美国国立卫生研究院国家癌症研究所淋巴恶性肿瘤科

Diffuse large B cell lymphoma (DLBCL) is an aggressive, profoundly heterogeneous cancer, presenting a challenge for precision medicine. Bruton’s tyrosine kinase (BTK) inhibitors block B cell receptor (BCR) signaling and are particularly effective in certain molecular subtypes of DLBCL that rely on chronic active BCR signaling to promote oncogenic NF-kB. The MCD genetic subtype, which often acquires mutations in the BCR subunit, CD79B, and in the innate immune adapter, MYD88L265P, typically resists chemotherapy but responds exceptionally to BTK inhibitors. However, the underlying mechanisms of response to BTK inhibitors are poorly understood. Herein, we find a non-canonical form of chronic selective autophagy in MCD DLBCL that targets ubiquitinated MYD88L265P for degradation in a TBK1-dependent manner. MCD tumors acquire genetic and epigenetic alterations that attenuate this autophagic tumor suppressive pathway. In contrast, BTK inhibitors promote autophagic degradation of MYD88L265P, thus explaining their exceptional clinical benefit in MCD DLBCL.

弥漫大B细胞淋巴瘤(diffuse large B cell lymphoma，DLBCL)是一种侵袭性强、高度异质性的肿瘤，这对精准医疗来说是巨大的挑战。目前的研究发现，通过布鲁顿酪氨酸激酶(BTK)抑制剂阻断B细胞受体(BCR)信号，对某些分子亚型的DLBCL很有效，这些DLBCL依赖慢性活性BCR信号促进致癌性NF-kB信号通路。MCD基因亚型是DLBCL在BCR亚基、CD79B和先天性免疫适配器蛋白MYD88L265P中获得突变的亚型，通常对化疗耐药，但对BTK抑制剂有反应。然而，目前MCD对BTK抑制剂有反应的潜在机制还不明确。在本研究中，研究者在MCD DLBCL中发现了一种非经典形式的慢性选择性自噬，它以TBK1依赖的方式靶向降解泛素化的MYD88L265P。MCD肿瘤获得的遗传和表观遗传学改变，减弱了这种自噬肿瘤抑制通路。相反，BTK抑制剂能促进MYD88L265P的自噬降解，从而解释了它在治疗MCD DLBCL中的特殊临床作用。

5.Interferon-stimulated neutrophils as a predictor of immunotherapy response.

干扰素刺激的中性粒细胞可以作为免疫治疗反应的预测因子。

以色列理工学院拉帕波特医学院细胞生物学和癌症科学

Despite the remarkable success of anti-cancer immunotherapy, its effectiveness remains confined to a subset of patients—emphasizing the importance of predictive biomarkers in clinical decision-making and further mechanistic understanding of treatment response. Current biomarkers, however, lack the power required to accurately stratify patients. Here, we identify interferon-stimulated, Ly6Ehi neutrophils as a blood-borne biomarker of anti-PD1 response in mice at baseline. Ly6Ehi neutrophils are induced by tumor-intrinsic activation of the STING (stimulator of interferon genes) signaling pathway and possess the ability to directly sensitize otherwise non-responsive tumors to anti-PD1 therapy, in part through IL12b-dependent activation of cytotoxic T cells. By translating our pre-clinical findings to a cohort of patients with non-small cell lung cancer and melanoma (n = 109), and to public data (n = 1440), we demonstrate the ability of Ly6Ehi neutrophils to predict immunotherapy response in humans with high accuracy (average AUC≈0.9). Overall, our study identifies a functionally active biomarker for use in both mice and humans.

尽管抗癌免疫治疗取得了显著成功，但其有效性仍然局限于一部分患者，这突显了预测性生物标志物在临床决策中的重要性，及其对于进一步理解治疗反应机制的必要性。然而，当前的生物标志物无法准确地将患者分层。在这项研究中，研究者发现干扰素刺激的 Ly6Ehi中性粒细胞可以作为小鼠对抗 PD1 抗体治疗反应的血液生物标志物。这些中性粒细胞是由肿瘤内部 STING（干扰素基因激活器）信号通路的激活诱导的，并且具有直接使原本对抗PD1抗体治疗不敏感的肿瘤敏感化的能力，另外，部分中性粒细胞还通过 IL12b 依赖的方式激活细胞毒性 T 细胞。此外，研究还将这些临床前的发现应用到了非小细胞肺癌和黑色素瘤患者队列（n = 109）以及公共数据（n = 1440）中，证明了 Ly6Ehi中性粒细胞有高精度预测免疫治疗反应的能力（平均 AUC≈0.9）。总的来说，该研究确定了一种生物标志物，可用于预测小鼠和人类免疫治疗反应。

6.Inosine induces stemness features in CAR-T cells and enhances potency.

肌苷能诱导 CAR-T 细胞的干细胞特性并增强其功能。

斯坦福大学医学院癌症研究所癌细胞治疗中心

Adenosine (Ado) mediates immune suppression in the tumor microenvironment and exhausted CD8+ CAR-T cells express CD39 and CD73, which mediate proximal steps in Ado generation. Here, we sought to enhance CAR-T cell potency by knocking out CD39, CD73, or adenosine receptor 2a (A2aR) but observed only modest effects. In contrast, overexpression of Ado deaminase (ADA-OE), which metabolizes Ado to inosine (INO), induced stemness and enhanced CAR-T functionality. Similarly, CAR-T cell exposure to INO augmented function and induced features of stemness. INO induced profound metabolic reprogramming, diminishing glycolysis, increasing mitochondrial and glycolytic capacity, glutaminolysis and polyamine synthesis, and reprogrammed the epigenome toward greater stemness. Clinical scale manufacturing using INO generated enhanced potency CAR-T cell products meeting criteria for clinical dosing. These results identify INO as a potent modulator of CAR-T cell metabolism and epigenetic stemness programming and deliver an enhanced potency platform for cell manufacturing.

腺苷（Ado）在肿瘤微环境中有免疫抑制的作用，但CD8+ CAR-T细胞表达的CD39和CD73会参与腺苷的生成。因此，该研究希望通过敲除CD39、CD73或腺苷受体2a（A2aR）来增强CAR-T细胞的功能，但治疗效果只得到了轻微的改善。相反，该研究发现，增加腺苷脱氨酶（ADA-OE）的表达会将腺苷代谢成肌苷（INO），从而使CAR-T细胞表现出干细胞的特征并增强其功能。同样地，暴露于肌苷中的CAR-T细胞也表现出增强的功能和干细胞性特征。从机制上解释，肌苷能诱导CAR-T细胞的深度代谢重组，减少了糖酵解作用，增加了线粒体和糖酵解的能力，促进了谷氨酰胺代谢和多胺合成，并且使细胞表观遗传组更倾向于干细胞状态。用肌苷生产出效力增强的CAR-T细胞，能使产品达到临床剂量的标准。这些结果表明肌苷是一种强效的CAR-T细胞代谢和干性的调节剂，并提供了一个增强CAR-T细胞功能的平台。

7.Integrative analysis of neuroblastoma by single-cell RNA sequencing identifies the NECTIN2-TIGIT axis as a target for immunotherapy.

基于单细胞RNA测序的神经母细胞瘤整合分析鉴定出NECTIN2-TIGIT轴可以作为免疫治疗的靶点。

荷兰玛希玛公主儿科肿瘤中心

Pediatric patients with high-risk neuroblastoma have poor survival rates and urgently need more effective treatment options with less side effects. Since novel and improved immunotherapies may fill this need, we dissect the immunoregulatory interactions in neuroblastoma by single-cell RNA-sequencing of 24 tumors (10 pre- and 14 post-chemotherapy, including 5 pairs) to identify strategies for optimizing immunotherapy efficacy. Neuroblastomas are infiltrated by natural killer (NK), T and B cells, and immunosuppressive myeloid populations. NK cells show reduced cytotoxicity and T cells have a dysfunctional profile. Interaction analysis reveals a vast immunoregulatory network and identifies NECTIN2-TIGIT as a crucial immune checkpoint. Combined blockade of TIGIT and PD-L1 significantly reduces neuroblastoma growth, with complete responses (CR) in vivo. Moreover, addition of TIGIT+PD-L1 blockade to standard relapse treatment in a chemotherapy-resistant Th-ALKF1174L/MYCN 129/SvJ syngeneic model induces CR. In conclusion, our integrative analysis provides promising targets and a rationale for immunotherapeutic combination strategies.

儿童高危神经母细胞瘤患者生存率低，因此急需更有效、副作用较小的治疗方法。鉴于新型和改进的免疫疗法可能满足这一需求，该研究通过对24个肿瘤（包括10个化疗前和14个化疗后，其中5对样本是配对的）进行单细胞RNA测序，以揭示神经母细胞瘤中的免疫调节相互作用，并确定优化免疫治疗效果的策略。结果显示，神经母细胞瘤中存在自然杀伤细胞（NK细胞）、T细胞、B细胞和免疫抑制性的髓样细胞群的浸润。其中，NK细胞的细胞毒性降低，T细胞呈现功能失调。相互作用分析揭示了广泛的免疫调节网络，并确定了NECTIN2-TIGIT是一个关键的免疫检查点。联合阻断TIGIT和PD-L1能显著抑制神经母细胞瘤的生长，在体内实现完全缓解（CR）。此外，在化疗耐药的Th-ALKF1174L/MYCN 129/SvJ 同种移植模型中，将TIGIT+PD-L1阻断加入标准复发治疗方案，也能实现CR。综上，该研究的整合分析为寻找肿瘤治疗靶点和制定免疫治疗联合策略提供了线索。

8.A comprehensive clinically informed map of dependencies in cancer cells and framework for target prioritization.

一个基于详细的临床信息绘制的癌细胞依赖关系图和目标优先级框架

英国惠康桑格研究所

Genetic screens in cancer cell lines inform gene function and drug discovery. More comprehensive screen datasets with multi-omics data are needed to enhance opportunities to functionally map genetic vulnerabilities. Here, we construct a second-generation map of cancer dependencies by annotating 930 cancer cell lines with multi-omic data and analyze relationships between molecular markers and cancer dependencies derived from CRISPR-Cas9 screens. We identify dependency-associated gene expression markers beyond driver genes, and observe many gene addiction relationships driven by gain of function rather than synthetic lethal effects. By combining clinically informed dependency-marker associations with protein-protein interaction networks, we identify 370 anti-cancer priority targets for 27 cancer types, many of which have network-based evidence of a functional link with a marker in a cancer type. Mapping these targets to sequenced tumor cohorts identifies tractable targets in different cancer types. This target prioritization map enhances understanding of gene dependencies and identifies candidate anti-cancer targets for drug development.

在癌症研究中，对癌细胞系进行基因筛查，可以了解基因功能并发现潜在治疗药物。为了更好地了解基因易感性，并为药物研发提供更多机会，我们需要更全面的筛查数据集，其中包含多组学数据。因此，该研究利用多组学数据对930个癌细胞系进行了注释，分析了来自CRISPR-Cas9筛查的分子标记与癌症依赖之间的联系，并构建了第二代癌症依赖关系图。在这个过程中，研究发现了一些驱动基因以外的表达癌症依赖关联分子标记物的基因，并且观察到许多基因与癌症的关系是由基因自身功能增强驱动的，而不是和其他基因发生合成致死效应引起的。通过结合临床信息支持的癌症依赖标记和蛋白质相互作用网络，该研究鉴定了27种癌症类型的370个抗癌优先靶点。这些靶点在网络中显示出与某些癌症的标记物有功能联系。将这些靶点映射到测序的肿瘤队列中，能发现不同癌症类型中可处理的靶点。总的来说，这个靶点优先级图加强了我们对基因依赖性的理解，并为药物研发提供了候选抗癌靶点。

Brain metastasis (BrM) is a common malignancy, predominantly originating from lung, melanoma, and breast cancers. The vasculature is a key component of the BrM tumor microenvironment with critical roles in regulating metastatic seeding and progression. However, the heterogeneity of the major BrM vascular components, namely endothelial and mural cells, is still poorly understood. We perform single-cell and bulk RNA-sequencing of sorted vascular cell types and detect multiple subtypes enriched specifically in BrM compared to non-tumor brain, including previously unrecognized immune regulatory subtypes. We integrate the human data with mouse models, creating a platform to interrogate vascular targets for the treatment of BrM. We find that the CD276 immune checkpoint molecule is significantly upregulated in the BrM vasculature, and anti-CD276 blocking antibodies prolonged survival in preclinical trials. This study provides important insights into the complex interactions between the vasculature, immune cells, and cancer cells, with translational relevance for designing therapeutic interventions.

脑转移（BrM）肿瘤是一种常见的恶性肿瘤，主要来自肺癌、黑色素瘤和乳腺癌。血管系统是BrM肿瘤微环境的关键组成部分，在调控肿瘤转移种植和进展的过程中扮演着重要角色。然而，我们对BrM的血管组分，即内皮细胞和壁细胞的异质性仍然知之甚少。因此，该研究对分选的血管细胞类型进行了单细胞和批量RNA测序，发现与非肿瘤脑相比，BrM中存在特异的多个细胞亚型的富集，包括先前未被认识的免疫调节细胞亚型。另外，该研究将人类数据与小鼠模型相结合，建立了一个平台，用于研究治疗BrM的血管靶点。结果发现CD276免疫检查点分子在BrM血管中显著上调，并且在临床前试验中使用抗CD276阻断抗体能延长BrM的生存期。总的来说，这项研究为血管、免疫细胞和癌细胞之间的复杂相互作用提供了重要的见解，具有转化意义，可用于设计治疗干预的措施。

3.Cancer-associated fibroblast phenotypes are associated with patient outcome in non-small cell lung cancer

癌症相关的成纤维细胞表型与非小细胞肺癌患者的预后相关

瑞士苏黎世大学定量生物医学系

Despite advances in treatment, lung cancer survival rates remain low. A better understanding of the cellular heterogeneity and interplay of cancer-associated fibroblasts (CAFs) within the tumor microenvironment will support the development of personalized therapies. We report a spatially resolved single-cell imaging mass cytometry (IMC) analysis of CAFs in a non-small cell lung cancer cohort of 1,070 patients. We identify four prognostic patient groups based on 11 CAF phenotypes with distinct spatial distributions and show that CAFs are independent prognostic factors for patient survival. The presence of tumor-like CAFs is strongly correlated with poor prognosis. In contrast, inflammatory CAFs and interferon-response CAFs are associated with inflamed tumor microenvironments and higher patient survival. High density of matrix CAFs is correlated with low immune infiltration and is negatively correlated with patient survival. In summary, our data identify phenotypic and spatial features of CAFs that are associated with patient outcome in NSCLC.

尽管肺癌在治疗方面已经取得了很多进展，但肺癌的生存率仍然较低。对肿瘤微环境中癌症相关的成纤维细胞（CAFs）的细胞异质性和互作进行更深入的了解，将有助于开发个性化治疗方案。因此，该研究对1,070名非小细胞肺癌患者的CAFs进行了空间单细胞成像质谱细胞学（IMC）分析。结果，研究基于11种在肿瘤中具有不同空间分布的CAFs鉴定出了四个不同的患者预后群体，并表明CAFs是患者生存的独立预后因素。比如，肿瘤样CAFs与不良预后强相关，相反，炎症性CAFs和干扰素响应性CAFs与炎症性肿瘤微环境和更高的患者生存率相关。高密度的基质型CAFs与低免疫浸润相关，并且与患者生存率呈负相关。总的来说，该研究的数据发现了在非小细胞肺癌中与患者预后相关的CAFs表型和空间特征。

4.Adeno-to-squamous transition drives resistance to KRAS inhibition in LKB1 mutant lung cancer

腺癌向鳞癌的转变驱动LKB1突变型肺癌对KRAS抑制剂产生耐药性。

中国科学院分子细胞科学卓越中心，上海生物化学与细胞生物学研究所

KRASG12C inhibitors (adagrasib and sotorasib) have shown clinical promise in targeting KRASG12C-mutated lung cancers; however, most patients eventually develop resistance. In lung patients with adenocarcinoma with KRASG12C and STK11/LKB1 co-mutations, we find an enrichment of the squamous cell carcinoma gene signature in pre-treatment biopsies correlates with a poor response to adagrasib. Studies of Lkb1-deficient KRASG12C and KrasG12D lung cancer mouse models and organoids treated with KRAS inhibitors reveal tumors invoke a lineage plasticity program, adeno-to-squamous transition (AST), that enables resistance to KRAS inhibition. Transcriptomic and epigenomic analyses reveal △Np63 drives AST and modulates response to KRAS inhibition. We identify an intermediate high-plastic cell state marked by expression of an AST plasticity signature and Krt6a. Notably, expression of the AST plasticity signature and KRT6A at baseline correlates with poor adagrasib responses. These data indicate the role of AST in KRAS inhibitor resistance and provide predictive biomarkers for KRAS-targeted therapies in lung cancer.

KRASG12C抑制剂（如adagrasib和sotorasib）在治疗KRASG12C突变的肺癌中显示出较好的临床潜力，但大多数患者最终会出现耐药性。在针对KRASG12C和STK11/LKB1共突变的肺腺癌患者的研究中，研究者发现术前腺癌活检样本鳞癌基因表达特征的富集与患者对adagrasib的不良反应相关。研究对Lkb1缺失的KRASG12C和KrasG12D肺癌小鼠模型和类器官采用KRAS抑制剂治疗，发现治疗后的肿瘤会启动一种细胞谱系可塑性程序，即腺癌向鳞癌的转变（AST），从而使肿瘤对KRAS抑制剂产生耐药性。转录组和表观基因组分析显示，△Np63促进了AST并调节了对KRAS抑制剂的反应。研究还发现了一种中间高可塑性细胞状态，其特征是表达AST可塑性标志物和Krt6a。值得注意的是，基线时AST可塑性标志物和KRT6A的表达与adagrasib的不良反应相关。这些数据表明AST在肺癌对KRAS抑制剂产生耐药性中具有重要作用，并为肺癌的KRAS靶向治疗的效果提供了可预测的生物标志物。

5.Immune heterogeneity in small-cell lung cancer and vulnerability to immune checkpoint blockade

小细胞肺癌中的免疫异质性及其对免疫检查点阻断治疗的易感性

美国基因泰克公司

Atezolizumab (anti-PD-L1), combined with carboplatin and etoposide (CE), is now a standard of care for extensive-stage small-cell lung cancer (ES-SCLC). A clearer understanding of therapeutically relevant SCLC subsets could identify rational combination strategies and improve outcomes. We conduct transcriptomic analyses and non-negative matrix factorization on 271 pre-treatment patient tumor samples from IMpower133 and identify four subsets with general concordance to previously reported SCLC subtypes (SCLC-A, -N, -P, and -I). Deeper investigation into the immune heterogeneity uncovers two subsets with differing neuroendocrine (NE) versus non-neuroendocrine (non-NE) phenotypes, demonstrating immune cell infiltration hallmarks. The NE tumors with low tumor-associated macrophage (TAM) but high T-effector signals demonstrate longer overall survival with PD-L1 blockade and CE versus CE alone than non-NE tumors with high TAM and high T-effector signal. Our study offers a clinically relevant approach to discriminate SCLC patients likely benefitting most from immunotherapies and highlights the complex mechanisms underlying immunotherapy responses.

阿替利珠单抗（抗PD-L1）联合卡铂和依托泊苷（CE）现已成为广泛期小细胞肺癌（ES-SCLC）的标准治疗方案。深入了解治疗相关的SCLC亚型有助于制定合理的联合治疗策略，并改善治疗效果。因此，该研究对来自IMpower133的271例患者的术前肿瘤样本进行了转录组分析和非负矩阵因子分解，确定了四个SCLC亚型子集，与先前报道的SCLC亚型（SCLC-A、-N、-P和-I）大体一致。对免疫异质性的深入研究发现，其中两个亚型，一个表现出神经内分泌（NE）表型，另一个表现出非神经内分泌（non-NE）表型，并显示出免疫细胞浸润的特征。NE肿瘤具有低肿瘤相关巨噬细胞（TAM）但高T效应物信号的特点，在接受PD-L1阻断和CE治疗时的总体生存期较长，非-NE肿瘤有高TAM和高T效应物信号的特点，在接受CE治疗时的总体生存期较短。总的来说，该研究提供了一种临床相关的方法，用于区分哪些SCLC患者最可能从免疫治疗中获益，并凸显了免疫治疗反应的复杂机制。

6.Multi-omic profiling of follicular lymphoma reveals changes in tissue architecture and enhanced stromal remodeling in high-risk patients

滤泡性淋巴瘤的多组学分析揭示了高危患者组织结构的变化和增强的基质重塑特征

美国国立卫生研究院淋巴细胞生物学组和高级组织成像中心，免疫系统生物学实验室

Follicular lymphoma (FL) is a generally incurable malignancy that evolves from developmentally blocked germinal center (GC) B cells. To promote survival and immune escape, tumor B cells undergo significant genetic changes and extensively remodel the lymphoid microenvironment. Dynamic interactions between tumor B cells and the tumor microenvironment (TME) are hypothesized to contribute to the broad spectrum of clinical behaviors observed among FL patients. Despite the urgent need, existing clinical tools do not reliably predict disease behavior. Using a multi-modal strategy, we examined cell-intrinsic and -extrinsic factors governing progression and therapeutic outcomes in FL patients enrolled onto a prospective clinical trial. By leveraging the strengths of each platform, we identify several tumor-specific features and microenvironmental patterns enriched in individuals who experience early relapse, the most high-risk FL patients. These features include stromal desmoplasia and changes to the follicular growth pattern present 20 months before first progression and first relapse.

滤泡性淋巴瘤（FL）是一种通常难以治愈的恶性肿瘤，其起源于发育受阻的生发中心（GC）B细胞。为了促进肿瘤存活和免疫逃逸，肿瘤B细胞经历了显著的遗传变化，并广泛重塑淋巴微环境。据推测，肿瘤B细胞与肿瘤微环境（TME）之间的动态相互作用可能有助于解释FL患者所呈现的广泛临床行为谱。但现有的临床工具却不能可靠地预测疾病行为，因此急需可靠的临床工具。通过多模态策略，该研究通过前瞻性临床试验，检查了影响FL患者病程和治疗结果的细胞内和细胞外因素。结合每个平台的优势，研究确定了一些在早期复发的个体中富集的肿瘤特异性特征和微环境模式，这些个体往往是FL患者中风险最高的患者。这些特征包括纤维结缔组织增生和滤泡生长模式的改变，并且在首次进展和首次复发前20个月就能被发现。

Issue 4, April 08, 2024, p497-722

在2024年4月，Cancer Cell共发表17篇文章，其中包括Commentary 1篇，Preview 4篇，Review 1篇，Article 10篇，Correction 1篇。

1.Pharmacogenomic profiling of intra-tumor heterogeneity using a large organoid biobank of liver cancer

利用大型肝癌类器官样本库对肿瘤内异质性进行药物基因组分析

北京大学第一医院肿瘤转化研究中心

Inter- and intra-tumor heterogeneity is a major hurdle in primary liver cancer (PLC) precision therapy. Here, we establish a PLC biobank, consisting of 399 tumor organoids derived from 144 patients, which recapitulates histopathology and genomic landscape of parental tumors, and is reliable for drug sensitivity screening, as evidenced by both in vivo models and patient response. Integrative analysis dissects PLC heterogeneity, regarding genomic/transcriptomic characteristics and sensitivity to seven clinically relevant drugs, as well as clinical associations. Pharmacogenomic analysis identifies and validates multi-gene expression signatures predicting drug response for better patient stratification. Furthermore, we reveal c-Jun as a major mediator of lenvatinib resistance through JNK and β-catenin signaling. A compound (PKUF-01) comprising moieties of lenvatinib and veratramine (c-Jun inhibitor) is synthesized and screened, exhibiting a marked synergistic effect. Together, our study characterizes the landscape of PLC heterogeneity, develops predictive biomarker panels, and identifies a lenvatinib-resistant mechanism for combination therapy.

肝癌的肿瘤内和肿瘤间的异质性是原发性肝癌（PLC）精准治疗面临的主要障碍。在这项研究中，研究者建立了一个PLC生物样本库，包括来自144名患者的399个肿瘤类器官样本。这些样本忠实地保留了原始肿瘤的组织病理学和基因组景观，并通过体内模型和患者反应验证了其在药物敏感性筛选方面的可靠性。通过综合分析，该研究解析了PLC的异质性，考虑了肿瘤的基因组/转录组特征及其对七种临床相关药物的敏感性，以及临床相关性。药物基因组学分析鉴定和验证了多基因表达特征，可用于预测药物反应，有助于患者分层。此外，研究还发现c-Jun能通过JNK和β-连环蛋白信号通路介导乐伐替尼的耐药，并合成筛选了一种化合物（PKUF-01），它结合了乐伐替尼和维拉特拉明（c-Jun抑制剂）的成分，展现出了两种成分显著的协同效应。总的来说，该研究描绘了PLC的异质性景观，建立了一套预测生物标志物的方法，并发现了乐伐替尼耐药机制，为联合治疗提供了重要线索。

2.Single-cell systems pharmacology identifies development-driven drug response and combination therapy in B cell acute lymphoblastic leukemia

通过单细胞系统药理学在B细胞急性淋巴细胞白血病中发现了由肿瘤发展驱动的药物反应和对应的联合治疗方案

美国圣犹达儿童研究医院计算生物系

Leukemia can arise at various stages of the hematopoietic differentiation hierarchy, but the impact of developmental arrest on drug sensitivity is unclear. Applying network-based analyses to single-cell transcriptomes of human B cells, we define genome-wide signaling circuitry for each B cell differentiation stage. Using this reference, we comprehensively map the developmental states of B cell acute lymphoblastic leukemia (B-ALL), revealing its strong correlation with sensitivity to asparaginase, a commonly used chemotherapeutic agent. Single-cell multi-omics analyses of primary B-ALL blasts reveal marked intra-leukemia heterogeneity in asparaginase response: resistance is linked to pre-pro-B-like cells, with sensitivity associated with the pro-B-like population. By targeting BCL2, a driver within the pre-pro-B like cell signaling network, we find that venetoclax significantly potentiates asparaginase efficacy in vitro and in vivo. These findings demonstrate a single-cell systems pharmacology framework to predict effective combination therapies based on intra-leukemia heterogeneity in developmental state, with potentially broad applications beyond B-ALL.

白血病可在造血过程的不同阶段发生，但白血病中造血细胞的发育阻碍对药物敏感性的影响尚不清楚。因此，该研究利用单细胞转录组数据对人类B细胞进行了网络分析，为B细胞的每个分化阶段定义了基因信号网络。以此为参考，该研究全面地描绘了B细胞急性淋巴细胞白血病（B-ALL）的发育状态，并发现其与门冬酰胺酶敏感性强相关，这是一种常用的化疗药物。对原发性B细胞急性淋巴白血病的原始细胞的单细胞多组学分析显示，肿瘤细胞对门冬酰胺酶的反应存在明显的内部异质性，比如抗性与前祖B细胞样细胞相关联，而敏感性与祖B细胞样细胞群体相关。通过针对前祖B细胞样细胞信号传导网络中的关键因子BCL2，该研究发现维奈托克（BCL2抑制剂）可以在体内和体外显著地提高门冬酰胺酶的疗效。这些发现展示了一种单细胞系统药理学框架，可根据白血病内部的发育状态异质性来预测有效的联合治疗方案，这种框架不仅限于B-ALL，具有广泛的应用前景。

3.Long-lasting mRNA-encoded interleukin-2 restores CD8+ T cell neoantigen immunity in MHC class I-deficient cancers

长效mRNA编码的IL-2可以在MHC-I缺陷型癌症中恢复CD8+ T细胞对新抗原的免疫能力

德国约翰内斯古腾堡大学医学中心转化肿瘤学

Major histocompatibility complex (MHC) class I antigen presentation deficiency is a common cancer immune escape mechanism, but the mechanistic implications and potential strategies to address this challenge remain poorly understood. Studying β2-microglobulin (β2M) deficient mouse tumor models, we find that MHC class I loss leads to a substantial immune desertification of the tumor microenvironment (TME) and broad resistance to immune-, chemo-, and radiotherapy. We show that treatment with long-lasting mRNA-encoded interleukin-2 (IL-2) restores an immune cell infiltrated, IFNγ-promoted, highly proinflammatory TME signature, and when combined with a tumor-targeting monoclonal antibody (mAB), can overcome therapeutic resistance. Unexpectedly, the effectiveness of this treatment is driven by IFNγ-releasing CD8+ T cells that recognize neoantigens cross-presented by TME-resident activated macrophages. These macrophages acquire augmented antigen presentation proficiency and other M1-phenotype-associated features under IL-2 treatment. Our findings highlight the importance of restoring neoantigen-specific immune responses in the treatment of cancers with MHC class I deficiencies.

MHC I类抗原呈递缺失是一种常见的癌症免疫逃逸机制，但我们对其中的机制和解决这一问题的方法仍知之甚少。由此，该研究通过研究β2-微球蛋白（β2M）缺陷的小鼠肿瘤模型，发现MHC I类分子的丢失会导致肿瘤微环境（TME）的免疫荒漠化以及对免疫、化疗和放疗的广泛抵抗。研究发现，用长效mRNA编码的白细胞介素-2（IL-2）来治疗可以恢复TME免疫细胞浸润的、IFNγ促进的高度炎症性的特征，并且当IL-2与肿瘤靶向的单克隆抗体（mAB）联合使用时，可以克服单用的治疗抵抗。出人意料的是，这种治疗是由释放IFNγ的CD8+ T细胞驱动的，它们能识别由TME中激活的巨噬细胞交叉呈递的新抗原。因为这些巨噬细胞在IL-2的治疗下获得了增强的抗原呈递能力和M1型巨噬细胞的相关特征。总的来说，该研究强调了在治疗MHC I类缺陷的癌症中恢复新抗原特异性免疫应答的重要性。

4.ARID1A orchestrates SWI/SNF-mediated sequential binding of transcription factors with ARID1A loss driving pre-memory B cell fate and lymphomagenesis

ARID1A是调控SWI/SNF介导的转录因子顺序结合的亚基，ARID1A的缺失会影响前记忆B细胞的命运和驱动淋巴瘤的发生

美国纽约康奈尔大学威尔康奈尔医学院血液学和肿瘤学研究室

ARID1A, a subunit of the canonical BAF nucleosome remodeling complex, is commonly mutated in lymphomas. We show that ARID1A orchestrates B cell fate during the germinal center (GC) response, facilitating cooperative and sequential binding of PU.1 and NF-kB at crucial genes for cytokine and CD40 signaling. The absence of ARID1A tilts GC cell fate toward immature IgM+CD80-PD-L2- memory B cells, known for their potential to re-enter new GCs. When combined with BCL2 oncogene, ARID1A haploinsufficiency hastens the progression of aggressive follicular lymphomas (FLs) in mice. Patients with FL with ARID1A-inactivating mutations preferentially display an immature memory B cell-like state with increased transformation risk to aggressive disease. These observations offer mechanistic understanding into the emergence of both indolent and aggressive ARID1A-mutant lymphomas through the formation of immature memory-like clonal precursors. Lastly, we demonstrate that ARID1A mutation induces synthetic lethality to SMARCA2/4 inhibition, paving the way for potential precision therapy for high-risk patients.

ARID1A是经典BAF核小体重塑复合物的一个亚基，常在淋巴瘤中发生突变。该研究发现ARID1A会在生发中心（GC）反应期间调控B细胞的命运，促进PU.1和NF-kB在细胞因子和CD40信号通路的关键基因上的合作和顺序结合。而ARID1A的缺失会使GC的B细胞命运倾向于不成熟的IgM+CD80PD-L2记忆B细胞，这些细胞往往能够重新进入新的GC。另外，当ARID1A与BCL2致癌基因相结合时，ARID1A的半失效加速了小鼠中侵袭性滤泡性淋巴瘤（FL）的进展。研究还发现，有ARID1A失活突变的FL患者优先表现出类似不成熟记忆B细胞的状态，并且这类患者转化为侵袭性疾病的风险更高。总的来说，上述观察结果发现，不成熟的记忆样克隆前体B细胞的形成，是ARID1A突变引起侵袭性的淋巴瘤的关键机制。最后，该研究证明了ARID1A突变和SMARCA2/4抑制剂有合成致死作用，这为高风险患者提供了潜在的精准治疗途径。

5.SMARCA4 is a haploinsufficient B cell lymphoma tumor suppressor that fine-tunes centrocyte cell fate decisions

SMARCA4是一个半失效的B细胞淋巴瘤抑癌基因，能调控中心细胞的命运走向。

美国德州大学安德森癌症中心淋巴瘤与骨髓瘤科

SMARCA4 encodes one of two mutually exclusive ATPase subunits in the BRG/BRM associated factor (BAF) complex that is recruited by transcription factors (TFs) to drive chromatin accessibility and transcriptional activation. SMARCA4 is among the most recurrently mutated genes in human cancer, including 30% of germinal center (GC)-derived Burkitt lymphomas. In mice, GC-specific Smarca4 haploinsufficiency cooperated with MYC over-expression to drive lymphomagenesis. Furthermore, monoallelic Smarca4 deletion drove GC hyperplasia with centroblast polarization via significantly increased rates of centrocyte recycling to the dark zone. Mechanistically, Smarca4 loss reduced the activity of TFs that are activated in centrocytes to drive GC-exit, including SPI1 (PU.1), IRF family, and NF-kB. Loss of activity for these factors phenocopied aberrant BCL6 activity within murine centrocytes and human Burkitt lymphoma cells. SMARCA4 therefore facilitates chromatin accessibility for TFs that shape centrocyte trajectories, and loss of fine-control of these programs biases toward centroblast cell-fate, GC hyperplasia and lymphoma.

SMARCA4编码BRG/BRM相关因子（BAF）复合物中的两个互斥的ATP酶亚基之一，该复合物被转录因子（TFs）招募以推动染色质可及性和转录激活。SMARCA4是人类癌症中最常见的突变基因之一，30%的生发中心（GC）来源的伯基特淋巴瘤都有该基因的突变。在小鼠中，GC特异性的Smarca4半失效联合MYC的过表达，会促进淋巴瘤的发生。此外，单等位基因的Smara4缺失会通过显著增加中心母细胞重新循环到暗区的速率，驱动GC增生并使中心母细胞极化。从机制上讲，Smarca4的丢失降低了在中心细胞中激活的转录因子的活性，这些转录因子通常能驱动B细胞从GC离开，包括SPI1（PU.1）、IRF家族和NF-kB。这些因子在小鼠中的中心细胞和人类伯基特淋巴瘤细胞中的活性丧失，使细胞的BCL6表现出异常的活性。总的来说，SMARCA4提高了调控中心细胞发育轨迹的转录因子的染色质可及性，这些调控程序的失控会使中心母细胞的命运发生偏移、导致GC增生和淋巴瘤。

6.Multimodal stimulation screens reveal unique and shared genes limiting T cell fitness

多模式刺激筛选揭示了限制T细胞适应性的特异性和共同基因

荷兰癌症研究所分子肿瘤学和免疫学分部

Genes limiting T cell antitumor activity may serve as therapeutic targets. It has not been systematically studied whether there are regulators that uniquely or broadly contribute to T cell fitness. We perform genomescale CRISPR-Cas9 knockout screens in primary CD8 T cells to uncover genes negatively impacting fitness upon three modes of stimulation: (1) intense, triggering activation-induced cell death (AICD); (2) acute, triggering expansion; (3) chronic, causing dysfunction. Besides established regulators, we uncover genes controlling T cell fitness either specifically or commonly upon differential stimulation. Dap5 ablation, ranking highly in all three screens, increases translation while enhancing tumor killing. Loss of Icam1-mediated homotypic T cell clustering amplifies cell expansion and effector functions after both acute and intense stimulation. Lastly, Ctbp1 inactivation induces functional T cell persistence exclusively upon chronic stimulation. Our results functionally annotate fitness regulators based on their unique or shared contribution to traits limiting T cell antitumor activity.

限制T细胞抗肿瘤活性的基因可能成为抗肿瘤的治疗靶点。但目前还不清楚是否存在特异或广泛调控T细胞适应性的基因。因此，该研究在原代CD8 T细胞中进行了基因组规模的CRISPR-Cas9敲除筛选，以揭示在三种刺激模式下对细胞适应性产生负性影响的基因：（1）强烈刺激，引起T细胞的激活诱导细胞死亡（AICD）；（2）急性刺激，诱导T细胞扩增；（3）慢性刺激，导致T细胞功能失调。结果发现，除了已知的调节因子外，该研究发现了一些新的能在不同刺激下调控T细胞适应性的基因，包括刺激特异性的和共同的。其中，Dap5的消除在三种筛选中排名较高，提高了T细胞的翻译能力并增强了肿瘤杀伤作用。另外，当时失去Icam1介导的同种型T细胞聚集时，急性和强烈刺激都会刺激T细胞扩增和增强T细胞的功能效应。最后，Ctbp1失活仅在慢性刺激下能诱导功能性T细胞的持久性。总的来说，该研究的结果根据这些适应性调节因子对限制T细胞抗肿瘤活性的贡献，对它们进行了功能注释。

7.Retinoic acid receptor activation reprograms senescence response and enhances anti-tumor activity of natural killer cells

激活视黄酸受体能重编程衰老反应并增强自然杀伤细胞的抗肿瘤活性

瑞士肿瘤研究所

Cellular senescence can exert dual effects in tumors, either suppressing or promoting tumor progression. The senescence-associated secretory phenotype (SASP), released by senescent cells, plays a crucial role in this dichotomy. Consequently, the clinical challenge lies in developing therapies that safely enhance senescence in cancer, favoring tumor-suppressive SASP factors over tumor-promoting ones. Here, we identify the retinoic-acid-receptor (RAR) agonist adapalene as an effective pro-senescence compound in prostate cancer (PCa). Reactivation of RARs triggers a robust senescence response and a tumor-suppressive SASP. In preclinical mouse models of PCa, the combination of adapalene and docetaxel promotes a tumor-suppressive SASP that enhances natural killer (NK) cell-mediated tumor clearance more effectively than either agent alone. This approach increases the efficacy of the allogenic infusion of human NK cells in mice injected with human PCa cells, suggesting an alternative therapeutic strategy to stimulate the anti-tumor immune response in "immunologically cold" tumors.

细胞衰老在肿瘤中可能产生双重效应，既可以抑制肿瘤的发展，也可能促进其进展。衰老细胞释放会释放一系列生物分子（包括细胞因子，生长因子等），称为衰老相关的分泌表型（SASP），它们在其中起着至关重要的作用。因此，临床上的挑战在于开发能够安全促进肿瘤细胞衰老，有利于肿瘤抑制的SASP，而不是促进肿瘤进展的SASP。因此，在这项研究中，研究者发现视黄酸受体（RAR）激动剂阿达博林是一种在前列腺癌（PCa）中有效的促肿瘤衰老化合物。RAR的重新激活能引发肿瘤强烈的衰老反应和并产生抑制肿瘤的SASP。在临床前的PCa小鼠模型中，阿达博林和多西他赛的联合使用促进了一种抑制肿瘤的SASP的产生，这种SASP比单独使用任何一种药物更能有效地增强自然杀伤（NK）细胞介导的肿瘤清除作用。研究在注射了人类PCa细胞的小鼠体内验证了这种方法的疗效，为刺激“免疫冷”肿瘤的抗肿瘤免疫反应提供了一种替代治疗方法。

8.Mapping functional to morphological variation reveals the basis of regional extracellular matrix subversion and nerve invasion in pancreatic cancer

通过将肿瘤细胞的功能变异映射到形态学变异，揭示了胰腺癌中区域性细胞外基质转变和神经侵袭的基础。

意大利欧洲肿瘤研究所(IRCCS)

Intratumor morphological heterogeneity of pancreatic ductal adenocarcinoma (PDAC) predicts clinical outcomes but is only partially understood at the molecular level. To elucidate the gene expression programs underpinning intratumor morphological variation in PDAC, we investigated and deconvoluted at single cell level the molecular profiles of histologically distinct clusters of PDAC cells. We identified three major morphological and functional variants that co-exist in varying proportions in all PDACs, display limited genetic diversity, and are associated with a distinct organization of the extracellular matrix: a glandular variant with classical ductal features; a transitional variant displaying abortive ductal structures and mixed endodermal and myofibroblast-like gene expression; and a poorly differentiated variant lacking ductal features and basement membrane, and showing neuronal lineage priming. Ex vivo and in vitro evidence supports the occurrence of dynamic transitions among these variants in part influenced by extracellular matrix composition and stiffness and associated with local, specifically neural, invasion.

胰腺导管腺癌（PDAC）的肿瘤内形态异质性可以用来预测临床结局，但我们对PDAC肿瘤内分子水平上的异质性了解很少。为了阐明PDAC肿瘤内形态变异的基因表达程序，该研究在单细胞水平上解析了PDAC的不同组织学细胞簇的分子特征。结果显示，该研究一共鉴定出了三种主要的形态和功能细胞群，它们在所有PDAC组织中以不同比例共存，显示有限的遗传多样性，并与细胞外基质的不同结构相关联，比如，具有经典导管特征的腺体细胞；有未成熟导管结构和混合内胚层并且有肌纤维母细胞样基因表达的过渡细胞；缺乏导管特征和基底膜，并表现出神经细胞谱系的初步特征的未分化细胞。体外和体内的证据支持了这些细胞之间会发生动态转变，这些转变会在一定程度上受到细胞外基质的组成和刚度的影响，并与肿瘤的局部侵袭，特别是神经侵袭相关。

9.PDGFRα+ITGA11+ fibroblasts foster early-stage cancer lymphovascular invasion and lymphatic metastasis via ITGA11-SELE interplay

PDGFRα+ITGA11+成纤维细胞通过ITGA11-SELE相互作用促进早期癌症的淋巴血管侵袭和淋巴转移

中山大学孙逸仙纪念医院

Cancer-associated fibroblasts (CAFs) exhibit considerable heterogeneity in advanced cancers; however, the functional annotation and mechanism of CAFs in early-stage cancers remain elusive. Utilizing single-cell RNA sequencing and spatial transcriptomic, we identify a previously unknown PDGFRa+ITGA11+ CAF subset in early-stage bladder cancer (BCa). Multicenter clinical analysis of a 910-case cohort confirms that PDGFRa+ITGA11+ CAFs are associated with lymphovascular invasion (LVI) and poor prognosis in early-stage BCa. These CAFs facilitate LVI and lymph node (LN) metastasis in early-stage BCa, as evidenced in a PDGFRa+ITGA11+ CAFs-specific deficient mouse model. Mechanistically, PDGFRa+ITGA11+ CAFs promote lymphangiogenesis via recognizing ITGA11 surface receptor SELE on lymphatic endothelial cells to activate SRC-p-VEGFR3-MAPK pathway. Further, CHI3L1 from PDGFRa+ITGA11+ CAFs aligns the surrounding matrix to assist cancer cell intravasation, fostering early-stage BCa LVI and LN metastasis. Collectively, our study reveals the crucial role of PDGFRa+ITGA11+ CAFs in shaping metastatic landscape, informing the treatment of early-stage BCa LVI.

在晚期癌症中，肿瘤相关的成纤维细胞（CAFs）展现出相当大的异质性；然而，在早期癌症中，CAFs的功能和机制仍然不为人知。因此，该研究通过单细胞RNA测序和空间转录组学，在早期膀胱癌（BCa）中发现了一个未报道过的PDGFRa+ITGA11+ CAF亚群。通过对910例病例的多中心临床分析，证实了PDGFRa+ITGA11+ CAF与早期BCa中的淋巴血管侵袭（LVI）和不良预后相关。这些CAFs促进了早期BCa的LVI和淋巴结（LN）转移，并在PDGFRa+ITGA11+ CAF特异性缺失的小鼠模型中得到了证实。机制上，PDGFRa+ITGA11+ CAF通过识别淋巴内皮细胞上的ITGA11表面受体SELE来激活SRC-p-VEGFR3-MAPK通路，从而促进淋巴管新生。此外，来自PDGFRa+ITGA11+ CAF的CHI3L1重塑了癌细胞周围的基质，协助癌细胞内皮化，促进早期BCa的LVI和LN转移。综上所述，该研究揭示了PDGFRa+ITGA11+ CAF在形成转移性肿瘤景观中的关键作用，并为早期BCa的LVI治疗提供了重要信息。

10.Genetic interactions reveal distinct biological and therapeutic implications in breast cancer

基因相互作用揭示了乳腺癌中不同的生物学和治疗启示

复旦大学上海肿瘤中心乳腺外科乳腺癌重点实验室

Co-occurrence and mutual exclusivity of genomic alterations may reflect the existence of genetic interactions, potentially shaping distinct biological phenotypes and impacting therapeutic response in breast cancer. However, our understanding of them remains limited. Herein, we investigate a large-scale multi-omics cohort (n=873) and a real-world clinical sequencing cohort (n=4,405) including several clinical trials with detailed treatment outcomes and perform functional validation in patient-derived organoids, tumor fragments, and in vivo models. Through this comprehensive approach, we construct a network comprising co-alterations and mutually exclusive events and characterize their therapeutic potential and underlying biological basis. Notably, we identify associations between TP53mut-AURKAamp and endocrine therapy resistance, germline BRCA1mut-MYCamp and improved sensitivity to PARP inhibitors, and TP53mut-MYBamp and immunotherapy resistance. Furthermore, we reveal that precision treatment strategies informed by co-alterations hold promise to improve patient outcomes. Our study highlights the significance of genetic interactions in guiding genome-informed treatment decisions beyond single driver alterations.

乳腺癌中基因组改变的共同发生和互斥可能反映了基因相互作用的存在，这些相互作用可能塑造了不同的生物学表型，并影响了治疗反应。然而，我们对它们的理解仍然有限。在这项研究中，研究者调查了一个大规模多组学队列（n = 873）和一个现实世界的临床测序队列（n = 4,405），其中包括几项具有详细治疗结果的临床试验，并在患者来源的类器官、肿瘤组织碎片和体内模型中进行功能验证。通过这种全面的方法，该研究构建了一个包括基因共同改变和互斥事件的网络，并表征了基因共同改变和互斥对治疗潜力的影响和潜在的生物学基础。值得注意的是，研究发现了TP53突变-AURKA扩增与肿瘤的内分泌治疗抵抗、BRCA1突变-MYC扩增与肿瘤对PARP抑制剂的敏感性提高以及TP53突变-MYB扩增与肿瘤的免疫治疗抵抗之间的关联。此外，该研究还发现根据基因共同改变制定的精准治疗策略有望改善患者预后。总的来说，该研究凸显了基因相互作用对于指导治疗决策的重要性，甚至超越了单一驱动基因改变对治疗决策的影响。

汇报人： 夏晓旭

导师：赵宇  任建君

审核：任建君  邱轲