Lan Lin, PhD
Assistant Professor of Pathology and Laboratory Medicine
University of Pennsylvania Perelman School of Medicine
Contact InformationThe Children's Hospital of Philadelphia
Perelman School of Medicine, University of Pennsylvania
Colket Translational Research Building 9052
3501 Civic Center Blvd
Philadelphia, PA, 19104
Office: 215-590-1966
Email: linlan@chop.edu
Research Expertise
The Lin Lab studies RNA modifications (“epitranscriptomics”) in human health and disease. Post-transcriptional RNA processing and modifications are key mechanisms for gene regulation and functional diversity in eukaryotic cells. We develop and apply high-throughput sequencing strategies and transcriptome engineering technologies to study the regulation and function of RNA modifications, including alternative splicing, A-to-I RNA editing, and m6A RNA methylation.
Long-read sequencing technologies are revolutionizing genomic research. These technologies have exciting transcriptomic applications, allowing direct resolution of transcript isoform structures and interrogation of repetitive RNA sequences. Using state-of-the-art nanopore long-read sequencing platform, we develop and apply new strategies to discover and quantify diverse RNA species in bulk tissues and single cells. By comparing the repertoire of full-length RNA transcripts between normal and diseased states (e.g. tumors and rare Mendelian disorders), we hope to discover molecular markers and develop RNA guided diagnostics and therapeutics for these diseases.
RNA editing has emerged as an important and widespread mechanism for generating transcriptome diversity in eukaryotic cells. Aberrant RNA editing has been implicated in a variety of diseases including neurological diseases and cancer. The most abundant type of RNA editing is the A-to-I RNA editing (the deamination of adenosine to inosine) mediated by the ADAR family of RNA editing enzymes. We combine genomic, bioinformatic, and molecular approaches to study the regulation, genetic variation, and function of A-to-I RNA editing, as well as the roles of RNA editing in shaping complex traits and diseases.
N6-methyladenosine (m6A) is an abundant and dynamically regulated class of RNA base modification in mRNAs and non-coding RNAs. It affects multiple aspects of RNA metabolism and controls developmental transitions by regulating mRNA decay and translation. We are developing sensitive sequencing methods to detect RNA m6A methylation in a wider array of clinical and biological samples and using transcriptome engineering technologies to investigate the regulatory and functional consequences of m6A methylation.
Education
B.S. (Biotechnology), Beijing University, 2001
Ph.D. (Cellular and Molecular Pathology), University of California, Los Angeles, 2007
Specialty Certification
Postgraduate Training
Postdoctoral Fellow, University of Iowa, Internal Medicine, 2007-2011
Awards and Honors
Student Travel Award, Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, 2004
Student Travel Award, Department of Pathology & Laboratory Mediicne, David Geffen School of Medicine, UCLA, 2005
Student Travel Award, American Society of Hematology 47th Annual Meeting, 2005
1st Prize, PathFinders Poster Competition, Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, UCLA, 2005
Dissertation Year Fellowship, UCLA, 2006-2007
Postdoctoral Travel Award, American Society for Biochemistry and Molecular Biology, 2009 Annual Meeting, 2009
Postdoctoral Travel Award, American Society for Biochemistry and Molecular Biology, 2010 Annual Meeting, 2010
Klaus Hummeler High-Impact Publication Award, CHOP, 2025
Memberships and Professional Organizations
RNA Society, 2024 - Present
American Society of Human Genetics, 2024 - Present
American Society of Gene & Cell Therapy, 2024 - Present
Web Links
Selected Publications
ATLAS-seq: A microfluidic single-cell TCR screen for antigen-reactive TCRs
Luo S, Notaro A, Lin L, Nature Commun, 2024
Long-read RNA sequencing: a transformative technology for exploring transcriptome complexity in human diseases
Ament XH, DeBruyne N, Wang F, Lin L, Molecular Therapy, 2024
Splicing defects in rare diseases: transcriptomics and machine learning strategies towards genetic diagnosis
Wang R, Helbig I, Edmondson AC, Lin L, Xing Y, Briefings in Bioinformatics 24(5): bbad284, 2023, PMID:37580177
TEQUILA-seq: a versatile and low-cost method for targeted long-read RNA sequencing
Wang F, Xu Y, Wang R, Zhang B, Smith N, Notaro A, Gaerlan S, Kutschera E, Kadash-Edmondson K, Xing Y, Lin L, Nature Commun 14(4760): , 2023, PMID:37553321
ESPRESSO: Robust discovery and quantification of transcript isoforms from error-prone long-read RNA-seq data
Gao Y+*, Wang F*, Wang R, Kutschera E, Xu Y, Xie S, Wang Y, Kadash-Edmondson K, Lin L, Xing Y+, Science Advances 9(3): , 2023, PMID:36662851
m6A deposition is regulated by PRMT1-mediated arginine methylation of METTL14 in its disordered C-terminal region
Wang Z, Pan Z, Adhikari S, Harada BT, Shen L, Yuan W, Abeywardana T, Al-Hadid Q, Stark JM, He C, Lin L*, Yang Y*., EMBO J 40(5): , 2021, PMID:33459381
isoCirc catalogs full-length circular RNA isoforms in human transcriptomes
Xin R, Gao Y, Gao Y, Wang R, Kadash-Edmondson KE, Liu B, Wang Y, Lin L, Xing Y., Nat Commun 12(): 266, 2021, PMID:33436621
The Natural Compound Neobractatin Induces Cell Cycle Arrest by Regulating E2F1 and Gadd45α.
Zheng Z, Wu M, Zhang J, Fu W, Xu N, Lao Y, Lin L*, Xu H*, Frontiers in Oncology 9(): 654, 2019, PMID:31380287
A panoramic view of RNA modifications: exploring new frontiers.
Zhang Z, Park E, Lin L, Xing Y,, Genome Biology 19(11): , 2018, PMID:29382368
The expanding landscape of alternative splicing variation in human populations
Park E, Pan Z, Zhang Z, Lin L, Xing Y, Am J Hum Genet 102(1): 11-26, 2018
