The paper identifies a conserved cis-acting element, REX, that enables extreme long-range enhancer-promoter interactions in mammals by increasing the genomic interaction range of enhancers.

Nature · Jul 2, 2025Peer-reviewedGenomics

APOE Christchurch enhances a disease-associated microglial response to plaque but suppresses response to tau pathology

Kristine M. Tran, Nellie E. Kwang, Claire Ann Butler, Ángela Gómez-Arboledas, Shimako Kawauchi, Cassandra Mar, Donna Chao, Rocio A. Barahona, Celia Da Cunha, Kate Inman Tsourmas, Zechuan Shi, Shuling Wang, Sherilyn Collins, Amber Walker, Kai‐Xuan Shi, , Kim N. Green

The paper investigates how the APOE Christchurch variant affects microglial responses to amyloid and tau pathology in mouse models, finding it enhances plaque-related responses but suppresses tau-related inflammation.

Molecular Neurodegeneration · Jan 22, 2025Peer-reviewedNeuroscience

Rapid and Quantitative Functional Interrogation of Human Enhancer Variant Activity in Live Mice

Ethan W. Hollingsworth, Taryn Audrey Liu, Joshua A. Alcantara, Cindy X. Chen, Sandra H. Jacinto, Evgeny Z. Kvon

This paper introduces dual-enSERT, a tool for rapidly measuring enhancer variant activity in live mice, and shows it can identify shared genetic mechanisms in non-coding variant pathogenesis.

Nature Communications · Jan 6, 2025Peer-reviewedGenomics

Molecular Signatures for Microbe-Associated Colorectal Cancers

Ibrahim M. Sayed, Daniella T. Vo, Joshua A. Alcantara, Kaili Inouye, Rama F. Pranadinata, Linda Luo, Clement Richard Boland, Nidhi P. Goyal, Dennis John Kuo, Sherry C. Huang, Debashis Sahoo, Pradipta Ghosh, Soumita Das

The paper identifies a Microbe-Associated Colorectal Cancer Signature (MACS) induced by Fusobacterium nucleatum in genetically predisposed hosts, linking microbial infection to early CRC initiation.

bioRxiv · May 26, 2024 · PreprintMicrobiology

Systematic phenotyping and characterization of the 3xTg-AD mouse model of Alzheimer's Disease

Dominic I. Javonillo, Kristine M. Tran, Jimmy Phan, Edna E. Hingco, Enikö A. Kramár, Celia da Cunha, Stefânia Forner, Shimako Kawauchi, Giedre Milinkeviciute, Ángela Gómez-Arboledas, Jonathan C. Neumann, Crystal E. Banh, Michelle Dieu Thao Huynh, Dina P. Matheos, Narges Rezaie, , Frank M. LaFerla

This paper characterizes the 3xTg-AD mouse model of Alzheimer's Disease across its lifespan and compares it with the 5xFAD model to assess pathology and model drift.

Frontiers in Neuroscience · Jan 24, 2022Peer-reviewedNeuroscience

Systematic Phenotyping and Characterization of the 5xFAD mouse model of Alzheimer's Disease

Stefânia Forner, Shimako Kawauchi, Gabriela Balderrama-Gutierrez, Enikö A. Kramár, Dina P. Matheos, Jimmy Phan, Dominic I. Javonillo, Kristine M. Tran, Edna E. Hingco, Celia da Cunha, Narges Rezaie, Joshua A. Alcantara, David Baglietto‐Vargas, Camden S. Jansen, Jonathan C. Neumann, , Kim N. Green

The paper performs a comprehensive phenotypic analysis of the 5xFAD mouse model across its lifespan, identifying novel age-related pathological features.

Scientific Data · Oct 15, 2021Peer-reviewedNeuroscience