In this work, we systematically benchmarked four widely used peak-calling tools, MACS2, SEACR, GoPeaks, and LanceOtron, for the CUT&RUN assay. Here, we compared each tool’s sensitivity, precision, and overall performance across datasets with different fragment sizes, signal strengths, and background noise. We found that no single method dominates in every scenario: for example, some tools perform better on broad peaks, others on narrow peaks; some are more robust to low signal-to-noise. These insights provide practical guidance in choosing peak callers depending on the CUT&RUN experimental design and highlight trade-offs that are often overlooked.

In this review, we explored the groundbreaking application of CAR-T cell therapy in CRC. While initially successful in blood cancers, CAR-T therapy is now being developed for solid tumors like CRC, with promising preclinical and early clinical trial results. The article examines key targets such as GUCY2C, LGR5, and CDH17, as well as emerging strategies like logic-gated and armored CAR-T designs. It also highlights the challenges posed by the tumor microenvironment and offers insights into patient selection based on genomic and epigenomic tumor subtypes and immune profiles. Together, these advances signal a new frontier in personalized immunotherapy for CRC.

This work provides an in-depth examination of the methodologies, computational tools, and frameworks developed to map the three-dimensional (3D) architecture of the genome, focusing on both ligation-based and ligation-free techniques.

Epigenome-based Classification (EpiC) leverages patterns of histone modifications to stratify CRC tumors with higher precision, capturing additional tumor heterogeneity not visible through genomic or transcriptomic data alone. This integration of epigenomic data could complement existing classifications (e.g. CMS, CRIS, PDS) by identifying new therapeutic targets and providing insights into the tumor's regulatory landscape, thereby supporting the development of more tailored and effective therapeutic strategies.