Biology subjects

Fisk, B.

Publications and source records attributed to Fisk, B..

3 recordsLinked to original sources

bioRxiv2023

Endothelial cells are a key target of IFN-g during response to combined PD-1/CTLA-4 ICB treatment in a mouse model of bladder cancer

To explore mechanisms of response to combined PD-1/CTLA-4 immune checkpoint blockade (ICB) treatment in individual cell types, we generated scRNA-seq using a mouse model of invasive urothelial carcinoma with three conditions: untreated tumor, treated tumor, and tumor treated after CD4+ T cell depletion. After classifying tumor cells based on detection of somatic variants and assigning non-tumor cell types using SingleR, we performed differential expression analysis, overrepresentation analysis, and gene set enrichment analysis (GSEA) within each cell type. GSEA revealed that endothelial cells were enriched for upregulated IFN-g response genes when comparing treated cells to both untreated cells and cells treated after CD4+ T cell depletion. Functional analysis showed that knocking out IFNgR1 in endothelial cells inhibited treatment response. Together, these results indicated that IFN-g signaling in endothelial cells is a key mediator of ICB induced anti-tumor activity.

cancer biology↗

bioRxiv2022

Enhancing Hepatic MBOAT7 Expression Does Not Improve Nonalcoholic Steatohepatitis in Mice

Background & AimsGenetic analyses of human NASH have revealed polymorphisms near the membrane bound O-acyl transferase domain containing 7 (MBOAT7) gene associated with worsened liver injury. NAFLD/NASH also appears to decrease MBOAT7 expression or activity independent of these polymorphisms. Thus, we hypothesized that enhancing MBOAT7 function in NASH would improve pathology. Approach & ResultsMale C57BL6/J mice were infected with adeno-associated virus 8 (AAV8) expressing MBOAT7 under control of the hepatocyte-specific thyroid hormone-binding globulin promoter, or control virus expressing green fluorescent protein (GFP). Mice were infected after NASH induction with either choline-deficient high-fat diet or Gubra Amylin NASH diet and compared to low-fat fed control mice. Both NASH diets increased liver weights, liver triglycerides, and plasma alanine and aspartate aminotransferase (ALT and AST) markers of liver injury, which were modestly yet significantly improved by MBOAT7 overexpression. However, NASH liver histology assessed by categorical scoring was not substantially improved by MBOAT7 overexpression. MBOAT7 regulates the formation of phosphatidylinositol (PI) predominantly by arachidonoylation of lysophosphatidylinositol (LPI). Shotgun lipidomics of NASH GFP-control livers suggested decreased MBOAT7 activity in that LPI content was elevated, and both total and arachidonoylated-PI were reduced. Surprisingly, MBOAT7 overexpression did not rescue the content of most arachidonoylated PI species but did normalize or increase the abundance of several oleate and linoleate-containing PI species. Free arachidonic acid was elevated but the MBOAT7 substrate arachidonoyl-CoA was found to be low in all NASH livers compared to low-fat fed mice, likely due to decreased expression of both long-chain acyl-CoA synthetases (ACSL) 1 and 4 in NASH livers compared to controls. ConclusionsThese results suggest MBOAT7 overexpression fails to measurably improve NASH pathology potentially due to insufficient abundance of its arachidonoyl-CoA substrate in fatty livers.

pathology↗

bioRxiv2021

Single Cell T Cell Receptor Repertoire Profiling for Dogs

BackgroundSpontaneous cancers in companion dogs are increasingly recognized as robust models of human disease. This recognition has led to translational clinical trials in companion dogs with osteosarcoma, lymphoma, melanoma, squamous cell carcinoma, and soft tissue sarcoma. The ability to precisely track tumor-specific immune responses in such clinical trials would benefit from reagents to perform species-specific single cell T cell receptor sequencing (scTCRseq). This technology defines clones of T cells reacting to immune interventions and can help identify the specific epitope of response. Single cell gene expression data give insights into the activity and polarization of the T cell. To date, scTCRseq has not been demonstrated for canine samples. MethodsSamples from two responding dogs in a trial of an autologous deglycosylated melanoma vaccine were selected to demonstrate applicability of scTCRseq in a cancer immunotherapy setting. A single-cell suspension of cryopreserved peripheral blood mononuclear cells (PBMC) was prepared for 10X single cell sequencing. Full length 10X cDNA was amplified using a custom-designed nested PCR of the alpha/beta V(D)J region. A library made from this enriched product (scTCRseq) and a 10X gene expression (GEX) library (scRNAseq) were sequenced on the NovaSeq 6000. Results1,850-2,172 estimated V(D)J-expressing cells yielded 87-103.7 million reads with 73.8%-75.8% mapped to a V(D)J gene (beta/alpha chains ratio 1.5:1). 43 TRAJ, 29 TRAV, 12 TRBJ, and 22 TRBV gene segments were observed representing 72.9%, 51.8%, 100%, and 62.9% of all known V and J gene segments respectively. A large diversity of clonotypes was captured with 966-1,253 TRA/TRB clonotypes identified. Both dogs also exhibited a small number of highly abundant T cell clonotypes suggesting the presence of an anti-tumor T cell population. GEX enriched libraries successfully defined large clusters of CD8+ and CD4+ T cells that overlapped with V(D)J-expressing cells. DiscussionThe developed reagents successfully generated scTCRseq data, for the first time, which allowed the T cell repertoire to be surveyed in dogs responding to anti-tumor immunotherapy. These reagents will allow longitudinal tracking of anti-tumor T cell dynamics in canine cancer immunotherapy trials.

genomics↗