Annie Trinh

All Publications

• A tunable, ultrasensitive threshold in enzymatic activity governs the DNA methylation landscape. Biophysical journal Bonsu, K. A., Laszik, N., Trinh, A., Downing, T. L., Read, E. L. 2026; 125 (7): 1802-1819

  Abstract

  DNA methylation is a widely studied epigenetic mark, affecting gene expression and cellular function at multiple levels. DNA methylation in the mammalian genome occurs primarily at cytosine-phosphate-guanine (CpG) dinucleotides, and patterning of the methylation landscape (i.e., the presence or absence of CpG methylation at a given genomic location) exhibits a generally bimodal distribution. Although much is known about the enzymatic writers and erasers of CpG methylation, it is not fully understood how these enzymes, along with genetic, chromatin, and regulatory factors, control the genome-wide methylation landscape. In this study, methylation is analyzed at annotated CpG islands (CGIs) and independent CpGs as a function of their proximity to other CpG substrates. Analysis is aided by a computationally efficient stochastic mathematical model of methylation dynamics, enabling parameterization from data. We find that methylation exhibits a switch-like dependence on local CpG density with a threshold of 7-8 CpGs per 100 bp and a Hill coefficient of 4-5. The threshold and steepness of the switch is modified in cell lines in which key enzymes are knocked out. Modeling further elucidates how enzymatic parameters, including catalytic rates and lengthscales of inter-CpG interaction, tune the properties of the switch. Together, the results support a model in which competition between opposing TET1-3 demethylating enzymes and DNA methyltransferases (DNMT3A/B) results in an ultrasensitive switch, analogous to the protein phosphorylation switch (termed "zero-order ultrasensitivity"). Our study provides insight to the mechanisms underlying establishment and maintenance of bimodal DNA methylation landscapes, and further provides a flexible pipeline for gleaning molecular insights to the cellular methylation machinery across cell-specific, epigenomic data sets.

  View details for DOI 10.1016/j.bpj.2026.03.013

  View details for PubMedID 41814656

• Challenging Reward Structures and Organizational Cultures that Propagate Stem Cell Hyperbole. Stem cell reviews and reports Trinh, A., Turner, L. 2025; 21 (8): 2810-2819

  Abstract

  How science is communicated shapes public understanding of science and informs decision-making by patients, research participants, policymakers, public funding agencies, private philanthropic organizations, and corporations. Responsible science communication is a collective responsibility of scientists. Accurate reporting is also a crucial feature of news media coverage of scientific research. Unfortunately, scientists, journalists, and other parties sometimes make hyperbolic claims that go beyond available evidence and exaggerate the significance of particular research findings. This phenomenon is evident in the rapidly evolving and highly competitive fields of stem cell biology and regenerative medicine, though hyperbolic representations have also been documented in such fields as artificial intelligence, genomics, precision medicine, and synthetic biology. Stem cell hyperbole is shaped and promoted by systemic factors. We highlight the continued significance of responsible communication of stem cell science across news media and social media, especially in an era where there are powerful incentives to make hyperbolic claims. While such norms as truthfulness, accuracy, and accountability might seem self-evident, contemporary incentive structures and organizational cultures play an important role in promoting hyperbolic representations and other inaccurate representations of scientific research. Finally, we propose recommendations for supporting and sustaining research cultures that prioritize honesty and accuracy in science communication and public engagement.

  View details for DOI 10.1007/s12015-025-10955-z

  View details for PubMedID 40820056

  View details for PubMedCentralID PMC12504345

• Methylation pseudotime analysis for label-free profiling of the temporal chromatin landscape with long-read sequencing. bioRxiv : the preprint server for biology Trinh, A., Akhtar, N., Bonsu, K., Laszik, N., Mendelevich, A., Wen, T., Morival, J. L., Diune, K. E., Frazeur, M., Vega, J. E., Gimelbrant, A. A., Read, E. L., Downing, T. L. 2025

  Abstract

  Faithful epigenetic inheritance across cell divisions is essential to maintaining cell identity and involves numerous epigenetic modifications, whose roles in establishing chromatin architecture are less understood. Technological approaches to temporally order epigenetic modifications throughout the cell cycle often face limitations in sequence resolution and rely on potentially damaging mitotic labeling or conversion steps. Herein, we present M ethylation P seudotime A nalysis T hrough read-level H eterogeneity (MPATH), a label- and conversion-free method to infer post-replication DNA strand maturity from methylation patterns across single molecules. We use MPATH to temporally order hydroxymethylation throughout mitotic inheritance, revealing that CpGs within cis-regulatory elements undergo transitions between methylation states at sub-cell-cycle timescales. When applied to long reads generated by NOMe-seq, MPATH uncovered relationships between nucleosome occupancy and DNA maturity. Finally, extension of MPATH to phased reads reveals allele-specific trends in pseudotime distribution associated with X chromosome activity. Our findings suggest that when coupled with multimodal sequencing strategies, MPATH could provide valuable insights into chromatin restoration dynamics.

  View details for DOI 10.1101/2025.03.03.641287

  View details for PubMedID 40161794

  View details for PubMedCentralID PMC11952338

• Targeting the ADPKD methylome using nanoparticle-mediated combination therapy APL BIOENGINEERING Trinh, A., Huang, Y., Shao, H., Ram, A., Morival, J., Wang, J., Chung, E., Downing, T. L. L. 2023; 7 (2): 026111

  Abstract

  DNA methylation aberrancies are found in autosomal dominant polycystic kidney disease (ADPKD), which suggests the methylome to be a promising therapeutic target. However, the impact of combining DNA methylation inhibitors (DNMTi) and ADPKD drugs in treating ADPKD and on disease-associated methylation patterns has not been fully explored. To test this, ADPKD drugs, metformin and tolvaptan (MT), were delivered in combination with DNMTi 5-aza-2'-deoxycytidine (Aza) to 2D or 3D cystic Pkd1 heterozygous renal epithelial cells (PKD1-Het cells) as free drugs or within nanoparticles to enable direct delivery for future in vivo applications. We found Aza synergizes with MT to reduce cell viability and cystic growth. Reduced representation bisulfite sequencing (RRBS) was performed across four groups: PBS, Free-Aza (Aza), Free-Aza+MT (F-MTAza), and Nanoparticle-Aza+MT (NP-MTAza). Global methylation patterns showed that while Aza alone induces a unimodal intermediate methylation landscape, Aza+MT recovers the bimodality reminiscent of somatic methylomes. Importantly, site-specific methylation changes associated with F-MTAza and NP-MTAza were largely conserved including hypomethylation at ADPKD-associated genes. Notably, we report hypomethylation of cancer-associated genes implicated in ADPKD pathogenesis as well as new target genes that may provide additional therapeutic effects. Overall, this study motivates future work to further elucidate the regulatory mechanisms of observed drug synergy and apply these combination therapies in vivo.

  View details for DOI 10.1063/5.0151408

  View details for Web of Science ID 001005215200001

  View details for PubMedID 37305656

  View details for PubMedCentralID PMC10257530

• DNA Methylation Dynamics During Esophageal Epithelial Regeneration Following Repair with Acellular Silk Fibroin Grafts in Rat. Advanced biology Urban, L. A., Li, J., Gundogdu, G., Trinh, A., Shao, H., Nguyen, T., Mauney, J. R., Downing, T. L. 2023; 7 (5): e2200160

  Abstract

  Esophageal pathologies such as atresia and benign strictures often require surgical reconstruction with autologous tissues to restore organ continuity. Complications such as donor site morbidity and limited tissue availability have spurred the development of acellular grafts for esophageal tissue replacement. Acellular biomaterials for esophageal repair rely on the activation of intrinsic regenerative mechanisms to mediate de novo tissue formation at implantation sites. Previous research has identified signaling cascades involved in neoepithelial formation in a rat model of onlay esophagoplasty with acellular silk fibroin grafts, including phosphoinositide 3-kinase (PI3K), and protein kinase B (Akt) signaling. However, it is currently unknown how these mechanisms are governed by DNA methylation (DNAme) during esophageal wound healing processes. Reduced-representation bisulfite sequencing is performed to characterize temporal DNAme dynamics in host and regenerated tissues up to 1 week postimplantation. Overall, global hypermethylation is observed at postreconstruction timepoints and an inverse correlation between promoter DNAme and the expression levels of differentially expressed proteins during regeneration. Site-specific hypomethylation targets genes associated with immune activation, while hypermethylation occurs within gene bodies encoding PI3K-Akt signaling components during the tissue remodeling period. The data provide insight into the epigenetic mechanisms during esophageal regeneration following surgical repair with acellular grafts.

  View details for DOI 10.1002/adbi.202200160

  View details for PubMedID 36658732

  View details for PubMedCentralID PMC10401397

• The impact of age-related hypomethylated DNA on immune signaling upon cellular demise. Trends in immunology Urban, L. A., Trinh, A., Pearlman, E., Siryaporn, A., Downing, T. L. 2021; 42 (6): 464-468

  Abstract

  Aging is associated with decreased antigen-specific immunity and increased chronic inflammation. While DNA-sensing pathways might be involved, the molecular factors underlying these age-related aberrancies in immune signaling are unclear. Here, we consider the potential role of aging-induced hypomethylated DNA as a putative stimulant of age-associated inflammation.

  View details for DOI 10.1016/j.it.2021.04.005

  View details for PubMedID 33994111

  View details for PubMedCentralID PMC9650629

• Biophysical and epigenetic regulation of cancer stemness, invasiveness and immune action. Current tissue microenvironment reports Veerasubramanian, P. K., Trinh, A., Akhtar, N., Liu, W. F., Downing, T. L. 2020; 1 (4): 277-300

  Abstract

  The tumor microenvironment (TME) is an amalgam of multiple dysregulated biophysical cues that can alter cellular behavior through mechanotransductive signaling and epigenetic modifications. Through this review, we seek to characterize the extent of biophysical and epigenetic regulation of cancer stemness and tumor-associated immune cells in order to identify ideal targets for cancer therapy.Recent studies have identified cancer stemness and immune action as significant contributors to neoplastic disease, due to their susceptibility to microenvironmental influences. Matrix stiffening, altered vasculature, and resultant hypoxia within the TME can influence cancer stem cell (CSC) and immune cell behavior, as well as alter the epigenetic landscapes involved in cancer development.This review highlights the importance of aberrant biophysical cues in driving cancer progression through altered behavior of CSCs and immune cells, which in turn sustains further biophysical dysregulation. We examine current and potential therapeutic approaches that break this self-sustaining cycle of disease progression by targeting the presented biophysical and epigenetic signatures of cancer. We also summarize strategies including the normalization of the TME, targeted drug delivery, and inhibition of cancer-enabling epigenetic players.

  View details for DOI 10.1007/s43152-020-00021-w

  View details for PubMedID 33817661

  View details for PubMedCentralID PMC8015331