Faculty Bibliography

Immune checkpoint blockade (ICB) has been a remarkable clinical advance for cancer; however, the majority of patients do not respond to ICB therapy. We show that metastatic disease in the pleural and peritoneal cavities is associated with poor clinical outcomes after ICB therapy. Cavity-resident macrophages express high levels of Tim-4, a receptor for phosphatidylserine (PS), and this is associated with reduced numbers of CD8⁺ T cells with tumor-reactive features in pleural effusions and peritoneal ascites from patients with cancer. We mechanistically demonstrate that viable and cytotoxic anti-tumor CD8⁺ T cells upregulate PS and this renders them susceptible to sequestration away from tumor targets and proliferation suppression by Tim-4⁺ macrophages. Tim-4 blockade abrogates this sequestration and proliferation suppression and enhances anti-tumor efficacy in models of anti-PD-1 therapy and adoptive T cell therapy in mice. Thus, Tim-4⁺ cavity-resident macrophages limit the efficacy of immunotherapies in these microenvironments.

This standardized protocol describes the preparation of PCR amplified and purified samples from human cell lines passaged and collected from CRISPR screening. High-quality samples can be used to perform next-generation sequencing (NGS) to uncover changes in sgRNA abundance from the timepoint at which library-transduced cells are selected to the timepoint when the screen is ended. Here, we describe proper calculation methods for library representation and show how to overcome potential issues often encountered by researchers. For complete information on the use and execution of this protocol, please refer to Wohlhieter et al. (2020).

Seneca Valley virus (SVV) is a picornavirus with potency in selectively infecting and lysing cancerous cells. The cellular receptor for SVV mediating the selective tropism for tumors is anthrax toxin receptor 1 (ANTXR1), a type I transmembrane protein expressed in tumors. Similar to other mammalian receptors, ANTXR1 has been shown to harbor N-linked glycosylation sites in its extracellular vWA domain. However, the exact role of ANTXR1 glycosylation on SVV attachment and cellular entry was unknown. Here we show that N-linked glycosylation in the ANTXR1 vWA domain is necessary for SVV attachment and entry. In our study, tandem mass spectrometry analysis of recombinant ANTXR1-Fc revealed the presence of complex glycans at N166, N184 in the vWA domain, and N81 in the Fc domain. Symmetry-expanded cryo-EM reconstruction of SVV-ANTXR1-Fc further validated the presence of N166 and N184 in the vWA domain. Cell blocking, co-immunoprecipitation, and plaque formation assays confirmed that deglycosylation of ANTXR1 prevents SVV attachment and subsequent entry. Overall, our results identified N-glycosylation in ANTXR1 as a necessary post-translational modification for establishing stable interactions with SVV. We anticipate our findings will aid in selecting patients for future cancer therapeutics, where screening for both ANTXR1 and its glycosylation could lead to an improved outcome from SVV therapy.

Background: A minority of small cell lung carcinomas (SCLC) has minimal or absent expression of neuroendocrine (NE) markers, which can present a diagnostic challenge. Recent studies have suggested that POU2F3-a marker of chemosensory tuft cell lineage-is expressed specifically in NE-low SCLC. Here, we aimed to examine expression of POU2F3 in SCLC with extremely low or negative NE markers and to determine its specificity relative to non-NE lung carcinomas.
Design(s): POU2F3 expression was examined immunohistochemically in 152 SCLC and 116 non-small cell lung carcinomas (NSCLC; 53 adenocarcinomas, 63 squamous cell carcinomas). SCLC comprised 144 unselected cases and 8 additional pre-selected NE-minimal or negative SCLC. All SCLC were tested for 4 conventional NE markers (CNM; synaptophysin, chromogranin, CD56, and INSM1), and tumors with combined NE score (average H-score of 4 CNM) <50 were defined as NE-low and those with score <10 (staining isolated cells only) as NE-minimal. TTF-1 expression was also evaluated.
Result(s): POU2F3 was expressed in 8% of unselected SCLC (11/140), but was completely negative in all 116 NSCLC. In the whole cohort, compared to POU2F3-negative cases (n=134), POU2F3-positive SCLC (n=18) had fewer positive CNM (mean 1.8 vs 3.7, p<0.0001), lower combined NE score (mean 60 vs 183, p<0.0001) and lower rate of TTF-1 expression (6% vs 81%, p<0.0001), respectively. A total of 15 SCLC were NE-low (n=10), NEminimal (n=4) or NE-entirely negative (n=1). POU2F3 was positive in 10/15 (67%) of these cases, including all 5 NE-minimal/negative SCLC. POU2F3 expression in these cases was typically strong and diffuse (mean H-score 147; range 60-235).
Conclusion(s): POU2F3 expression is highly specific for SCLC relative to NSCLC, and is significantly enriched in NE-low SCLC, particularly in cases with minimal or negative NE marker expression. We suggest that POU2F3 represents a novel helpful diagnostic marker of SCLC

Background: There has been growing data suggesting that small cell lung carcinoma (SCLC) comprises distinct subtypes defined by expression of transcriptional regulators - ASCL1, NEUROD1, YAP1 and POU2F3. Pre-clinical data suggest distinct therapeutic vulnerabilities of these subtypes, prompting an interest in identifying them in patient samples. We have recently characterized these subtypes immunohistochemically (IHC) and histologically in a large cohort of clinical samples. As cytologic specimens commonly represent sole diagnostic specimen for SCLC patients, here we aimed to determine whether the distribution of subtype-defining markers is equivalent in cytologic and surgical specimens.
Design(s): The expression of ASCL1, NEUROD1, POU2F3 and YAP1 was analyzed by IHC in cytologic specimens (n=26, formalin-fixed blocks) of SCLC, and distribution was compared to that of surgical specimens (n=148). We also compared the distribution of conventional neuroendocrine markers (CNM; synaptophysin, chromogranin, CD56, and INSM1) and their association with novel marker-defined subtypes in cytologic preparations.
Result(s): Cytologic specimens included EBUS-FNA (n=24) and pleural fluid (n=2). ASCL1, NEUROD1, POU2F3 and YAP1 had a similar distribution in cytologic vs surgical specimens both qualitatively and by quantitative H-score analysis (Table 1A, p=0.1-0.9). Distribution of marker defined subtypes based on combined (Table 1B) and relative (Table 1C) expression levels of ASCL1 and NEUROD1 was also similar in the two specimen types (p=0.2-1). POU2F3 was expressed exclusively in ASCL1/NEUROD1 double-negative cases in both specimen types, and was associated with low or minimal expression of CNMs, as defined by lower combined neuroendocrine score (average H-score of 4 CNM), compared to other subtypes (mean 70 vs 177 in cytology specimens, respectively; p<0.01).
Conclusion(s): Expression of SCLC subtype-defining markers can be reliably assessed by IHC in formalin fixed cytologic preparations and is comparable to that of surgical specimens. Potential utility of POU2F3 as a diagnostic marker in SCLC with minimal or absent CNM expression warrants further study

The coronavirus disease 2019 (COVID-19) pandemic has claimed the lives of over one million people worldwide. The causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a member of the Coronaviridae family of viruses that can cause respiratory infections of varying severity. The cellular host factors and pathways co-opted during SARS-CoV-2 and related coronavirus life cycles remain ill defined. To address this gap, we performed genome-scale CRISPR knockout screens during infection by SARS-CoV-2 and three seasonal coronaviruses (HCoV-OC43, HCoV-NL63, and HCoV-229E). These screens uncovered host factors and pathways with pan-coronavirus and virus-specific functional roles, including major dependency on glycosaminoglycan biosynthesis, sterol regulatory element-binding protein (SREBP) signaling, bone morphogenetic protein (BMP) signaling, and glycosylphosphatidylinositol biosynthesis, as well as a requirement for several poorly characterized proteins. We identified an absolute requirement for the VMP1, TMEM41, and TMEM64 (VTT) domain-containing protein transmembrane protein 41B (TMEM41B) for infection by SARS-CoV-2 and three seasonal coronaviruses. This human coronavirus host factor compendium represents a rich resource to develop new therapeutic strategies for acute COVID-19 and potential future coronavirus pandemics.

Flaviviruses pose a constant threat to human health. These RNA viruses are transmitted by the bite of infected mosquitoes and ticks and regularly cause outbreaks. To identify host factors required for flavivirus infection, we performed full-genome loss of function CRISPR-Cas9 screens. Based on these results, we focused our efforts on characterizing the roles that TMEM41B and VMP1 play in the virus replication cycle. Our mechanistic studies on TMEM41B revealed that all members of the Flaviviridae family that we tested require TMEM41B. We tested 12 additional virus families and found that SARS-CoV-2 of the Coronaviridae also required TMEM41B for infection. Remarkably, single nucleotide polymorphisms present at nearly 20% in East Asian populations reduce flavivirus infection. Based on our mechanistic studies, we propose that TMEM41B is recruited to flavivirus RNA replication complexes to facilitate membrane curvature, which creates a protected environment for viral genome replication.