Maggie P. Y. Lam
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View article: SALVE: prediction of interorgan communication with transcriptome latent space representation
SALVE: prediction of interorgan communication with transcriptome latent space representation Open
We describe a bioinformatics strategy to find associations between the secretome-coding genes and functional pathways of two organs. This approach may be used to find cross-talk signals between the heart, adipose, liver, and other tissues.…
View article: SALVE: prediction of interorgan communication with transcriptome latent space representation
SALVE: prediction of interorgan communication with transcriptome latent space representation Open
Massive transcriptomics data allow gene relationships to be discovered from their correlated expression. We describe SALVE, a method to infer the associations between secretome-encoding transcripts and gene modules in a distal organ from R…
View article: High Molecular Weight DNA Extraction of Pomegranate v1
High Molecular Weight DNA Extraction of Pomegranate v1 Open
The purpose of this protocol is to share a modified CTAB DNA extraction method that can be generally applied to all plants, but is especially effective in extracting High Molecular Weight (HMW) DNA from plants with high concentrations of s…
View article: A ratiometric catalog of protein isoform shifts in the cardiac fetal gene program
A ratiometric catalog of protein isoform shifts in the cardiac fetal gene program Open
Pathological cardiac remodeling is associated with the reactivation of fetal genes, yet the extent of the heart's fetal gene program and its impact on proteome compositions remain incompletely understood. Here, using a proteome-wide protei…
View article: Deuterium labeling enables proteome-wide turnover kinetics analysis in cell culture
Deuterium labeling enables proteome-wide turnover kinetics analysis in cell culture Open
Protein turnover is a critical component of gene expression regulation and cellular homeostasis, yet methods for measuring turnover rates that are scalable and applicable to different models are still needed. We introduce an improved D2O (…
View article: Deuterium labeling enables proteome wide turnover kinetics analysis in cell culture
Deuterium labeling enables proteome wide turnover kinetics analysis in cell culture Open
Summary The half-life of proteins is tightly regulated and underlies many cellular processes. It remains unclear the extent to which proteins are dynamically synthesized and degraded in different cell types and cell states. We introduce an…
View article: Protein Turnover Dynamics Analysis With Subcellular Spatial Resolution
Protein Turnover Dynamics Analysis With Subcellular Spatial Resolution Open
Protein synthesis and degradation (i.e., turnover) forms an important part of protein homeostasis and has been implicated in many age-associated diseases. Different cellular locations, such as organelles and membraneless compartments, ofte…
View article: Improved determination of protein turnover rate with heavy water labeling by mass isotopomer ratio selection
Improved determination of protein turnover rate with heavy water labeling by mass isotopomer ratio selection Open
The synthesis and degradation rates of proteins form an essential component of gene expression control. Heavy water labeling has been used in conjunction with mass spectrometry to measure protein turnover rates, but the optimal analytical …
View article: A Ratiometric Catalog of Protein Isoform Shifts in the Cardiac Fetal Gene Program
A Ratiometric Catalog of Protein Isoform Shifts in the Cardiac Fetal Gene Program Open
Pathological cardiac remodeling is associated with the reactivation of fetal genes, yet the extent of the heart’s fetal gene program and its impact on proteome compositions remain incompletely understood. Here, using a new proteome-wide pr…
View article: Tissue Usage Preference and Intrinsically Disordered Region Remodeling of Alternative Splicing Derived Proteoforms in the Heart
Tissue Usage Preference and Intrinsically Disordered Region Remodeling of Alternative Splicing Derived Proteoforms in the Heart Open
A computational analysis of mass spectrometry data was performed to uncover alternative splicing derived protein variants across chambers of the human heart. Evidence for 216 non-canonical isoforms was apparent in the atrium and the ventri…
View article: Tissue Usage Preference and Intrinsically Disordered Region Remodeling of Alternative Splicing Derived Proteoforms in the Heart
Tissue Usage Preference and Intrinsically Disordered Region Remodeling of Alternative Splicing Derived Proteoforms in the Heart Open
A computational analysis of mass spectrometry data was performed to uncover alternative splicing derived protein variants across chambers of the human heart. Evidence for 216 non-canonical isoforms was apparent in the atrium and the ventri…
View article: Co-culture with normal and senescent AC16 cardiomyocytes modulates fibrotic response in primary human ventricular fibroblasts
Co-culture with normal and senescent AC16 cardiomyocytes modulates fibrotic response in primary human ventricular fibroblasts Open
Transwell co-culture with human AC16 cardiomyocyte-like cells modifies the response of primary human ventricular fibroblasts to TGF-β stimulation. Fibrotic response markers including collagen I (COL1A1) and ɑ-smooth muscle actin (ACTA2) ar…
View article: Senescence in human AC16 cardiac cells is associated with thymidine kinase induction and histone loss
Senescence in human AC16 cardiac cells is associated with thymidine kinase induction and histone loss Open
AC16 cells are a transformed human cardiac cell line commonly used to study cardiomyocyte biology. We show that reduced proliferation and senescence markers can be robustly induced in AC16 cells cultured in low serum condition and treated …
View article: Simultaneous proteome localization and turnover analysis reveals spatiotemporal features of protein homeostasis disruptions
Simultaneous proteome localization and turnover analysis reveals spatiotemporal features of protein homeostasis disruptions Open
The functions of proteins depend on their spatial and temporal distributions, which are not directly measured by static protein abundance. Under endoplasmic reticulum (ER) stress, the unfolded protein response (UPR) pathway remediates prot…
View article: Protein prediction models support widespread post-transcriptional regulation of protein abundance by interacting partners
Protein prediction models support widespread post-transcriptional regulation of protein abundance by interacting partners Open
Protein and mRNA levels correlate only moderately. The availability of proteogenomics data sets with protein and transcript measurements from matching samples is providing new opportunities to assess the degree to which protein levels in a…
View article: Sex-specific responses to slow progressive pressure overload in a large animal model of HFpEF
Sex-specific responses to slow progressive pressure overload in a large animal model of HFpEF Open
We performed a comprehensive assessment to evaluate the effects of slow progressive pressure overload on cardiopulmonary function in a large animal model of heart failure with preserved ejection fraction (HFpEF) in males and females. Funct…
View article: Proteogenomics reveals sex-biased aging genes and coordinated splicing in cardiac aging
Proteogenomics reveals sex-biased aging genes and coordinated splicing in cardiac aging Open
Han et al. used proteogenomics to compare male and female mouse hearts at 4 and 20 mo. Sex-biased cardiac genes function in mitochondrial metabolism, translation, autophagy, and other processes. Hundreds of cardiac genes show sex-by-age in…
View article: HDAC6 modulates myofibril stiffness and diastolic function of the heart
HDAC6 modulates myofibril stiffness and diastolic function of the heart Open
Passive stiffness of the heart is determined largely by extracellular matrix and titin, which functions as a molecular spring within sarcomeres. Titin stiffening is associated with the development of diastolic dysfunction (DD), while augme…
View article: Protein prediction models support widespread post-transcriptional regulation of protein abundance by interacting partners
Protein prediction models support widespread post-transcriptional regulation of protein abundance by interacting partners Open
Protein and mRNA levels correlate only moderately. The availability of proteogenomics data sets with protein and transcript measurements from matching samples is providing new opportunities to assess the degree to which protein levels in a…
View article: Proteogenomic characterization of age and sex interactions in cardiac gene expression
Proteogenomic characterization of age and sex interactions in cardiac gene expression Open
Supplemental Data for "Proteogenomic characterization of age and sex interactions in cardiac gene expression"
View article: Proteogenomic characterization of age and sex interactions in cardiac gene expression
Proteogenomic characterization of age and sex interactions in cardiac gene expression Open
Supplemental Data for "Proteogenomic characterization of age and sex interactions in cardiac gene expression"
View article: Proteogenomic characterization of age and sex interactions in cardiac gene expression
Proteogenomic characterization of age and sex interactions in cardiac gene expression Open
Supplemental Data for "Proteogenomic characterization of age and sex interactions in cardiac gene expression"
View article: Proteogenomic characterization of age and sex interactions in cardiac gene expression
Proteogenomic characterization of age and sex interactions in cardiac gene expression Open
Supplemental Data for "Proteogenomic characterization of age and sex interactions in cardiac gene expression"
View article: Shotgun Proteomics Sample Processing Automated by an Open-Source Lab Robot
Shotgun Proteomics Sample Processing Automated by an Open-Source Lab Robot Open
Mass spectrometry-based shotgun proteomics experiments require multiple sample preparation steps, including enzymatic protein digestion and clean-up, which can take up significant person-hours of bench labor and present a source of batch-t…
View article: Transcriptome features of striated muscle aging and predictability of protein level changes
Transcriptome features of striated muscle aging and predictability of protein level changes Open
We performed total RNA sequencing and multi-omics analysis comparing skeletal muscle and cardiac muscle in young adult (4 months) vs. early aging (20 months) mice to examine the molecular mechanisms of striated muscle aging. We observed th…
View article: Transcriptome features of striated muscle aging and predictability of protein level changes
Transcriptome features of striated muscle aging and predictability of protein level changes Open
RNA and protein levels correlate only partially and some transcripts are better correlated with their protein counterparts than others. This suggests that in aging and disease studies, some transcriptomics markers may carry more informatio…