Petri Lab

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About 

Our laboratory investigates epitranscriptomic and post-transcriptional mechanisms underlying disease onset and progression. We pair wet-lab experimental workflows with integrated bioinformatics to deliver multiomic approaches to m6A RNA modifications, alternative splicing, and differential transcript usage. Building on research into endocrine therapy resistance in breast cancer and environmental pollutant exposures in metabolic dysfunction-associated steatotic liver disease (MASLD), our program extends these comparative multiomic strategies to other hormone-responsive and metabolic conditions, including endometriosis and polycystic ovary syndrome (PCOS).We combine long-read direct RNA sequencing (Oxford Nanopore), short-read sequencing, single-nucleus transcriptomics, and mass spectrometry with custom computational pipelines integrating transcriptomics, proteomics, and metabolomics. By unifying bench-top biochemistry and dry-lab bioinformatics, we aim to uncover novel epitranscriptomic biomarkers, elucidate RNA-level dysregulation across complex disease models, and identify actionable therapeutic targets at the intersection of endocrinology, toxicology, and RNA biology.

Key Research Areas

  • Core Mechanisms: m6A RNA modifications, alternative splicing, differential transcript usage.
  • MASLD, breast cancer, endometriosis, and PCOS.
  • Methodology: Oxford Nanopore direct RNA-seq, short-read RNA-seq, snRNA-seq, mass spectrometry, and integrated bioinformatic pipelines across multiomics (transcriptomics, proteomics, metabolomics).
  • Hybrid wet-lab biochemistry and dry-lab computational biology.

Current Projects

  • “m6A epitranscriptome drivers of endocrine-resistant breast cancer” funded by a grant from the Office of the Assistant Secretary of Defense for Health Affairs, in the amount of $1,313,309.00, through the Breast Cancer Research Program under Award No. HT9425-23-1-0017: Klinge, C.M., (PI), Clem, B.C. (MPI)
  • NIH 1 R01ES036210-01A1 “RNA modifications in apolipoprotein regulation by environmental exposures” Klinge, C.M., (PI), Cave, M.C. (MPI) 

Team 

Subheaders as needed for roles etc.

Recent Publications

  • Piell, K.M, Vallarta, A.J., Wilt, A.E., Avila-Valdes, B.L., Sumlut, M.H., Goli, N., Petri, B.J., He, L., Zhang, X., Clem, B.F., and Klinge, C.M. Regulation of PSAT1 and PHGDH by m6A in Endocrine-Resistant Breast Cancer Cells.  Biochim Biophys Acta (BBA) Mol. Basis Dis. 1872:168266, 2026.  Epub 15 Apr 2026    PMID: 41997307  doi: https://doi.org/10.1016/j.bbadis.2026.168266
  • Petri, B.J., Piell, K.M, Wahlang, B., Chariker, J.H., Rouchka, E.C., Cave, M.C., and Klinge, C.M.  Long-read isoform sequencing reveals Aroclor1260-induced isoform usage in mouse liver. Genes 17:126 , 2026. Epub 25 Jan 2026 doi:10.3390/genes17020126 
  • Petri, B.J., Piell, K.M., Avila-Valdes, B.L., Stanley, C.G., Winkler, LJ., Brown, J.T., Ulett, R., Sanchez, G., Chariker, J.H., Rouchka, E.C., and Klinge, C.M. Integrated Nanopore and short-read RNA sequencing identifies dysregulation of METTL3- m6A modifications in endocrine therapy- sensitive and resistant breast cancer cells. Functional & Integrative Genomics 25: 149, 2025 Epub 2025 July 9, doi:10.1007/s10142-025-01658-2  PMID: 40632306 
  • Klinge, C.M., (corresponding author); Chariker, J.H., Piell, K.M., Petri, B.J., Rouchka E.C., and Cave, M.C. Polychlorinated biphenyl exposure alters tRNA transcriptome in high fat diet-fed mouse liver. Non-coding RNA 11: 41, 2025.   Epub 2025 May 22 doi: 10.3390/ncrna11030041 PMID 40559619  PMCID: PMC12195632
  • Piell, K.M., Poulton, C.C., Stanley, C.G., Schultz, D.J., and Klinge, C.M. Integrated Metabolomics and Transcriptomics Analysis of Anacardic Acid Inhibition of Breast Cancer Cell Viability. Int. J. Mol. Sci. 25:7044, 2024 Epub. 2024 June 27   PMID: 39000156  PMCID: PMC11241071 DOI: 10.3390/ijms25137044
  • Petri, B.J., Piell, K.M., Xu, J., Cai, L., Rai, S.N., Li, M., Wilkey, D.W., Merchant, M.L., Cave, M.C., and Klinge C.M. Chronic Aroclor 1260 Exposure Alters the Mouse Liver Proteome, Selenoproteins, and Metals in Steatotic Liver Disease. Environ. Toxicol. Pharmacol. 107: 104430, 2024.  Epub. 2024 Mar 27. PMID: 38552755 PMCID: PMC11044900 doi:https://doi.org/10.1016/j.etap.2024.104430 
  • Petri, B.J., Piell, K.M., Wahlang, B., Head, K.Z., Rouchka, E.C., Park, J.W., Hwang, J.Y., Banerjee, M., Cave, M.C., and Klinge C.M. Altered splicing factor and alternative splicing events in a mouse model of diet- and polychlorinated biphenyl-induced liver disease. Environ. Toxicol. Pharmacol. 103: 104260, 2023. Epub. 2023 September 6.  PMID: 37683712 PMCID: PMC10591945   DOI: 10.1016/j.etap.2023.104260
  • Petri, B.J., Cave, M.C., and Klinge, C.M. Changes in m6A in Steatotic Liver Disease.  Genes 14: 1653, 2023. Epub 2023 August 19; doi: 10.3390/genes14081653; PMID: 37628704 PMCID PMC10454815  
  • Petri, B.J., Piell, K.M., Wilt, A., Howser, A.D., Winkler, L., Whitworth, M.R., Valdes, B.L., Lehman, N., Clem, B.F., and Klinge C.M. microRNA Regulation of the Serine Synthesis Pathway in Endocrine-resistant Breast Cancer Cells. Endocrine-Related Cancer 30: e230148, 2023. Epub. 2023 August 1. PMID: 37650685 PMCID: PMC10546957  DOI: 10.1530/ERC-23-0148

  • Petri, B.J. and Klinge, C.M. m6A Readers, Writers, Erasers, and the m6A Epitranscriptome in Breast Cancer. J. Mol. Endocrinol. 70: e220110, 2023. Epub 2022 November 11; DOI: 10.1530/JME-22-0110; PMID: 36367225 PMCID: PMC9790079

    Complete List of Published Work in PubMed

Petri Lab

Biochemistry and Molecular Genetics

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HSC-A, Rm 715

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