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Homeostasis in the gut is achieved by impeccable functioning of tissue resident immune cells that reside and closely interact with the epithelium. The tissue resident immune cells of the intestinal epithelium are predominantly lymphocytes, known as intraepithelial lymphocytes (IELs) and mainly consist of TCRαβ T cells and TCRgd T cells. These IELs are well known to sense microbes, nutrients, and cellular stress but their role in intestinal cancer progression has been controversial. On one hand, gd Τ cells are the primary source of IL-17, an important proinflammatory cytokine that aid in colorectal cancer (CRC) progression. On the other hand, mice lacking gd Τ cells have been showed to have an increased risk of developing carcinogen-induced CRC. Here we used two different mouse model of colon cancer to investigate the role of gd T IELs in colon tumor growth. We showed that in both orthotopic implantation of cancer cells in the colon, and inflammation-driven colon cancer models, gd T cells are essentials to limit tumor growth. Indeed, mice lacking gd T cells had increased tumor incidence with high-grade adenomas compared to control mice. We also performed gene expression analysis of the adenomas in control mice and in mice lacking gd T cells. They revealed distinct transcription profiles with CRC-associated gene expression profile, including inflammatory genes and epithelial to mesenchymal transition genes, particularly enriched in adenomas from gd T cell deficient mice. Moreover, using human tissue microarrays, we investigated whether the presence of gd T cells in tumors of patients with advanced CRC could be used to predict disease outcomes. We revealed that patient disease-free survival was improved if gd T cells could be detected within tumors. Therefore, we showed that gd T cells are primordial in limiting colorectal cancer progression in both mice and humans. Citation Format: Sonia Ghilas, Dinesh Raghu, Kelly Tran, Yang Liao, Bhupinder Pal, Shoukat Sterle, Christine Dijkstra, Marina Yakou, Pavitha Parathan, John Mariadason, Matthias Ernst, Andreas Behren, Grant Drummond, Wei Shi, Lisa A. Mielke. Intestinal intraepithelial T cells limit colorectal cancer progression [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr PR007.

Mielke et al. show that TCF-1 limits IL-17–producing CD8+ T (Tc17) cell development from double-positive thymocytes through the sequential suppression of MAF and RORγt, while cementing conventional CD8+ T cell fate., Interleukin (IL)-17–producing CD8+ T (Tc17) cells have emerged as key players in host-microbiota interactions, infection, and cancer. The factors that drive their development, in contrast to interferon (IFN)-γ–producing effector CD8+ T cells, are not clear. Here we demonstrate that the transcription factor TCF-1 (Tcf7) regulates CD8+ T cell fate decisions in double-positive (DP) thymocytes through the sequential suppression of MAF and RORγt, in parallel with TCF-1–driven modulation of chromatin state. Ablation of TCF-1 resulted in enhanced Tc17 cell development and exposed a gene set signature to drive tissue repair and lipid metabolism, which was distinct from other CD8+ T cell subsets. IL-17–producing CD8+ T cells isolated from healthy humans were also distinct from CD8+IL-17− T cells and enriched in pathways driven by MAF and RORγt. Overall, our study reveals how TCF-1 exerts central control of T cell differentiation in the thymus by normally repressing Tc17 differentiation and promoting an effector fate outcome.

Prostate cancer is a common cause of cancer-related death in men. E6AP (E6-Associated Protein), an E3 ubiquitin ligase and a transcription cofactor, is elevated in a subset of prostate cancer patients. Genetic manipulations of E6AP in prostate cancer cells expose a role of E6AP in promoting growth and survival of prostate cancer cells in vitro and in vivo. However, the effect of E6AP on prostate cancer cells is broad and it cannot be explained fully by previously identified tumor suppressor targets of E6AP, promyelocytic leukemia protein and p27. To explore additional players that are regulated downstream of E6AP, we combined a transcriptomic and proteomic approach. We identified and quantified 16,130 transcripts and 7,209 proteins in castration resistant prostate cancer cell line, DU145. A total of 2,763 transcripts and 308 proteins were significantly altered on knockdown of E6AP. Pathway analyses supported the known phenotypic effects of E6AP knockdown in prostate cancer cells and in parallel exposed novel potential links of E6AP with cancer metabolism, DNA damage repair and immune response. Changes in expression of the top candidates were confirmed using real-time polymerase chain reaction. Of these, clusterin, a stress-induced chaperone protein, commonly deregulated in prostate cancer, was pursued further. Knockdown of E6AP resulted in increased clusterin transcript and protein levels in vitro and in vivo. Concomitant knockdown of E6AP and clusterin supported the contribution of clusterin to the phenotype induced by E6AP. Overall, results from this study provide insight into the potential biological pathways controlled by E6AP in prostate cancer cells and identifies clusterin as a novel target of E6AP.

Prostate cancer (PC) is the most common cancer in men. Elevated levels of E3 ligase, E6-Associated Protein (E6AP) were previously linked to PC, consistent with increased protein expression in a subset of PC patients. In cancers, irregular E3 ligase activity drives proteasomal degradation of tumor suppressor proteins. Accordingly, E3 ligase inhibitors define a rational therapy to restore tumor suppression. The relevant tumor suppressors targeted by E6AP in PC are yet to be fully identified. In this study we show that p27, a key cell cycle regulator, is a target of E6AP in PC. Down regulation of E6AP increases p27 expression and enhances its nuclear accumulation in PC. We demonstrate that E6AP regulates p27 expression by inhibiting its transcription in an E2F1-dependent manner. Concomitant knockdown of E6AP and p27 partially restores PC cell growth, supporting the contribution of p27 to the overall effect of E6AP on prostate tumorigenesis. Overall, we unravelled the E6AP-p27 axis as a new promoter of PC, exposing an attractive target for therapy through the restoration of tumor suppression.

Mutation of the key tumour suppressor p53 defines a transition in the progression towards aggressive and metastatic breast cancer (BC) with the poorest outcome. Specifically, the p53 mutation frequency exceeds 50% in triple-negative BC. Key regulators of mutant p53 that facilitate its oncogenic functions are potential therapeutic targets. We report here that the MDM4 protein is frequently abundant in the context of mutant p53 in basal-like BC samples. Importantly, we show that MDM4 plays a critical role in the proliferation of these BC cells. We demonstrate that conditional knockdown (KD) of MDM4 provokes growth inhibition across a range of BC subtypes with mutant p53, including luminal, Her2+ and triple-negative BCs. In vivo, MDM4 was shown to be crucial for the establishment and progression of tumours. This growth inhibition was mediated, at least in part, by the cell cycle inhibitor p27. Depletion of p27 together with MDM4 KD led to recovery of the proliferative capacity of cells that were growth-inhibited by MDM4 KD alone. Consistently, we identified low levels of p27 expression in basal-like tumours corresponding to high levels of MDM4 and p53. This predicts a signature for a subset of tumours that may be amenable to therapies targeted towards MDM4 and mutant p53. The therapeutic potential of MDM4 as a target in BC with mutant p53 was shown in vitro by use of a small-molecule inhibitor. Overall, our study supports MDM4 as a novel therapeutic target for BC expressing mutant p53. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

T cell factor-1 (TCF-1), encoded by Tcf7, is a transcription factor and histone deacetylase (HDAC) essential for commitment to both the T cell and the innate lymphoid cell (ILC) lineages in mammals. In this review, we discuss the multifunctional role of TCF-1 in establishing these lineages and the requirement for TCF-1 throughout lineage differentiation and maintenance of lineage stability. We highlight recent reports showing promise for TCF-1 as a novel biomarker to identify recently characterized subsets of exhausted CD8+ T cells that may help to predict patient responses to immune checkpoint blockade (ICB).

Restoration of tumor suppression is an attractive onco-therapeutic approach. It is particularly relevant when a tumor suppressor is excessively degraded by an overactive oncogenic E3 ligase. We previously discovered that the E6-associated protein (E6AP; as classified in the human papilloma virus context) is an E3 ligase that has an important role in the cellular stress response, and it directly targets the tumor-suppressor promyelocytic leukemia protein (PML) for proteasomal degradation. In this study, we have examined the role of the E6AP-PML axis in prostate cancer (PC). We show that knockdown (KD) of E6AP expression attenuates growth of PC cell lines in vitro. We validated this finding in vivo using cell line xenografts, patient-derived xenografts and mouse genetics. We found that KD of E6AP attenuates cancer cell growth by promoting cellular senescence in vivo, which correlates with restoration of tumor suppression by PML. In addition, we show that KD of E6AP sensitizes cells to radiation-induced death. Overall, our findings demonstrate a role for E6AP in the promotion of PC and support E6AP targeting as a novel approach for PC treatment, either alone or in combination with radiation.

The Knowledge Base (KB) used for real-world applications, such as booking a movie or restaurant reservation, keeps changing over time. End-to-end neural networks trained for these task-oriented dialogs are expected to be immune to any changes in the KB. However, existing approaches breakdown when asked to handle such changes. We propose an encoder-decoder architecture (BoSsNet) with a novel Bag-of-Sequences (BoSs) memory, which facilitates the disentangled learning of the response’s language model and its knowledge incorporation. Consequently, the KB can be modified with new knowledge without a drop in interpretability. We find that BoSsNeT outperforms state-of-the-art models, with considerable improvements (>10%) on bAbI OOV test sets and other human-human datasets. We also systematically modify existing datasets to measure disentanglement and show BoSsNeT to be robust to KB modifications.

Recent end-to-end task oriented dialog systems use memory architectures to incorporate external knowledge in their dialogs. Current work makes simplifying assumptions about the structure of the knowledge base, such as the use of triples to represent knowledge, and combines dialog utterances (context) as well as knowledge base (KB) results as part of the same memory. This causes an explosion in the memory size, and makes the reasoning over memory harder. In addition, such a memory design forces hierarchical properties of the data to be fit into a triple structure of memory. This requires the memory reader to infer relationships across otherwise connected attributes. In this paper we relax the strong assumptions made by existing architectures and separate memories used for modeling dialog context and KB results. Instead of using triples to store KB results, we introduce a novel multi-level memory architecture consisting of cells for each query and their corresponding results. The multi-level memory first addresses queries, followed by results and finally each key-value pair within a result. We conduct detailed experiments on three publicly available task oriented dialog data sets and we find that our method conclusively outperforms current state-of-the-art models. We report a 15-25% increase in both entity F1 and BLEU scores., Comment: Accepted as full paper at NAACL 2019

Plumbagin (1), a naphthoquinone, induces cell death and affects various signaling pathways in cancer cells. Wnt signaling is active constitutively in colorectal cancer and plays an important role in its progression and pathogenesis. It was hypothesized that 1 is likely to modulate Wnt signaling, and this compound was studied for its effect on this pathway in human colorectal cancer cells. Plumbagin (1) was found to downregulate Wnt signaling when assessed by a TOPFlash/FOPFlash reporter activity assay and also decreased the expression of several coactivators and downstream targets of Wnt signaling such as ?-catenin, TCF7L2, p300, Bcl9l, c-Myc, vimentin, and cyclinD1 in SW620 colorectal cancer cells. Using isogenic HCT116p53+/+ and HCT116p53-/- colorectal cancer cells, it was found that compound 1-mediated downregulation of Wnt signaling is p53-independent. Interestingly, treatment with 1 upregulated the expression of HBP1 (a negative regulator of Wnt signaling) in these cells. The results obtained show for the first time that downregulation of Wnt signaling could be one of the molecular mechanisms by which plumbagin exerts its inhibitory effects in human colorectal cancer cells. � 2014 The American Chemical Society and American Society of Pharmacognosy.

Mutation of the key tumour suppressor p53 defines a transition in the progression towards aggressive and metastatic breast cancer (BC) with the poorest outcome. Specifically, the p53 mutation frequency exceeds 50% in triple-negative BC. Key regulators of mutant p53 that facilitate its oncogenic functions are potential therapeutic targets. We report here that the MDM4 protein is frequently abundant in the context of mutant p53 in basal-like BC samples. Importantly, we show that MDM4 plays a critical role in the proliferation of these BC cells. We demonstrate that conditional knockdown (KD) of MDM4 provokes growth inhibition across a range of BC subtypes with mutant p53, including luminal, Her2

Availability of genome sequence of human and different pathogens has advanced proteomics research for various clinical applications. One of the prime goals of proteomics is identification and characterization of biomarkers for cancer and other fatal human diseases to aid an early diagnosis and monitor disease progression. However, rapid detection of low abundance biomarkers from the complex biological samples under clinically relevant conditions is extremely difficult, and it requires the development of ultrasensitive, robust and high-throughput technological platform. In order to overcome several technical limitations associated with sensitivity, dynamic range, detection time and multiplexing, proteomics has started integrating several emerging disciplines such as nanotechnology, which has led to the development of a novel analytical platform known as ‘nanoproteomics’. Among the diverse classes of nanomaterials, the quantum dots, gold nanoparticles, carbon nanotubes and silicon nanowires are the most promising candidates for diagnostic applications. Nanoproteomics offers several advantages such as ultralow detection, short assay time, high-throughput capability and low sample consumption. In this article, we have discussed the application of nanoproteomics for biomarker discovery in various diseases with special emphasis on various types of cancer. Furthermore, we have discussed the prospects, merits and limitations of nanoproteomics.