Epigenomic analysis of formalin-fixed paraffin-embedded samples by CUT&Tag

Benchmark of chromatin-protein interaction methods in haploid round spermatids

Introduction

Chromatin-protein interactions are fundamental for regulation of gene transcription. While chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) has long been the gold standard for mapping these interactions, emerging techniques such as CUT&RUN and CUT&Tag, which offer advantages such as low-input requirements and high signal-to-noise ratios, have aroused great attention. However, research addressing the potential biases introduced by enzyme-based tagmentation approaches and comparative assessment with ChIP-seq remain absent.

Methods

This study aims to systematically evaluate and compare the performance of ChIP-seq, CUT&Tag, and CUT&RUN for profiling genome-wide transcription factors and histone modification binding.

Results

Our analysis revealed that all three methods reliably detect histone modifications and transcription factor enrichment, with CUT&Tag standing out for its comparatively higher signal-to-noise ratio. Detailed peak comparison revealed unique and overlapping enrichment among the three techniques. Additionally, CUT&Tag can identify novel CTCF peaks compared with the other two methods. A strong correlation was observed between CUT&Tag signal intensity and chromatin accessibility, highlighting its ability to generate high-resolution signals in accessible regions.

Discussion

The systematic comparison summarizes the differences between CUT&Tag and CUT&RUN in terms of the signal-to-noise ratio and bias toward accessible chromatin. Considering the experimental procedures, signal specificity, and inherent biases, we recommend tailoring the choice of method to the type of chromatin-protein interaction under study. CUT&Tag offers a promising alternative for applications requiring high sensitivity and reduced background noise.

Global modulation of gene expression and transcriptome size in aneuploid combinations of maize

Genomic imbalance refers to the more severe phenotypic consequences of changing a single chromosome compared to changing the whole genomic set. Previous genomic imbalance studies in maize have identified gene expression modulation in aneuploids of single chromosome arms. Here, the modulation of gene expression in more complex aneuploids, e.g., monosomy of one chromosome arm and trisomy of another was examined to determine the extent that combination aneuploids were additive, multiplicative, or rebalanced in terms of their effect on gene expression. A series of genetic crosses was performed to produce one, two, and three copies of one arm with independent one, two, and three copies of the other arm in each of the three genotypes for the opposite arm. In total, 31 combinations were analyzed. By examining RNA modulation, we found that cis genes on varied chromosome arms are generally more dosage-compensated in aneuploid combinations than in single aneuploidy even though some showed a clear dosage effect. For genes on the unvaried chromosomes (trans), there is greater modulation in most of the aneuploidy combinations. Finally, 22 of the 31 combinations were found to have an altered transcriptome size, suggesting that extensive stoichiometric changes of genomic regions upset global messenger RNA (mRNA) transcription. Overall, these results have important implications for understanding the role of genomic stoichiometry for mechanisms of gene expression, the evolution of dosage-sensitive duplicated genes, the evolution of sex chromosomes, the rapid growth adaptation of aneuploid cancer cells, and the control of quantitative traits.

Total whole-arm chromosome losses predict malignancy in human cancer

Aneuploidy is observed as gains or losses of whole chromosomes or chromosome arms and is a common hallmark of cancer. Whereas models for the generation of aneuploidy in cancer invoke mitotic chromosome segregation errors, whole-arm losses might occur simply as a result of centromere breakage. We recently showed that elevated RNA Polymerase II level over the S-phase-dependent histone genes predicts rapid recurrence of human meningioma and is correlated with total whole-arm losses relative to gains. To explain this imbalance in arm losses over gains, we have proposed that histone overexpression at S-phase competes with the histone H3 variant CENP-A, resulting in centromere breaks and whole-arm losses. To test whether centromere breaks alone can drive aneuploidy, we ask whether total whole-arm aneuploids can predict outcomes across different cancer types in large RNA and whole-genome sequencing databanks. We find that total whole-arm losses generally predict outcome, suggesting that centromere breakage is a major initiating factor leading to aneuploidy and the resulting changes in the selective landscape that drive most cancers. We also present evidence that centromere breakage alone is sufficient to account for whole-arm losses and gains, contrary to mitotic spindle error models for the generation of aneuploidy. Our results suggest that therapeutic intervention targeting histone overexpression has the potential to reduce aneuploidy and slow cancer progression.

Chromatin profiling to identify biomarkers in inflammatory bowel diseases

PURPOSE OF REVIEW

Chromatin plays a critical role in gene regulation and disease pathogenesis. In inflammatory bowel disease (IBD), alterations in chromatin structure contribute to disease heterogeneity and impact treatment responses. This review explores chromatin accessibility and chromatin-associated proteins as biomarkers for IBD and highlights recent technological advancements enabling targeted biomarker discovery and novel therapies.

RECENT FINDINGS

Advancements in high-throughput sequencing have enabled genome-wide profiling of chromatin interactions in IBD. Studies have identified distinct chromatin landscapes in Crohn's disease (CD) and ulcerative colitis (UC), revealing stable regulatory shifts independent of inflammation.

SUMMARY

Chromatin profiling offers a novel approach for identifying biomarkers and therapeutic targets in IBD. Integrating chromatin accessibility data with transcriptomic and epigenomic analyses can refine disease classification and guide personalized treatment strategies. Emerging techniques compatible with formalin-fixed paraffin-embedded (FFPE) samples enhance clinical applicability, bridging the gap between molecular research and precision gastroenterology.

Total whole-arm chromosome losses predict malignancy in human cancer

Aneuploidy is observed as gains or losses of whole chromosomes or chromosome arms and is a common hallmark of cancer. Whereas models for the generation of aneuploidy in cancer invoke mitotic chromosome segregation errors, whole-arm losses might occur simply as a result of centromere breakage. We recently showed that elevated RNA Polymerase II (RNAPII) level over S-phase-dependent histone genes predicts rapid recurrence of human meningioma and is correlated with total whole-arm losses relative to gains. To explain this imbalance in arm losses over gains, we have proposed that histone overexpression at S-phase competes with the histone H3 variant CENP-A, resulting in centromere breaks and whole-arm losses. To test whether centromere breaks alone can drive aneuploidy, we ask whether total whole-arm aneuploids can predict outcome across different cancer types in large RNA and whole-genome sequencing databanks. We find that total whole-arm losses generally predict outcome, suggesting that centromere breakage is a major initiating factor leading to aneuploidy and the resulting changes in the selective landscape that drive most cancers. We also present evidence that centromere breakage alone is sufficient to account for whole-arm losses and gains, contrary to mitotic spindle error models for generation of aneuploidy. Our results suggest that therapeutic intervention targeting histone overexpression has the potential of reducing aneuploidy and slowing cancer progression.

Significance Statement

Gain or loss of whole chromosome arms following centromere breaks is frequent in cancer, but whether or not there is a common initiating event is unknown. Here we show that the total number of whole-arm losses predicts patient outcomes across cancer types, suggesting a causal relationship. This general excess of losses over gains is not predicted by mitotic error models of aneuploidy but rather suggests that centromere breaks themselves initiate whole-arm aneuploidies. Insofar as aneuploidy reshapes the selective landscapes that drive most cancers, our results have potential clinical implications.

Proposal of a Safe Transport Protocol and Its Utility of Antigen-Preserving Tissue for Formalin-Fixed Porcine Renal Samples

Background: Formalin is widely used as a standard fixative in histopathological analysis; however, its high toxicity and strict regulatory restrictions create challenges for the safe transport and external evaluation of specimens. In translational research utilizing large animal models, establishing a reliable transport protocol that preserves both tissue structure and antigenicity remains essential. Objective: This study aimed to develop and validate a protocol for the safe transport of formalin-fixed renal specimens while maintaining their histopathological and immunohistochemical integrity. Methods: Using a porcine model, renal specimens were fixed in formalin and subsequently substituted with physiological saline or 70% ethanol before transport. These were compared with specimens transported in formalin without substitution. Following transportation, hematoxylin and eosin (HE) staining and immunohistochemistry (Nephrin, E-cadherin, CD3) were performed to assess tissue integrity, antigenicity, and structural preservation. Additionally, sample degradation, antigen loss, and potential leakage were evaluated. Results: Specimens substituted with saline or ethanol retained cellular structure and antigenicity comparable to those transported in formalin, with no significant deterioration in histological or immunohistochemical quality. Furthermore, no leakage or sample damage was observed during transport, demonstrating the feasibility of this replacement protocol for routine pathological assessments. Conclusions: These findings suggest that formalin substitution with saline or ethanol provides a viable alternative for specimen transport, ensuring both biosafety and analytical integrity. This protocol may enhance specimen handling in preclinical research, regulatory compliance, and international collaboration in pathology and regenerative medicine.

Understanding developing kidneys and Wilms tumors one cell at a time

Single-cell sequencing-based techniques are revolutionizing all fields of biomedical sciences, including normal kidney development and how this is disturbed in the development of Wilms tumor. The many different techniques and the differences between them can obscure which technique is best used to answer which question. In this review we summarize the techniques currently available, discuss which have been used in kidney development or Wilms tumor context, and which techniques can or should be combined to maximize the increase in biological understanding we can get from them.

Distinct structural and functional heterochromatin partitioning of lamin B1 and lamin B2 revealed using genome-wide nicking enzyme epitope targeted DNA sequencing

Gene expression is regulated by chromatin DNA methylation and other features, including histone post-translational modifications (PTMs), chromatin remodelers and transcription factor occupancy. A complete understanding of gene regulation will require the mapping of these chromatin features in small cell number samples. Here we describe a novel genome-wide chromatin profiling technology, named as Nicking Enzyme Epitope targeted DNA sequencing (NEED-seq). NEED-seq offers antibody-targeted controlled nicking by Nt.CviPII-pGL fusion to study specific protein-DNA complexes in formaldehyde fixed cells, allowing for both visual and genomic resolution of epitope bound chromatin. When applied to nuclei, NEED-seq yielded genome-wide profile of chromatin-associated proteins and histone PTMs. Additionally, NEED-seq of lamin B1 and B2 demonstrated their association with heterochromatin. Lamin B1- and B2-associated domains (LAD) segregated to three different states, and states with stronger LAD correlated with heterochromatic marks. Hi-C analysis displayed A and B compartment with equal lamin B1 and B2 distribution, although methylated DNA remained high in B compartment. LAD clustering with Hi-C resulted in subcompartments, with lamin B1 and B2 partitioning to facultative and constitutive heterochromatin, respectively, and were associated with neuronal development. Thus, lamin B1 and B2 show structural and functional partitioning in mammalian nucleus.

RNA polymerase II at histone genes predicts outcome in human cancer

Genome-wide hypertranscription is common in human cancer and predicts poor prognosis. To understand how hypertranscription might drive cancer, we applied our formalin-fixed paraffin-embedded (FFPE)-cleavage under targeted accessible chromatin method for mapping RNA polymerase II (RNAPII) genome-wide in FFPE sections. We demonstrate global RNAPII elevations in mouse gliomas and assorted human tumors in small clinical samples and discover regional elevations corresponding to de novo HER2 amplifications punctuated by likely selective sweeps. RNAPII occupancy at S-phase-dependent histone genes correlated with WHO grade in meningiomas, accurately predicted rapid recurrence, and corresponded to whole-arm chromosome losses. Elevated RNAPII at histone genes in meningiomas and diverse breast cancers is consistent with histone production being rate-limiting for S-phase progression and histone gene hypertranscription driving overproliferation and aneuploidy in cancer, with general implications for precision oncology.

RNA Polymerase II hypertranscription at histone genes in cancer FFPE samples

Genome-wide hypertranscription is common in human cancer and predicts poor prognosis. To understand how hypertranscription might drive cancer, we applied our FFPE-CUTAC method for mapping RNA Polymerase II (RNAPII) genome-wide in formalin-fixed paraffin-embedded (FFPE) sections. We demonstrate global RNAPII elevations in mouse gliomas and assorted human tumors in small clinical samples and discover regional elevations corresponding to de novo HER2 amplifications punctuated by likely selective sweeps. RNAPII occupancy at replication-coupled histone genes correlated with WHO grade in meningiomas, accurately predicted rapid recurrence, and corresponded to whole-arm chromosome losses. Elevated RNAPII at histone genes in meningiomas and diverse breast cancers is consistent with histone production being rate-limiting for S-phase progression and histone gene hypertranscription driving overproliferation and aneuploidy in cancer, with general implications for precision oncology.

Emerging Approaches to Profile Accessible Chromatin from Formalin-Fixed Paraffin-Embedded Sections

Nucleosomes are non-uniformly distributed across eukaryotic genomes, with stretches of 'open' chromatin strongly associated with transcriptionally active promoters and enhancers. Understanding chromatin accessibility patterns in normal tissue and how they are altered in pathologies can provide critical insights to development and disease. With the advent of high-throughput sequencing, a variety of strategies have been devised to identify open regions across the genome, including DNase-seq, MNase-seq, FAIRE-seq, ATAC-seq, and NicE-seq. However, the broad application of such methods to FFPE (formalin-fixed paraffin-embedded) tissues has been curtailed by the major technical challenges imposed by highly fixed and often damaged genomic material. Here, we review the most common approaches for mapping open chromatin regions, recent optimizations to overcome the challenges of working with FFPE tissue, and a brief overview of a typical data pipeline with analysis considerations.