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Loss of histone H3K27 Trimethylation (H3K27me3) immunohistochemical expression is commonly used as an ancillary test and a surrogate marker for the diagnosis of malignant peripheral nerve sheath tumor (MPNST). A potential histological mimic of MPNST is sarcomatoid carcinoma. Prompted by an index specimen of sarcomatoid carcinoma with H3K27me3 loss and the lack of literature on such phenomenon, we sought to determine the frequency of H3K27me3 loss of expression in a cohort of sarcomatoid carcinomas. Fifty specimens of primary and metastatic sarcomatoid carcinomas with spindle cell morphology mimicking MPNST were prospectively and retrospectively retrieved from our institutional archives and stained with an antibody to H3K27me3. H3K27me3 staining was lost in 4 of the 50 specimens (8%). These specimens included a primary sarcomatoid urothelial carcinoma of the bladder resection, two local recurrences (sarcomatoid squamous cell carcinoma of the larynx and oral cavity) as well as a metastatic sarcomatoid renal cell carcinoma. Next-generation sequencing performed on all four specimens demonstrated gene mutations and copy number alterations with TP53, FANC (FANCD2 and FANCI), and TERT being the most common gene mutations and CDKN2A/B copy number loss and 11q region amplification being the most common copy number gene alterations. Mutations involving NF1, SUZ12, or EED were absent in all tested specimens. In conclusion, H3K27me3 expression may be lost in as many as 8% of sarcomatoid carcinomas which can pose as a potential diagnostic pitfall, especially in challenging sarcomatoid carcinoma specimens with absent keratin staining. [ABSTRACT FROM AUTHOR]

Common fragile sites (CFSs) are specific regions of all individuals' genome that are predisposed to DNA double strand breaks (DSBs) and undergo subsequent rearrangements. CFS formation can be induced in vitro by mild level of DNA replication stress, such as DNA polymerase inhibition or nucleotide pool disturbance. The mechanisms of CFS formation have been linked to DNA replication timing control, transcription activities, as well as chromatin organization. However, it is unclear what specific cis- or trans-factors regulate the interplay between replication and transcription that determineCFS formation. We recently reported genome-wide mapping of DNA DSBs under replication stress induced by aphidicolin in human lymphoblastoids for the first time. Here, we systematically compared these DSBs with regards to nearby epigenomic features mapped in the same cell line from published studies. We demonstrate that aphidicolin-induced DSBs are strongly correlated with histone 3 lysine 36 trimethylation, a marker for active transcription. We further demonstrate that this DSB signature is a composite effect by the dual treatment of aphidicolin and its solvent, dimethylsulfoxide, the latter of which potently induces transcription on its own. We also present complementing evidence for the association between DSBs and 3D chromosome architectural domains with high density gene cluster and active transcription. Additionally, we show that while DSBswere detected at all but one of the fourteen finely mapped CFSs, they were not enriched in the CFS core sequences and rather demarcated the CFS core region. Related to this point, DSB density was not higher in large genes of greater than 300 kb, contrary to reported enrichment of CFS sites at these large genes. Finally, replication timing analyses demonstrate that the CFS core region contain initiation events, suggesting that altered replication dynamics are responsible for CFS formation in relatively higher level of replication stress. [ABSTRACT FROM AUTHOR]

Common fragile sites (CFSs) are specific regions of all individuals’ genome that are predisposed to DNA double strand breaks (DSBs) and undergo subsequent rearrangements. CFS formation can be induced in vitro by mild level of DNA replication stress, such as DNA polymerase inhibition or nucleotide pool disturbance. The mechanisms of CFS formation have been linked to DNA replication timing control, transcription activities, as well as chromatin organization. However, it is unclear what specific cis- or trans-factors regulate the interplay between replication and transcription that determine CFS formation. We recently reported genome-wide mapping of DNA DSBs under replication stress induced by aphidicolin in human lymphoblastoids for the first time. Here, we systematically compared these DSBs with regards to nearby epigenomic features mapped in the same cell line from published studies. We demonstrate that aphidicolin-induced DSBs are strongly correlated with histone 3 lysine 36 trimethylation, a marker for active transcription. We further demonstrate that this DSB signature is a composite effect by the dual treatment of aphidicolin and its solvent, dimethylsulfoxide, the latter of which potently induces transcription on its own. We also present complementing evidence for the association between DSBs and 3D chromosome architectural domains with high density gene cluster and active transcription. Additionally, we show that while DSBs were detected at all but one of the fourteen finely mapped CFSs, they were not enriched in the CFS core sequences and rather demarcated the CFS core region. Related to this point, DSB density was not higher in large genes of greater than 300 kb, contrary to reported enrichment of CFS sites at these large genes. Finally, replication timing analyses demonstrate that the CFS core region contain initiation events, suggesting that altered replication dynamics are responsible for CFS formation in relatively higher level of replication stress.