160 results match your criteria: "Advanced Clinical Biosystems Research Institute.[Affiliation]"
J Allergy Clin Immunol
January 2025
National Jewish Health, Denver, CO, USA. Electronic address:
Background: Inhibition of IL-4/IL-13 driven inflammation by dupilumab has shown significant clinical benefits in treatment of atopic dermatitis (AD).
Objective: To assess longitudinal protein and metabolite composition in AD skin during dupilumab treatment.
Methods: Skin tape strip (STS) were collected from lesional/non-lesional skin of 20 AD patients during 16-week dupilumab treatment and from 20 healthy volunteers (HV) followed for 16-weeks.
J Proteome Res
January 2025
Department of Computational Biomedicine, Cedars Sinai Medical Center, Los Angeles, California 90048, United States.
Single cell transcriptomics (SCT) has revolutionized our understanding of cellular heterogeneity, yet the emergence of single cell proteomics (SCP) promises a more functional view of cellular dynamics. A challenge is that not all mass spectrometry facilities can perform SCP, and not all laboratories have access to cell sorting equipment required for SCP, which together motivate an interest in sending bulk cell samples through the mail for sorting and SCP analysis. Shipping requires cell storage, which has an unknown effect on SCP results.
View Article and Find Full Text PDFMol Cell Proteomics
January 2025
Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048; Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048; Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048. Electronic address:
Single cell proteomics was performed on human induced pluripotent stem cells (iPSCs), iPSC-derived cardiomyocytes, and adult cardiomyocytes. Over 700 proteins could be simultaneously measured in each cell revealing unique subpopulations. A sub-set of iPSCs expressed higher levels of Lin28a and Tra-1-60 towards the outer edge of cell colonies.
View Article and Find Full Text PDFInt J Mol Sci
December 2024
Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
The prevalence of cardiovascular disease varies with sex, and the impact of intrinsic sex-based differences on vasculature is not well understood. Animal models can provide important insights into some aspects of human biology; however, not all discoveries in animal systems translate well to humans. To explore the impact of chromosomal sex on proteomic phenotypes, we used iPSC-derived vascular smooth muscle cells from healthy donors of both sexes to identify sex-based proteomic differences and their possible effects on cardiovascular pathophysiology.
View Article and Find Full Text PDFNature
January 2025
State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.
Int Immunopharmacol
January 2025
Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Advanced Clinical Biosystems Research Institute, Precision Biomarker Laboratories, Cedars Sinai Medical Center, Los Angeles, CA, USA. Electronic address:
Objective: This study aimed to investigate the tumorigenic role and regulatory pathways of peptidyl arginine deiminase 2 (PAD-2) in A549 lung cancer cells following treatment with small interfering RNA (PADI-2 siRNA) or the pharmacological pan-PAD inhibitor BB-Cl amidine.
Materials And Methods: A549 lung cancer cells were treated with PADI-2 siRNA to knock down PADI-2 expression or with BB-Cl amidine to inhibit PAD2 activity. The effects on cell proliferation, migration, invasion, and cell cycle phases were assessed.
Cisplatin-based chemotherapy is used across many common tumor types, but resistance reduces the likelihood of long-term survival. We previously found the puromycin-sensitive aminopeptidase, NPEPPS, as a druggable driver of cisplatin resistance in vitro and in vivo and in patient-derived organoids. Here, we present a general mechanism where NPEPPS interacts with the volume-regulated anion channels (VRACs) to control cisplatin import into cells and thus regulate cisplatin response across a range of cancer types.
View Article and Find Full Text PDFNature
December 2024
State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.
The human body contains trillions of cells, classified into specific cell types, with diverse morphologies and functions. In addition, cells of the same type can assume different states within an individual's body during their lifetime. Understanding the complexities of the proteome in the context of a human organism and its many potential states is a necessary requirement to understanding human biology, but these complexities can neither be predicted from the genome, nor have they been systematically measurable with available technologies.
View Article and Find Full Text PDFEur Heart J
January 2025
Cedars-Sinai Medical Center, Smidt Heart Institute, 127 S San Vicente Blvd Pavilion, Los Angeles, CA 90048, USA.
Sci Rep
November 2024
Department of Electrical & Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA, 22203, USA.
Bioinformatics software tools are essential to identify informative molecular features that define different phenotypic sample groups. Among the most fundamental and interrelated tasks are missing value imputation, signature gene detection, and differential pattern visualization. However, many commonly used analytics tools can be problematic when handling biologically diverse samples if either informative missingness possess high missing rates with mixed missing mechanisms, or multiple sample groups are compared and visualized in parallel.
View Article and Find Full Text PDFJ Proteome Res
December 2024
Institute for Systems Biology, Seattle, Washington 98109, United States.
Biomed Pharmacother
November 2024
Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Advanced Clinical Biosystems Research Institute, Precision Biomarker Laboratories, Cedars-Sinai Medical Center, Los Angeles, CA, USA. Electronic address:
Background: Dilated cardiomyopathy (DCM) is characterized by enlarged, weakened heart ventricles due to chronic fibrosis. Dysfunctional senescent myofibroblasts and excessive citrullination have been implicated in fibrotic diseases. Peptidylarginine deiminases (PADs) are involved in the citrullination of ECM proteins.
View Article and Find Full Text PDFBrain
October 2024
Neurobiology and Behavior, Univ. of California Irvine, Irvine, CA 92697, USA.
Nat Cardiovasc Res
August 2024
Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA.
ACS Meas Sci Au
August 2024
Department of Computational Biomedicine, Cedars Sinai Medical Center, Los Angeles, California 90048, United States.
J Proteome Res
September 2024
Precision Biomarker Laboratories, Cedars-Sinai Medical Center, Beverly Hills, California 90211, United States.
This Technical Note presents a comprehensive proteomics workflow for the new combination of Orbitrap and Astral mass analyzers across biofluids, cells, and tissues. Central to our workflow is the integration of Adaptive Focused Acoustics (AFA) technology for cells and tissue lysis to ensure robust and reproducible sample preparation in a high-throughput manner. Furthermore, we automated the detergent-compatible single-pot, solid-phase-enhanced sample Preparation (SP3) method for protein digestion.
View Article and Find Full Text PDFbioRxiv
July 2024
Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles CA, 90048, USA.
Single-cell omics data analysis pipelines are complicated to design and difficult to share or reproduce. We describe a web platform that enables no-code analysis pipeline design, simple computing via the Open Science Grid, and sharing of entire data analysis pipelines, their input data, and interactive results. We expect this platform to increase the accessibility and reproducibility of single-cell omics.
View Article and Find Full Text PDFbioRxiv
July 2024
Department of Computational Biomedicine, Cedars Sinai Medical Center, Los Angeles CA 90048.
Proteomes are well known to poorly correlate with transcriptomes measured from the same sample. While connected, the complex processes that impact the relationships between transcript and protein quantities remains an open research topic. Many studies have attempted to predict proteomes from transcriptomes with limited success.
View Article and Find Full Text PDFJ Proteome Res
August 2024
Department of Computational Biomedicine, Cedars Sinai Medical Center, Los Angeles, California 90048, United States.
Noninvasive detection of protein biomarkers in plasma is crucial for clinical purposes. Liquid chromatography-mass spectrometry (LC-MS) is the gold standard technique for plasma proteome analysis, but despite recent advances, it remains limited by throughput, cost, and coverage. Here, we introduce a new hybrid method that integrates direct infusion shotgun proteome analysis (DISPA) with nanoparticle (NP) protein corona enrichment for high-throughput and efficient plasma proteomic profiling.
View Article and Find Full Text PDFActa Neuropathol
July 2024
Department of Neurosurgery, Maxine Dunitz Neurosurgical Research Institute, Cedars-Sinai Medical Center, 127 S. San Vicente Blvd., A6212, Los Angeles, CA, 90048, USA.
Mol Metab
August 2024
Department of Cardiology, Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA. Electronic address:
Objectives: Cachexia is a metabolic disorder and comorbidity with cancer and heart failure. The syndrome impacts more than thirty million people worldwide, accounting for 20% of all cancer deaths. In acute myeloid leukemia, somatic mutations of the metabolic enzyme isocitrate dehydrogenase 1 and 2 cause the production of the oncometabolite D2-hydroxyglutarate (D2-HG).
View Article and Find Full Text PDFNat Commun
June 2024
Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
The global scientific response to COVID 19 highlighted the urgent need for increased throughput and capacity in bioanalytical laboratories, especially for the precise quantification of proteins that pertain to health and disease. Acoustic ejection mass spectrometry (AEMS) represents a much-needed paradigm shift for ultra-fast biomarker screening. Here, a quantitative AEMS assays is presented, employing peptide immunocapture to enrich (i) 10 acute phase response (APR) protein markers from plasma, and (ii) SARS-CoV-2 NCAP peptides from nasopharyngeal swabs.
View Article and Find Full Text PDFRes Sq
May 2024
Department of Electrical & Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, USA.
Bioinformatics software tools are essential to identify informative molecular features that define different phenotypic sample groups. Among the most fundamental and interrelated tasks are missing value imputation, signature gene detection, and differential pattern visualization. However, many commonly used analytics tools can be problematic when handling biologically diverse samples if either informative missingness possess high missing rates with mixed missing mechanisms, or multiple sample groups are compared and visualized in parallel.
View Article and Find Full Text PDFCirc Genom Precis Med
June 2024
Department of Physiology (E.E.N., M.S., D.W.D.K., J.v.d.V.), Amsterdam UMC, the Netherlands.
Clin Proteomics
June 2024
Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA.
Background: Descending thoracic aortic aneurysms and dissections can go undetected until severe and catastrophic, and few clinical indices exist to screen for aneurysms or predict risk of dissection.
Methods: This study generated a plasma proteomic dataset from 75 patients with descending type B dissection (Type B) and 62 patients with descending thoracic aortic aneurysm (DTAA). Standard statistical approaches were compared to supervised machine learning (ML) algorithms to distinguish Type B from DTAA cases.