tbuckley/cabot-search huggingface dataset:
GametesOmics: A Comprehensive Multi-omics Database for Exploring the Gametogenesis in Humans and Mice
Authors: Jianting An, Jing Wang, Siming Kong, Shi Song, Wei Chen, Peng Yuan, Qilong He, Yidong Chen, Ye Li, Yi Yang, Wei Wang, Rong Li, Liying Yan, Zhiqiang Yan, Jie Qiao
Journal: Genomics Proteomics & Bioinformatics (2023)

Gametogenesis plays an important role in the reproduction and evolution of species. The transcriptomic and epigenetic alterations in this process can influence the reproductive capacity, fertilization, and embryonic development. The rapidly increasing single-cell studies have provided valuable multi-omics resources. However, data from different layers and sequencing platforms have not been uniformed and integrated, which greatly limits their use for exploring the molecular mechanisms that underlie oogenesis and spermatogenesis. Here, we develop GametesOmics, a comprehensive database that integrates the data of gene expression, DNA methylation, and chromatin accessibility during oogenesis and spermatogenesis in humans and mice. GametesOmics provides a user-friendly website and various tools, including Search and Advanced Search for querying the expression and epigenetic modification(s) of each gene; Tools with Differentially expressed gene (DEG) analysis for identifying DEGs, Correlation analysis for demonstrating the genetic and epigenetic changes, Visualization for displaying single-cell clusters and screening marker genes as well as master transcription factors (TFs), and MethylView for studying the genomic distribution of epigenetic modifications. GametesOmics also provides Genome Browser and Ortholog for tracking and comparing gene expression, DNA methylation, and chromatin accessibility between humans and mice. GametesOmics offers a comprehensive resource for biologists and clinicians to decipher the cell fate transition in germ cell development, and can be accessed at http://gametesomics.cn/.
Omics for deciphering oral microecology
Authors: Yongwang Lin, Xiaoyue Liang, Zhengyi Li, Tao Gong, Biao Ren, Yuqing Li, Xian Peng
Journal: International Journal of Oral Science (2024)

Abstract The human oral microbiome harbors one of the most diverse microbial communities in the human body, playing critical roles in oral and systemic health. Recent technological innovations are propelling the characterization and manipulation of oral microbiota. High-throughput sequencing enables comprehensive taxonomic and functional profiling of oral microbiomes. New long-read platforms improve genome assembly from complex samples. Single-cell genomics provides insights into uncultured taxa. Advanced imaging modalities including fluorescence, mass spectrometry, and Raman spectroscopy have enabled the visualization of the spatial organization and interactions of oral microbes with increasing resolution. Fluorescence techniques link phylogenetic identity with localization. Mass spectrometry imaging reveals metabolic niches and activities while Raman spectroscopy generates rapid biomolecular fingerprints for classification. Culturomics facilitates the isolation and cultivation of novel fastidious oral taxa using high-throughput approaches. Ongoing integration of these technologies holds the promise of transforming our understanding of oral microbiome assembly, gene expression, metabolites, microenvironments, virulence mechanisms, and microbe-host interfaces in the context of health and disease. However, significant knowledge gaps persist regarding community origins, developmental trajectories, homeostasis versus dysbiosis triggers, functional biomarkers, and strategies to deliberately reshape the oral microbiome for therapeutic benefit. The convergence of sequencing, imaging, cultureomics, synthetic systems, and biomimetic models will provide unprecedented insights into the oral microbiome and offer opportunities to predict, prevent, diagnose, and treat associated oral diseases.
Abstract PR009: SMARCAL1 is a dual regulator of innate immune signaling and PD-L1 expression that promotes tumor immune evasion
Authors: Giuseppe Leuzzi, Alessandro Vasciaveo, Angelo Taglialatela, Xiao Chen, Tessa M. Firestone, Allison R. Hickman, Wendy Mao, Tanay Thakar, Alina Vaitsiankova, Jen-Wei Huang, Raquel Cuella-Martin, Samuel B. Hayward, Jordan S. Kesner, Ali Ghasemzadeh, Tarun S. Nambiar, Patricia Ho, Alexander Rialdi, Maxime Hebrard, Yinglu Li, Jinmei Gao, Saarang Gopinath, Oluwatobi A. Adeleke, Bryan Venters, Charles G. Drake, Richard Baer, Benjamin Izar, Ernesto Guccione, Michael-Christopher Keogh, Raphael Guerois, Lu Sun, Chao Lu, Andrea Califano, Alberto Ciccia
Journal: Cancer Research (2024)

Abstract Genomic instability can trigger cancer-intrinsic innate immune responses that promote tumor rejection. However, cancer cells often evade these responses by overexpressing immune checkpoint regulators, such as PD-L1. Here, we identify the SNF2-family DNA translocase SMARCAL1 as a factor that favors tumor immune evasion by a dual mechanism involving both the suppression of innate immune signaling and the induction of PD-L1-mediated immune checkpoint responses. Mechanistically, SMARCAL1 relieves endogenous DNA damage and suppresses cGAS-STING-dependent immune signaling during cancer cell growth. Simultaneously, it cooperates with the AP-1 family member JUN to maintain chromatin accessibility at a transcriptional regulatory element in the PD-L1 gene, thereby promoting PD-L1 expression in cancer cells. Loss of SMARCAL1 enhances anti-tumor immune responses and sensitizes tumors to immune checkpoint blockade in a mouse melanoma model. Collectively, these studies uncover SMARCAL1 as a valuable target for cancer immunotherapy. Citation Format: Giuseppe Leuzzi, Alessandro Vasciaveo, Angelo Taglialatela, Xiao Chen, Tessa M. Firestone, Allison R. Hickman, Wendy Mao, Tanay Thakar, Alina Vaitsiankova, Jen-Wei Huang, Raquel Cuella-Martin, Samuel B. Hayward, Jordan S. Kesner, Ali Ghasemzadeh, Tarun S. Nambiar, Patricia Ho, Alexander Rialdi, Maxime Hebrard, Yinglu Li, Jinmei Gao, Saarang Gopinath, Oluwatobi A. Adeleke, Bryan Venters, Charles G. Drake, Richard Baer, Benjamin Izar, Ernesto Guccione, Michael-Christopher Keogh, Raphael Guerois, Lu Sun, Chao Lu, Andrea Califano, Alberto Ciccia. SMARCAL1 is a dual regulator of innate immune signaling and PD-L1 expression that promotes tumor immune evasion [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Damage Repair: From Basic Science to Future Clinical Application; 2024 Jan 9-11; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2024;84(1 Suppl):Abstract nr PR009.
Abstract A003: HPV infection causes dependence on alternative DNA damage response pathways providing cancer specific targets for radiosensitization
Authors: Michael Goldstein, Akhil Kotwal, Nishanth Gabriel, William Buchser, Monica Sentmanat, Stephanie Markovina, Julie Schwarz, Xia Cui
Journal: Cancer Research (2024)

Abstract Targeted radiosensitization is an attractive approach to improving the efficacy of radiotherapy in cancer treatment. However, drugs targeting ubiquitous DNA damage response (DDR) pathways are not cancer specific and can increase radiation related side effects. Thus, there is an unmet clinical need for tumor specific molecular targets. To address this need we sought to identify DNA damage signaling pathways that are unique to cancer cells. We hypothesized that by expressing its genome in host cells high-risk Human Papilloma Virus (HPV) can rewire DNA damage signaling making HPV-positive tumor cells dependent on alternative pathways to survive radiation, which can be exploited for targeted radiosensitization of HPV-induced cancers. Using a CRISPR/Cas9 screen in cells that selectively express HPV16 proteins E6 or E7 we uncovered genes that cells rely on to survive radiation-induced DNA damage in the context of E6 or E7 expression. We demonstrate that targeting these newly identified genes sensitizes cancer cells to radiation specifically in the presence of E6 or E7. We provide mechanistic insights showing that E6 and E7 alter the cellular epigenome by inhibiting histone lysine acetylation and tri-methylation, respectively. In this setting, a member of a centromeric protein complex identified in the screen is critical for mitotic progression and survival in E6-expressing cells following radiation exposure. Deletion of this factor resulted in delayed mitotic progression, chromosomal missegregation and rapid post-mitotic death in irradiated HPV-positive cells, a phenotype that was mitigated by ablation of E6 expression. Furthermore, we identified an E3 ubiquitin ligase that promotes survival in E7-expressing cells following radiation exposure by alleviating perturbations during DNA replication. Together, we have uncovered DDR pathways that are critical for cell survival after radiation exposure specifically in HPV-positive cells. Our findings suggest that expression of viral proteins E6 and E7 rewires DNA damage signaling networks causing dependence on alternative response pathways. We propose that these pathways can be targeted for tumor-specific radiosensitization of HPV-induced cancers. Citation Format: Michael Goldstein, Akhil Kotwal, Nishanth Gabriel, William Buchser, Monica Sentmanat, Stephanie Markovina, Julie Schwarz, Xia Cui. HPV infection causes dependence on alternative DNA damage response pathways providing cancer specific targets for radiosensitization [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Damage Repair: From Basic Science to Future Clinical Application; 2024 Jan 9-11; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2024;84(1 Suppl):Abstract nr A003.
Information decomposition and the informational architecture of the brain
Authors: Andrea I. Luppi, Fernando E. Rosas, Pedro A.M. Mediano, David K. Menon, Emmanuel A. Stamatakis
Journal: Trends in Cognitive Sciences (2024)

To explain how the brain orchestrates information-processing for cognition, we must understand information itself. Importantly, information is not a monolithic entity. Information decomposition techniques provide a way to split information into its constituent elements: unique, redundant, and synergistic information. We review how disentangling synergistic and redundant interactions is redefining our understanding of integrative brain function and its neural organisation. To explain how the brain navigates the trade-offs between redundancy and synergy, we review converging evidence integrating the structural, molecular, and functional underpinnings of synergy and redundancy; their roles in cognition and computation; and how they might arise over evolution and development. Overall, disentangling synergistic and redundant information provides a guiding principle for understanding the informational architecture of the brain and cognition.
Age-Related Macular Degeneration
Authors: Monika Fleckenstein, Steffen Schmitz-Valckenberg, Usha Chakravarthy
Journal: JAMA (2024)

Importance Age-related macular degeneration (AMD) affects approximately 20 million people in the US and 196 million people worldwide. AMD is a leading cause of severe vision impairment in older people and is expected to affect approximately 288 million people worldwide by 2040. Observations Older age, genetic factors, and environmental factors, such as cigarette smoking, are associated with development of AMD. AMD occurs when extracellular deposits accumulate in the outer retina, ultimately leading to photoreceptor degeneration and loss of central vision. The late stages of AMD are characterized by outer retinal atrophy, termed geographic atrophy , or neovascularization associated with subretinal and/or intraretinal exudation, termed exudative neovascular AMD . The annual incidence of AMD ranges from 0.3 per 1000 in people who are aged 55 to 59 years to 36.7 per 1000 in people aged 90 years or older. The estimated heritability of late-stage AMD is approximately 71% (95% CI, 18%-88%). Long-term prospective cohort studies show a significantly higher AMD incidence in people who smoke more than 20 cigarettes per day compared with people who never smoked. AMD is diagnosed primarily with clinical examination that includes a special lens that focuses light of the slit lamp through the pupil. Exudative neovascular AMD is best identified using angiography and by optical coherence tomography. Individuals with AMD who take nutritional supplements consisting of high-dose vitamin C, vitamin E, carotenoids, and zinc have a 20% probability to progress to late-stage AMD at 5 years vs a 28% probability for those taking a placebo. In exudative neovascular AMD, 94.6% of patients receiving monthly intravitreal anti–vascular endothelial growth factor (anti-VEGF) injections experience less than a 15-letter visual acuity loss after 12 months compared with 62.2% receiving sham treatment. Conclusions and Relevance The prevalence of AMD is anticipated to increase worldwide to 288 million individuals by 2040. Intravitreally administered anti-VEGF treatment is first-line therapy for exudative neovascular AMD.
Integrated gut metabolome and microbiome fingerprinting reveals that dysbiosis precedes allergic inflammation in IgE‐mediated pediatric cow's milk allergy
Authors: Ellen De Paepe, Vera Plekhova, Pablo Vangeenderhuysen, Nele Baeck, Dominique Bullens, Tania Claeys, Marilyn De Graeve, Kristien Kamoen, Anneleen Notebaert, Tom Van de Wiele, Wim Van Den Broeck, Koen Vanlede, Myriam Van Winckel, Lars Vereecke, Chris Elliott, Eric Cox, Lynn Vanhaecke
Journal: Allergy (2024)

Abstract Background IgE‐mediated cow's milk allergy (IgE‐CMA) is one of the first allergies to arise in early childhood and may result from exposure to various milk allergens, of which β‐lactoglobulin (BLG) and casein are the most important. Understanding the underlying mechanisms behind IgE‐CMA is imperative for the discovery of novel biomarkers and the design of innovative treatment and prevention strategies. Methods We report a longitudinal in vivo murine model, in which two mice strains (BALB/c and C57Bl/6) were sensitized to BLG using either cholera toxin or an oil emulsion ( n = 6 per group). After sensitization, mice were challenged orally, their clinical signs monitored, antibody (IgE and IgG1) and cytokine levels (IL‐4 and IFN‐γ) measured, and fecal samples subjected to metabolomics. The results of the murine models were further extrapolated to fecal microbiome‐metabolome data from our population of IgE‐CMA ( n = 22) and healthy ( n = 23) children (Trial: NCT04249973), on which polar metabolomics, lipidomics and 16S rRNA metasequencing were performed. In vitro gastrointestinal digestions and multi‐omics corroborated the microbial origin of proposed metabolic changes. Results During mice sensitization, we observed multiple microbially derived metabolic alterations, most importantly bile acid, energy and tryptophan metabolites, that preceded allergic inflammation. We confirmed microbial dysbiosis, and its associated effect on metabolic alterations in our patient cohort, through in vitro digestions and multi‐omics, which was accompanied by metabolic signatures of low‐grade inflammation. Conclusion Our results indicate that gut dysbiosis precedes allergic inflammation and nurtures a chronic low‐grade inflammation in children on elimination diets, opening important new opportunities for future prevention and treatment strategies.
Exposed endoscopic full-thickness resection with reopenable clip-over-the-line method for a duodenal neuroendocrine tumor
Authors: Hitoshi Mori, Noriya Uedo, Satoki Shichijo, Tomoki Michida, Ryu Ishihara
Journal: Endoscopy (2024)

The nonexposed endoscopic full-thickness resection (EFTR) device is available for endoscopic removal of duodenal subepithelial tumors, but the large application cap may make it difficult to resect lesions located in complex areas of the duodenum. Moreover, to insert the device into the duodenum, balloon dilation is often required, thus resection of a lesion behind the pyloric ring is difficult. Exposed EFTR can remove lesions in difficult sites; however, a secure closure method for the full-thickness wound is necessary for the success of the procedure. We report a case of exposed EFTR and full-thickness wound closure by reopenable clip-over-the-line method [1] for duodenal neuroendocrine tumor (NET).
Transcriptome Dynamics and Cell Dialogs Between Oocytes and Granulosa Cells in Mouse Follicle Development
Authors: Wenju Liu, Chuan Chen, Yawei Gao, Xinyu Cui, Yuhan Zhang, Liang Gu, Yuanlin He, Jing Li, Shaorong Gao, Rui Gao, Cizhong Jiang
Journal: Genomics Proteomics & Bioinformatics (2023)

The development and maturation of follicles is a sophisticated and multistage process. The dynamic gene expression of oocytes and their surrounding somatic cells and the dialogs between these cells are critical to this process. In this study, we accurately classified the oocyte and follicle development into nine stages and profiled the gene expression of mouse oocytes and their surrounding granulosa cells and cumulus cells. The clustering of the transcriptomes showed the trajectories of two distinct development courses of oocytes and their surrounding somatic cells. Gene expression changes precipitously increased at Type 4 stage and drastically dropped afterward within both oocytes and granulosa cells. Moreover, the number of differentially expressed genes between oocytes and granulosa cells dramatically increased at Type 4 stage, most of which persistently passed on to the later stages. Strikingly, cell communications within and between oocytes and granulosa cells became active from Type 4 stage onward. Cell dialogs connected oocytes and granulosa cells in both unidirectional and bidirectional manners. TGFB2/3, TGFBR2/3, INHBA/B, and ACVR1/1B/2B of TGF-β signaling pathway functioned in the follicle development. NOTCH signaling pathway regulated the development of granulosa cells. Additionally, many maternally DNA methylation- or H3K27me3-imprinted genes remained active in granulosa cells but silent in oocytes during oogenesis. Collectively, Type 4 stage is the key turning point when significant transcription changes diverge the fate of oocytes and granulosa cells, and the cell dialogs become active to assure follicle development. These findings shed new insights on the transcriptome dynamics and cell dialogs facilitating the development and maturation of oocytes and follicles.
Abstract A001: Discovery of imidazo [4,5-c]pyridin-2-ones as selective inhibitors of DNA-dependent protein kinase and effective radiosensitizers
Authors: Michael P. Hay, Cho R. Hong, Lydia P. Liew, Benjamin D. Dickson, Way W. Wong, Sophia F. O'Brien-Gortner, Rebecca Airey, Jagdish Jaiswal, William R. Wilson, Stephen M. Jamieson
Journal: Cancer Research (2024)

Abstract Inhibition of the repair of radiation-induced DNA double strand breaks (DSB) offers the potential to sensitize tumors to radiation therapy. The dominant role of non-homologous end-joining in the repair of radiation-induced DSBs indicates that DNA-dependent protein kinase (DNA-PK) is an excellent target for the development of radiosensitizers. We report the discovery of a new chemical class of kinase inhibitor based on the imidazo[4,5-c]pyridin-2-one scaffold. The class was developed by scaffold-hopping from the pan phosphoinositide 3-kinsase (PI3K) and PI3K-like kinase (PIKK) inhibitor dactolisib. Iterative development culminated in the identification of SN39536 as a low nM DNA-PK inhibitor with excellent selectivity. Further modification led to the discovery of the more potent and more selective SN40905. Both SN39536 and SN40905 were effective inhibitors of DNA-PK kinase activity in a biochemical assay with substantial selectivity for DNA-PK across the PIKK and PI3K families. Both compounds selectively inhibited growth of HAP1 PRKDC wild-type cells when combined with radiation, but not the corresponding PRKDC-/- cells. SN39536 and SN40905 were effective radiosensitizers of colorectal carcinoma (HCT116), non-small cell lung cancer (H460, H1299, and A549), pancreatic (BxPC-3, PANC-1, and MiaPaCa-2) and head and neck squamous cell carcinoma (FaDu and UT-SCC-74B) cells determined using a clonogenic survival endpoint. Both SN39536 and SN40905 displayed high oral bioavailability. When administered PO at a range of non-toxic doses, both SN39536 and SN40905 provided significant additional tumor cell killing of HCT116, UT-SCC-74B, and BxPC-3 tumor xenografts in combination with a single (13 Gy) radiation treatment determined by ex vivo clonogenic survival assays. SN39536 also provided substantial tumor growth inhibition of HCT116 tumor xenografts in combination with RAD (10 Gy). SN39536 and SN40905 represent a new, potent, and selective class of DNA-PK inhibitors with significant potential as radiosensitizers for the treatment of human cancers. Citation Format: Michael P. Hay, Cho R. Hong, Lydia P. Liew, Benjamin D. Dickson, Way W. Wong, Sophia F. O'Brien-Gortner, Rebecca Airey, Jagdish Jaiswal, William R. Wilson, Stephen M. Jamieson. Discovery of imidazo [4,5-c]pyridin-2-ones as selective inhibitors of DNA-dependent protein kinase and effective radiosensitizers [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Damage Repair: From Basic Science to Future Clinical Application; 2024 Jan 9-11; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2024;84(1 Suppl):Abstract nr A001.