Advances in mass spectrometry(MS)have enabled high-throughput analysis of proteomes in biological systems.The state-of-the-art MS data analysis relies on database search algorithms to quantify proteins by identifying ...Advances in mass spectrometry(MS)have enabled high-throughput analysis of proteomes in biological systems.The state-of-the-art MS data analysis relies on database search algorithms to quantify proteins by identifying peptide–spectrum matches(PSMs),which convert mass spectra to peptide sequences.Different database search algorithms use distinct search strategies and thus may identify unique PSMs.However,no existing approaches can aggregate all user-specified database search algorithms with a guaranteed increase in the number of identified peptides and a control on the false discovery rate(FDR).To fill in this gap,we proposed a statistical framework,Aggregation of Peptide Identification Results(APIR),that is universally compatible with all database search algorithms.Notably,under an FDR threshold,APIR is guaranteed to identify at least as many,if not more,peptides as individual database search algorithms do.Evaluation of APIR on a complex proteomics standard dataset showed that APIR outpowers individual database search algorithms and empirically controls the FDR.Real data studies showed that APIR can identify disease-related proteins and post-translational modifications missed by some individual database search algorithms.The APIR framework is easily extendable to aggregating discoveries made by multiple algorithms in other high-throughput biomedical data analysis,e.g.,differential gene expression analysis on RNA sequencing data.The APIR R package is available at https://github.com/yiling0210/APIR.展开更多
This year （2018） marks the 60th anniversary of the ＂central dogma＂, summarized as ＂DNA makes RNA makes protein＂, which was originally proposed by Francis Crick in 1958. Three years later, messenger RNA was ident...This year （2018） marks the 60th anniversary of the ＂central dogma＂, summarized as ＂DNA makes RNA makes protein＂, which was originally proposed by Francis Crick in 1958. Three years later, messenger RNA was identified as the template of protein synthesis. After 60 years of discovery, including discovery of the split nature of eukaryotic genes （Le., splicing）, it becomes evident that messenger RNAs are not merely messengers, but a hub of co- and post-transcriptional regulation, which is fundamental to amplify the complexity encoded in the genome of higher eukaryotic organisms. The mature forms of RNA of protein-coding genes and their abundance have to be tightly regulated through multiple steps of sophisticated processing, including capping, splicing and polyadenylation. In addition, their function also critically depends on proper localization -- sometimes trafficking to the remote parts of the cell such as dendrites and axons of neurons -- and proper control of their stability. Furthermore, thousands of long and small noncoding RNAs are produced to play a wide range of roles in gene regulation. From our perspective, two overarching goals for RNA biology include （i） characterizing the spatial-temporal regulation of various RNA species and elucidating the underlying regulatory mechanisms; （ii） understanding the functional impact of such regulation on human physiology and disease.展开更多
Leucine-rich repeat containing 15(LRRC15)has emerged as an attractive biomarker and target for cancer therapy.Transforming growth factor-β(TGFβ)induces the expression of this plasma membrane protein specifically in ...Leucine-rich repeat containing 15(LRRC15)has emerged as an attractive biomarker and target for cancer therapy.Transforming growth factor-β(TGFβ)induces the expression of this plasma membrane protein specifically in aggressive and treatment resistant tumor cells derived from mesenchymal stem cells,with minimal expression observed in non-neoplastic tissues.We have developed a humanized monoclonal antibody,DUNP19,that specifically binds with high affinity to a phylogenetically conserved LRRC15 epitope and is rapidly internalized upon LRRC15 binding.In multiple subcutaneous and orthotopic tumor xenograft mouse models,Lutetium-177 labeled DUNP19([^(177)Lu]Lu-DUNP19)enabled non-invasive imaging and molecularly precise radiotherapy to LRRC15-expressing cancer cells and murine cancer-associated fibroblasts,effectively halting tumor progression and prolonging survival with minimal toxicity.Transcriptomic analyses of[^(177)Lu]Lu-DUNP19-treated tumors reveal a loss of pro-tumorigenic mechanisms,including a previously reported TGF β-induced LRRC15+signature associated with immunotherapy resistance.In a syngeneic tumor model,administration of[^(177)Lu]Lu-DUNP19 significantly potentiated checkpoint-blockade therapy,yielding durable complete responses.Together,these results demonstrate that radio-theranostic targeting of LRRC15 with DUNP19 is a compelling precision medicine platform for image-guided diagnosis,eradication,and reprogramming of LRRC15+tumor tissue that drives immunoresistance and disease aggressiveness in a wide range of currently untreatable malignancies.展开更多
基金supported by the following grants:the National Cancer Institute,USA(a part of the National Institutes of Health,USAGrant No.T32LM012424)to Yiling Elaine Chen+8 种基金the National Cancer Institute,USA(Grant No.K08CA201591)the Margaret E Early Medical Research Trust,USAthe Pediatric Cancer Research Foundation,USA to Leo David Wangthe National Cancer Institute under Cancer Center Support Grant,USA(Grant No.P30CA033572)to the MS facility at the City of Hopethe National Institute of General Medical Sciences,USA(a part of the National Institutes of Health,USAGrant Nos.R01GM120507 and R35GM140888)the National Science Foundation,USA(Grant Nos.DBI-1846216 and DMS-2113754)the Johnson&Johnson WiSTEM2D Award,USA,the Sloan Research Fellowship,USAthe UCLA David Geffen School of Medicine W.M.Keck Foundation Junior Faculty Award,USA,to Jingyi Jessica Li.
文摘Advances in mass spectrometry(MS)have enabled high-throughput analysis of proteomes in biological systems.The state-of-the-art MS data analysis relies on database search algorithms to quantify proteins by identifying peptide–spectrum matches(PSMs),which convert mass spectra to peptide sequences.Different database search algorithms use distinct search strategies and thus may identify unique PSMs.However,no existing approaches can aggregate all user-specified database search algorithms with a guaranteed increase in the number of identified peptides and a control on the false discovery rate(FDR).To fill in this gap,we proposed a statistical framework,Aggregation of Peptide Identification Results(APIR),that is universally compatible with all database search algorithms.Notably,under an FDR threshold,APIR is guaranteed to identify at least as many,if not more,peptides as individual database search algorithms do.Evaluation of APIR on a complex proteomics standard dataset showed that APIR outpowers individual database search algorithms and empirically controls the FDR.Real data studies showed that APIR can identify disease-related proteins and post-translational modifications missed by some individual database search algorithms.The APIR framework is easily extendable to aggregating discoveries made by multiple algorithms in other high-throughput biomedical data analysis,e.g.,differential gene expression analysis on RNA sequencing data.The APIR R package is available at https://github.com/yiling0210/APIR.
文摘This year （2018） marks the 60th anniversary of the ＂central dogma＂, summarized as ＂DNA makes RNA makes protein＂, which was originally proposed by Francis Crick in 1958. Three years later, messenger RNA was identified as the template of protein synthesis. After 60 years of discovery, including discovery of the split nature of eukaryotic genes （Le., splicing）, it becomes evident that messenger RNAs are not merely messengers, but a hub of co- and post-transcriptional regulation, which is fundamental to amplify the complexity encoded in the genome of higher eukaryotic organisms. The mature forms of RNA of protein-coding genes and their abundance have to be tightly regulated through multiple steps of sophisticated processing, including capping, splicing and polyadenylation. In addition, their function also critically depends on proper localization -- sometimes trafficking to the remote parts of the cell such as dendrites and axons of neurons -- and proper control of their stability. Furthermore, thousands of long and small noncoding RNAs are produced to play a wide range of roles in gene regulation. From our perspective, two overarching goals for RNA biology include （i） characterizing the spatial-temporal regulation of various RNA species and elucidating the underlying regulatory mechanisms; （ii） understanding the functional impact of such regulation on human physiology and disease.
基金supported in part by the Outsmarting Osteosarcoma Hero Award(Because of Sydney)the UCLA Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research Rose Hill Foundation Innovator Award+23 种基金supported by NCI R01CA201035,R01CA240711,R01CA229893DoD W81XWH-18-1-0223UCLA SPORE in Prostate Cancer(P50 CA092131)JCCC Cancer support grant from NIH P30 CA016042(PI:Teitell)Knut and Alice Wallenberg FoundationBertha Kamprad FoundationDavid H.Koch Prostate Cancer Foundation Young Investigator AwardSwedish Research CouncilSwedish Cancer SocietySIPEA FoundationSwedish Childhood Cancer FoundationJohn and Augusta Perssons FoundationRoyal Physiographic Society of LundFranke and Margareta Bergqvist FoundationCrafoord FoundationLund University Medical Faculty research time allocation award,IngaBrittArne Lundberg Research Foundation,the German Research Foundation(552440240)the German Cancer Consortium(DKTK)the German Federal Ministry of Education and Research(BMBFgrant no.01KD2206A/SATURN3)funding support from the Children’s Discovery Institute of the St.Louis Children’s Hospital.Confocal laser scanning microscopy was performed at the Advanced Light Microscopy/Spectroscopy Laboratory(RRID:SCR_022789)the Leica Microsystems Center of Excellence at the California NanoSystems Institute at UCLA with funding support from NIH Shared Instrumentation Grant S10OD025017Flow cytometry was performed in the UCLA Jonsson Comprehensive Cancer Center(JCCC)Center for AIDS Research Flow Cytometry Core Facility that is supported by National Institutes of Health awards P30 CA016042 and 5P30 AI028697。
文摘Leucine-rich repeat containing 15(LRRC15)has emerged as an attractive biomarker and target for cancer therapy.Transforming growth factor-β(TGFβ)induces the expression of this plasma membrane protein specifically in aggressive and treatment resistant tumor cells derived from mesenchymal stem cells,with minimal expression observed in non-neoplastic tissues.We have developed a humanized monoclonal antibody,DUNP19,that specifically binds with high affinity to a phylogenetically conserved LRRC15 epitope and is rapidly internalized upon LRRC15 binding.In multiple subcutaneous and orthotopic tumor xenograft mouse models,Lutetium-177 labeled DUNP19([^(177)Lu]Lu-DUNP19)enabled non-invasive imaging and molecularly precise radiotherapy to LRRC15-expressing cancer cells and murine cancer-associated fibroblasts,effectively halting tumor progression and prolonging survival with minimal toxicity.Transcriptomic analyses of[^(177)Lu]Lu-DUNP19-treated tumors reveal a loss of pro-tumorigenic mechanisms,including a previously reported TGF β-induced LRRC15+signature associated with immunotherapy resistance.In a syngeneic tumor model,administration of[^(177)Lu]Lu-DUNP19 significantly potentiated checkpoint-blockade therapy,yielding durable complete responses.Together,these results demonstrate that radio-theranostic targeting of LRRC15 with DUNP19 is a compelling precision medicine platform for image-guided diagnosis,eradication,and reprogramming of LRRC15+tumor tissue that drives immunoresistance and disease aggressiveness in a wide range of currently untreatable malignancies.
