The daily renewal of the corpus epithelium is fuelled by adult stem cells residing within tubular glands, but the identity of these stem cells remains controversial. Lgr5 marks homeostatic stem cells and 'reserve' stem cells in multiple tissues. Here, we report Lgr5 expression in a subpopulation of chief cells in mouse and human corpus glands. Using a non-variegated Lgr5-2A-CreERT2 mouse model, we show by lineage tracing that Lgr5-expressing chief cells do not behave as corpus stem cells during homeostasis, but are recruited to function as stem cells to effect epithelial renewal following injury by activating Wnt signalling. Ablation of Lgr5 cells severely impairs epithelial homeostasis in the corpus, indicating an essential role for these Lgr5 cells in maintaining the homeostatic stem cell pool. We additionally define Lgr5 chief cells as a major cell-of-origin of gastric cancer. These findings reveal clinically relevant insights into homeostasis, repair and cancer in the corpus.

Chemo-resistance is one of the major causes of cancer-related deaths. Here we used single-cell transcriptomics to investigate divergent modes of chemo-resistance in tumor cells. We observed that higher degree of phenotypic intra-tumor heterogeneity (ITH) favors selection of pre-existing drug-resistant cells, whereas phenotypically homogeneous cells engage covert epigenetic mechanisms to trans-differentiate under drug-selection. This adaptation was driven by selection-induced gain of H3K27ac marks on bivalently poised resistance-associated chromatin, and therefore not expressed in the treatment-naïve setting. Mechanistic interrogation of this phenomenon revealed that drug-induced adaptation was acquired upon the loss of stem factor SOX2, and a concomitant gain of SOX9. Strikingly we observed an enrichment of SOX9 at drug-induced H3K27ac sites, suggesting that tumor evolution could be driven by stem cell-switch-mediated epigenetic plasticity. Importantly, JQ1 mediated inhibition of BRD4 could reverse drug-induced adaptation. These results provide mechanistic insights into the modes of therapy-induced cellular plasticity and underscore the use of epigenetic inhibitors in targeting tumor evolution.

Signaling between cancer and nonmalignant (stromal) cells in the tumor microenvironment (TME) is a key to tumor progression. Here, we deconvoluted bulk tumor transcriptomes to infer cross-talk between ligands and receptors on cancer and stromal cells in the TME of 20 solid tumor types. This approach recovered known transcriptional hallmarks of cancer and stromal cells and was concordant with single-cell, in situ hybridization and IHC data. Inferred autocrine cancer cell interactions varied between tissues but often converged on Ephrin, BMP, and FGFR-signaling pathways. Analysis of immune checkpoints nominated interactions with high levels of cancer-to-immune cross-talk across distinct tumor types. Strikingly, PD-L1 was found to be highly expressed in stromal rather than cancer cells. Overall, our study presents a new resource for hypothesis generation and exploration of cross-talk in the TME. Significance: This study provides deconvoluted bulk tumor transcriptomes across multiple cancer types to infer cross-talk in the tumor microenvironment.

No abstract

Signaling between cancer and nonmalignant (stromal) cells in the tumor microenvironment (TME) is key to tumorigenesis yet challenging to decipher from tumor transcriptomes. Here, we report an unbiased, data-driven approach to deconvolute bulk tumor transcriptomes and predict crosstalk between ligands and receptors on cancer and stromal cells in the TME of 20 solid tumor types. Our approach recovers known transcriptional hallmarks of cancer and stromal cells and is concordant with single-cell and immunohistochemistry data, underlining its robustness. Pan-cancer analysis reveals previously unrecognized features of cancer-stromal crosstalk. We find that autocrine cancer cell cross-talk varied between tissues but often converged on known cancer signaling pathways. In contrast, many stromal cross-talk interactions were highly conserved across tumor types. Interestingly, the immune checkpoint ligand PD-L1 was overexpressed in stromal rather than cancer cells across all tumor types. Moreover, we predicted and experimentally validated aberrant ligand and receptor expression in cancer cells of basal and luminal breast cancer, respectively. Collectively, our findings validate a data-driven method for tumor transcriptome deconvolution and establishes a new resource for hypothesis generation and downstream functional interrogation of the TME in tumorigenesis and disease progression.

<div>Abstract<p>Signaling between cancer and nonmalignant (stromal) cells in the tumor microenvironment (TME) is a key to tumor progression. Here, we deconvoluted bulk tumor transcriptomes to infer cross-talk between ligands and receptors on cancer and stromal cells in the TME of 20 solid tumor types. This approach recovered known transcriptional hallmarks of cancer and stromal cells and was concordant with single-cell, <i>in situ</i> hybridization and IHC data. Inferred autocrine cancer cell interactions varied between tissues but often converged on Ephrin, BMP, and FGFR-signaling pathways. Analysis of immune checkpoints nominated interactions with high levels of cancer-to-immune cross-talk across distinct tumor types. Strikingly, PD-L1 was found to be highly expressed in stromal rather than cancer cells. Overall, our study presents a new resource for hypothesis generation and exploration of cross-talk in the TME.</p>Significance:<p>This study provides deconvoluted bulk tumor transcriptomes across multiple cancer types to infer cross-talk in the tumor microenvironment.</p></div>

No abstract

S2.4 Veterinary mycology research, September 21, 2022, 3:00 PM - 4:30 PM Oomycosis is an emerging disease of humans and animals caused by oomycetes in the Stramenopiles-Alveolata-Rhizaria super group, mainly Pythium insidiosum and occasionally Lagenidium giganteum or Paralagenidum species. In surface freshwater, oomycetes produce motile biflagellate asexual zoospores with marked chemotactic attraction to epithelial surfaces of vertebrate hosts. Infection is the result of encystation and invasion of damaged skin or gastrointestinal mucosa. Of ∼ 4200 cases of pythiosis reported globally between 1980 and 2021 only ∼ 20% involved humans while 80% involved animals, mainly horses, dogs, and cattle. Most human cases occur in India and Thailand, whereas most animal infections were reported in the United States and Brazil. Pythiosis has been reported in mainland China, but the burden of the disease is low and comprises &lt;1% of overall cases in humans. Neither pythiosis nor lagenidiosis has been previously reported in humans or animals in Hong Kong. From January 2018 to January 2022, the Veterinary Diagnostic Laboratory of City University of Hong Kong diagnosed 10 cases of oomycosis (5 canine, 5 feline) after identification of non-parallel walled, irregularly branching, and poorly septate hyphae in the center of necrotic regions of histological sections of formalin-fixed paraffin-embedded tissues (FFPET). Species identity was confirmed by PCR and sequencing of 28S rDNA from DNA extracts of FFPET. There were 8 cases of P. insidiosum and 2 of L. giganteum infection. Serum ELISA was positive for Pythium antibodies in 5/6 cases tested and negative for Pythium/Lagenidium/Paralagenidum antibodies in a German shepherd dog (GSD) with disseminated disease caused by L. giganteum. Affected dogs were young to middle-aged at presentation (9 months to 5 years old). Two dogs had focal cutaneous infections, two had extensive gastrointestinal involvement, and the GSD had disseminated disease with cutaneous, mediastinal, and abdominal involvement. Affected cats were young (8 weeks to 18 months) and presented with subcutaneous/cutaneous disease. Three cats had a distinctive perianal ring of bulging subcutaneous granulation tissue, including one that also had an ulcerated, proliferative and necrotic lesion involving two adjacent hind-limb digits. One cat had facial subcutaneous swelling with mandibular lymph node enlargement and the remaining cat presented with extensive circumferential swelling of one hind limb from the distal paw to the mid-stifle. All cats tested negative for the Feline leukemia virus and Feline immunodeficiency virus. Traumatic or surgical wounds preceding infection were identified in a kitten caught in a rodent glue-trap with skin wounds, in a cat with facial involvement that had an injured globe surgically enucleated, and in a dog with cutaneous pythiosis that had chronic dermatitis. Treatment data were available for one canine case. The GSD with lagenidiosis was treated with combination antimicrobial therapy including voriconazole, terbinafine, minocycline, and azithromycin. The dog responded poorly. Mefenoxam was substituted for voriconazole and hyperbaric oxygen therapy was administered. After initial response, the dog succumbed 4 months from diagnosis. We have had success with the treatment of four feline cases using combination therapy including surgical debridement, immunotherapy with a Pythium vaccine, and combinations of antifungal drugs (posaconazole and terbinafine), and/or antimicrobials (doxycycline/minocycline and azithromycin).