Editorial:Transcriptome analysis in tumor microenvironment and tumor heterogeneity

Cancer,a disease as intricate as it is devastating,continues to challenge the medical and scientific community[1].Its complex nature is epitomized by the tumor microenvironment and tumor heterogeneity.As we delve deeper into the realms of cancer research,the advent of transcriptome analysis has emerged as a powerful torchbearer,illuminating our understanding of these enigmatic facets of cancer biology[2].

Tumor heterogeneity of gastric cancer: From the perspective of tumor-initiating cell

Gastric cancer(GC) remains one of the most common and malignant types of cancer due to its rapid progression, distant metastasis, and resistance to conventional chemotherapy, although efforts have been made to understand the underlying mechanism of this resistance and to improve clinical outcome. It is well recognized that tumor heterogeneity, a fundamental feature of malignancy, plays an essential role in the cancer development and chemoresistance. The model of tumor-initiating cell(TIC) has been proposed to explain the genetic, histological, and phenotypical heterogeneity of GC. TIC accounts for a minor subpopulation of tumor cells with key characteristics including high tumorigenicity, maintenance of self-renewal potential, giving rise to both tumorigenic and non-tumorigenic cancer cells, and resistance to chemotherapy. Regarding tumor-initiating cell of GC(GATIC), substantial studies have been performed to(1) identify the putative specific cell markers for purification and functional validation of GATICs;(2) trace the origin of GATICs; and(3) decode the regulatory mechanism of GATICs. Furthermore, recent studies demonstrate the plasticity of GATIC and the interaction between GATIC and its surrounding factors(TIC niche or tumor microenvironment). All these investigations pave the way for the development of GATIC-targeted therapy, which is in the phase of preclinical studies and clinical trials. Here, we interpret the heterogeneity of GC from the perspectives of TIC by reviewing the above-mentioned fundamental and clinical studies of GATICs. Problems encountered during the GATIC investigations and the potential solutions are also discussed.

Patient-derived non-small cell lung cancer xenograft mirrors complex tumor heterogeneity

Objective:Patient-derived xenograft(PDX)models have shown great promise in preclinical and translational applications,but their consistency with primary tumors in phenotypic,genetic,and pharmacodynamic heterogeneity has not been well-studied.This study aimed to establish a PDX repository for non-small cell lung cancer(NSCLC)and to further elucidate whether it could preserve the heterogeneity within and between tumors in patients.Methods:A total of 75 surgically resected NSCLC specimens were implanted into immunodeficient NOD/SCID mice.Based on the successful establishment of the NSCLC PDX model,we compared the expressions of vimentin,Ki67,EGFR,and PD-L1 proteins between cancer tissues and PDX models using hematoxylin and eosin staining and immunohistochemical staining.In addition,we detected whole gene expression profiling between primary tumors and PDX generations.We also performed whole exome sequencing(WES)analysis in 17 first generation xenografts to further assess whether PDXs retained the patient heterogeneities.Finally,paclitaxel,cisplatin,doxorubicin,atezolizumab,afatininb,and AZD4547 were used to evaluate the responses of PDX models to the standard-of-care agents.Results:A large collection of serially transplantable PDX models for NSCLC were successfully developed.The histology and pathological immunohistochemistry of PDX xenografts were consistent with the patients’tumor samples.WES and RNA-seq further confirmed that PDX accurately replicated the molecular heterogeneities of primary tumors.Similar to clinical patients,PDX models responded differentially to the standard-of-care treatment,including chemo-,targeted-and immuno-therapeutics.Conclusions:Our established PDX models of NSCLC faithfully reproduced the molecular,histopathological,and therapeutic characteristics,as well as the corresponding tumor heterogeneities,which provides a clinically relevant platform for drug screening,biomarker discovery,and translational research.

Intratumoral heterogeneity of hepatocellular carcinoma: From singlecell to population-based studies

Hepatocellular carcinoma(HCC)is characterized by high heterogeneity in both intratumoral and interpatient manners.While interpatient heterogeneity is related to personalized therapy,intratumoral heterogeneity(ITH)largely influences the efficacy of therapies in individuals.ITH contributes to tumor growth,metastasis,recurrence,and drug resistance and consequently limits the prognosis of patients with HCC.There is an urgent need to understand the causes,characteristics,and consequences of tumor heterogeneity in HCC for the purposes of guiding clinical practice and improving survival.Here,we summarize the studies and technologies that describe ITH in HCC to gain insight into the origin and evolutionary process of heterogeneity.In parallel,evidence is collected to delineate the dynamic relationship between ITH and the tumor ecosystem.We suggest that conducting comprehensive studies of ITH using single-cell approaches in temporal and spatial dimensions,combined with population-based clinical trials,will help to clarify the clinical implications of ITH,develop novel intervention strategies,and improve patient prognosis.

Advances in the role of circulating tumor cell heterogeneity in metastatic small cell lung cancer

Small cell lung cancer(SCLC),a highly aggressive malignancy,is rapidly at an extensive stage once diagnosed and is one of the leading causes of death from malignancy.In the past decade,the treatment of SCLC has largely remained unchanged,and chemotherapy remains the cornerstone of SCLC treatment.The therapeutic value of adding immune checkpoint inhibitors to chemotherapy for SCLC is low,and only a few SCLC patients have shown a response to immune checkpoint inhibitors.Circulating tumor cells(CTCs)are tumor cells shed from solid tumor masses into the peripheral circulation and are key to tumor metastasis.Single-cell sequencing has revealed that the genetic profiles of individual CTCs are highly heterogeneous and contribute to the poor outcome and prognosis of SCLC patients.Theoretically,phenotypic analysis of CTCs may be able to predict the diagnostic significance of new potential targets for metastatic tumors.In this paper,we will discuss in depth the heterogeneity of CTCs in SCLC and the value of CTCs for the diagnosis and prognosis of SCLC and as relevant tumor markers in metastatic SCLC.

Heterogeneity of neutrophils in cancer:one size does not fit all

Neutrophils play an essential role in the defense against bacterial infections and orchestrate both the innate and adaptive immune responses.With their abundant numbers,diverse function and short life span,these cells are at the forefront of immune responses,and have gained attention in recent years because of their presence in tumor sites.Neutrophil involvement pertains to tumor cells'ability to construct a suitable tumor microenvironment(TME)that accelerates their own growth and malignancy,by facilitating their interaction with surrounding cells through the circulatory and lymphatic systems,thereby influencing tumor development and progression.Studies have indicated both pro-and anti-tumor properties of infiltrating neutrophils.The TME can exploit neutrophil function,recruitment,and even production,thus resulting in pro-tumor properties of neutrophils,including promotion of genetic instability,tumor cell proliferation,angiogenesis and suppression of anti-tumor or inflammatory response.In contrast,neutrophils can mediate anti-tumor resistance by direct cytotoxicity to the tumor cells or by facilitating anti-tumor functions via crosstalk with T cells.Here,we summarize current knowledge regarding the effects of neutrophil heterogeneity under homeostatic and tumor conditions,including neutrophil phenotype and function,in cancer biology.

Heterogeneity and renal mass biopsy:a review of its role and reliability

Increased abdominal imaging has led to an increase in the detection of the incidental small renal mass(SRM). With increasing recognition that the malignant potential of SRMs is heterogeneous, ranging from benign(15%-20%) to aggressive(20%), enthusiasm for more conservative management strategies in the elderly and infirmed, such as active surveillance(AS), have grown considerably. As the management of the SRM evolves to incorporate ablative techniques and AS for low risk disease, the role of renal mass biopsy(RMB) to help guide individualized therapy is evolving. Historically, the role of RMB was limited to the evaluation of suspected metastatic disease, renal abscess, or lymphoma. However, in the contemporary era, the role of biopsy has grown, most notably to identify patients who harbor benign lesions and for whom treatment, particularly the elderly or frail, may be avoided. When performing a RMB to guide initial clinical decision making for small, localized tumors, the most relevant questions are often relegated to proof of malignancy and documentation(if possible) of grade. However, significant intratumoral heterogeneity has been identified in clear cell renal cell carcinoma(ccRCC) that may lead to an underestimation of the genetic complexity of a tumor when single-biopsy procedures are used. Heterogeneous genomic landscapes and branched parallel evolution of ccRCCs with spatially separated subclones creates an illusion of clonal dominance when assessed by single biopsies and raises important questions regarding how tumors can be optimally sampled and whether future evolutionary tumor branches might be predictable and ultimately targetable. This work raises profound questions concerning the genetic landscape of cancer and how tumor heterogeneity may affect, and possibly confound, targeted diagnostic and therapeutic interventions. In this review, we discuss the current role of RMB, the implications of tumor heterogeneity on diagnostic accuracy, and highlight promising future directions.

Circulating tumor cells: Biological features and survival mechanisms

Circulating tumor cells(CTCs)are neoplastic cells that are detached from primary tumors and enter circulation.Enumeration and characterization of CTCs are of significance in cancer diagnosis,prognosis,and treatment monitoring.CTC survival in the bloodstream is a limiting step for the development of metastases in distant organs.Recent technological advances,especially in single-cell molecular analyses have uncovered heterogeneous CTC survival mechanisms.Undergoing epithelial-to-mesenchymal transition(EMT),increasing stem cell-like properties,and forming cell clusters enable CTCs to adapt to the harsh microenvironment of the circulation.Expressing and releasing several immunosuppressive molecules help CTCs escape from anti-cancer immune mechanisms.This review article summarizes the biological characteristics of CTCs and focuses on the recent understanding of the mechanisms by which CTCs survive in circulation.Additionally,the clinical and therapeutic implications of CTCs are discussed.

HPV18 E6 and E7 Intratumour Heterogeneity in Esophageal Cancer

The development of esophageal cancer accompanied by the presence of human papillomavirus (HPV) DNA into the host genome. By evaluating the expression of this virus for tumor cell origin and also their cell grows and migrations, we examined esophageal cancer clonality in the context of intra-tumor heterogeneity. In this research, we have checked the expression of HPV18 E6 and E7 in different single cell clones by the manual cell picking method in the HPV positive esophageal cancer (EC109), EC109 cell line used as a negative control, and Hela cell line used as the positive control. Quantitative real-time PCR (QRT-PCR) was run to detect the expression levels of HPV E6 and E7, Cell Counting Kit-8 (CCK-8) assay was used to examine cell proliferation, invasion assays performed using Costar chambers and wounding assay to study cell migrations in vitro. We investigated the intra-tumor heterogeneity of HPV E6 and E7 in esophageal cancer and the evaluation of the growth and migrations at the clonal level, using 10 single cell clones. In particular clones, C7 & C10 displayed a highly variable expression in both HPV E6 and E7 and weak in four clones (C1, C3, C4, and C9) consequently, the cell invasion, proliferation, and migration increase with increasing the level of HPV expression and inverse. In conclusion, the resulting based on single cell cloning showed the relationship between HPV and cell growth and migration in esophageal cancer. Future study in HPV DNA integration needed to explore the mains specific integration site of HPV DNA in esophageal cancer and molecular monitoring of the HPV for future prevention researches and also effective therapeutic strategies.

异时性多复发灶耐药基因分子异质性的胃肠道间质瘤1例报告及文献复习

目的:分析1例长期伊马替尼治疗后多部位、异时性复发病灶敏感/耐药共存的少见胃肠道间质瘤(GISTs)患者的临床资料,揭示GISTs继发突变的异质性是复发耐药过程中的重要属性。方法:收集1例复发GISTs患者的临床资料,采用HE染色法进行组织学观察,免疫组织化学染色检测相关蛋白表达,一代和二代测序技术分析肿瘤基因变异情况。结果:患者,男性,66岁,因胃间质瘤行胃部分切除术。一代测序技术检测结果显示为原癌基因,受体酪氨酸激酶(KIT)基因11号外显子缺失突变(p.551-554del)。伊马替尼治疗1年左右,停药4个月后复发,患者出现脾区病灶,继续采用伊马替尼一线治疗,脾区病灶得到控制。59个月后盆腔发现新病灶,采用伊马替尼加量(600 mg·d^(-1))并舒尼替尼二线治疗,治疗2个月后CT检查结果显示患者脾区病灶大小趋于稳定,而盆腔新病灶体积持续增大。二代测序技术检测结果显示两复发灶在原有KIT基因11号外显子缺失突变的基础上,分别继发KIT基因13号外显子(p.V654A)和17号外显子(p.Y823D)突变。结论:GISTs在靶向药物选择作用的压力下,肿瘤生物学行为表现出复杂性,即时间异质性、空间异型性和分子异质性,不同复发灶可以出现不同的耐药机制。

单细胞RNA测序技术在肺癌肿瘤微环境研究中的进展

免疫微环境对肿瘤的发生发展起着关键作用。近年来,随着高通量测序技术的飞速发展,研究人员对肿瘤微环境中的免疫细胞组成及其功能有了更深入的了解。然而,传统的群体测序技术难以解析单个细胞层面的异质性,限制了对肿瘤微环境复杂性的全面理解。单细胞RNA测序技术的兴起,为揭示肺癌免疫微环境的异质性带来了新的机遇。当前以T细胞为中心的免疫治疗在临床中容易出现免疫原性耐药或者免疫相关性肺炎等影响预后的副作用,其关键因素是肿瘤微环境中免疫细胞与肿瘤细胞的相互作用发生了变化。而单细胞RNA测序技术可以从细胞间互作、拟时序分析等角度揭示肿瘤微环境中不同亚群间的起源与作用,进而发现新的细胞亚群或新生生物标志物,为揭示免疫治疗的耐药及疗效监测等提供新的途径。该综述系统回顾了单细胞RNA测序技术在揭示肺癌特别是免疫治疗后肺癌微环境异质性方面的最新研究进展,为促进肺癌免疫治疗的精准化与个体化提供参考。

组织成像质谱流式在消化系统肿瘤中的应用

组织成像质谱流式(IMC)是一种融合了质谱、高分辨激光消融、免疫组织/细胞化学的新技术。以独特的高维视角全面、精准地描绘组织和肿瘤微环境中复杂的表型、信号通路、肿瘤免疫的相互作用,在消化系统肿瘤中广泛应用。本文围绕IMC在描绘肿瘤微环境全景图、揭示肿瘤空间异质性、阐明肿瘤药理学机制、助力新药开发、动态评估免疫治疗疗效在消化系统肿瘤中应用展开综述。

肿瘤相关中性粒细胞的异质性及潜在的临床意义

恶性肿瘤组织中肿瘤相关中性粒细胞(TAN)是肿瘤微环境的重要组成部分。TAN在肿瘤中的作用具有两面性。一方面,TAN可直接杀伤肿瘤细胞,或介导其他免疫细胞协同抗肿瘤。另一方面,TAN也可促进肿瘤血管生成、重塑细胞外基质及参与肿瘤细胞免疫逃逸。以上TAN功能的异质性是其在肿瘤微环境中多种复杂机制的交互调控下形成的,对肿瘤的发展或抑制产生重要的作用。因此,阐明TAN的异质性、不同亚群转化机制及其潜在的临床意义显得尤为重要,不仅有助于开发针对促肿瘤型中性粒细胞亚群的抑制类药物和疗法,还可进一步促进免疫治疗更多获益人群的新评估标准建立和筛选。

单细胞转录组测序在黑色素瘤中的研究进展

黑色素瘤是皮肤癌中致死性最高的一种恶性肿瘤,其发生、发展机制复杂,具有高度侵袭性、转移性和致死性,患者预后差。因此,加强该病基础研究尤为重要。单细胞转录组测序作为近年来快速发展的新技术,以其特有的优势如探索细胞亚群的异质性、鉴定稀有细胞、使用生物信息算法揭示不同组织细胞的分化轨迹等,极大地推动了黑色素瘤的基础与临床研究发展。本文就黑色素瘤单细胞转录组测序研究中肿瘤异质性和肿瘤免疫方面的进展进行综述。

单细胞转录组测序解析化疗后舌鳞癌免疫细胞动态图谱和肿瘤细胞耐药异质性

目的:探究舌鳞癌免疫和肿瘤细胞亚群的转录组异质性和化疗相关的变化。方法:研究收集了首都医科大学附属北京口腔医院口腔颌面头颈肿瘤科确诊舌鳞状细胞癌(简称舌鳞癌)、接受相同化疗方案却出现化疗疗效差异的2位患者的化疗前、后的肿瘤和外周血单核细胞样本共8例,进行单细胞转录组测序,并对测序结果进行数据分析。使用多重免疫荧光技术观察T细胞化疗前后变化和疗效出现差异的患者之间肿瘤细胞marker基因表达情况对比。结果:根据经典marker基因的表达将获得的细胞分成T细胞和NK细胞、B细胞和浆细胞、上皮细胞等12个主要的细胞亚群。数据分析结果显示,化疗后舌鳞癌免疫和肿瘤亚群细胞图谱发生了显著变化。2位化疗效果不同的患者在特定亚型的T细胞、NK细胞和髓样细胞表现出转录组异质性和化疗相关变化,多重免疫荧光实验发现化疗后舌鳞癌肿瘤微环境中Tregs细胞减少,而CTL细胞增加。此外,该研究探索了化疗前后肿瘤细胞的异质性,并定义了三组具有不同生物学特征和恶性程度的肿瘤细胞亚群。多重免疫荧光显示疗效较差者的原发肿瘤组织比疗效好者具有更多高度恶性组肿瘤细胞。结论:研究结果解析了化疗后舌鳞癌免疫和肿瘤细胞的异质性,对影响舌鳞癌化疗效果的因素提出了新的见解,有助于识别潜在免疫治疗靶点。

PET/CT在淋巴瘤异质性评估中的价值

淋巴瘤是一种以淋巴细胞为主要来源的高度异质性肿瘤。^(18)F-FDG PET/CT通过对肿瘤细胞状态和肿瘤微环境变化的异质性FDG摄取进行评估,被广泛用于嗜FDG淋巴瘤分期、再分期及治疗反应评估。但常规PET参数在全面评估肿瘤异质性方面存在不足。本文总结PET/CT在淋巴瘤诊断、分期、治疗及预后评估中的作用,并探讨PET/CT未来发展方向,包括新PET参数的探索、新试剂的开发和人工智能的融合,这些领域在淋巴瘤检测、异质性量化、鉴别、中期疗效评估和预测预后等方面取得了重大突破。

单细胞测序在口腔鳞状细胞癌研究中的价值

单细胞测序(single-cell sequencing,SCS)在口腔鳞状细胞癌(oral squamous cell carcinoma,OSCC)研究中具有巨大潜力。随着SCS技术的发展,其灵敏度和准确度不断提高且成本逐渐降低,SCS将成为肿瘤研究的重要技术工具。SCS技术通过在单个细胞分辨率下识别基因组突变所导致的差异基因表达和表观遗传学信息改变,为发现新的细胞特异性标志物和细胞类型提供巨大帮助。在OSCC研究中,SCS不仅有助于揭示癌细胞的异质性以及更准确地理解肿瘤微环境,也有助于深入探讨恶性细胞、免疫细胞及基质细胞三者间的相互作用,揭示它们在肿瘤发生、发展中的相互影响及作用。利用SCS对肿瘤中的免疫细胞进行分类、理解免疫逃逸机制,将为免疫治疗的有效开展提供关键支持。本综述介绍SCS技术的发展现状,并回顾和讨论该技术在OSCC领域中的最新研究进展和应用前景。

单细胞RNA测序技术在胶质母细胞瘤研究中的应用

胶质母细胞瘤是成人脑部最常见的原发恶性肿瘤,尽管近年来在改善预后方面做出了巨大的努力,其中位生存期仍低于20个月,且存活时间超过20个月的患者不到5%。胶质母细胞瘤的标准治疗方案为最大限度的手术切除,联合放疗及替莫唑胺化疗。单细胞RNA测序(scRNA-seq)技术精准分析每个独特的细胞,使我们能够更好地理解肿瘤的异质性、肿瘤细胞的演化过程、肿瘤免疫微环境中各类细胞的特殊功能及细胞间相互作用,从而为临床的个体化治疗提供新思路。该综述重点关注scRNA-seq技术在胶质母细胞瘤的异质性、肿瘤免疫微环境、细胞通讯以及治疗研究中的应用。

ecDNA在小细胞肺癌致癌相关性、异质性和耐药性的机制研究进展

随着染色体外DNA(extrachromosomal DNA,ecDNA)研究的深入,研究发现ecDNA大多只存在于肿瘤细胞内,并且在肿瘤异质性和耐药中起着关键作用。ecDNA存在于多种恶性肿瘤中,但在正常细胞中极少出现。因为ecDNA具有强大的癌基因扩增和动态改变能力,故肿瘤细胞中含有ecDNA的患者临床预后更差。目前的研究已经证实小细胞肺癌(small cell lung cancer,SCLC)患者癌细胞中存在ecDNA。本文综述了ecDNA的形成机制并以此为基础讨论了ecDNA在癌细胞中扩增的过程,其促进肿瘤生长,复发和转移的机制以及ecDNA与SCLC高耐药性的关系。最后本文总结了ecDNA富集的SCLC的治疗方向,为未来进一步的研究提供一定指导。

Clinical implications of single cell sequencing for bladder cancer

Bladder cancer(BC)is the 10th most common cancer worldwide,with about 0.5 million reported new cases and about 0.2 million deaths per year.In this scoping review,we summarize the current evidence regarding the clinical implications of single-cell sequencing for bladder cancer based on PRISMA guidelines.We searched PubMed,CENTRAL,Embase,and supplemented with manual searches through the Scopus,and Web of Science for published studies until February 2023.We included original studies that used at least one single-cell technology to study bladder cancer.Forty-one publications were included in the review.Twenty-nine studies showed that this technology can identify cell subtypes in the tumor microenvironment that may predict prognosis or response to immune checkpoint inhibition therapy.Two studies were able to diagnose BC by identifying neoplastic cells through single-cell sequencing urine samples.The remaining studies were mainly a preclinical exploration of tumor microenvironment at single cell level.Single-cell sequencing technology can discriminate heterogeneity in bladder tumor cells and determine the key molecular properties that can lead to the discovery of novel perspectives on cancer management.This nascent tool can advance the early diagnosis,prognosis judgment,and targeted therapy of bladder cancer.