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      Recent insights into the therapeutic strategies targeting the pseudokinase PTK7 in cancer

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          Abstract

          The generation of drugs counteracting deregulated protein kinases has been a major focus in cancer therapy development. Breakthroughs in this effort have produced many therapeutic agents to the benefit of patients, mostly through the development of chemical or antibody-based drugs targeting active kinases. These strategies are challenged when considering catalytically inactive protein kinases (or pseudokinases), which represent 10% of the human kinome with many of relevance in cancer. Among the so-called pseudotyrosine kinases, the PTK7 receptor tyrosine kinase (RTK) stands as a bona fide target overexpressed in several solid tumors and hematological malignancies and linked to metastasis, poor prognosis, and resistance to treatment. Despite the lack of catalytic activity, PTK7 has signaling capacities through heterodimerization with active RTKs and offers pharmacological targeting opportunities through its inactive kinase domain. Moreover, PTK7-targeting strategies based on antibody-drug conjugates, aptamers, and CAR-T cell-based therapies have demonstrated encouraging results in preclinical and clinical settings. We review the most recent data assigning to PTK7 a prominent role in cancer progression as well as current preclinical and clinical targeting strategies against RTK family pseudokinases including PTK7.

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          The protein kinase complement of the human genome.

          G. Manning (2002)
          We have catalogued the protein kinase complement of the human genome (the "kinome") using public and proprietary genomic, complementary DNA, and expressed sequence tag (EST) sequences. This provides a starting point for comprehensive analysis of protein phosphorylation in normal and disease states, as well as a detailed view of the current state of human genome analysis through a focus on one large gene family. We identify 518 putative protein kinase genes, of which 71 have not previously been reported or described as kinases, and we extend or correct the protein sequences of 56 more kinases. New genes include members of well-studied families as well as previously unidentified families, some of which are conserved in model organisms. Classification and comparison with model organism kinomes identified orthologous groups and highlighted expansions specific to human and other lineages. We also identified 106 protein kinase pseudogenes. Chromosomal mapping revealed several small clusters of kinase genes and revealed that 244 kinases map to disease loci or cancer amplicons.
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            Comprehensive Molecular Characterization of Human Colon and Rectal Cancer

            Summary To characterize somatic alterations in colorectal carcinoma (CRC), we conducted genome-scale analysis of 276 samples, analyzing exome sequence, DNA copy number, promoter methylation, mRNA and microRNA expression. A subset (97) underwent low-depth-of-coverage whole-genome sequencing. 16% of CRC have hypermutation, three quarters of which have the expected high microsatellite instability (MSI), usually with hypermethylation and MLH1 silencing, but one quarter has somatic mismatch repair gene mutations. Excluding hypermutated cancers, colon and rectum cancers have remarkably similar patterns of genomic alteration. Twenty-four genes are significantly mutated. In addition to the expected APC, TP53, SMAD4, PIK3CA and KRAS mutations, we found frequent mutations in ARID1A, SOX9, and FAM123B/WTX. Recurrent copy number alterations include potentially drug-targetable amplifications of ERBB2 and newly discovered amplification of IGF2. Recurrent chromosomal translocations include fusion of NAV2 and WNT pathway member TCF7L1. Integrative analyses suggest new markers for aggressive CRC and important role for MYC-directed transcriptional activation and repression.
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              Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase

              High-affinity nucleic acid ligands for a protein were isolated by a procedure that depends on alternate cycles of ligand selection from pools of variant sequences and amplification of the bound species. Multiple rounds exponentially enrich the population for the highest affinity species that can be clonally isolated and characterized. In particular one eight-base region of an RNA that interacts with the T4 DNA polymerase was chosen and randomized. Two different sequences were selected by this procedure from the calculated pool of 65,536 species. One is the wild-type sequence found in the bacteriophage mRNA; one is varied from wild type at four positions. The binding constants of these two RNA's to T4 DNA polymerase are equivalent. These protocols with minimal modification can yield high-affinity ligands for any protein that binds nucleic acids as part of its function; high-affinity ligands could conceivably be developed for any target molecule.
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                Author and article information

                Contributors
                jean-paul.borg@inserm.fr
                Journal
                Oncogene
                Oncogene
                Oncogene
                Nature Publishing Group UK (London )
                0950-9232
                1476-5594
                21 May 2024
                21 May 2024
                2024
                : 43
                : 26
                : 1973-1984
                Affiliations
                [1 ]GRID grid.463833.9, ISNI 0000 0004 0572 0656, Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe labellisée Ligue ‘Cell polarity, , Cell signaling and Cancer’, ; Marseille, France
                [2 ]Institut Universitaire de France, ( https://ror.org/055khg266) Paris, France
                [3 ]Present Address: adMare BioInnovations, Vancouver, BC Canada
                Author information
                http://orcid.org/0000-0001-8418-3382
                Article
                3060
                10.1038/s41388-024-03060-x
                11196218
                38773263
                e71f1b02-2819-4b9f-bd8b-a7cc81071c73
                © The Author(s) 2024

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 12 March 2024
                : 2 May 2024
                : 3 May 2024
                Funding
                Funded by: FundRef https://doi.org/10.13039/501100004099, Ligue Contre le Cancer;
                Funded by: FundRef https://doi.org/10.13039/501100004795, Institut Universitaire de France (IUF);
                Funded by: FundRef https://doi.org/10.13039/501100006364, Institut National Du Cancer (French National Cancer Institute);
                Award ID: PLBIO 2017-157
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100004097, Fondation ARC pour la Recherche sur le Cancer (ARC Foundation for Cancer Research);
                Funded by: FundRef https://doi.org/10.13039/501100004793, Ministère de l'Education Nationale, de l'Enseignement Supérieur et de la Recherche (MENESR);
                Categories
                Review Article
                Custom metadata
                © Springer Nature Limited 2024

                Oncology & Radiotherapy
                oncogenes,extracellular signalling molecules
                Oncology & Radiotherapy
                oncogenes, extracellular signalling molecules

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