PO.TB09.01 · 肿瘤生物学
通过对患者样本进行深度单细胞多组学分析揭示TP53突变型急性髓系白血病中的谱系依赖性调控程序
Dependent lineage regulatory programs in TP53-mutated acute myeloid leukemia revealed through deep single-cell multi-omic profiling of patient samples
作者与单位 Authors & Affiliations
摘要 Abstract
中文摘要
TP53突变型（TP53m）急性髓系白血病（AML）是一种临床上难治且生物学上独特的疾病。为通过造血过程研究该疾病的分子基础，我们整合了单细胞RNA测序（10x以及长读长Oxford Nanopore测序）、开放染色质图谱（scATAC-seq）、用于捕捉结构变异和拷贝数改变的全基因组测序（WGS），以及来自49例TP53m AML患者、7例TP53野生型（WT）AML患者和4名健康供者的骨髓样本的深度panel DNA测序。
定相基因分型联合WGS揭示，双等位基因缺失与染色体内断裂相关，而单等位基因缺失则倾向于数目性染色体改变。TP53m克隆遍布于干/祖细胞和髓系-红系谱系，但在成熟淋巴细胞中比例下降。虽然共发生的AML驱动突变影响TP53m克隆的谱系偏向，但我们观察到HSC/MPP、LMPP和晚期红系区室的扩增。
在以HSC/MPP为主的疾病中，TP53m细胞表现出翻译和线粒体呼吸程序的抑制，并富集与慢性炎症应激相关的“p53-LSC”特征。这提示其通过代谢静息进行适应，从而在炎症压力下获得持存能力。在以LMPP为主的扩增中，我们观察到MYC/E2F靶基因的富集。结合拟时序的转录组邻域分析显示，红系区室具有异质性，成熟度较低的嗜碱性细胞富集TP53m克隆，而成熟度较高的正染性细胞富集TP53野生型克隆，将这一转变提名为分化延迟/阻滞的临界点。与此一致，在以红系为主的患者中，晚期红系细胞表现出GATA-1和KLF1（红系转录因子）活性受损，且TP53m克隆表现出增强的GATA2、SPI1和CEBPD调控子活性。在红系分化中，TP53m克隆相较于TP53野生型克隆表现出EIF2AK1(HRI)→eIF2alpha介导的整合应激反应（ISR）的转录活性增强。上述红系区室内的差异表达分析显示TP53m克隆中ISR被激活；SESN2、DDIT4和DDIT3/CHOP显著上调，ATF3和XBP1呈上升趋势，同时GATA2升高。复制/线粒体处理相关组分（GINS2、RPA3、ABCB8）显著下调。这些数据共同支持一个模型，即GATA-1/KLF1功能缺陷是TP53m克隆红系内阻滞的基础，这可能归因于HRI-ISR环路的激活。
这些针对TP53m AML的详细分子分化阶段特异性分析提供了机制性见解，并为功能性研究和合成致死研究提供了平台，以特异性靶向TP53m白血病细胞。
查看英文原文 English abstract
TP53 -mutated ( TP53 m) Acute myeloid leukemia (AML) represents a clinically intractable and biologically distinct disease. To study the molecular basis of this disease through hemopoiesis, we integrated single-cell RNA-seq (10x and long-read Oxford Nanopore sequencing) with open chromatin profiles (scATAC-seq), whole-genome (WGS) to capture structural variants and copy number alterations, and deep panel DNA sequencing from bone marrow samples taken from a cohort of 49 TP53 m AML patients, 7 TP53 wild type (WT) AML patients, and 4 healthy donors.
Phased genotyping plus WGS revealed biallelic loss to be associated with intrachromosomal breakage, whereas monoallelic loss favored numerical chromosomal alterations. TP53 m clones pervaded stem/progenitors and myeloerythroid lineages but were proportionally depleted in mature lymphocytes. While co-occurring AML driver mutations influence the lineage biases of TP53m clones, we observed expansion of HSC/MPP, LMPP, and late erythroid compartments.
In HSC/MPP dominant disease, TP53m cells displayed suppression of translational and mitochondrial-respiratory programs, with enrichment of a “p53-LSC” signature linked to chronic inflammatory stress. This suggests adaptation through metabolic quiescence, conferring persistence under inflammatory pressure. In LMPP-dominant expansion, we observed enriched MYC/E2F targets. Transcriptomic neighborhood analysis with pseudotime showed the erythroid compartment to be heterogeneous, with less mature basophilic cells enriched for TP53 m clones, whereas more mature orthochromatic cells were enriched for TP53 wt clones, nominating this transition as a tipping point for differentiation delay/arrest. Consistently, in erythroid dominant patients, late-stage erythroid cells demonstrated impaired GATA-1 and KLF1 (erythroid TFs) activities, and TP53 m clones showed heightened GATA2, SPI1, and CEBPD regulon activity. TP53 m versus TP53 wt clones in erythroid differentiation showed heightened transcriptional activity of the EIF2AK1(HRI)→eIF2alpha mediated integrated stress response (ISR). Differential expression analysis within the aforementioned erythroid compartment showed ISR activation in TP53m clones; SESN2 , DDIT4 , and DDIT3 /CHOP significantly up, with ATF3 , and XBP1 , up-trending, together with increased GATA2 . Replication/mitochondrial-handling components ( GINS2 , RPA3 , ABCB8 ) were significantly downregulated. These data together support a model in which deficient GATA-1/KLF1 function underpins the intra erythroid arrest of TP53 m clones possibly due to activated HRI-ISR circuitry.
These detailed molecular differentiation stage specific analyses of TP53 m AML provide mechanistic insights and a platform for functional and synthetic lethal studies to specifically target TP53 m leukemic cells.
利益披露 Disclosure
F. A. Radtke, None.
B. S. Jaiswal,
Bristol Myers Squibb Employment, Stock.
G. Lopez,
Bristol Myers Squibb Employment, Stock.
J. Zhao,
Bristol Myers Squibb Employment, Stock.
S. Banerjee,
Bristol Myers Squibb Employment, Stock.
D. Hemerich Brennan,
Bristol Myers Squibb Employment, Stock.
Y. Zhao,
Bristol Myers Squibb Employment, Stock.
V. Körber,
BASF Stock.
Novartis Stock.
Sandoz Stock.
Sanofi Stock.
M. Metzner, None..
R. Moore, None..
B. Stoilova, None..
B. Usukhbayar, None..
D. Cruz Hernandez, None.
M. Ortiz Estevez,
Bristol Myers Squibb Employment, Stock.
A. O’Donohue,
Bristol Myers Squibb Employment, Stock, Stock Option.
D. Lopes de Menezes,
Bristol Myers Squibb Employment, Stock, Stock Option, Patent, Other Intellectual Property.
R. N. Suragani,
Bristol Myers Squibb Employment, Stock.
A. K. Gandhi,
Bristol Myers Squibb Employment, Stock Option.
P. Vyas,
Yellowstone Biosciences Limited Employment, g., Board of Directors, non-salaried role), Other Business Ownership.
Bristol Myers Squibb/Celgene Independent Contractor.
Pfizer Independent Contractor.
Jazz Independent Contractor.
Abbvie Independent Contractor.
Daiichi Sankyo Independent Contractor.
Astellas Independent Contractor.
GSK Independent Contractor.
Servier Independent Contractor.