Abstract 2835: Lamin AC deficiency promotes genomic instability through increased R-loop accumulation
Authors: Christopher William Schultz, Sourav Saha, Anjali Dhall, Yang Zhang, Parth Desai, Lorinc Pongor, David A. Scheiblin, Valentin Magidson, Yilun Sun, Christophe Redon, Suresh Kumar, Manan Krishnamurthy, Henrique B. Dias, Vasilisa Askenova, Elizabeth Giordanio, Nobuyuki Takahashi, Michael Nirula, Yasuhiro Arakawa, Ukhyun Jo, Beverly A. Teacher, Mirit I. Aladjem, Stephen Lockett, Marry Dasso, Yves Pommier, Ajit K. Sharma, Anish Thomas
Journal: Cancer Research (2025)

Abstract Lamin A/C (LMNA), a key component of the nuclear envelope, plays an essential role in maintaining nuclear integrity and regulating genome organization. While LMNA dysregulation has been linked to genomic instability in both cancer and aging, the specific mechanisms remain poorly understood. We investigated the role of LMNA in small cell lung cancer (SCLC), a highly lethal form of lung cancer characterized by neuroendocrine (NE) differentiation, low LMNA expression, and extreme genomic instability. We show that LMNA depletion leads to increased R-loop formation, transcription-replication conflicts, replication stress, DNA breaks, the formation of micronuclei and increases sensitivity to TOP1 and ATR inhibition. Mechanistically, LMNA loss compromises RNA export efficiency by disrupting the nuclear pore complex distribution causing clumping and reducing incorporation of phenylalanine-glycine-nucleoporins (FG-nucleoporins). We found that LMNA expression is dynamically regulated during SCLC differentiation from NE to a non-NE state by EZH2, a component of the polycomb repressive complex that epigenetically silences LMNA. Inhibition of EZH2 restored LMNA expression in SCLC cells, and functionally led to a reduction in R-loops. Low LMNA levels were associated with significantly reduced survival in SCLC patients implicating R-loops as potential detrimental factor in SCLC patients. To confirm this, we utilized multiplexed immunofluorescence and confirmed LMNA protein was inversely correlated with R-loops both within the same SCLC tumor and across SCLC tumors using an SCLC rapid autopsy sample alongside an SCLC tumor microarray. Interestingly, low expression of canonical R-loop suppressing genes (RNASEH1, BRD4, SETX and DHX9) also predicted poorer prognosis in SCLC patients, supporting R-loops as a detrimental factor for SCLC prognosis. Critically, we were able to replicate key findings linking low LMNA to decreased FG-nucleoporin incorporation and increased R-loops using patient derived young and old fibroblasts lines demonstrating generalizability of this finding across disease models. Our results reveal a novel mechanism by which LMNA safeguards genome integrity by repressing R-loops, with important implications for both cancer and aging. Citation Format: Christopher William Schultz, Sourav Saha, Anjali Dhall, Yang Zhang, Parth Desai, Lorinc Pongor, David A. Scheiblin, Valentin Magidson, Yilun Sun, Christophe Redon, Suresh Kumar, Manan Krishnamurthy, Henrique B. Dias, Vasilisa Askenova, Elizabeth Giordanio, Nobuyuki Takahashi, Michael Nirula, Yasuhiro Arakawa, Ukhyun Jo, Beverly A. Teacher, Mirit I. Aladjem, Stephen Lockett, Marry Dasso, Yves Pommier, Ajit K. Sharma, Anish Thomas. Lamin AC deficiency promotes genomic instability through increased R-loop accumulation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2835.