Steven A. Carr YOU? Author Swipe

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Elevated synaptic PKA activity and abnormal striatal dopamine signaling in Akap11 mutant mice, a genetic model of schizophrenia and bipolar disorder Open

Bryan J. Song, Yang Ge, Ally Nicolella, Min Jee Kwon, Kevin Bonanno , et al. · 2025

Loss-of-function mutations in AKAP11 (a protein kinase A (PKA)-binding protein) greatly increase the risk of bipolar disorder and schizophrenia. To determine the neurobiological functions of AKAP11, we conduct multi-omic and neurobiologica…

Supplementary Data from Proteomic Profiling of Extracellular Matrix Components from Patient Metastases Identifies Consistently Elevated Proteins for Developing Nanobodies That Target Primary Tumors and Metastases Open

Noor Jailkhani, Karl R. Clauser, Howard H. Mak, Steffen Rickelt, Chenxi Tian , et al. · 2025

Supplementary methods and materials.

Table S2 from Integrative Proteogenomics and Forward Genetics Reveal a Novel Mitotic Vulnerability in Triple-Negative Breast Cancer Open

Nicholas J. Neill, Shankha Satpathy, Karsten Krug, Jitendra K. Meena, Nivetha Ramesh Babu , et al. · 2025

Table S2: Proteogenomic fold-change data (PTPN12 normal vs deficient) (related to Figure 2).

Data from Integrative Proteogenomics and Forward Genetics Reveal a Novel Mitotic Vulnerability in Triple-Negative Breast Cancer Open

Nicholas J. Neill, Shankha Satpathy, Karsten Krug, Jitendra K. Meena, Nivetha Ramesh Babu , et al. · 2025

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with few effective targeted therapies. Taxanes and other microtubule-targeting agents (MTA) are first-line chemotherapies for TNBC; however, the molecular mecha…

Table S1 from Integrative Proteogenomics and Forward Genetics Reveal a Novel Mitotic Vulnerability in Triple-Negative Breast Cancer Open

Nicholas J. Neill, Shankha Satpathy, Karsten Krug, Jitendra K. Meena, Nivetha Ramesh Babu , et al. · 2025

Table S1: PDX proteogenomic data (related to Figure 2).

Table S4 from Integrative Proteogenomics and Forward Genetics Reveal a Novel Mitotic Vulnerability in Triple-Negative Breast Cancer Open

Nicholas J. Neill, Shankha Satpathy, Karsten Krug, Jitendra K. Meena, Nivetha Ramesh Babu , et al. · 2025

Table S4: Integrated GSEA analysis (related to Figure 3).

Figure S1 from Integrative Proteogenomics and Forward Genetics Reveal a Novel Mitotic Vulnerability in Triple-Negative Breast Cancer Open

Nicholas J. Neill, Shankha Satpathy, Karsten Krug, Jitendra K. Meena, Nivetha Ramesh Babu , et al. · 2025

Figure S1: Integration of proteogenomics and functional genetics to reveal novel vulnerabilities in TNBC (related to Figure 1).

Characterization of the plasma proteome of multiple myeloma and its precursor conditions and identification of a prognostic high-risk signature of progression Open

Elizabeth D. Lightbody, Romanos Sklavenitis-Pistofidis, Christine‐Ivy Liacos, Nang Kham Su, Katherine Towle , et al. · 2025

Introduction Multiple Myeloma (MM) precursors Monoclonal Gammopathy of Undetermined Significance (MGUS) and Smoldering Multiple Myeloma (SMM) have variable risk of progression to MM and identifying which patients may progress is challengin…

Table S3 from Integrative Proteogenomics and Forward Genetics Reveal a Novel Mitotic Vulnerability in Triple-Negative Breast Cancer Open

Nicholas J. Neill, Shankha Satpathy, Karsten Krug, Jitendra K. Meena, Nivetha Ramesh Babu , et al. · 2025

Table S3: PTPN12-selective growth modifiers (related to Figure 3).

Figure S6 from Integrative Proteogenomics and Forward Genetics Reveal a Novel Mitotic Vulnerability in Triple-Negative Breast Cancer Open

Nicholas J. Neill, Shankha Satpathy, Karsten Krug, Jitendra K. Meena, Nivetha Ramesh Babu , et al. · 2025

Figure S6: PTPN12-deficient primary TNBC are sensitive to taxane chemotherapy (related to Figure 6).

Figure S5 from Integrative Proteogenomics and Forward Genetics Reveal a Novel Mitotic Vulnerability in Triple-Negative Breast Cancer Open

Nicholas J. Neill, Shankha Satpathy, Karsten Krug, Jitendra K. Meena, Nivetha Ramesh Babu , et al. · 2025

Figure S5: PTPN12-deficient cells exhibit mitotic defects dependent on APCFZR1 hyperactivation (related to Figure 5).

Pomalidomide downregulates FIZ1 to induce fetal hemoglobin in adult erythroid progenitors Open

Zachary Hyman, Steven A. Carr · 2025

Reactivation of fetal hemoglobin (HbF) expression has been a target for the treatment of hemoglobinopathies such as sickle cell disease (SCD) and β-thalassemia for several decades. While gene therapy has recently been approved as a cure fo…

Figure S2 from Integrative Proteogenomics and Forward Genetics Reveal a Novel Mitotic Vulnerability in Triple-Negative Breast Cancer Open

Nicholas J. Neill, Shankha Satpathy, Karsten Krug, Jitendra K. Meena, Nivetha Ramesh Babu , et al. · 2025

Figure S2: PTPN12-deficient models exhibit downregulation of cell cycle and mitotic pathways (related to Figure 2).

Figure S4 from Integrative Proteogenomics and Forward Genetics Reveal a Novel Mitotic Vulnerability in Triple-Negative Breast Cancer Open

Nicholas J. Neill, Shankha Satpathy, Karsten Krug, Jitendra K. Meena, Nivetha Ramesh Babu , et al. · 2025

Figure S4: PTPN12 deficiency causes aberrant degradation of APCFZR1 substrates (related to Figure 4).

Figure S3 from Integrative Proteogenomics and Forward Genetics Reveal a Novel Mitotic Vulnerability in Triple-Negative Breast Cancer Open

Nicholas J. Neill, Shankha Satpathy, Karsten Krug, Jitendra K. Meena, Nivetha Ramesh Babu , et al. · 2025

Figure S3: PTPN12-deficient cells are vulnerable to perturbation of mitotic regulators (related to Figure 3).

887 Mechanistic role of signal peptide peptidase in Qa-1-mediated antigen presentation and tumor immunity Open

Clara Wolfe, Kyle Ockerman, Roya Solhi Abarghani, Arun-Kumar Kaliya-Perumal, Grant Brennan , et al. · 2025

119 Endogenous retroviruses as tumor-specific antigens in clear cell renal cell carcinoma: A new avenue for immunotherapy Open

Qinqin Jiang, David A. Braun, Karl R. Clauser, Vijyendra Ramesh, Justin S. Becker , et al. · 2025

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer Open

Hui Zhang, Tao Liu, Zhen Zhang, Samuel Payne, Bai Zhang , et al. · 2025

Microscaled Cell Surface Proteomics for Cryo-Preserved Cells and Tissue Samples Open

Jørgen Thorup, Sarah A Johnston, Moe Haines, Margaret Rush, Edwin Sedodo , et al. · 2025

Cell surface proteins (CSPs) regulate key cellular functions and represent valuable targets for diagnostics and therapeutics. Despite advances in proteomic workflows, CSP analysis from cryopreserved or low-input clinical samples remains li…

Impact of clinical factors and season on inflammatory cytokines in biologic-treated and untreated asthma Open

Tanawin Nopsopon, Javier Cabrera-Pérez, Pui Y. Lee, Kailey Brodeur, Njira Lugogo , et al. · 2025

In-situ glial cell-surface proteomics identifies pro-longevity factors in Drosophila Open

Mariana Marques, Bo Sun, Ye-Jin Park, Tyler Jackson, Tzu‐Chiao Lu , et al. · 2025

Much focus has shifted towards understanding how glial dysfunction contributes to age-related neurodegeneration due to the critical roles glial cells play in maintaining healthy brain function. Cell-cell interactions, which are largely med…

Genetic landscape of DNMT3A R882H reveals mechanism of aberrant oligomerization Open

Emma M. Garcia, Olivia R. Lavidor, Shaunak Raval, Nicholas Z. Lue, Jessica K. Liang , et al. · 2025

Summary DNA methyltransferase 3A (DNMT3A) is a de novo DNA methyltransferase that is recurrently mutated in hematological malignancies and developmental disorders. The most prevalent mutation, R882H, compromises DNMT3A activity in a domina…

HIF2-driven PTHrP Causes Cachexia and Hypercalcemia in Kidney Cancer: Treatment with HIF2 Inhibitors Open

Muhannad Abu‐Remaileh, Laura Stransky, Nikita Bhalerao, Nitin H. Shirole, Qinqin Jiang , et al. · 2025

Kidney cancer frequently causes paraneoplastic syndromes, including hypercalcemia and cachexia, but the underlying mechanisms are incompletely understood. The most common form of kidney cancer, clear cell renal cell carcinoma, is frequentl…

Endocytome profiling uncovers cell-surface protein dynamics underlying neuronal connectivity Open

Colleen N. McLaughlin, Hui Ji, Ken C. Dong, Chuanyun Xu, Kenneth Kin Lam Wong , et al. · 2025

Endocytosis actively remodels the neuronal surface proteome to drive diverse cellular processes, yet its global extent and circuit-level consequences have defied comprehensive interrogation. Here, we introduce endocytome profiling: a syste…

A genetically engineered vertebrate animal model of <i>NAA15</i>-related heart disease uncovers myocardial growth, contractility, and mitochondrial defects Open

Warlen Pereira Piedade, Olivia Weeks, Alexander A. Akerberg, M Molnár, Jennifer Galdieri , et al. · 2025

Delineating the genetic and environmental instigators of congenital heart disease (CHD), affecting up to 1% of newborns, will improve preventative, diagnostic, and therapeutic efforts to mitigate the disease. Although mutations in the N-al…

Directed evolution of LaccID for cell surface proximity labeling and electron microscopy Open

Song-Yi Lee, Heegwang Roh, David González-Pérez, Mason Mackey, Daniel Hoces , et al. · 2025

Discovery of chromatin-based determinants of azacytidine and decitabine anti-cancer activity Open

Rishi V. Puram, Qiangzong Yin, YuhJong Liu, Justine C. Rutter, Daniel P. Bondeson , et al. · 2025

The DNA-incorporating nucleoside analogs azacytidine (AZA) and decitabine (DEC) have clinical efficacy in blood cancers, yet the precise mechanism by which these agents kill cancer cells has remained unresolved -- specifically, whether the…

CD33-CD45 Interaction Reveals a Mechanistic Link to Alzheimer’s Disease Susceptibility Open

Nicole Vo, Cory D. Rillahan, Zena K. Chatila, Daniel M. Virga, Jennifer L. Hall , et al. · 2025

The innate immune gene CD 33, encoding a myeloid inhibitory sialic acid-binding receptor, is associated with Alzheimer’s disease (AD) susceptibility. The AD-associated rs3865444 CC risk variant reduces splicing of the sialic acid-binding d…

Integrative analysis of lung adenocarcinoma across diverse ethnicities and exposures Open

Shankha Satpathy, Natalie M. Clark, Yi‐Ju Chen, Noshad Hosseini, Ya-Hsuan Chang , et al. · 2025

Lung adenocarcinomas (LUAD) are a pressing global health problem with enduring lethality and rapidly shifting epidemiology. Proteogenomic studies integrating proteomics and post-translational modifications with genomics can identify clinic…

High-Throughput Proteomic and Phosphoproteomic Analysis of Formalin-Fixed Paraffin-Embedded Tissues Open

Moe Haines, John R Thorup, Simone Gohsman, Claudia Ctortecka, Chelsea J. Newton , et al. · 2025

Formalin-fixed, paraffin-embedded (FFPE) patient tissues are a valuable resource for proteomic studies with the potential to associate derived molecular insights with clinical annotations and outcomes. Here, we present an optimized, partia…

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