Protocol for profiling in vitro intratumor heterogeneity using spatially annotated single-cell sequencing

Here, we present a protocol for spatially annotated single-cell sequencing, a technique for spatially profiling intratumor heterogeneity with deep single-cell RNA sequencing and single-cell resolution. By combining live-cell imaging and photopatterned illumination, we describe steps to identify regions of interest in an in vitro tumor model, label the selected cells with photoactivatable dyes, and isolate and subject them to scRNAseq. This protocol can be applied to a range of cell lines and could be expanded to tissue sections. For complete details on the use and execution of this protocol, please refer to Smit et al. (2022).1.

Abstract 6105: Unravelling the mechanistic basis of chromoplexy, a mutational process driving early cancer genome evolution

Genome evolution can happen gradually or via bursts of rearrangements. Chromoplexy is an example of a process driving rapid genome evolution. This mutational signature is detected in ~18% of human cancers (PCAWG Consortium, 2020) and is frequently observed in prostate adenocarcinoma, lymphoid malignancies, and thyroid adenocarcinoma. Chromoplexy is inferred to happen as one catastrophic event that generates copy-neutral chains of translocations involving multiple chromosomes (Baca et al., 2013). Existing studies of chromoplexy monitor the outcome of massive cancer genome reorganization, thus early molecular events leading to catastrophic chromosome rearrangements remain elusive. In this work, we aimed to recapitulate molecular mechanisms underlying chromoplexy. For this, we set out to establish a cell line model and use fluorescence-based reporter systems to enrich for and allow isolation of cells containing signatures of chromoplexy. We additionally address whether colocalization of multiple double-strand breaks, for example in transcription hubs or abnormal nuclear structures, might stimulate chained inter- and intra- chromosomal translocations typical for chromoplexy. If successful, this work will provide a mechanistic understanding of an important mutational process driving rapid genome evolution in cancer, congenital disease, and potentially organismal evolution.

Citation Format: Nataliia Serbyn, Myrthe M. Smit, Vimathi S. Gummalla, Gregory J. Brunette, David S. Pellman. Unravelling the mechanistic basis of chromoplexy, a mutational process driving early cancer genome evolution. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6105.

Spatially Annotated Single Cell Sequencing for Unraveling Intratumor Heterogeneity

Intratumor heterogeneity is a major obstacle to effective cancer treatment. Current methods to study intratumor heterogeneity using single-cell RNA sequencing (scRNA-seq) lack information on the spatial organization of cells. While state-of-the art spatial transcriptomics methods capture the spatial distribution, they either lack single cell resolution or have relatively low transcript counts. Here, we introduce spatially annotated single cell sequencing, based on the previously developed functional single cell sequencing (FUNseq) technique, to spatially profile tumor cells with deep scRNA-seq and single cell resolution. Using our approach, we profiled cells located at different distances from the center of a 2D epithelial cell mass. By profiling the cell patch in concentric bands of varying width, we showed that cells at the outermost edge of the patch responded strongest to their local microenvironment, behaved most invasively, and activated the process of epithelial-to-mesenchymal transition (EMT) to migrate to low-confluence areas. We inferred cell-cell communication networks and demonstrated that cells in the outermost ∼10 cell wide band, which we termed the invasive edge, induced similar phenotypic plasticity in neighboring regions. Applying FUNseq to spatially annotate and profile tumor cells enables deep characterization of tumor subpopulations, thereby unraveling the mechanistic basis for intratumor heterogeneity.

Prevalence of the AMHR2 mutation in Miniature Schnauzers and genetic investigation of a Belgian Malinois with persistent Müllerian duct syndrome

Persistent Müllerian duct syndrome (PMDS) is a sex-limited disorder in which males develop portions of the female reproductive tract. Important consequences of PMDS are cryptorchidism and its sequelae of infertility and increased risk of testicular cancer. Anti-Müllerian hormone (AMH) and its receptor (AMHR2) induce the regression of the Müllerian ducts in male embryos. In Miniature Schnauzer dogs, the genetic basis has been identified as an autosomal recessive nonsense mutation in AMHR2, but the allele frequency of the mutation is unknown. Thus, the primary objective of this study was to estimate the prevalence of the AMHR2 mutation in North American Miniature Schnauzers, in order to ascertain the value of genetic testing in this breed. An additional objective was to determine whether mutations in AMH or AMHR2 were responsible for PMDS in a Belgian Malinois; this would aid development of a genetic test for the Belgian Malinois breed. Genomic DNA from 216 Miniature Schnauzers (including one known PMDS case) was genotyped for the AMHR2 mutation, and DNA from a single PMDS-affected Belgian Malinois was sequenced for all coding exons of AMH and AMHR2. The Miniature Schnauzer cohort had an AMHR2 mutation allele frequency of 0.16 and a carrier genotypic frequency of 0.27. The genetic basis for PMDS in the Belgian Malinois was not determined, as no coding or splicing mutations were identified in either AMH or AMHR2. These findings support a benefit to AMHR2 mutation testing Miniature Schnauzers used for breeding or with cryptorchidism.

Distribution of viral antigen in tissues of new-born lambs infected with Rift Valley fever virus

The distribution of Rift Valley fever (RVF) viral antigen was studied by immunohistochemistry in the liver, spleen, prescapular lymph node, lungs and kidneys ot eight experimentally infected new-born lambs and in four new-born lambs that died of RVF during the 1974-75 RVF epidemic. The eight experimentally infected lambs were euthanazed at 6, 12, 18, 24, 30, 33, 48 and 51 h post-infection (p.i.), respectively. Immunohistochemical staining utilized polyclonal hyperimmune mouse ascites fluid to RVF virus and peroxidase-diaminobenzidine was substrate. Virus antigen was most prominent in the liver and was detected as early as 18 h p.i. in the cytoplasm of hepatocytes that were sparsely scattered throughout the lobules. At 24-33 h p.i. antigen was also present in or adjacent to small foci of hepatocellular necrosis. At 48-51 h p.i. and in one of the field cases, positive staining was widespread and most consistently present in the cytoplasm of large numbers of degenerated or necrotic hepatocytes and in a new acidophilic bodies. Immunohistochemical staining was rarely observed in hepatocyte nuclei. Almost diffuse histochemical staining was observed in disintegrated cells and in the cytoplasm of necrotic hepatocytes throughout the liver in the other three field cases with pannecrosis; only the primary foci necrosis and a narrow periportal rim of intact hepatocytes did not stain. No staining was observed in bile duct epithelium, endothelial and Kupffer cells in the initial stages of Infection, supporting the contention that hepatocytes constitute the primary site of RVF virus replication in new-born lambs. Few cells stained positively in the spleen, prescapular lymph node, lungs and kidneys.

The diagnosis of Wesselsbron disease in a new-born lamb by immunohistochemical staining of viral antigen

Wesselsbron disease (WSL) was diagnosed in a 2-d-old lamb on a farm in the north-eastern Free State Province where a few abortions and neonatal deaths occurred in sheep in April 1994. The liver of the lamb was slightly swollen and orange-brown and, microscopically, it revealed single or small groups of necrotic hepatocytes that were randomly scattered throughout the lobules. Other histopathologic hepatic lesions included the presence of acidophilic bodies, intranuclear inclusion bodies in a few hepatocytes, neutrophils in the parenchyma, mild Kupffer-cell and bile-ductular proliferation and infiltration of mixed inflammatory cells in the portal tracts. Immunohistochemical staining of sections of formalin-fixed specimens of the liver with polyclonal antibody against WSL virus revealed positive staining in acidophilic bodies, cytoplasmic fragments of necrotic liver cells, the cytoplasm of degenerated hepatocytes and, rarely, in intranuclear inclusions. Positive staining was also obtained in liver sections from two newborn lambs experimentally infected with WSL virus. The results of this investigation showed that the immunohistochemical staining of sections of formalin-fixed liver can be used to confirm the diagnosis of WSL in new-born lambs.

Application of immunoperoxidase techniques to formalin-fixed brain tissue for the diagnosis of rabies in southern Africa

Two immunoperoxidase techniques, viz. avidin-biotin complex (ABC) and peroxidase-anti-peroxidase (PAP) procedures, were applied to paraffin-wax-embedded brain-tissue sections, from brains which had been fixed in 10% formalin, to demonstrate the presence of rabies-virus antigen by light microscopy. These techniques positively identified both "viverrid" and "canid" rabies-virus antigen in tissues sections of species commonly infected with rabies virus in southern Africa, viz. the domestic dog (Canis familiaris), yellow mongoose (Cynictus penicillata), black-backed jackal (Canis mesomelas), bat-eared fox (Otocyon megalotus), cattle (Bos taurus), sheep (Ovis aries) and humans. With both of these techniques rabies-virus antigen stained as sharply demarcated, brown precipitates within the cytoplasm of neurons. The virtual absence of background staining enabled identification of fine granules of viral antigen, often referred to as "virus dust", within axons, dendrites and cytoplasm of the nerve cell body. Staining with the ABC procedure clearer, more deeply-coloured precipitates than the PAP method.