioRxiv2026

Proteomics and single-cell transcriptomics identify LRP1 as a diagnostic biomarker for atypical fibroxanthoma and pleomorphic dermal sarcoma.

Atypical fibroxanthoma (AFX) and pleomorphic dermal sarcoma (PDS) are cutaneous neoplasms that fall along a spectrum. PDS is more aggressive than AFX with higher rates of local and distant metastases. Diagnostic biomarkers for AFX and PDS are lacking and therefore these tumors are diagnosed only after excluding other dermal spindle cell neoplasms, including cutaneous leiomyosarcoma (cLMS), spindle cell melanoma (SCM), and sarcomatoid squamous cell carcinoma (sSCC). To identify clinically valuable biomarkers, we contrast the tumors within the diagnostic differential using single-cell RNA sequencing and bulk proteomic data. Gene Ontology (GO) analysis of transcripts and proteins enriched in AFX/PDS identified multiple shared pathways associated with cell adherence and the extracellular matrix. We identify that LRP1, LTBP2, and NAV1 are all enriched in AFX/PDS over other tumors in the differential at both the level of mRNA and protein. IHC reveals that LRP1 is 90% sensitive and 73% specific for AFX/PDS in a cohort of AFX, PDS, cLMS, SCM, and sSCC. This outperforms published data for CD10, which is currently used clinically (sensitivity 83.5% and specificity 50%). When used in conjunction with LTBP2, specificity for AFX/PDS within the differential rises from 73% to 93%. These findings suggest that LRP1, particularly if evaluated in conjunction with existing stains, can improve diagnostic accuracy for AFX and PDS.

cancer biology↗

bioRxiv2025

Characterization of an immunodeficiency-associated EZH2 variant

Regulation of gene expression is central to the development of immune cells and their ability to respond to infection. As part of a clinical evaluation, we identified two sisters with recurrent infections, hypogammaglobulinemia, and memory B cell deficiency, diagnosed as common variable immunodeficiency. Whole exome sequencing identified a heterozygous variant (Leu50Ser, L50S) in a conserved region of EZH2, the catalytic subunit of the epigenetic gene repressor Polycomb Repressive Complex 2 (PRC2). EZH2-catalyzed histone H3 lysine 27 methylation (H3K27me) in bulk was not overall significantly disrupted by this variant, in patient samples or cell lines expressing EZH2-L50S. EZH2-L50S protein is expressed similar to wild-type and can form PRC2. However, we find that specific genomic regions that normally have high wild-type levels of H3K27me3 are deficient in the L50S context, particularly around gene promoters. EZH2-L50S is still recruited to these sites, but is not as active. Using recombinant purified PRC2, we determine that L50S affects methylation of nucleosomes and disrupts allosteric stimulation that normally amplifies H3K27me3, consistent with the location of L50 in the allosteric regulatory region of PRC2. Thus, variation of EZH2 L50, occurring at low frequency in the population may interfere with normal B cell gene expression patterns, contributing to immunodeficiency. This study has implications for genetic variation in PRC2 in the general population.

molecular biology↗

bioRxiv2020

RNA matchmaking remodels lncRNA structure and promotes PRC2 activity

Human Polycomb Repressive Complex 2 (PRC2) catalysis of histone H3 lysine 27 methylation at certain loci depends on long noncoding RNAs (lncRNAs). Yet, in apparent contradiction, RNA is a potent catalytic inhibitor of PRC2. Here we show that intermolecular RNA-RNA interactions between the lncRNA HOTAIR and its target genes can relieve RNA inhibition of PRC2. RNA matchmaking is promoted by heterogenous nuclear ribonucleoprotein (hnRNP) B1, which uses multiple protein domains to bind regions of HOTAIR via multi-valent protein-RNA interactions. Chemical probing demonstrates that RNA matchmaking changes HOTAIR RNA structure. Genome-wide HOTAIR/PRC2 activity occurs at genes whose transcripts can make favorable RNA-RNA interactions with HOTAIR. We demonstrate that RNA-RNA matches of HOTAIR with target gene RNAs can relieve the inhibitory effect of a single lncRNA for PRC2 activity. Our work highlights an intrinsic switch that allows PRC2 activity in specific RNA contexts, which could explain how many lncRNAs work with PRC2.

biochemistry↗