Reciprocal inhibition between TP63 and STAT1 regulates anti-tumor immune response through interferon-γ signaling in squamous cancer.

Squamous cell carcinomas (SCCs) are common and aggressive malignancies. Immune check point blockade (ICB) therapy using PD-1/PD-L1 antibodies has been approved in several types of advanced SCCs. However, low response rate and treatment resistance are common. Improving the efficacy of ICB therapy requires better understanding of the mechanism of immune evasion. Here, we identify that the SCC-master transcription factor TP63 suppresses interferon-γ (IFNγ) signaling. TP63 inhibition leads to increased CD8+ T cell infiltration and heighten tumor killing in in vivo syngeneic mouse model and ex vivo co-culture system, respectively. Moreover, expression of TP63 is negatively correlated with CD8+ T cell infiltration and activation in patients with SCC. Silencing of TP63 enhances the anti-tumor efficacy of PD-1 blockade by promoting CD8+ T cell infiltration and functionality. Mechanistically, TP63 and STAT1 mutually suppress each other to regulate the IFNγ signaling by co-occupying and co-regulating their own promoters and enhancers. Together, our findings elucidate a tumor-extrinsic function of TP63 in promoting immune evasion of SCC cells. Over-expression of TP63 may serve as a biomarker predicting the outcome of SCC patients treated with ICB therapy, and targeting TP63/STAT/IFNγ axis may enhance the efficacy of ICB therapy for this deadly cancer.

Epigenomic analyses identify FOXM1 as a key regulator of anti-tumor immune response in esophageal adenocarcinoma.

Unlike most cancer types, the incidence of esophageal adenocarcinoma (EAC) has rapidly escalated in the western world over recent decades. Using whole genome bisulfite sequencing (WGBS), we identify the transcription factor (TF) FOXM1 as an important epigenetic regulator of EAC. FOXM1 plays a critical role in cellular proliferation and tumor growth in EAC patient-derived organoids and cell line models. We identify ERBB2 as an upstream regulator of the expression and transcriptional activity of FOXM1. Unexpectedly, gene set enrichment analysis (GSEA) unbiased screen reveals a prominent anti-correlation between FOXM1 and immune response pathways. Indeed, syngeneic mouse models show that FOXM1 inhibits the infiltration of CD8+ T cells into the tumor microenvironment. Consistently, FOXM1 suppresses CD8+ T cell chemotaxis in vitro and antigen-dependent CD8+ T cell killing. This study characterizes FOXM1 as a significant EAC-promoting TF and elucidates its novel function in regulating anti-tumor immune response.

Integrating cfDNA liquid biopsy and organoid-based drug screening reveals PI3K signaling as a promising therapeutic target in colorectal cancer.

BACKGROUND: The current precision medicine relies on biomarkers, which are mainly obtained through next-generation sequencing (NGS). However, this model failed to find effective drugs for most cancer patients. This study tried to combine liquid biopsy with functional drug tests using organoid models to find potential drugs for cancer patients. METHODS: Colorectal cancer (CRC) patients were prospectively enrolled and blood samples were collected from patients before the start of treatment. Targeted deep sequencing of cfDNA samples was performed using a 14-gene panel. Gastrointestinal (GI) cancer organoids were established and PI3K and mTOR inhibitors were evaluated on organoid models. RESULTS: A total of 195 mutations were detected across 58 cfDNA samples. The most frequently mutated genes were KRAS, TP53, PIK3CA, and BRAF, all of which exhibited higher mutation rates than tissue biopsy. Although 81% of variants had an allele frequency of less than 1%, certain mutations in KRAS, TP53, and SMAD4 had high allele frequencies exceeding 10%. Notably, among the seven patients with high allele frequency mutations, six had metastatic tumors, indicating that a high allele frequency of ctDNA could potentially serve as a biomarker of later-stage cancer. A high rate of PIK3CA mutation (31 out of 67, or 46.3%) was discovered in CRC patients, suggesting possible tumor progression mechanisms and targeted therapy opportunities. To evaluate the value of anti PI3K strategy in GI cancer, different lines of GI cancer organoids were established. The organoids recapitulated the morphologies of the original tumors. Organoids were generally insensitive to PI3K inhibitors. However, CRC-3 and GC-4 showed response to mTOR inhibitor Everolimus, and GC-3 was sensitive to PI3Kδ inhibitor Idelalisib. The CRC organoid with a PIK3CA mutation showed greater sensitivity to the PI3K inhibitor Alpelisib than wildtype organoids, suggesting potential treatment options for the corresponding patients. CONCLUSION: Liquid biopsy holds significant promise for improving precision treatment and tumor prognosis in colorectal cancer patients. The combination of biomarker-based drug prediction with organoid-based functional drug sensitivity assay may lead to more effective cancer treatment.

TSCRE: a comprehensive database for tumor-specific cis-regulatory elements.

Cis-regulatory elements (CREs) and super cis-regulatory elements (SCREs) are non-coding DNA regions which influence the transcription of nearby genes and play critical roles in development. Dysregulated CRE and SCRE activities have been reported to alter the expression of oncogenes and tumor suppressors, thereby regulating cancer hallmarks. To address the strong need for a comprehensive catalogue of dysregulated CREs and SCREs in human cancers, we present TSCRE (http://tscre.zsqylab.com/), an open resource providing tumor-specific and cell type-specific CREs and SCREs derived from the re-analysis of publicly available histone modification profiles. Currently, TSCRE contains 1 864 941 dysregulated CREs and 68 253 dysregulated SCREs identified from 1366 human patient samples spanning 17 different cancer types and 9 histone marks. Over 95% of these elements have been validated in public resources. TSCRE offers comprehensive annotations for each element, including associated genes, expression patterns, clinical prognosis, somatic mutations, transcript factor binding sites, cancer-type specificity, and drug response. Additionally, TSCRE integrates pathway and transcript factor enrichment analyses for each study, enabling in-depth functional and mechanistic investigations. Furthermore, TSCRE provides an interactive interface for users to explore any CRE and SCRE of interest. We believe TSCRE will be a highly valuable platform for the community to discover candidate cancer biomarkers.

Testosterone administration decreases sensitivity to angry facial expressions in healthy males: A computational modeling approach.

Previous research indicates that higher testosterone levels are related to increased aggressive and dominant behaviors, particularly in males. One possible mechanism for these hormone-behavior associations could involve threat perception. However, the causal influence of testosterone on men's recognition of threatening facial expressions remains unknown. Here, we tested the causal effect of exogenous testosterone on men's sensitivity to facial threat by combining a psychophysical task with computational modeling. We administered a single dose (150 mg) of testosterone or placebo gel to healthy young men (n = 120) in a double-blind, placebo-controlled, between-participant design. Participants were presented with morphed emotional faces mixing anger/fear and neutral expressions and made judgments about the emotional expression. Across typical regression analysis, signal detection analysis, and drift diffusion modeling, our results consistently showed that individuals who received testosterone (versus placebo) exhibited a lower perceived sensitivity to angry facial expressions. But we observed no significant effects of testosterone administration on fearful facial expressions. The findings indicate that testosterone attenuates sensitivity to facial threat, especially angry facial expressions, which could lead to a misestimation of others' dominance and an increase in one's own aggressive and dominant behaviors.

Dopaminergic-related Anatomical Pattern of Dorsal Striatum in Schizophrenia.

Striatal dopaminergic overactivity was hypothesized as the core pathophysiology of schizophrenia. However, morphological alterations of striatum in schizophrenia remains exclusive, largely because brain regional heterogeneity limited traditional group-mean based approach. Leveraging third-party brain maps of neurotransmitter and cognition behaviours, we developed a pattern-based representation feature score (ReFS) to investigate structural spatial pattern variation in schizophrenia. Structural ReFS of subcortical regions, particularly the striatum, were linked to schizophrenia diagnosis, symptom severity, and genetic susceptibility. Dopaminergic-ReFS of striatum was increased in schizophrenia patients and reliably reproduced across 13 datasets. The pattern-based ReFS effectively captured the shared genetic pathways underlying both schizophrenia and striatum. The results provide convergent, multimodal suggest the central role of striatal spatial patterns in schizophrenia psychopathologies and and open new avenues to develop individualized treatments for psychotic disorders.

ARID1A Deficiency Regulates Anti-Tumor Immune Response in Esophageal Adenocarcinoma.

ARID1A, a member of the chromatin remodeling SWI/SNF complex, is frequently lost in many cancer types, including esophageal adenocarcinoma (EAC). Here, we study the impact of ARID1A deficiency on the anti-tumor immune response in EAC. We find that EAC tumors with ARID1A mutations are associated with enhanced tumor-infiltrating CD8+ T cell levels. ARID1A-deficient EAC cells exhibit heightened IFN response signaling and promote CD8+ T cell recruitment and cytolytic activity. Moreover, we demonstrate that ARID1A regulates fatty acid metabolism genes in EAC, showing that fatty acid metabolism could also regulate CD8+ T cell recruitment and CD8+ T cell cytolytic activity in EAC cells. These results suggest that ARID1A deficiency shapes both tumor immunity and lipid metabolism in EAC, with significant implications for immune checkpoint blockade therapy in EAC.

Asponchimides A-E: new enantiomeric N-acetyldopamine trimers from Aspongopus chinensis.

Five new racemic N-acetyldopamine (NADA) trimers, asponchimides A-E (1-5), were isolated from Aspongopus chinensis, a prominent traditional Chinese medicinal insect employed for alleviating pain, treating indigestion, and addressing kidney ailments. Compounds 1-5 were successfully resolved by chiral high-performance liquid chromatography (HPLC), yielding five pairs of enantiomers: (+)- and (-)-asponchimides A-E (1a/1b-5a/5b). Their structural identities were discerned by extensive spectroscopic analyses, including high-resolution mass spectrometry (HRMS), ultraviolet-visible (UV-Vis) spectroscopy, infrared (IR) spectroscopy, and nuclear magnetic resonance (NMR), and their absolute configurations were determined by electronic circular dichroism (ECD) calculations. Compounds 1-5 are pioneering instances of NADA trimers featuring a Δ7 double bond. When subjected to a series of bioassays, a majority of the compounds exhibited weak inhibitory activity against nitric oxide (NO) production in LPS-induced RAW 264.7 cells.

Comprehensive analyses of partially methylated domains and differentially methylated regions in esophageal cancer reveal both cell-type- and cancer-specific epigenetic regulation.

BACKGROUND: As one of the most common malignancies, esophageal cancer has two subtypes, squamous cell carcinoma and adenocarcinoma, arising from distinct cells-of-origin. Distinguishing cell-type-specific molecular features from cancer-specific characteristics is challenging. RESULTS: We analyze whole-genome bisulfite sequencing data on 45 esophageal tumor and nonmalignant samples from both subtypes. We develop a novel sequence-aware method to identify large partially methylated domains (PMDs), revealing profound heterogeneity at both methylation level and genomic distribution of PMDs across tumor samples. We identify subtype-specific PMDs that are associated with repressive transcription, chromatin B compartments and high somatic mutation rate. While genomic locations of these PMDs are pre-established in normal cells, the degree of loss is significantly higher in tumors. We find that cell-type-specific deposition of H3K36me2 may underlie genomic distribution of PMDs. At a smaller genomic scale, both cell-type- and cancer-specific differentially methylated regions (DMRs) are identified for each subtype. Using binding motif analysis within these DMRs, we show that a cell-type-specific transcription factor HNF4A maintains the binding sites that it generates in normal cells, while establishing new binding sites cooperatively with novel partners such as FOSL1 in esophageal adenocarcinoma. Finally, leveraging pan-tissue single-cell and pan-cancer epigenomic datasets, we demonstrate that a substantial fraction of cell-type-specific PMDs and DMRs identified here in esophageal cancer are actually markers that co-occur in other cancers originating from related cell types. CONCLUSIONS: These findings advance our understanding of DNA methylation dynamics at various genomic scales in normal and malignant states, providing novel mechanistic insights into cell-type- and cancer-specific epigenetic regulations.

Treatment for ovarian clear cell carcinoma with combined inhibition of WEE1 and ATR.

BACKGROUND: Standard platinum-based therapy for ovarian cancer is inefficient against ovarian clear cell carcinoma (OCCC). OCCC is a distinct subtype of epithelial ovarian cancer. OCCC constitutes 25% of ovarian cancers in East Asia (Japan, Korea, China, Singapore) and 6-10% in Europe and North America. The cancer is characterized by frequent inactivation of ARID1A and 10% of cases of endometriosis progression to OCCC. The aim of this study was to identify drugs that are either FDA-approved or in clinical trials for the treatment of OCCC. RESULTS: High throughput screening of 166 compounds that are either FDA-approved, in clinical trials or are in pre-clinical studies identified several cytotoxic compounds against OCCC. ARID1A knockdown cells were more sensitive to inhibitors of either mTOR (PP242), dual mTOR/PI3K (GDC0941), ATR (AZD6738) or MDM2 (RG7388) compared to control cells. Also, compounds targeting BH3 domain (AZD4320) and SRC (AZD0530) displayed preferential cytotoxicity against ARID1A mutant cell lines. In addition, WEE1 inhibitor (AZD1775) showed broad cytotoxicity toward OCCC cell lines, irrespective of ARID1A status. CONCLUSIONS: In a selection of 166 compounds we showed that inhibitors of ATR and WEE1 were cytotoxic against a panel of OCCC cell lines. These two drugs are already in other clinical trials, making them ideal candidates for treatment of OCCC.

Studying the effect of self-selected background music on reading task with eye movements.

Using background music (BGM) during learning is a common behavior, yet whether BGM can facilitate or hinder learning remains inconclusive and the underlying mechanism is largely an open question. This study aims to elucidate the effect of self-selected BGM on reading task for learners with different characteristics. Particularly, learners' reading task performance, metacognition, and eye movements were examined, in relation to their personal traits including language proficiency, working memory capacity, music experience and personality. Data were collected from a between-subject experiment with 100 non-native English speakers who were randomly assigned into two groups. Those in the experimental group read English passages with music of their own choice played in the background, while those in the control group performed the same task in silence. Results showed no salient differences on passage comprehension accuracy or metacognition between the two groups. Comparisons on fine-grained eye movement measures reveal that BGM imposed heavier cognitive load on post-lexical processes but not on lexical processes. It was also revealed that students with higher English proficiency level or more frequent BGM usage in daily self-learning/reading experienced less cognitive load when reading with their BGM, whereas students with higher working memory capacity (WMC) invested more mental effort than those with lower WMC in the BGM condition. These findings further scientific understanding of how BGM interacts with cognitive tasks in the foreground, and provide practical guidance for learners and learning environment designers on making the most of BGM for instruction and learning.

Differential audiovisual information processing in emotion recognition: An eye-tracking study.

Recent research has suggested that dynamic emotion recognition involves strong audiovisual association; that is, facial or vocal information alone automatically induces perceptual processes in the other modality. We hypothesized that different emotions may differ in the automaticity of audiovisual association, resulting in differential audiovisual information processing. Participants judged the emotion of a talking-head video under audiovisual, video-only (with no sound), and audio-only (with a static neutral face) conditions. Among the six basic emotions, disgust had the largest audiovisual advantage over the unimodal conditions in recognition accuracy. In addition, in the recognition of all the emotions except for disgust, participants' eye-movement patterns did not change significantly across the three conditions, suggesting mandatory audiovisual information processing. In contrast, in disgust recognition, participants' eye movements in the audiovisual condition were less eyes-focused than the video-only condition and more eyes-focused than the audio-only condition, suggesting that audio information in the audiovisual condition interfered with eye-movement planning for important features (eyes) for disgust. In addition, those whose eye-movement pattern was affected less by concurrent disgusted voice information benefited more in recognition accuracy. Disgust recognition is learned later in life and thus may involve a reduced amount of audiovisual associative learning. Consequently, audiovisual association in disgust recognition is less automatic and demands more attentional resources than other emotions. Thus, audiovisual information processing in emotion recognition depends on the automaticity of audiovisual association of the emotion resulting from associative learning. This finding has important implications for real-life emotion recognition and multimodal learning. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

Generation and multiomic profiling of a TP53/CDKN2A double-knockout gastroesophageal junction organoid model.

Inactivation of the tumor suppressor genes tumor protein p53 (TP53) and cyclin-dependent kinase inhibitor 2A (CDKN2A) occurs early during gastroesophageal junction (GEJ) tumorigenesis. However, because of a paucity of GEJ-specific disease models, cancer-promoting consequences of TP53 and CDKN2A inactivation at the GEJ have not been characterized. Here, we report the development of a wild-type primary human GEJ organoid model and a CRISPR-edited transformed GEJ organoid model. CRISPR-Cas9-mediated TP53 and CDKN2A knockout (TP53/CDKN2AKO) in GEJ organoids induced morphologic dysplasia and proneoplastic features in vitro and tumor formation in vivo. Lipidomic profiling identified several platelet-activating factors (PTAFs) among the most up-regulated lipids in CRISPR-edited organoids. PTAF/PTAF receptor (PTAFR) abrogation by siRNA knockdown or a pharmacologic inhibitor (WEB2086) reduced proliferation and other proneoplastic features of TP53/CDKN2AKO GEJ organoids in vitro and tumor formation in vivo. In addition, murine xenografts of Eso26, an established human esophageal adenocarcinoma cell line, were suppressed by WEB2086. Mechanistically, TP53/CDKN2A dual inactivation disrupted both the transcriptome and the DNA methylome, likely mediated by key transcription factors, particularly forkhead box M1 (FOXM1). FOXM1 activated PTAFR transcription by binding to the PTAFR promoter, further amplifying the PTAF-PTAFR pathway. Together, these studies established a robust model system for investigating early GEJ neoplastic events, identified crucial metabolic and epigenomic changes occurring during GEJ model tumorigenesis, and revealed a potential cancer therapeutic strategy. This work provides insights into proneoplastic mechanisms associated with TP53/CDKN2A inactivation in early GEJ neoplasia, which may facilitate early diagnosis and prevention of GEJ neoplasms.

Understanding the role of eye movement consistency in face recognition and autism through integrating deep neural networks and hidden Markov models.

Greater eyes-focused eye movement pattern during face recognition is associated with better performance in adults but not in children. We test the hypothesis that higher eye movement consistency across trials, instead of a greater eyes-focused pattern, predicts better performance in children since it reflects capacity in developing visual routines. We first simulated visual routine development through combining deep neural network and hidden Markov model that jointly learn perceptual representations and eye movement strategies for face recognition. The model accounted for the advantage of eyes-focused pattern in adults, and predicted that in children (partially trained models) consistency but not pattern of eye movements predicted recognition performance. This result was then verified with data from typically developing children. In addition, lower eye movement consistency in children was associated with autism diagnosis, particularly autistic traits in social skills. Thus, children's face recognition involves visual routine development through social exposure, indexed by eye movement consistency.

Making a saccade enhances Stroop and Simon conflict control.

Cognitive control is an important ability instantiated in many situations such as conflict control (e.g., Stroop/Simon task) and the control of eye movements (e.g., saccades). However, it is unclear whether eye movement control shares a common cognitive control system with the conflict control. In Experiment 1, we asked participants to make a prosaccade or antisaccade and then to identify the color of a lateralized color word (i.e., a Stroop-Simon stimulus). The stimulus onset asynchrony (SOA) between the saccadic cue and the Stroop-Simon stimulus was manipulated to be either short (200 ms) or long (600 ms). Results showed that the Stroop effect at the response level and the (negative) Simon effect were smaller when the SOA was short than long, demonstrating a decline of response control over time after making a saccade. Moreover, this temporal change of the Simon effect was more pronounced in the antisaccade session than in the prosaccade session. Furthermore, individuals who had better performance in the antisaccade task performed better in the response control of Stroop interference. When the saccade task was removed in Experiment 2, the temporal declines of the response control observed in Experiment 1 were absent. Experiment 3 replicated the key results of Experiment 1 by replacing the Stroop-Simon task with a typical Simon task and separately testing the typical Stroop and Simon tasks. Overall, our findings suggest that a common system is shared between the control of eye movements and the conflict control at the response level.

Serial dependence of facial identity for own- and other-race faces.

It is well established that individuals are better at recognising faces of their own-race compared with other-races; however, there is ongoing debate regarding the perceptual mechanisms that may be involved and therefore sensitive to face-race. Here, we ask whether serial dependence of facial identity, a bias where the perception of a face's identity is biased towards a previously presented face, shows an other-race effect. Serial dependence is associated with face recognition ability and appears to operate on high-level, face-selective representations, like other candidate mechanisms (e.g., holistic processing). We therefore expected to find an other-race effect for serial dependence for our Caucasian and Asian participants. While participants showed robust effects of serial dependence for all faces, only Caucasian participants showed stronger serial dependence for own-race faces. Intriguingly, we found that individual variation in own-race, but not other-race, serial dependence was significantly associated with face recognition abilities. Preliminary evidence also suggested that other-race contact is associated with other-race serial dependence. In conclusion, though we did not find an overall difference in serial dependence for own- versus other-race faces in both participant groups, our results highlight that this bias may be functionally different for own- versus other-race faces and sensitive to racial experience.

Activation of bivalent factor DLX5 cooperates with master regulator TP63 to promote squamous cell carcinoma.

To reconstruct systematically hyperactive transcription factor (TF)-dependent transcription networks in squamous cell carcinomas (SCCs), a computational method (ELMER) was applied to 1293 pan-SCC patient samples, and 44 hyperactive SCC TFs were identified. As a top candidate, DLX5 exhibits a notable bifurcate re-configuration of its bivalent promoter in cancer. Specifically, DLX5 maintains a bivalent state in normal tissues; its promoter is hypermethylation, leading to DLX5 transcriptional silencing in esophageal adenocarcinoma (EAC). In stark contrast, DLX5 promoter gains active histone marks and becomes transcriptionally activated in ESCC, which is directly mediated by SOX2. Functionally, silencing of DLX5 substantially inhibits SCC viability both in vitro and in vivo. Mechanistically, DLX5 cooperates with TP63 in regulating ∼2000 enhancers and promoters, which converge on activating cancer-promoting pathways. Together, our data establish a novel and strong SCC-promoting factor and elucidate a new epigenomic mechanism - bifurcate chromatin re-configuration - during cancer development.

A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb target genes.

CpG Island promoter genes make up more than half of human genes, and a subset regulated by Polycomb-Repressive Complex 2 (PRC2+-CGI) become DNA hypermethylated and silenced in cancer. Here, we perform a systematic analysis of CGI genes across TCGA cancer types, finding that PRC2+-CGI genes are frequently prone to transcriptional upregulation as well. These upregulated PRC2+-CGI genes control important pathways such as Epithelial-Mesenchymal Transition (EMT) and TNFα-associated inflammatory response, and have greater cancer-type specificity than other CGI genes. Using publicly available chromatin datasets and genetic perturbations, we show that transcription factor binding sites (TFBSs) within distal enhancers underlie transcriptional activation of PRC2+-CGI genes, coinciding with loss of the PRC2-associated mark H3K27me3 at the linked promoter. In contrast, PRC2-free CGI genes are predominantly regulated by promoter TFBSs which are common to most cancer types. Surprisingly, a large subset of PRC2+-CGI genes that are upregulated in one cancer type are also hypermethylated/silenced in at least one other cancer type, underscoring the high degree of regulatory plasticity of these genes, likely derived from their complex regulatory control during normal development.