Research Profile

John LaCava, Ph.D.

Group Leader, Associate Professor, European Research Institute for the Biology of Ageing
Research Associate Professor, The Rockefeller University
Managing Director, B13LOGY LLC

Emerging Lines of Investigation (select examples)

Major Funding (≥ $50k, previous 5 years)

2022

LINE-1 expression in cancer correlates with p53 mutation, copy number alteration, and S phase checkpoint. PNAS. DOI: 10.1073/pnas.2115999119

Targeting DNA topoisomerases or checkpoint kinases results in an overload of chaperone systems, triggering aggregation of a metastable subproteome. eLife. DOI: 10.7554/eLife.70726


2021

IgG and IgA autoantibodies against L1 ORF1p expressed in granulocytes correlate with granulocyte consumption and disease activity in pediatric systemic lupus erythematosus. Arthritis Research & Therapy. DOI: 10.1186/s13075-021-02538-3


2020

Affinity proteomic dissection of the human nuclear cap-binding complex interactome. Nucleic Acids Research. DOI: 10.1093/nar/gkaa743

NCBP3 positively impacts mRNA biogenesis. Nucleic Acids Research. DOI: 10.1093/nar/gkaa744

National Cancer Institute Think-Tank Meeting Report on Proteomic Cartography and Biomarkers at the Single-Cell Level: Interrogation of Premalignant Lesions. Journal of Proteome Research. DOI: 10.1021/acs.jproteome.0c00021

LINE-1 ORF2p expression is nearly imperceptible in human cancers. Mobile DNA. DOI: 10.1186/s13100-019-0191-2


2019

To the editor in reply to Dr. Crow’s letter. Arthritis Rheumatology. DOI: 10.1002/art.41104

High prevalence and disease correlation of autoantibodies against p40 encoded by long interspersed nuclear elements (LINE-1) in systemic lupus erythematosus. Arthritis & Rheumatology. DOI: 10.1002/art.41054

Identification of RNase-sensitive LINE-1 Ribonucleoprotein Interactions by Differential Affinity Immobilization. Bio-protocol. DOI: 10.21769/BioProtoc.3200

RNA Binding Proteins as Regulators of Retrotransposon‐Induced Exonization. Bioessays. DOI: 10.1002/bies.201800263


2018

Targeting the CALR Interactome in Myeloproliferative Neoplasms. JCI Insight. DOI 10.1172/jci.insight.122703

Polycomb Complexes Associate with Enhancers and Promote Oncogenic Transcriptional Programs in Cancer through Multiple Mechanisms. Nature Communications. DOI: 10.1038/s41467-018-05728-x

Functions of unconventional mammalian translational GTPases GTPBP1 and GTPBP2. Genes & Development. DOI: 10.1101/gad.314724.118

Dissection of affinity captured LINE-1 macromolecular complexes. eLife. DOI: 10.7554/eLife.30094

LINE-1 protein localization and functional dynamics during the cell cycle. eLife. DOI: 10.7554/eLife.30058

Characterizing ZC3H18, a multi-domain protein at the interface of RNA production and destruction decisions. Cell Reports. DOI: 10.1016/j.celrep.2017.12.037


2017

Tumor suppressor NPRL2 induces ROS production and DNA damage response. Scientific Reports. DOI: 10.1038/s41598-017-15497-0

The Polycomb group protein CBX6 is an essential regulator of embryonic stem cell identity. Nature Communications. DOI: 10.1038/s41467-017-01464-w

RNA Degradation Assay Using RNA Exosome Complexes, Affinity-purified from HEK-293 Cells. Bio-protocol. DOI: 10.21769/BioProtoc.2239

Affinity Purification of the RNA Degradation Complex, the Exosome, from HEK-293 Cells. Bio-protocol. DOI: 10.21769/BioProtoc.2238


2016

Purification and Analysis of Endogenous Human RNA Exosome Complexes. RNA. DOI: 10.1261/rna.057760.116

Protein complex affinity capture from cryomilled mammalian cells. Journal of Visualized Experiments. DOI: 10.3791/54518


2015

Rapid, Optimized Interactomic Screening. Nature Methods. DOI: 10.1038/nmeth.3395

Affinity proteomics to study endogenous protein complexes: Pointers, pitfalls, preferences and perspectives. BioTechniques. DOI: 10.2144/000114262


2014

Expression and detection of LINE-1 ORF-encoded proteins. Mobile Genetic Elements. DOI: 10.4161/mge.29319


2013

The human cap-binding complex is functionally connected to the nuclear RNA exosome. Nature Structural & Molecular Biology. DOI: 10.1038/nsmb.2703

Affinity proteomics reveals human host factors implicated in discrete stages of LINE-1 retrotransposition. Cell. DOI: 10.1016/j.cell.2013.10.021

Improved native isolation of endogenous Protein A-tagged protein complexes. BioTechniques. DOI: 10.2144/000114012


2012

Improved methodology for the affinity isolation of human protein complexes expressed at near endogenous levels. BioTechniques. DOI: 10.2144/000113864


2006

RNA-quality control by the exosome. Nature Reviews Molecular Cell Biology. DOI: 10.1038/nrm1964


2005

RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell. DOI: 10.1016/j.cell.2005.04.029

2023

Affinity-Based Interactome Analysis of Endogenous LINE-1 Macromolecules. In M.R. Branco & A. de Mendoza Soler (Eds.) Transposable Elements: Methods and Protocols. Springer. DOI: 10.1007/978-1-0716-2883-6_12


2020

The Eukaryotic Exosome: Methods and Protocols. Methods in Molecular Biology Series (Springer). Vol: 2062. Eds. LaCava, J & Vaňáčová, Š. DOI: 10.1007/978-1-4939-9822-7

Affinity Proteomic Analysis of the Human Exosome and Its Cofactor Complexes. In J. LaCava & Š. Vaňáčová (Eds.), The Eukaryotic RNA Exosome: Methods and Protocols. Springer. DOI: 10.1007/978-1-4939-9822-7_15


2016

Protein Complex Purification by Affinity Capture. In B. Andrews, C. Boone, T. Davis, & S. Fields (Eds.), Budding Yeast: A Laboratory Manual. Cold Spring Harbor Laboratory Press. DOI: 10.1101/pdb.top077545. Includes 3 companion protocols: DOI: 10.1101/pdb.prot087932; DOI: 10.1101/pdb.prot087940; DOI: 10.1101/pdb.prot087957

Characterization of L1-RNPs. 2016. In J.L. Garcia (Ed.), Transposons and Retrotransposons: Methods and Protocols. Springer. DOI: 10.1007/978-1-4939-3372-3_20

2015

Oroskar, A.A., A.R. Oroskar, J.P. LaCava, & M.P. Rout . 2015. Apparatus and Method for Parallel Collection and Analysis of the Proteome and Complex Compositions. US Patent No. 9,084,994.