About

Matthew D. Weitzman, Ph.D., is a Professor of Pathology and Laboratory Medicine at the University of Pennsylvania Perelman School of Medicine. His research focuses on understanding cellular host responses to virus infection and the environment encountered and manipulated by viruses. His laboratory employs an integrated experimental approach combining biochemistry, molecular biology, genetics, and cell biology to study multiple viruses, including Adenovirus, Herpes Simplex Virus (HSV-1), and Adeno-Associated Virus (AAV). These studies aim to elucidate the dynamic interactions between viral genomes and host defense mechanisms, particularly the DNA repair pathways, which are crucial for maintaining genome integrity and preventing diseases such as cancer. Weitzman’s work has significant implications for developing efficient viral vectors for gene therapy and understanding the evolution of the human genome in response to viral conflicts. He has contributed to the field by discovering how cellular DNA damage response apparatus acts as a defense against viral assault and how viruses counteract these host defenses, providing insights into fundamental cell biology and potential therapeutic strategies.

Research topics

• Medicine
• Virology
• Pathology
• Political Science
• Immunology
• Biology

Selected publications

• Identification of E3 ligase substrates and PROTAC-induced ubiquitylation sites using proximity-based identification of ubiquitin sites (PrIUS)

  Communications Biology · 2026-04-09

  articleOpen accessSenior author

  The ubiquitin system regulates virtually all cellular processes, yet the vast majority of ubiquitylation sites identified in the human proteome cannot be attributed to specific E3 ligases. This knowledge gap hampers our understanding of ubiquitin signaling and the development of therapeutics leveraging the ubiquitylation system. Here we present Proximity-based Identification of Ubiquitin Sites (PrIUS), a versatile mass spectrometry-based approach combining proximity-dependent biotinylation (BioID) with ubiquitin remnant (diGly) enrichment. PrIUS enables simultaneous identification of E3 ligase interactors and direct mapping of substrate ubiquitylation sites within a single workflow. Using the E3 ligase NEDD4L, we demonstrated that E3 interactomes are inherently rich for diGly-modified peptides that remain largely undetectable without PTM-specific enrichment. PrIUS identified hundreds of high-confidence ubiquitylation sites, successfully distinguished substrates from non-substrate interactors (including adapters and E2 enzymes), and identified non-degradative ubiquitylation events. We also demonstrate utility for characterizing targeted protein degrader mechanisms by precisely mapping PROTAC-induced ubiquitylation sites. PrIUS thus provides a useful approach for elucidating E3-substrate relationships and characterizing mechanisms for emerging degrader therapeutics at amino acid resolution.

  PublisherOA PDFDOI

• Mysteries of adenovirus packaging

  Journal of Virology · 2025-04-17 · 2 citations

  reviewOpen accessSenior author

  ABSTRACT It is conventionally held that most DNA viruses package their genomes by one of two fundamental mechanisms: described by the sequential or concurrent models of assembly and packaging. Sequential packaging involves the translocation of a viral genome into a pre-formed capsid, often referred to as the pro-capsid. In contrast, concurrent packaging does not require the assembly of a pro-capsid. Instead, the genome is condensed, and the capsid shell is formed around the genome. The accumulation of empty particles in adenovirus infected cells has led to the assumption that adenovirus packaging may be best described by the sequential model. However, existing models fail to adequately explain all experimental observations, leaving many mysteries of adenovirus genome packaging unresolved. In this review, we describe key findings in adenovirus assembly and packaging, and we discuss them in the context of the competing models of sequential versus concurrent packaging. We discuss recent findings that have redefined our understanding of adenovirus packaging, including the role of viral biomolecular condensates and visualization of viral assembly and packaging in situ . These advances have renewed interest in the concurrent model of packaging. We anticipate that lessons learned from adenovirus packaging will be highly valuable for the advancement of viral vectors and gene-delivery technologies. In reviewing this topic, we hope to stimulate discussion and facilitate future investigation that will ultimately resolve gaps in knowledge and expand our understanding of DNA virus genome packaging.

  PublisherDOI

• Probing condensate microenvironments with a micropeptide killswitch

  Nature · 2025-06-04 · 22 citations

  articleOpen access

  Abstract Biomolecular condensates are thought to create subcellular microenvironments that have different physicochemical properties compared with their surrounding nucleoplasm or cytoplasm 1–5 . However, probing the microenvironments of condensates and their relationship to biological function is a major challenge because tools to selectively manipulate specific condensates in living cells are limited 6–9 . Here, we develop a non-natural micropeptide (that is, the killswitch) and a nanobody-based recruitment system as a universal approach to probe endogenous condensates, and demonstrate direct links between condensate microenvironments and function in cells. The killswitch is a hydrophobic, aromatic-rich sequence with the ability to self-associate, and has no homology to human proteins. When recruited to endogenous and disease-specific condensates in human cells, the killswitch immobilized condensate-forming proteins, leading to both predicted and unexpected effects. Targeting the killswitch to the nucleolar protein NPM1 altered nucleolar composition and reduced the mobility of a ribosomal protein in nucleoli. Targeting the killswitch to fusion oncoprotein condensates altered condensate compositions and inhibited the proliferation of condensate-driven leukaemia cells. In adenoviral nuclear condensates, the killswitch inhibited partitioning of capsid proteins into condensates and suppressed viral particle assembly. The results suggest that the microenvironment within cellular condensates has an essential contribution to non-stoichiometric enrichment and mobility of effector proteins. The killswitch is a widely applicable tool to alter the material properties of endogenous condensates and, as a consequence, to probe functions of condensates linked to diverse physiological and pathological processes.

  PublisherOA PDFDOI

• Double-strand break repair pathways differentially affect processing and transduction by dual AAV vectors

  Nature Communications · 2025-02-11 · 6 citations

  articleOpen access

  Recombinant adeno-associated viral vectors (rAAV) are a powerful tool for gene delivery but have a limited DNA carrying capacity. Efforts to expand this genetic payload have focused on engineering the vector components, such as dual trans-splicing vectors which double the delivery size by exploiting the natural concatenation of rAAV genomes in host nuclei. We hypothesized that inefficient dual vector transduction could be improved by modulating host factors which affect concatenation. Since factors mediating concatenation are not well defined, we performed a genome-wide screen to identify host cell regulators. We discover that Homologous Recombination (HR) is inhibitory to dual vector transduction. We demonstrate that depletion or inhibition of HR factors BRCA1 and Rad51 significantly increase reconstitution of a large split transgene by increasing both concatenation and expression from rAAVs. Our results define roles for DNA damage repair in rAAV transduction and highlight the potential for pharmacological intervention to increase genetic payload of rAAV vectors.

  PublisherOA PDFDOI

• Phosphorylation regulates viral biomolecular condensates to promote infectious progeny production

  The EMBO Journal · 2024-01-02 · 12 citations

  articleOpen accessSenior authorCorresponding

  Biomolecular condensates (BMCs) play important roles in diverse biological processes. Many viruses form BMCs which have been implicated in various functions critical for the productive infection of host cells. The adenovirus L1-52/55 kilodalton protein (52K) was recently shown to form viral BMCs that coordinate viral genome packaging and capsid assembly. Although critical for packaging, we do not know how viral condensates are regulated during adenovirus infection. Here we show that phosphorylation of serine residues 28 and 75 within the N-terminal intrinsically disordered region of 52K modulates viral condensates in vitro and in cells, promoting liquid-like properties. Furthermore, we demonstrate that phosphorylation of 52K promotes viral genome packaging and the production of infectious progeny particles. Collectively, our findings provide insights into how viral condensate properties are regulated and maintained in a state conducive to their function in viral progeny production. In addition, our findings have implications for antiviral strategies aimed at targeting the regulation of viral BMCs to limit viral multiplication.

  PublisherDOI

• 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

• Identifying Protein Interactions with Viral DNA Genomes during Virus Infection

  Viruses · 2024-05-25 · 6 citations

  reviewOpen accessCorresponding

  Viruses exploit the host cell machinery to enable infection and propagation. This review discusses the complex landscape of DNA virus-host interactions, focusing primarily on herpesviruses and adenoviruses, which replicate in the nucleus of infected cells, and vaccinia virus, which replicates in the cytoplasm. We discuss experimental approaches used to discover and validate interactions of host proteins with viral genomes and how these interactions impact processes that occur during infection, including the host DNA damage response and viral genome replication, repair, and transcription. We highlight the current state of knowledge regarding virus-host protein interactions and also outline emerging areas and future directions for research.

  PublisherOA PDFDOI

• Figure S4 from Impaired Death Receptor Signaling in Leukemia Causes Antigen-Independent Resistance by Inducing CAR T-cell Dysfunction

  2023-04-03

  preprintOpen access

  <p>Persistent antigen exposure resulting from impaired T cell cytotoxicity machinery results in progressive CART19 dysfunction.</p>

  PublisherDOI

• Table S4 from Impaired Death Receptor Signaling in Leukemia Causes Antigen-Independent Resistance by Inducing CAR T-cell Dysfunction

  2023-04-03

  preprintOpen access

  <p>sgRNA and sequencing primers used</p>

  PublisherDOI

• Table S4 from Impaired Death Receptor Signaling in Leukemia Causes Antigen-Independent Resistance by Inducing CAR T-cell Dysfunction

  2023-04-03

  preprintOpen access

  <p>sgRNA and sequencing primers used</p>

  PublisherDOI

Recent grants

• NIH Grant R01AI067952

  NIH · $2.1M · 2011

• NIH Grant R21CA185799

  NIH · $402k · 2017

• NIH Grant R01NS082240

  NIH · $2.0M · 2018

• NIH Grant R01CA097093

  NIH · $5.2M · 2020

• NIH Grant R21AI081019

  NIH · $527k · 2011

Frequent coauthors

• Katharina E. Hayer

  70 shared

• Katarzyna Kulej

  University of Pennsylvania

  37 shared

• Ophir Shalem

  36 shared

• Eui Tae Kim

  Jeju National University

  35 shared

• Nathan Singh

  31 shared

• Saar Gill

  University of Pennsylvania

  31 shared

• Marco Ruella

  University of Pennsylvania

  31 shared

• Christin Herrmann

  University of Pennsylvania

  30 shared