About

Ophir Shalem, Ph.D., is an Associate Professor of Genetics at the University of Pennsylvania's Perelman School of Medicine. His research focuses on functional genomics, aiming to understand gene function through large-scale perturbation approaches. His lab develops novel perturbation and functional genomics methods and applies them to study a range of human diseases, including neurodegenerative disorders. Dr. Shalem's work involves integrating genomics approaches to uncover mechanisms underlying disease processes and gene regulation.

Research topics

• Medicine
• Computer Science
• Gerontology
• Pathology
• Geography
• Environmental health
• Cartography
• Genetics
• Biology
• Internal medicine
• Demography
• Neuroscience
• Psychology

Selected publications

• CRISPR associated enzymes are mislocalized to the cytoplasm in iPSC-derived neurons resulting in KRAB(KOX1)-specific degradation

  2026-04-24

  datasetSenior author
  PublisherDOI

• Abstract 2674 Intracellular Protein Editing to Enable Incorporation of Non-Canonical Residues into Endogenous Proteins

  Journal of Biological Chemistry · 2025-05-01

  articleOpen accessSenior author
  PublisherDOI

• Contrasting physiological and pathological tau phosphorylation

  Alzheimer s & Dementia · 2025-12-01

  articleOpen access

  BACKGROUND: Although phosphorylation to the microtubule-associated protein tau is strongly correlated with its aggregation and neurodegeneration in Alzheimer's disease, tau is also abundantly phosphorylated during normal, physiological development. Yet, tau phosphorylation is not associated with toxicity in developing brains. This divergence in the effects of phosphorylation to tau at different ages makes it of interest for further study. METHOD: Here, we compare site-specific effects of tau phosphorylation in developing and aged mouse brains. We further characterize combinatorial combinations of phosphorylation to tau in embryonic neurons to identify specific tau phospho-proteoforms. Lastly, we investigate the site-specific regulation of tau phosphorylation under physiological conditions. These experiments were achieved using mouse aging studies, sub-cellular fractionations assays in human iPSC-derived neurons and cell-free biophysical assays using semi-synthesized phosphorylated tau. RESULT: Although phosphorylation to tau is associated with insoluble tau in aged brains, we found that nearly 100% of phospho-tau is soluble in neonatal mouse brains. Furthermore, we identified the cellular-mechanism via which specific sites in tau are phosphorylated under physiological conditions of neuronal axon growth and collapse. Lastly, we identified specific combinatorial patterns of phosphorylation that are unique to the physiological state and thus distinct from disease-specific tau proteoforms. CONCLUSION: Our findings highlight the possibility of differential regulation of tau phosphorylation in the developing and adult brains. Overall, by contrasting physiological and pathological phosphorylation patterns to tau, we discern tau proteoforms that are unique to the disease state, and thus strong candidates for therapeutic clearance.

  PublisherOA PDFDOI

• Pooled tagging and hydrophobic targeting of endogenous proteins for unbiased mapping of unfolded protein responses

  Molecular Cell · 2025-04-23 · 5 citations

  articleOpen accessSenior author
  PublisherOA PDFDOI

• Tau aggregation results in an impaired ability to counteract microtubule destabilization via specific combinatorial tau phosphorylation patterns

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-08-12 · 1 citations

  preprintOpen access

  Tau phosphorylation is a defining feature of Alzheimer's disease, yet it also plays an essential physiological role in stabilizing microtubules (MTs) during normal neuronal development. While individual phosphorylation sites have been well-studied in pathology, it remains largely unknown how combinatorial phosphorylation is regulated under physiological conditions. Here, we uncover distinct, site-specific phosphorylation patterns on tau in developing human neurons. With top-down mass spectrometry we find that functional, endogenous tau is highly modified, with up to 21 phosphates per molecule. We identify patterns of co-occurrence between phosphorylation sites that are in proximity in the linear protein sequence, such as epitopes S202/T205/T212/T217 and T231/S235/S262. Moreover, these phospho-epitopes define discrete pools of tau and regulate tau-MT interactions in coordination, providing a mechanism for fine-tuning the binding of tau to MTs. Intriguingly, we find that co-occurring phospho-epitopes are dynamically regulated in response to changes in MT integrity; chemical perturbation of neuronal MTs promotes rapid tau dephosphorylation by phosphatase PP2a at most sites to enhance tau-MT interactions and counteract destabilization. We then use the PS19 tauopathy mouse model to demonstrate that developmental and pathological tau phosphorylation patterns partially overlap, and that co-occurring phospho-epitopes exhibit similar associations with the insoluble fraction in aged mice. Our results reveal an isoform-dependence on the effects of site-specific tau phosphorylation on its behavior. Together, these findings define a combinatorial phosphorylation code that modulates tau's physiological function in neurons and raises the possibility that MT destabilization precedes tau phosphorylation in disease. This work provides a mechanistic framework for distinguishing functional from pathological tau phosphorylation, with implications for the development of therapies that specifically target disease-associated tau proteoforms.

  PublisherOA PDFDOI

• TDP-43 loss induces cryptic polyadenylation in ALS/FTD

  Nature Neuroscience · 2025-10-21 · 16 citations

  articleOpen access

  Nuclear depletion and cytoplasmic aggregation of the RNA-binding protein TDP-43 are cellular hallmarks of amyotrophic lateral sclerosis (ALS). TDP-43 nuclear loss causes de-repression of cryptic exons, yet cryptic alternative polyadenylation (APA) events have been largely overlooked. In this study, we developed a bioinformatic pipeline to reliably identify alternative last exons, 3' untranslated region (3'UTR) extensions and intronic polyadenylation APA event types, and we identified cryptic APA sites induced by TDP-43 loss in induced pluripotent stem cell (iPSC)-derived neurons. TDP-43 binding sites are enriched at sites of these cryptic events, and TDP-43 can both repress and enhance APA. All categories of cryptic APA were also identified in ALS and frontotemporal dementia (FTD) postmortem brain tissue. RNA sequencing (RNA-seq), thiol(SH)-linked alkylation for the metabolic sequencing of RNA (SLAM-seq) and ribosome profiling (Ribo-seq) revealed that distinct cryptic APA categories have different downstream effects on transcript levels and that cryptic 3'UTR extensions can increase RNA stability, leading to increased translation. In summary, we demonstrate that TDP-43 nuclear depletion induces cryptic APA, expanding the palette of known consequences of TDP-43.

  PublisherOA PDFDOI

• Antisense oligonucleotide depletion of CCDC146 is a broad-spectrum therapeutic strategy for ALS

  Utrecht University Repository (Utrecht University) · 2025-08-19

  otherOpen access

  Amyotrophic lateral sclerosis (ALS) is a heritable and incurable disease defined by the degeneration of motor neurons (MNs), yet the genetics of ALS remain partially understood. Using a genomic deep learning-powered whole-genome analysis of 6,715 ALS patients, we identify four rare noncoding variants associated with patient survival, including chr7:76,009,472:C>T which is linked to a 70.6% reduction in survival. Genetic editing of this variant into iPSC-derived MNs increases CCDC146 expression and exacerbates ALS-specific phenotypes including TDP-43 mislocalization. We reveal that CCDC146 was located within the basal body of primary cilia in human MNs, and that cilia structure and function is impaired by CCDC146 overexpression but is restored by its depletion. Suppressing CCDC146 using an antisense oligonucleotide (ASO) completely rescues ALS-specific survival defects in neurons derived from both sporadic and familial patients, and it extends survival and reverses TDP-43 pathology in an aggressive ALS mouse model. Taken together, CCDC146 is a new modifier of ALS survival that acts via the primary cilia of MNs. ASO targeting of CCDC146 is a potential therapeutic approach for both sporadic and genetic forms of ALS, particularly because congenital absence of CCDC146 is well tolerated.

  Publisher

• CRISPR screen reveals modifiers of rAAV production including known rAAV infection genes playing an unexpected role in vector production

  Molecular Therapy — Methods & Clinical Development · 2025-01-18 · 2 citations

  articleOpen accessSenior author

  Recombinant adeno-associated virus (rAAV) vectors are an effective and well-established tool in the growing gene therapy field, with five U.S. Food and Drug Administration-approved AAV-mediated gene therapies already on the market and numerous more in clinical trials. However, manufacturing rAAV vectors is an expensive, timely, and labor-intensive process that limits the commercial use of AAV-mediated gene therapies. To address this limitation, we screened producer cells for genes that could be targeted to increase rAAV yield. Specifically, we performed a CRISPR-based genome-wide knockout (KO) screen in human embryonic kidney (HEK) 293 cells using an antibody specific to intact AAV2 capsids coupled with flow cytometry to identify genes that modulate rAAV production. We discovered that the KO of a group of heparan sulfate biosynthesis genes previously implicated in rAAV infectivity decreased rAAV production. Additionally, we identified several vesicular trafficking proteins for which KO in HEK 293 cells increased rAAV yields. Our findings provide evidence that host proteins associated with viral infection may have also been co-opted for viral assembly and that the genetic makeup of viral producer cells can be manipulated to increase particle yield.

  PublisherDOI

• Intracellular protein editing enables incorporation of noncanonical residues in endogenous proteins

  Science · 2025-05-01 · 22 citations

  articleOpen accessCorresponding

  The ability to study proteins in their native cellular context is crucial to our understanding of biology. In this work, we report a technology for intracellular protein editing, drawing from split intein-mediated protein splicing, genetic code expansion, and endogenous protein tagging. This approach enables us to rapidly and site-specifically install residues and chemical handles into a protein. We demonstrate the power of this platform to edit cellular proteins, inserting epitopes, protein-specific sequences, and noncanonical amino acids. Notably, we use an endogenous tagging approach to apply our protein editing technology to endogenous proteins with minimal perturbation. We anticipate that the protein editing technology presented in this work will be applied to a diverse set of problems and phenomena in live mammalian cells.

  PublisherOA PDFDOI

• The SMC5/6 complex prevents genotoxicity upon APOBEC3A-mediated replication stress

  The EMBO Journal · 2024-06-17 · 9 citations

  articleOpen access

  Mutational patterns caused by APOBEC3 cytidine deaminase activity are evident throughout human cancer genomes. In particular, the APOBEC3A family member is a potent genotoxin that causes substantial DNA damage in experimental systems and human tumors. However, the mechanisms that ensure genome stability in cells with active APOBEC3A are unknown. Through an unbiased genome-wide screen, we define the Structural Maintenance of Chromosomes 5/6 (SMC5/6) complex as essential for cell viability when APOBEC3A is active. We observe an absence of APOBEC3A mutagenesis in human tumors with SMC5/6 dysfunction, consistent with synthetic lethality. Cancer cells depleted of SMC5/6 incur substantial genome damage from APOBEC3A activity during DNA replication. Further, APOBEC3A activity results in replication tract lengthening which is dependent on PrimPol, consistent with re-initiation of DNA synthesis downstream of APOBEC3A-induced lesions. Loss of SMC5/6 abrogates elongated replication tracts and increases DNA breaks upon APOBEC3A activity. Our findings indicate that replication fork lengthening reflects a DNA damage response to APOBEC3A activity that promotes genome stability in an SMC5/6-dependent manner. Therefore, SMC5/6 presents a potential therapeutic vulnerability in tumors with active APOBEC3A.

  PublisherOA PDFDOI

Frequent coauthors

• Neville E. Sanjana

  New York University

  134 shared

• Feng Zhang

  International Peace Maternity & Child Health Hospital

  92 shared

• Kaijie Zheng

  Oak Ridge National Laboratory

  37 shared

• Aviv Regev

  Broad Institute

  36 shared

• Matthew D. Weitzman

  Children's Hospital of Philadelphia

  36 shared

• Stuart H. Orkin

  Dana-Farber/Boston Children's Cancer and Blood Disorders Center

  35 shared

• Katharina E. Hayer

  31 shared

• Feng Zhang

  First Affiliated Hospital of GuangXi Medical University

  29 shared

Labs

• Ophir Shalem LabPI

Education

• Ph.D., Molecular Genetics (labs of Prof. Tzachi Pilpel and Prof. Eran Segal)

  Weizmann Institute of Science

  2012

• M.Sc., Molecular Genetics (Prof. Tzachi Pilpel lab)

  Weizmann Institute of Science

  2007

• B.Sc., Computer Science

  Ben-Gurion University of the Negev

  2004