Biology subjects

Giuliano, A. E.

Publications and source records attributed to Giuliano, A. E..

3 recordsLinked to original sources

bioRxiv2023

A Practical Approach for Targeting Structural Variants Genome-wide in Plasma Cell-free DNA

Interrogating gene mutations and aberrant DNA methylation in plasma cell-free DNA (cfDNA) has become increasingly common for monitoring tumor burden in cancer patients. However, no tests currently target chromosomal structural variants (SVs) genome-wide. Here, we report a simple molecular and sequencing workflow, Genome-wide Analysis of Palindrome Formation (GAPF-seq), to probe DNA palindromes, a type of SV that often demarcates gene amplification. Low-coverage next-generation sequencing of palindrome-enriched DNA uncovered skewed chromosomal distributions of high-coverage 1-kb bins (HCBs) in tumor DNA. When combined with traditional machine learning, GAPF-seq differentiated 39 breast tumors from matched control DNA with an Area Under the Curve (AUC) of 0.955. A proof-of-concept liquid biopsy study using cfDNA from 27 prostate cancer patients and 24 control individuals yielded an average AUC of 0.896. HCBs on the X chromosome emerged as a nearly decisive feature and were linked to androgen receptor gene amplification. As a simple and agnostic liquid biopsy approach, GAPF-seq could fill this technological gap, offering unique cancer-specific SV profiles.

cancer biology↗

bioRxiv2022

TDP 2 modulates the expression of estrogen-responsive oncogenes

With its ligand estrogen, the estrogen receptor (ER) stimulates tumor cell growth by activating a global transcriptional program. This activation involves topoisomerase 2 (TOP2), which resolves topological problems by transiently creating and re-ligating DNA double-strand breaks (DSBs). Recent studies have uncovered the involvement of DNA repair proteins in the repair of TOP2-induced DSBs. These noncanonical repair pathways may serve as backup processes when TOP2 is halted and fails to re-ligate DSBs, but their impact on transcription remains elusive. In this study, we investigated the role of tyrosyl-DNA phosphodiesterase 2 (TDP2), an enzyme that acts for the removal of halted TOP2 from the 5-end of the DNA, in the estrogen-induced transcriptome. Using TDP2-deficient ER-positive cells and mice, we showed that TDP2 regulates the expression of oncogene MYC. MYC induction by estrogen was a very early event (1 hour) and TOP2-dependent. In TDP2-deficient cells, the induction of MYC by estrogen became prolonged and volatile. Bulk and single-cell RNA-seq identified the oncogenes MYC and CCND1 as genes whose estrogen response was regulated by TDP2. These results suggest that TDP2 may play a role in the repair of TOP2-induced DSBs in specific genomic loci and tightly regulates the expression of oncogenes.

molecular biology↗

bioRxiv2022

The molecular consequences of androgen activity in the human breast

The mammary gland has been extensively studied for estrogen and progesterone reactivity, but the molecular effects of androgen in the breast remain largely unexplored. Transgender men are recorded female at birth but identify as male and may undergo gender-affirming androgen therapy to align their physical characteristics and gender identity. Here we perform single cell resolution transcriptome, chromatin, and spatial profiling of androgen treated breasts from transgender men. We find male-biased androgen receptor gene targets are upregulated in cells expressing androgen receptor, and that paracrine signaling drives sex-relevant changes in other cell types. We observe an altered epithelium, shifts in immune populations, and a reduction of capillary vasculature. Finally, we find evidence of the metabolic impact of androgen and identify a gene regulatory network driving androgen-directed fat loss. This work elucidates the molecular consequences of androgen in the human breast at single cell resolution.

genomics↗