Spatiotemporal control of SMARCA5 by a MAPK-RUNX1 axis distinguishes mutant KRAS-driven pancreatic malignancy from tissue regeneration (CUT&Tag)

De-differentiation or trans-differentiation is a common response to injury in many tissues, and the processes predispose cells to cancer. Acute pancreatitis-induced acinar-to-ductal metaplasia (ADM) is similar to pancreatic ductal adenocarcinoma (PDAC) at both the chromatin level and gene expression level. Mutant KRAS induces chromatin remodeling activities required for both regeneration and tumorigenesis at the peak of ADM, and it blocks regeneration. We show that chromatin remodeler SMARCA5 (SNF2H) can promotes the regeneration defects caused by mutant KRAS by maintaining chromatin accessibility at regions specifically required for malignancy. Mechanistically, regeneration-related chromatin remodeling activities are shared between wild-type and mutant KRAS and they occur very early upon pancreatitis, while the malignancy-related chromatin regions become accessible much later. The activity of SMARCA5 is controlled spatiotemporally by transcription factor RUNX1, which is only accumulated at sufficient levels at late ADM lock-in stage. Finally, we show that the malignancy regulation activity of SMARCA5 is different from its general function in CTCF recruitment. In summary, we have identified a specific function of a general chromatin remodeler that is precisely controlled during acinar cell trans-differentiation to separate malignancy from tissue regeneration. Overall design: Through ChIP-seq,CUT&RUN and CUT&Tag experiments, we aim to investigate whether SMARCA5 binds to its regulated sites and whether SMARCA5 is recruited by RUNX1.

去分化（De-differentiation）与转分化（Trans-differentiation）是多数组织应对损伤的常见应答方式，且此类过程会增加细胞罹患癌症的风险。急性胰腺炎诱导的腺泡-导管上皮化生（ADM）在染色质水平与基因表达水平上均与胰腺导管腺癌（PDAC）高度相似。突变型KRAS可在腺泡-导管上皮化生的峰值阶段，诱导再生与肿瘤发生所需的染色质重塑活性，同时阻断组织再生过程。本研究发现，染色质重塑因子SMARCA5（SNF2H）可通过维持恶性转化特异性区域的染色质可及性，加剧突变型KRAS引发的再生缺陷。从机制层面来看，野生型与突变型KRAS共享与再生相关的染色质重塑活性，且该活性在胰腺炎发生早期即被激活；而与恶性转化相关的染色质区域则在更晚阶段才获得可及性。SMARCA5的活性受转录因子RUNX1的时空精准调控，后者仅在腺泡-导管上皮化生的晚期锁定阶段积累至足够水平。最后，本研究证实SMARCA5的恶性调控功能与其在CCCTC结合因子（CTCF）招募中的常规功能存在显著差异。综上，本研究明确了一类通用染色质重塑因子的特定功能：该功能在腺泡细胞转分化过程中受到精准调控，从而实现恶性转化与组织再生的功能区分。整体实验设计：通过染色质免疫共沉淀测序（ChIP-seq）、切割靶标下的DNA释放与测序（CUT&RUN）及切割与标签测序（CUT&Tag）实验，旨在探究SMARCA5是否结合其调控位点，以及SMARCA5是否受RUNX1招募。