Targetable lesions and proteomes predict therapy sensitivity through disease evolution in pediatric acute lymphoblastic leukemia
Nature Communications
DOI: 10.1038/s41467-023-42701-9
2023
SQuAPP—simple quantitative analysis of proteins and PTMs
Bioinformatics
Enes K Ergin and Anuli C Uzozie and Siyuan Chen and Ye Su and Philipp F Lange
DOI: 10.1093/bioinformatics/btac628
10/2022
Pathogenic BRCA1 variants disrupt PLK1-regulation of mitotic spindle orientation
Nature Communications
Zhengcheng He and Ryan Ghorayeb and Susanna Tan and Ke Chen and Amanda C. Lorentzian and Jack Bottyan and Syed Mohammed Musheer Aalam and Miguel Angel Pujana and Philipp F. Lange and Nagarajan Kannan and Connie J. Eaves and Christopher A. Maxwell
DOI: 10.1038/s41467-022-29885-2
04/2022
Multi-omic profiling of the leukemic microenvironment shows bone marrow interstitial fluid is distinct from peripheral blood plasma
Lorenz Nierves and Jian Guo and Siyuan Chen and Janice Tsui and Anuli Uzozie and Jonathan W. Bush and Tao Huan and Philipp F. Lange
DOI: 10.1101/2022.03.30.486272
04/2022
Persistence of targetable lesions, predicted therapy sensitivity and proteomes through disease evolution in pediatric acute lymphoblastic leukemia
Amanda C. Lorentzian and Jenna Rever and Enes K. Ergin and Meiyun Guo and Neha M. Akella and Nina Rolf and C. James Lim and Gregor S.D. Reid and Christopher A. Maxwell and Philipp F. Lange
DOI: 10.1101/2022.03.04.22271927
03/2022
Sensitive Identification of Known and Unknown Protease Activities by Unsupervised Linear Motif Deconvolution
Analytical Chemistry
Anuli C. Uzozie and Theodore G. Smith and Siyuan Chen and Philipp F. Lange
DOI: 10.1021/acs.analchem.1c04937
02/2022
A cross-standardized flow cytometry platform to assess phenotypic stability in precursor B-cell acute lymphoblastic leukemia (B-ALL) xenografts
Cytometry Part A
Nina Rolf and Lorraine Y. T. Liu and Angela Tsang and Philipp F. Lange and Chinten James Lim and Christopher A. Maxwell and Suzanne M. Vercauteren and Gregor S. D. Reid
DOI: 10.1002/cyto.a.24473
01/2022
HUNTER: Sensitive Automated Characterization of Proteolytic Systems by N Termini Enrichment from Microscale Specimen
Methods in Molecular Biology
DOI: 10.1007/978-1-0716-2124-0_8
2022
Shift of the insoluble content of the proteome in aging mouse brain
bioRxiv
Molzahn, C. and Kuechler, E. and Zemlyankina, I. and Nieves, L. and Ali, T. and Cole, G. and Wang, J. and Albu, R.F. and Zhu, M. and Cashman, N. and Gilch, S. and Karsan, A. and Lange, P.F. and Gsponer, J. and Mayor, T.
DOI: 10.1101/2022.12.13.520290
2022
Modification of BRCA1-associated breast cancer risk by HMMR overexpression
Nature Communications
Mateo, F. and He, Z. and Mei, L. and de Garibay, G.R. and Herranz, C. and García, N. and Lorentzian, A. and Baiges, A. and Blommaert, E. and Gómez, A. and Mirallas, O. and Garrido-Utrilla, A. and Palomero, L. and Espín, R. and Extremera, A.I. and Soler-Monsó, M.T. and Petit, A. and Li, R. and Brunet, J. and Chen, K. and Tan, S. and Eaves, C.J. and McCloskey, C. and Hakem, R. and Khokha, R. and Lange, P.F. and Lázaro, C. and Maxwell, C.A. and Pujana, M.A.
DOI: 10.1038/s41467-022-29335-z
2022
Isolation of Detergent Insoluble Proteins from Mouse Brain Tissue for Quantitative Analysis Using Data Independent Acquisition (DIA)
Methods in Molecular Biology
DOI: 10.1007/978-1-0716-2124-0_3
2022
Detectability of Biotin Tags by LC-MS/MS
Journal of Proteome Research
Nierves, L. and Lange, P.F.
DOI: 10.1021/acs.jproteome.0c01049
2021
Robust unsupervised deconvolution of linear motifs characterizes 68 protein modifications at proteome scale
Scientific Reports
Smith, T.G. and Uzozie, A.C. and Chen, S. and Lange, P.F.
DOI: 10.1038/s41598-021-01971-3
2021
PDX models reflect the proteome landscape of pediatric acute lymphoblastic leukemia but divert in select pathways
Journal of Experimental and Clinical Cancer Research
Uzozie, A.C. and Ergin, E.K. and Rolf, N. and Tsui, J. and Lorentzian, A. and Weng, S.S.H. and Nierves, L. and Smith, T.G. and Lim, C.J. and Maxwell, C.A. and Reid, G.S.D. and Lange, P.F.
DOI: 10.1186/s13046-021-01835-8
2021
Fold-Change Compression: An Unexplored but Correctable Quantitative Bias Caused by Nonlinear Electrospray Ionization Responses in Untargeted Metabolomics
Analytical Chemistry
Yu, H. and Xing, S. and Nierves, L. and Lange, P.F. and Huan, T.
DOI: 10.1021/acs.analchem.0c00246
2020
Multi-Omic Approach to Identify Phenotypic Modifiers Underlying Cerebral Demyelination in X-Linked Adrenoleukodystrophy
Frontiers in Cell and Developmental Biology
Richmond, P.A. and van der Kloet, F. and Vaz, F.M. and Lin, D. and Uzozie, A. and Graham, E. and Kobor, M. and Mostafavi, S. and Moerland, P.D. and Lange, P.F. and van Kampen, A.H.C. and Wasserman, W.W. and Engelen, M. and Kemp, S. and van Karnebeek, C.D.M.
DOI: 10.3389/fcell.2020.00520
2020
Tumor Variant Identification That Accounts for the Unique Molecular Landscape of Pediatric Malignancies
JNCI Cancer Spectrum
Amanda Lorentzian and Jaclyn A Biegel and D Gigi Ostrow and Nina Rolf and Chi-Chao Liu and S Rod Rassekh and Rebecca J Deyell and Timothy Triche and Kirk R Schultz and Jacob Rozmus and Gregor S D Reid and C James Lim and Philipp F Lange and Christopher A Maxwell
DOI: 10.1093/jncics/pky079
01/2019
Origins and clinical relevance of proteoforms in pediatric malignancies
Expert Review of Proteomics
Lorentzian, A. and Uzozie, A. and Lange, P.F.
DOI: 10.1080/14789450.2019.1575206
2019
Sensitive determination of proteolytic proteoforms in limited microscale proteome samples
Molecular and Cellular Proteomics
Weng, S.S.H. and Demir, F. and Ergin, E.K. and Dirnberger, S. and Uzozie, A. and Tuscher, D. and Nierves, L. and Tsui, J. and Huesgen, P.F. and Lange, P.F.
DOI: 10.1074/mcp.TIR119.001560
2019
HMMR acts in the PLK1-dependent spindle positioning pathway and supports neural development
eLife
Connell, M. and Chen, H. and Jiang, J. and Kuan, C.-W. and Fotovati, A. and Chu, T.L.H. and He, Z. and Lengyell, T.C. and Li, H. and Kroll, T. and Li, A.M. and Goldowitz, D. and Frappart, L. and Ploubidou, A. and Patel, M.S. and Pilarski, L.M. and Simpson, E.M. and Lange, P.F. and Allan, D.W. and Maxwell, C.A.
DOI: 10.7554/eLife.28672
2017
TAILS N-Terminomics and Proteomics Show Protein Degradation Dominates over Proteolytic Processing by Cathepsins in Pancreatic Tumors
Cell Reports
Prudova, A. and Gocheva, V. and auf dem Keller, U. and Eckhard, U. and Olson, O.C. and Akkari, L. and Butler, G.S. and Fortelny, N. and Lange, P.F. and Mark, J.C. and Joyce, J.A. and Overall, C.M.
DOI: 10.1016/j.celrep.2016.06.086
2016
Active site specificity profiling of the matrix metalloproteinase family: Proteomic identification of 4300 cleavage sites by nine MMPs explored with structural and synthetic peptide cleavage analyses
Matrix Biology
Eckhard, U. and Huesgen, P.F. and Schilling, O. and Bellac, C.L. and Butler, G.S. and Cox, J.H. and Dufour, A. and Goebeler, V. and Kappelhoff, R. and auf dem Keller, U. and Klein, T. and Lange, P.F. and Marino, G. and Morrison, C.J. and Prudova, A. and Rodriguez, D. and Starr, A.E. and Wang, Y. and Overall, C.M.
DOI: 10.1016/j.matbio.2015.09.003
2016
Active site specificity profiling datasets of matrix metalloproteinases (MMPs) 1, 2, 3, 7, 8, 9, 12, 13 and 14
Data in Brief
Eckhard, U. and Huesgen, P.F. and Schilling, O. and Bellac, C.L. and Butler, G.S. and Cox, J.H. and Dufour, A. and Goebeler, V. and Kappelhoff, R. and auf dem Keller, U. and Klein, T. and Lange, P.F. and Marino, G. and Morrison, C.J. and Prudova, A. and Rodriguez, D. and Starr, A.E. and Wang, Y. and Overall, C.M.
DOI: 10.1016/j.dib.2016.02.036
2016
Proteome TopFIND 3.0 with TopFINDer and PathFINDer: Database and analysis tools for the association of protein termini to pre- and post-translational events
Nucleic Acids Research
Fortelny, N. and Yang, S. and Pavlidis, P. and Lange, P.F. and Overall, C.M.
DOI: 10.1093/nar/gku1012
2015
COSMC knockdown mediated aberrant O-glycosylation promotes oncogenic properties in pancreatic cancer
Molecular Cancer
Hofmann, B.T. and Schlüter, L. and Lange, P. and Mercanoglu, B. and Ewald, F. and Fölster, A. and Picksak, A.-S. and Harder, S. and El Gammal, A.T. and Grupp, K. and Güngör, C. and Drenckhan, A. and Schlüter, H. and Wagener, C. and Izbicki, J.R. and Jücker, M. and Bockhorn, M. and Wolters-Eisfeld, G.
DOI: 10.1186/s12943-015-0386-1
2015
Active Site Specificity Profiling of the Matrix Metalloproteinase Family: Proteomic Identification of 4,300 Cleavage Sites by MMPs 1, 2, 3, 7, 8, 9, 12, 13, and 14.
2015
LysargiNase and tryptic digest of MDA-MB 231 cell lysates
2014
Network Analyses Reveal Pervasive Functional Regulation Between Proteases in the Human Protease Web
PLoS Biology
Fortelny, N. and Cox, J.H. and Kappelhoff, R. and Starr, A.E. and Lange, P.F. and Pavlidis, P. and Overall, C.M.
DOI: 10.1371/journal.pbio.1001869
2014
Ensembles of protein termini and specific proteolytic signatures as candidate biomarkers of disease
Proteomics - Clinical Applications
Huesgen, P.F. and Lange, P.F. and Overall, C.M.
DOI: 10.1002/prca.201300104
2014
Annotating N termini for the human proteome project: N termini and Na-acetylation status differentiate stable cleaved protein species from degradation remnants in the human erythrocyte proteome
Journal of Proteome Research
Lange, P.F. and Huesgen, P.F. and Nguyen, K. and Overall, C.M.
DOI: 10.1021/pr401191w
2014
Characterization of LysargiNase for use in phosphoproteomics experiments, partII
2014
LysargiNase mirrors trypsin for protein C-terminal and methylation-site identification
Nature Methods
Huesgen, P.F. and Lange, P.F. and Rogers, L.D. and Solis, N. and Eckhard, U. and Kleifeld, O. and Goulas, T. and Gomis-Rüth, F.X. and Overall, C.M.
DOI: 10.1038/nmeth.3177
2014
Macrophage matrix metalloproteinase-12 dampens inflammation and neutrophil influx in arthritis
Cell Reports
Bellac, C.L. and Dufour, A. and Krisinger, M.J. and Loonchanta, A. and Starr, A.E. and auf dem Keller, U. and Lange, P.F. and Goebeler, V. and Kappelhoff, R. and Butler, G.S. and Burtnick, L.D. and Conway, E.M. and Roberts, C.R. and Overall, C.M.
DOI: 10.1016/j.celrep.2014.09.006
2014
Proteomic Amino-Termini Profiling Reveals Targeting Information for Protein Import into Complex Plastids
PLoS ONE
Huesgen, P.F. and Alami, M. and Lange, P.F. and Foster, L.J. and Schröder, W.P. and Overall, C.M. and Green, B.R.
DOI: 10.1371/journal.pone.0074483
2013
Protein TAILS: When termini tell tales of proteolysis and function
Current Opinion in Chemical Biology
Lange, P.F. and Overall, C.M.
DOI: 10.1016/j.cbpa.2012.11.025
2013
TopFIND 2.0 - Linking protein termini with proteolytic processing and modifications altering protein function
Nucleic Acids Research
Lange, P.F. and Huesgen, P.F. and Overall, C.M.
DOI: 10.1093/nar/gkr1025
2012
Towards kit-like 18F-labeling of marimastat, a noncovalent inhibitor drug for in vivo PET imaging cancer associated matrix metalloproteases
MedChemComm
Li, Y. and Ting, R. and Harwig, C.W. and Auf Dem Keller, U. and Bellac, C.L. and Lange, P.F. and Inkster, J.A.H. and Schaffer, P. and Adam, M.J. and Ruth, T.J. and Overall, C.M. and Perrin, D.M.
DOI: 10.1039/c1md00117e
2011
TopFIND, a knowledgebase linking protein termini with function
Nature Methods
Lange, P.F. and Overall, C.M.
DOI: 10.1038/nmeth.1669
2011
Novel matrix metalloproteinase inhibitor [18F]marimastat- aryltrifluoroborate as a probe for in vivo positron emission tomography imaging in cancer
Cancer Research
Auf Dem Keller, U. and Bellac, C.L. and Li, Y. and Lou, Y. and Lange, P.F. and Ting, R. and Harwig, C. and Kappelhoff, R. and Dedhar, S. and Adam, M.J. and Ruth, T.J. and Bénard, F. and Perrin, D.M. and Overall, C.M.
DOI: 10.1158/0008-5472.CAN-10-1584
2010
ClC-7 requires Ostm1 as a beta-subunit to support bone resorption and lysosomal function
GBM Annual Spring meeting Mosbach 2007
Jens C. Fuhrmann and Philipp F. Lange and Lena Wartosch and Thomas J. Jentsch
DOI: 10.1240/sav_gbm_2007_m_001701
03/2007
ClC-7 requires Ostm1 as a ß-subunit to support bone resorption and lysosomal function
Nature
DOI: 10.1038/nature04535
2006