Carmel Grace McCullough

All Publications

• Resolving spatial subclonal genomic heterogeneity of loss of heterozygosity and extrachromosomal DNA in gliomas NATURE COMMUNICATIONS Webb, M. G., Chow, F., McCullough, C. G., Zhang, B., Lee, J. J. Y., Bassiouni, R., Garrett III, N. E., Hurth, K., Carpten, J. D., Zada, G., Craig, D. W. 2025; 16 (1): 5290

  Abstract

  Mapping the spatial organization of DNA-level somatic copy number changes in tumors can provide insight to understanding higher-level molecular and cellular processes that drive pathogenesis. We describe an integrated framework of spatial transcriptomics, tumor/normal DNA sequencing, and bulk RNA sequencing to identify shared and distinct characteristics of an initial cohort of eleven gliomas of varied pathology and a replication cohort of six high-grade glioblastomas. We identify focally amplified extrachromosomal DNA (ecDNA) in four of the eleven initial gliomas, with subclonal tumor heterogeneity in two EGFR-amplified grade IV glioblastomas. In a TP53-mutated glioblastoma, we detect a subclone with EGFR amplification on ecDNA coupled to chromosome 17 loss of heterozygosity. To validate subclonal somatic aneuploidy and copy number alterations associated with ecDNA double minutes, we examine the replication cohort, identifying MDM2/MDM4 ecDNA subclones in two glioblastomas. The spatial heterogeneity of EGFR and p53 inactivation underscores the role of ecDNA in enabling rapid oncogene amplification and enhancing tumor adaptability under selective pressure.

  View details for DOI 10.1038/s41467-025-59805-z

  View details for Web of Science ID 001507937400002

  View details for PubMedID 40514380

  View details for PubMedCentralID PMC12166086

• A spatiotemporal and machine-learning platform facilitates the manufacturing of hPSC-derived esophageal mucosa. Developmental cell Yang, Y., McCullough, C. G., Seninge, L., Guo, L., Kwon, W. J., Zhang, Y., Li, N. Y., Gaddam, S., Pan, C., Zhen, H., Torkelson, J., Glass, I. A., Charville, G. W., Que, J., Stuart, J. M., Ding, H., Oro, A. E. 2025

  Abstract

  Human pluripotent stem cell-derived tissue engineering offers great promise for designer cell-based personalized therapeutics, but harnessing such potential requires a deeper understanding of tissue-level interactions. We previously developed a cell replacement manufacturing method for ectoderm-derived skin epithelium. However, it remains challenging to manufacture the endoderm-derived esophageal epithelium despite possessing a similar stratified epithelial structure. Here, we employ single-cell and spatial technologies to generate a spatiotemporal multi-omics cell census for human esophageal development. We identify the cellular diversity, dynamics, and signal communications for the developing esophageal epithelium and stroma. Using Manatee, a machine-learning algorithm, we prioritize the combinations of candidate human developmental signals for in vitro derivation of esophageal basal cells. Functional validation of Manatee predictions leads to a clinically compatible system for manufacturing human esophageal mucosa.

  View details for DOI 10.1016/j.devcel.2024.12.030

  View details for PubMedID 39798574

• Common mitochondrial deletions in RNA-Seq: evaluation of bulk, single-cell, and spatial transcriptomic datasets COMMUNICATIONS BIOLOGY Omidsalar, A. A., Mccullough, C. G., Xu, L., Boedijono, S., Gerke, D., Webb, M. G., Manojlovic, Z., Sequeira, A., Lew, M. F., Santorelli, M., Serrano, G. E., Beach, T. G., Limon, A., Vawter, M. P., Hjelm, B. E. 2024; 7 (1): 200

  Abstract

  Common mitochondrial DNA (mtDNA) deletions are large structural variants in the mitochondrial genome that accumulate in metabolically active tissues with age and have been investigated in various diseases. We applied the Splice-Break2 pipeline (designed for high-throughput quantification of mtDNA deletions) to human RNA-Seq datasets and describe the methodological considerations for evaluating common deletions in bulk, single-cell, and spatial transcriptomics datasets. A robust evaluation of 1570 samples from 14 RNA-Seq studies showed: (i) the abundance of some common deletions detected in PCR-amplified mtDNA correlates with levels observed in RNA-Seq data; (ii) RNA-Seq library preparation method has a strong effect on deletion detection; (iii) deletions had a significant, positive correlation with age in brain and muscle; (iv) deletions were enriched in cortical grey matter, specifically in layers 3 and 5; and (v) brain regions with dopaminergic neurons (i.e., substantia nigra, ventral tegmental area, and caudate nucleus) had remarkable enrichment of common mtDNA deletions.

  View details for DOI 10.1038/s42003-024-05877-4

  View details for Web of Science ID 001163774500004

  View details for PubMedID 38368460

  View details for PubMedCentralID PMC10874445

• Utilizing RNA and outlier analysis to identify an intronic splice-altering variant in AP4S1 in a sibling pair with progressive spastic paraplegia HUMAN MUTATION McCullough, C. G., Szelinger, S., Belnap, N., Ramsey, K., Schrauwen, I., Claasen, A. M., Burke, L. W., Siniard, A. L., Huentelman, M. J., Narayanan, V., Craig, D. W. 2020; 41 (2): 412-419

  Abstract

  We report a likely pathogenic splice-altering AP4S1 intronic variant in two sisters with progressive spastic paraplegia, global developmental delay, shy character, and foot deformities. Sequencing was completed on whole-blood messenger RNA (mRNA) and analyzed for gene expression outliers after exome sequencing analysis failed to identify a causative variant. AP4S1 was identified as an outlier and contained a rare homozygous variant located three bases upstream of exon 5 (NC_000014.8(NM_007077.4):c.295-3C>A). Confirmed by additional RNA-seq, reverse-transcription polymerase chain reaction, and Sanger sequencing, this variant corresponded with exon 5, including skipping, altered isoform usage, and loss of expression from the canonical isoform 2 (NM_001128126.3). Previously, loss-of-function variants within AP4S1 were associated with a quadriplegic cerebral palsy-6 phenotype, AP-4 Deficiency Syndrome. In this study, the inclusion of mRNA-seq allowed for the identification of a previously missed splice-altering variant, and thereby expands the mutational spectrum of AP-4 Deficiency Syndrome to include impacts to some tissue-dependent isoforms.

  View details for DOI 10.1002/humu.23939

  View details for Web of Science ID 000496346400001

  View details for PubMedID 31660686