Bioinformatics modeling for KLF2-Binding downstream promoter motifs of cytotoxic T-cell regulation

Jason Chengwu Duan; Wenqin Li; Biaoru Li; Jason Chengwu Duan; Wenqin Li; Biaoru Li

doi:10.3934/Allergy.2026007

AIMS Allergy and Immunology

2026, Volume 10, Issue 2: 71-82. doi: 10.3934/Allergy.2026007

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Research article

Bioinformatics modeling for KLF2-Binding downstream promoter motifs of cytotoxic T-cell regulation

1.
Department of Biostatistics, University of California, Los Angeles, CA, USA
2.
Department of Chemistry, University of California, Irvine, CA 92697, USA
3.
Senior Faculty of Principal Research Scientist, Department of Pediatrics and GA Cancer Center, Children Hospital at GA, Augusta, GA 30913, USA

Received: 22 December 2025 Revised: 02 May 2026 Accepted: 19 May 2026 Published: 28 May 2026

To support the study of Krüppel-like factor 2 (KLF2) regulatory mechanisms on cytotoxic T lymphocytes (CTLs), we studied a possibility with a web-based bioinformatics module that enables researchers to identify putative KLF2-binding promoter regions in genomic DNA sequences. After a KLF2 protein structure with C2H2 zinc finger domain and binding-site analysis, we successfully set up a tool to integrate Python-based sequence parsing and motif identification routines to locate CACCC motifs near potential start codons (e.g., ATG) across reading frames associated with key CTL genes such as TNF-α and IFN-γ. The tool supports visualization and sequence upload functionality through a static website interface, making it accessible for researchers and clinicians investigating KLF2-mediated transcriptional control in tumor-infiltrating lymphocytes (TILs). This work supplements our primary study on spatial-temporal regulatory networks involved in TIL reactivation by KLF2 down-regulation.
Citation: Jason Chengwu Duan, Wenqin Li, Biaoru Li. Bioinformatics modeling for KLF2-Binding downstream promoter motifs of cytotoxic T-cell regulation[J]. AIMS Allergy and Immunology, 2026, 10(2): 71-82. doi: 10.3934/Allergy.2026007

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Abstract

To support the study of Krüppel-like factor 2 (KLF2) regulatory mechanisms on cytotoxic T lymphocytes (CTLs), we studied a possibility with a web-based bioinformatics module that enables researchers to identify putative KLF2-binding promoter regions in genomic DNA sequences. After a KLF2 protein structure with C2H2 zinc finger domain and binding-site analysis, we successfully set up a tool to integrate Python-based sequence parsing and motif identification routines to locate CACCC motifs near potential start codons (e.g., ATG) across reading frames associated with key CTL genes such as TNF-α and IFN-γ. The tool supports visualization and sequence upload functionality through a static website interface, making it accessible for researchers and clinicians investigating KLF2-mediated transcriptional control in tumor-infiltrating lymphocytes (TILs). This work supplements our primary study on spatial-temporal regulatory networks involved in TIL reactivation by KLF2 down-regulation.

Acknowledgments

With the support of Dr. H. D. Preisler, we have set up a method to analyze genomic profiles of CD3, CD4, and CD8 from TIL. This work was supported by National Cancer Institute IRG-91-022-09, USA (to BL).

Conflicts of interest

Biaoru Li is a member of the editorial board of the Allergy and Immunology and was not involved in the editorial review or the decision to publish this article. The authors declare no conflict of interest.

Author contributions

CWD (1) performs in silico experiments and WQL experimental fields, including biostatistics. BL conceived and designed the experiments.

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