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      KRT17 Promotes T-lymphocyte Infiltration Through the YTHDF2–CXCL10 Axis in Colorectal Cancer

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          Abstract

          KRT17 is highly expressed in deficient mismatch repair colorectal cancer, where it promotes T-cell infiltration via the YTHDF2–CXCL10 axis. KRT17 expression correlates with improved immunotherapy responsiveness, highlighting a potential prospective biomarker and therapeutic target for immunotherapy.

          Abstract

          Poor infiltration of T lymphocytes has been regarded as a crucial mechanism of tumor immune escape. Here, we demonstrate a protective role of KRT17 in colorectal cancer, where KRT17 reversed the tumor immunosuppressive microenvironment by increasing T-lymphocyte infiltration. High-throughput RNA sequencing suggested that KRT17 was significantly upregulated in deficient mismatch repair (dMMR) tumors compared with proficient mismatch repair (pMMR) tumors. In a colorectal cancer cohort of 446 cases, KRT17 expression positively correlated with better clinical outcomes. Krt17 overexpression decreased xenograft tumor growth in immune-competent mice. T-cell depletion in a murine model showed that the presence of T lymphocytes was necessary for Krt17-mediated disruption of tumorigenesis. Mass spectrometry and coimmunoprecipitation assays suggested KRT17 caused YTHDF2 degradation through the ubiquitin-proteasome system. Through high-throughput RNA immunoprecipitation sequencing, we found that CXCL10 was the target gene of the N6-methyladenosine (m 6A) “reader” YTHDF2. KRT17 synergized with anti–PD-1 for better tumor control in an immunotherapy-resistant murine model. In a cohort of patients with colorectal cancer receiving pembrolizumab, high KRT17 expression was found within the tumors of responders. Collectively, we elucidated a critical role of KRT17 in colorectal cancer to prevent immune escape. These findings present new insights into potential therapeutic strategies and effective markers of immunotherapy reactivity against pMMR tumors.

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          Fast gapped-read alignment with Bowtie 2.

          As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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            The PRIDE database and related tools and resources in 2019: improving support for quantification data

            Abstract The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world’s largest data repository of mass spectrometry-based proteomics data, and is one of the founding members of the global ProteomeXchange (PX) consortium. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2016. In the last 3 years, public data sharing through PRIDE (as part of PX) has definitely become the norm in the field. In parallel, data re-use of public proteomics data has increased enormously, with multiple applications. We first describe the new architecture of PRIDE Archive, the archival component of PRIDE. PRIDE Archive and the related data submission framework have been further developed to support the increase in submitted data volumes and additional data types. A new scalable and fault tolerant storage backend, Application Programming Interface and web interface have been implemented, as a part of an ongoing process. Additionally, we emphasize the improved support for quantitative proteomics data through the mzTab format. At last, we outline key statistics on the current data contents and volume of downloads, and how PRIDE data are starting to be disseminated to added-value resources including Ensembl, UniProt and Expression Atlas.
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              Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade

              The genomes of cancers deficient in mismatch repair contain exceptionally high numbers of somatic mutations. In a proof-of-concept study, we previously showed that colorectal cancers with mismatch repair deficiency were sensitive to immune checkpoint blockade with antibodies to programmed death receptor-1 (PD-1). We have now expanded this study to evaluate the efficacy of PD-1 blockade in patients with advanced mismatch repair-deficient cancers across 12 different tumor types. Objective radiographic responses were observed in 53% of patients, and complete responses were achieved in 21% of patients. Responses were durable, with median progression-free survival and overall survival still not reached. Functional analysis in a responding patient demonstrated rapid in vivo expansion of neoantigen-specific T cell clones that were reactive to mutant neopeptides found in the tumor. These data support the hypothesis that the large proportion of mutant neoantigens in mismatch repair-deficient cancers make them sensitive to immune checkpoint blockade, regardless of the cancers' tissue of origin.
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                Author and article information

                Journal
                Cancer Immunol Res
                Cancer Immunol Res
                Cancer Immunology Research
                American Association for Cancer Research
                2326-6066
                2326-6074
                05 July 2023
                02 May 2023
                : 11
                : 7
                : 875-894
                Affiliations
                [1 ]Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
                [2 ]Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
                [3 ]Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
                [4 ]Department of Colorectal Surgery, The First Clinical College of Changsha Medical University, Changsha Medical University, Changsha, China.
                Author notes
                [#]

                L. Kang, L. Huang, and X. Zheng contributed equally as coauthors of this article.

                [##]

                W. Liang, H. Liu, and Z. Zeng were co–senior authors of this article.

                [* ] Corresponding Authors: Liang Kang, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China. Phone: 86-203-845-5369; E-mail: kangl@ 123456mail.sysu.edu.cn ; Liang Huang, huangl75@ 123456mail.sysu.edu.cn ; and Xiaobin Zheng, zhengxbn@ 123456mail3.sysu.edu.cn

                Cancer Immunol Res 2023;11:875–94

                Author information
                https://orcid.org/0000-0002-4664-8772
                https://orcid.org/0000-0002-8932-4866
                https://orcid.org/0000-0001-8789-821X
                https://orcid.org/0009-0000-0158-769X
                https://orcid.org/0009-0007-6266-2340
                https://orcid.org/0000-0001-5235-9929
                https://orcid.org/0000-0002-0848-2898
                https://orcid.org/0009-0009-0352-3097
                https://orcid.org/0000-0001-8156-3283
                https://orcid.org/0000-0001-6725-9904
                https://orcid.org/0000-0001-9748-6411
                https://orcid.org/0000-0002-3086-5297
                https://orcid.org/0000-0001-7062-8280
                Article
                CIR-22-0814
                10.1158/2326-6066.CIR-22-0814
                10320689
                37129929
                82dcd56d-5d35-4d38-a7ed-ad2ac88f3fb3
                ©2023 The Authors; Published by the American Association for Cancer Research

                This open access article is distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) license.

                History
                : 13 October 2022
                : 26 January 2023
                : 27 April 2023
                Page count
                Pages: 20
                Funding
                Funded by: National Natural Science Foundation of China (NSFC), https://doi.org/10.13039/501100001809;
                Award ID: 82200569 and 82000515
                Award Recipient :
                Funded by: China Postdoctoral Science Foundation, https://doi.org/10.13039/501100002858;
                Award ID: 2021M703723
                Award Recipient :
                Funded by: Basic and Applied Basic Research Foundation of Guangdong Province (廣東省基礎與應用基礎研究專項資金), https://doi.org/10.13039/501100021171;
                Award ID: 2022A1515012498&#xFF0C
                Award ID: 2021A1515111011 and 2019A1515110043
                Award Recipient :
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                Research Articles

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