Anti-ROR1 CAR-T cells: Architecture and performance

Osorio-Rodríguez, Daniel Andrés; Camacho, Bernardo

doi:10.3389/fmed.2023.1121020

Cited by 8 publications

(2 citation statements)

References 148 publications

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“…By comparing brain organ samples from humans and great apes, it was found that the epithelial-mesenchymal transition regulator ZEB2 promotes the transformation of neural epithelium, which ultimately leads to the expansion of the human brain[51]. The membrane receptor ROR1, which is crucial for embryonic development and overexpressed in multiple cancers, has been shown to be a safe and practical target for CAR-T cell immunotherapy in clinical trials using non-human primates[52, 53].…”

Section: Resultsmentioning

confidence: 99%

Enhancing Recognition and Interpretation of Functional Phenotypic Sequences through Fine-Tuning Pre-Trained Genomic Models

Du,

Zhong,

Liu

2023

Preprint

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Decoding high-quality human genomic sequences requires comprehensive analysis of DNA sequence functionality. Through computational and experimental approaches, researchers study the genotype-phenotype relationship and generate important datasets that help unravel complicated genetic blueprints. This study explores the use of deep learning, particularly pre-trained models like DNA_bert_6 and human_gpt2-v1, in interpreting and representing human genome sequences. We meticulously construct multiple datasets linking genotypes and phenotypes to fine-tune pre-trained models for precise DNA sequence classification. Furthermore, we specifically focused on the human endogenous retrovirus (HERV) dataset with commendable classification performance (both binary and multi-classification accuracy and F1 values above 0.935 and 0.888, respectively). We evaluate the influence of sequence length on classification results and analyze the impact of feature extraction in the model’s hidden layers using the HERV dataset. To further understand the phenotype-specific patterns learned by the model, we perform enrichment, pathogenicity and conservation analyzes of specific motifs in the HERV sequence with high average local representation weight (LRAW) scores. Overall, the generated datasets further provide numerous additional genotype-phenotype datasets for evaluating the performance of genomic models. The findings highlight the potential of large models in learning DNA sequence representations, particularly when utilizing the HERV dataset, and provide valuable insights for future research. This work represents an innovative strategy that combines pre-trained model representations with classical omics methods for analyzing the functionality of genome sequences, fostering cross-fertilization between genomics and advanced AI. The source code and data are available athttps://github.com/GeorgeBGM/Genome_Fine-Tuning.

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Section: Resultsmentioning

confidence: 99%

Enhancing Recognition and Interpretation of Functional Phenotypic Sequences through Fine-Tuning Pre-Trained Genomic Models

Du,

Zhong,

Liu

2023

Preprint

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“…All data and custom scripts were collected and stored using Git version control. Code for raw data processing, analysis, and figure generation is available in the GitHub repository ( https://github.com/daniosro/Si_biomineralization_ANME_SRB ) ( 92 ). All other data are included in the manuscript and/or supporting information .…”

Section: Data Materials and Software Availabilitymentioning

confidence: 99%

Microbially induced precipitation of silica by anaerobic methane-oxidizing consortia and implications for microbial fossil preservation

Osorio-Rodriguez,

Metcalfe,

McGlynn

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

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Authigenic carbonate minerals can preserve biosignatures of microbial anaerobic oxidation of methane (AOM) in the rock record. It is not currently known whether the microorganisms that mediate sulfate-coupled AOM—often occurring as multicelled consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB)—are preserved as microfossils. Electron microscopy of ANME-SRB consortia in methane seep sediments has shown that these microorganisms can be associated with silicate minerals such as clays [Chen et al ., Sci. Rep. 4 , 1–9 (2014)], but the biogenicity of these phases, their geochemical composition, and their potential preservation in the rock record is poorly constrained. Long-term laboratory AOM enrichment cultures in sediment-free artificial seawater [Yu et al ., Appl. Environ. Microbiol. 88 , e02109-21 (2022)] resulted in precipitation of amorphous silicate particles (~200 nm) within clusters of exopolymer-rich AOM consortia from media undersaturated with respect to silica, suggestive of a microbially mediated process. The use of techniques like correlative fluorescence in situ hybridization (FISH), scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDS), and nanoscale secondary ion mass spectrometry (nanoSIMS) on AOM consortia from methane seep authigenic carbonates and sediments further revealed that they are enveloped in a silica-rich phase similar to the mineral phase on ANME-SRB consortia in enrichment cultures. Like in cyanobacteria [Moore et al ., Geology 48 , 862–866 (2020)], the Si-rich phases on ANME-SRB consortia identified here may enhance their preservation as microfossils. The morphology of these silica-rich precipitates, consistent with amorphous-type clay-like spheroids formed within organic assemblages, provides an additional mineralogical signature that may assist in the search for structural remnants of microbial consortia in rocks which formed in methane-rich environments from Earth and other planetary bodies.

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Targeted immunotherapy and nanomedicine for rhabdomyosarcoma: The way of the future

Morel,

Rössler,

Bernasconi

2024

Medicinal Research Reviews

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Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma of childhood. Histology separates two main subtypes: embryonal RMS (eRMS; 60%–70%) and alveolar RMS (aRMS; 20%–30%). The aggressive aRMS carry one of two characteristic chromosomal translocations that result in the expression of a PAX3::FOXO1 or PAX7::FOXO1 fusion transcription factor; therefore, aRMS are now classified as fusion‐positive (FP) RMS. Embryonal RMS have a better prognosis and are clinically indistinguishable from fusion‐negative (FN) RMS. Next to histology and molecular characteristics, RMS risk groupings are now available defining low risk tumors with excellent outcomes and advanced stage disease with poor prognosis, with an overall survival of about only 20% despite intensified multimodal treatment. Therefore, development of novel effective targeted strategies to increase survival and to decrease long‐term side effects is urgently needed. Recently, immunotherapies and nanomedicine have been emerging for potent and effective tumor treatments with minimal side effects, raising hopes for effective and safe cures for RMS patients. This review aims to describe the most relevant preclinical and clinical studies in immunotherapy and targeted nanomedicine performed so far in RMS and to provide an insight in future developments.

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Anti-ROR1 CAR-T cells: Architecture and performance

Cited by 8 publications

References 148 publications

Enhancing Recognition and Interpretation of Functional Phenotypic Sequences through Fine-Tuning Pre-Trained Genomic Models

Enhancing Recognition and Interpretation of Functional Phenotypic Sequences through Fine-Tuning Pre-Trained Genomic Models

Microbially induced precipitation of silica by anaerobic methane-oxidizing consortia and implications for microbial fossil preservation

Targeted immunotherapy and nanomedicine for rhabdomyosarcoma: The way of the future

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