Molecular Subtypes of Primary SCLC Tumors and Their Associations With Neuroendocrine and Therapeutic Markers

Prognostic significance of Ki-67 in assessing the risk of progression, relapse or metastasis in pheochromocytomas and paragangliomas

INTRODUCTION

Since the Fourth edition of the WHO classification, PPGLs have been recognized for their metastatic potential, though no clear features can accurately predict this behavior. The prognostic value of Ki-67 in assessing the risk of progression, relapse, or metastasis in PPGLs remains debated.

METHODS

This cohort study included 501 patients diagnosed with PPGLs at the First Hospital of Jilin University between 2000 and 2022, with clinical data, treatment details, pathological indicators, and germline gene test results collected. Bulk sequencing was performed on formalin-fixed paraffin-embedded (FFPE) primary tumor samples from 87 patients. Progression-free survival (PFS) was analyzed using multivariable Cox regression.

RESULTS

Among the 119 enrolled patients with PPGLs, the average age was 45.7 ± 14.0 years, and the median follow-up time was 46 months. A significant finding was the high expression of CDK1, a gene known to be significantly associated with the metastatic risk of PPGLs, in samples with Ki-67 ≥ 3% (p < 0.0001). More importantly, patients with PPGLs and a Ki-67 level ≥ 3% had a 3.59-fold higher risk of progression, relapse or metastasis compared to those with Ki-67 < 3% (HR = 4.59, 95% CI: 1.06-11.95), after adjusting for all confounding factors. In the composite model, the addition of Ki-67 enhanced the predictive ability of the combined model of SDHB, primary site, tumor size, and invade neighboring tissue (AUC = 0.888, 95% CI: 0.808-0.967 vs. AUC = 0.874, 95% CI: 0.783-0.965).

CONCLUSION

A Ki-67 level ≥ 3% is associated with an increased risk of progression, relapse or metastasis in patients with PPGLs.

Epstein-Barr virus-positive small cell neuroendocrine carcinoma of the nasopharynx: A clinicopathologic study of 7 cases and literature review

Epstein-Barr virus (EBV)-positive small cell neuroendocrine carcinoma (NEC) of the nasopharynx is a rare entity with poorly characterized clinicopathological and prognostic features. In this study, seven cases of EBV-positive nasopharyngeal small cell NEC will be compared to 6 EBV-negative cases of nasopharyngeal small cell NEC. The overall EBV-positive rate, defined by EBV-encoded small RNAs (EBERs) in situ hybridization of nasopharyngeal small cell NEC, was 53.8 % (7/13). The patients' age ranged from 38 to 73 years, with a median age of 56 years. There was a large preponderance of males, with a male-to-female ratio of 6:1. In the present study, EBV-positive nasopharyngeal small cell NEC had a significantly higher expression of POU2F3 (85.7 %, 6/7) than EBV-negative nasopharyngeal small cell NEC (16.7 %, 1/6). RNA sequencing revealed that EBV-positive nasopharyngeal small cell NEC was distinct from EBV-negative nasopharyngeal small cell NEC in the control group. There was no statistically significant difference in overall survival between patients with EBV-positive and EBV-negative nasopharyngeal small cell NEC in the present cohort. These findings suggest that EBV-positive nasopharyngeal small cell NEC may be closely associated with POU2F3. In addition, POU2F3 and ASCL1 may play important roles in the tumorigenesis of EBV-positive nasopharyngeal small cell NEC.

An organoid library unveils subtype-specific IGF-1 dependency via a YAP-AP1 axis in human small cell lung cancer

Small cell lung cancer (SCLC) is a devastating disease with limited therapeutic advancements. Although SCLC has recently been classified into four molecular subtypes, subtype-specific therapies are still lacking. Here, we established 40 patient-derived SCLC organoid lines with predominant TP53 and RB1 alterations and rare targetable genetic lesions. Transcriptome profiling divided the SCLC organoids into neuroendocrine (NE)-type SCLC and non-NE-type SCLC, with the latter characterized by YAP1 or POU2F3 expression. NE-type SCLC organoids grew independent of alveolar niche factors, whereas non-NE-type SCLC organoids relied on insulin-like growth factor (IGF)-1-driven YAP1 and AP1 activation. Therapeutic targeting of IGF-1, YAP1 and AP1 effectively suppressed the growth of non-NE-type organoids. Co-knockout of TP53 and RB1 in human alveolar cells altered their lineage toward the airway epithelium-like fate and conferred IGF-1 dependency, validating the subtype-phenotype connection. Our SCLC organoid library represents a valuable resource for developing biology-based therapies and has the potential to reshape the drug discovery landscape.

Molecular heterogeneity of small cell lung cancer and new therapeutic possibilities: a narrative review of the literature

Background and Objective

Small cell lung cancer (SCLC) is an aggressive disease commonly occurring in individuals with a history of heavy smoking. Despite recent approvals of chemotherapy and immunotherapy in the first-line treatment of extensive-stage SCLC, it maintains a poor prognosis. Moreover, only a small percentage of patients benefits from the addition of immunotherapy to platinum-based chemotherapy. The lack of significant progress in therapeutic options unrevealed the urgent need for a deeper understanding of tumor biology and easy-to-use predictive biomarkers, aiming to better tailor the treatment strategy. The aim of this review is to summarize recent evidence about the biology, molecular heterogeneity, as well as tumor microenvironment (TME) of SCLC and their forefront therapeutic implications.

Methods

A literature search was conducted using PubMed, focusing on articles published in English from 1981 to October 2024. Studies on SCLC biology and subclassification were selected for further analysis and integrated in the current narrative review.

Key Content and Findings

SCLC entity implies four distinct molecular subtypes based on transcription factors expression, specifically achaete-scute homolog 1 (ASCL1), neurogenic differentiation 1 (NEUROD1), POU class 2 homeobox 3 (POU2F3), and yes-associated protein 1 (YAP1), reflecting the tumor heterogeneity in terms of gene expression, transcriptional profiles, immune infiltration, and treatment sensitivity. Recently, a new subgroup, "SCLC-I", has been proposed to replace the YAP1 subtype, showing higher responsiveness to immunotherapy. The TME, implying immune cell infiltration and their interactions with cancer cells, plays a crucial role in determining SCLC's sensitivity to immunotherapy.

Conclusions

Advances in SCLC molecular characterization and the development of targeted therapies against specific molecular pathways might improve patients' clinical outcome, supporting a more personalized approach to this complex disease.

Functional characterization of the ATOH1 molecular subtype indicates a pro-metastatic role in small cell lung cancer

Molecular subtypes of small cell lung cancer (SCLC) have been described based on differential expression of the transcription factors (TFs) ASCL1, NEUROD1, and POU2F3 and immune-related genes. We previously reported an additional subtype based on expression of the neurogenic TF ATOH1 within our SCLC circulating tumor cell-derived explant (CDX) model biobank. Here, we show that ATOH1 protein is detected in 7 of 81 preclinical models and 16 of 102 clinical samples of SCLC. In CDX models, ATOH1 directly regulates neurogenesis and differentiation programs, consistent with roles in normal tissues. In ex vivo cultures of ATOH1+ CDXs, ATOH1 is required for cell survival. In vivo, ATOH1 depletion slows tumor growth and suppresses liver metastasis. Our data validate ATOH1 as a bona fide lineage-defining TF of SCLC with cell survival and pro-metastatic functions. Further investigation exploring ATOH1-driven vulnerabilities for targeted treatment with predictive biomarkers is warranted.

Clinicopathological characteristics of transcription factor-defined subtypes in bladder small cell carcinoma

BACKGROUND

Small cell carcinoma (SmCC) of the bladder is a rare and aggressive malignancy. Characterizing transcription factor (TF)-defined subtypes may provide insights into its biology and inform targeted therapies. This study investigates lineage-specific TF expression in bladder SmCC, its association with clinicopathological features, and comparisons with prostate SmCC.

METHODS

A retrospective analysis was conducted on 9 cases of bladder SmCC and 6 cases of prostate SmCC diagnosed at a single cancer hospital in Japan. Immunohistochemistry was performed for lineage-specific TFs (ASCL1, NEUROD1, POU2F3, and YAP1) and neuroendocrine and other markers. Statistical comparisons were made using Fisher's exact test and independent samples t-tests.

RESULTS

Combined SmCC morphology, including urothelial carcinoma (UC) (5 cases) and adenocarcinoma (2 cases), was more frequent in bladder SmCC than in prostate SmCC (78% [7 of 9 cases] vs. 17% [1 of 6 cases], p = 0.041). NEUROD1 was more frequently expressed in bladder SmCC than in prostate SmCC (67% [6 of 9 cases] vs. 0% [0 of 6 cases]; p = 0.028). NEUROD1 expression was more frequent in combined SmCC and UC bladder tumors than in other bladder SmCC tumors (100% [5 of 5 cases] vs. 25% [1 of 4 cases], p = 0.048). Conversely, HNF4A expression was absent in all combined SmCC and UC bladder tumors (0 of 5) but present in 75% (3 of 4) of other bladder SmCC tumors (p = 0.048). In 2 cases of bladder SmCC, NEUROD1 and POU2F3 were expressed in a mutually exclusive manner, with neuroendocrine markers expressed only in the NEUROD1-expressing component.

CONCLUSIONS

NEUROD1 is characteristically expressed in bladder SmCC, especially in SmCC combined with UC, suggesting a distinct phenotype from prostate SmCC. These findings highlight the potential for TF-based classification to improve diagnostic accuracy and inform therapeutic strategies.

Proteogenomic Characterization of High-Grade Lung Neuroendocrine Carcinoma Deciphers Molecular Diversity and Potential Biomarkers of Different Histological Subtypes in Chinese Population

High-grade lung neuroendocrine carcinomas (Lu-NECs) are clinically refractory malignancies with poor prognosis and limited therapeutic advances. The biological and molecular features underlying the histological heterogeneity of Lu-NECs are not fully understood. In this study, we present a multi-omics integration of whole-exome sequencing and deep proteomic profiling in 93 Chinese Lu-NECs to establish the first comprehensive proteogenomic atlas of this disease spectrum. Our analyses revealed a high degree of mutational concordance among the subtypes at the genomic level; however, distinct proteomic profiles enabled a clear differentiation of histological subtypes, unveiling subtype-specific molecular and biological features related to tumor metabolism, immunity, and proliferation. Furthermore, RB1 mutations confer divergent prognostic effects through subtype-specific cis- and trans-proteomic regulation. In addition, we identified potential protein biomarkers for histological subtype classification and risk stratification, which were validated by immunohistochemistry in an independent cohort. This study provides a valuable proteogenomic resource and insight into Lu-NEC heterogeneity.

Challenges of small cell lung cancer heterogeneity and phenotypic plasticity

Small cell lung cancer (SCLC) is an aggressive neuroendocrine malignancy with ~7% 5-year overall survival reflecting early metastasis and rapid acquired chemoresistance. Immunotherapy briefly extends overall survival in ~15% cases, yet predictive biomarkers are lacking. Targeted therapies are beginning to show promise, with a recently approved delta-like ligand 3 (DLL3)-targeted therapy impacting the treatment landscape. The increased availability of patient-faithful models, accumulating human tumour biobanks and numerous comprehensive molecular profiling studies have collectively facilitated the mapping and understanding of substantial intertumoural and intratumoural heterogeneity. Beyond the almost ubiquitous loss of wild-type p53 and RB1, SCLC is characterized by heterogeneously mis-regulated expression of MYC family members, yes-associated protein 1 (YAP1), NOTCH pathway signalling, anti-apoptotic BCL2 and epigenetic regulators. Molecular subtypes are based on the neurogenic transcription factors achaete-scute homologue 1 (ASCL1) and neurogenic differentiation factor 1 (NEUROD1), the rarer non-neuroendocrine transcription factor POU class 2 homeobox 3 (POU2F3), and immune- and inflammation-related signatures. Furthermore, SCLC shows phenotypic plasticity, including neuroendocrine-to-non-neuroendocrine transition driven by NOTCH signalling, which is associated with disease progression, chemoresistance and immune modulation and, in mouse models, with metastasis. Although these features pose substantial challenges, understanding the molecular vulnerabilities of transcription factor subtypes, the functional relevance of plasticity and cell cooperation offer opportunities for personalized therapies informed by liquid and tissue biomarkers.

Identifying reproducible transcription regulator coexpression patterns with single cell transcriptomics

The proliferation of single cell transcriptomics has potentiated our ability to unveil patterns that reflect dynamic cellular processes such as the regulation of gene transcription. In this study, we leverage a broad collection of single cell RNA-seq data to identify the gene partners whose expression is most coordinated with each human and mouse transcription regulator (TR). We assembled 120 human and 103 mouse scRNA-seq datasets from the literature (>28 million cells), constructing a single cell coexpression network for each. We aimed to understand the consistency of TR coexpression profiles across a broad sampling of biological contexts, rather than examine the preservation of context-specific signals. Our workflow therefore explicitly prioritizes the patterns that are most reproducible across cell types. Towards this goal, we characterize the similarity of each TR's coexpression within and across species. We create single cell coexpression rankings for each TR, demonstrating that this aggregated information recovers literature curated targets on par with ChIP-seq data. We then combine the coexpression and ChIP-seq information to identify candidate regulatory interactions supported across methods and species. Finally, we highlight interactions for the important neural TR ASCL1 to demonstrate how our compiled information can be adopted for community use.

Molecular and Immunohistochemical Classification of Extrapulmonary Small Cell Neuroendocrine Carcinomas: A Study of 181 Cases

Extrapulmonary small cell neuroendocrine carcinoma (EP-SCNC) is a rare malignancy with a poor prognosis. Most patients with EP-SCNC have metastatic disease upon presentation, and their average overall survival (OS) is less than 12 months. Our study aimed to conduct a complex analysis of EP-SCNC. One hundred eighty-one EP-SCNC tissue samples were subjected to a complex analysis. One hundred fifty-five tumors were pure EP-SCNC, whereas 26 were combined tumors. Immunohistochemistry for ASCL1, NEUROD1, YAP1, POU2F3, Rb1, p53, cyclin D1, p16, PTEN, DLL3, PD-L1, CD56, synaptophysin, chromogranin A, and INSM1 was performed, and 128 samples were analyzed molecularly using next-generation sequencing, comprising DNA and RNA analyses. Detailed results on immunohistochemical and molecular analyses were provided for each primary origin of EP-SCNC separately. Median survival for the whole cohort of patients was 8.94 months. Patient age (≥70 years), tumor mutational burden <15, and TP53 and BRCA2 mutations were negative prognostic factors. High expression of ASCL-1 was associated with shorter OS, whereas high expression of YAP1 was associated with longer OS. Patients with genitourinary tumors had significantly better OS than those with gastrointestinal tract EP-SCNC tumors. Rb1 expression loss was detected more often in genitourinary tract SCNCs. In contrast, p16 overexpression was found more often in genitourinary tract SCNCs. POU2F3 expression was detected more often in combined tumors, whereas NEUROD1 was detected more often in pure EP-SCNC. Regarding "druggable markers," DLL3 was expressed in 66% of tumors and PD-L1 in 17.4%. Detailed analyses of different prognostic and predictive markers are needed to better understand EP-SCNC biology and create more personalized therapy to improve patient prognosis.

Prognostic significance of ALK high expression in SCLC: a 9-year cohort analysis

Purpose

The aim of this study was to investigate the prognostic value of the abnormal expression of anaplastic lymphoma kinase (ALK) protein in patients with small cell lung cancer (SCLC) based on 9-year data from our center.

Methods

A retrospective cohort study was conducted to assess the clinical outcomes of patients with ALK-positive SCLC diagnosed in our hospital over the past 9 years. We used public databases to analyze the expression of ALK in pan-cancer and its prognostic value and analyzed the correlation between ALK and SCLC prognosis-related genes.

Results

A total of 685 patients diagnosed with SCLC underwent ALK testing, and 59 patients were identified to have abnormal expression of the ALK protein, with 10 cases showing strong expression, 14 cases displaying moderate expression, and 35 cases exhibiting weak expression. The median age of the ALK-positive cohort was 64 years (range: 58-70 years), 91.5% (54/59) were male, 61.0% (36/59) were smokers, and the median overall survival (mOS) was 7.0 months (95% CI: 4.5-9.5 months). Within this cohort, the mOS for the ALK (+) subgroup was 4.0 months (95% CI: 2.9-5.1 months), the mOS for the ALK (++) subgroup was 10.0 months (95% CI: 4.9-15.1 months), and the mOS for the ALK (+++) subgroup was 12.0 months (95% CI: 7.4-16.6 months). Kaplan-Meier revealed that the mOS of the ALKLow group was significantly worse than that of the ALKHigh group [mOS: 4.0 months (95% CI: 2.9-5.1 months) versus 11.0 months (95% CI: 8.3-13.7 months), p = 0.009]. Following covariate adjustment using a Cox regression model, it was indicated that the level of abnormal expression of the ALK protein was an independent prognostic factor for patients with SCLC (HR: 0.486, 95% CI: 0.271-0.871, p = 0.015).

Conclusion

The prognosis for patients with SCLC with strong abnormal expression of the ALK protein was significantly better than those with weak expression.

Current and future perspectives in extensive-stage small-cell lung cancer

Small-cell lung cancer (SCLC) is a highly aggressive and rapidly proliferative malignancy that has historically had limited therapeutic advancements. Recent advancements in the understanding of SCLC have led to attempts at subtyping the disease based on transcription factor characteristics, offering new insights into its biology and potential therapeutic targets. In addition, significant progress has been made in developing treatment regimens, providing new hope for improved patient outcomes. The introduction of immune checkpoint inhibitors, such as atezolizumab and durvalumab, in combination with traditional chemotherapy, has marked a significant advancement, demonstrating improved overall survival and progression-free survival compared to chemotherapy alone. Despite these advancements, the prognosis for extensive-stage SCLC (ES-SCLC), the more advanced form of SCLC, remains poor, highlighting the critical need for ongoing research and the development of novel therapeutic strategies. New treatment modalities, such as lurbinectedin and anti-Delta-like Canonical Notch Ligand 3 antibodies, are now included in the treatment options for refractory SCLC, and many more treatment strategies involving combination therapies are being studied. Advances in molecular profiling and the identification of biomarkers are aiding in the development of personalized treatment approaches. This review focuses on these recent advancements and emerging strategies in the treatment of ES-SCLC.

Lethal co-expression intolerance underlies the mutually exclusive expression of ASCL1 and NEUROD1 in SCLC cells

Small cell lung cancer (SCLC) subtypes, defined by the expression of lineage-specific transcription factors (TFs), are thought to be mutually exclusive, with intra-tumoral heterogeneities. This study investigated the mechanism underlying this phenomenon with the aim of identifying a novel vulnerability of SCLC. We profiled the expression status of ASCL1, NEUROD1, POU2F3, and YAP1 in 151 surgically obtained human SCLC samples. On subtyping, a high degree of mutual exclusivity was observed between ASCL1 and NEUROD1 expression at the cell, but not tissue, level. Inducible co-expression models of all combinations of ASCL1, NEUROD1, POU2F3, YAP1, and ATOH1 using SCLC cell lines showed that some expression combinations, such as ASCL1 and NEUROD1, exhibited mutual repression and caused growth inhibition and apoptosis. Gene expression and ATAC-seq analyses of the ASCL1 and NEUROD1 co-expression models revealed that co-expression of ASCL1 in NEUROD1-driven cells, and of NEUROD1 in ASCL1-driven cells, both (although more efficiently by the former) reprogrammed the cell lineage to favor the ectopically expressed factor, with rewiring of chromatin accessibility. Mechanistically, co-expressed NEUROD1 in ASCL1-driven SCLC cells caused apoptosis by downregulating BCL2, likely in a MYC-independent manner. In conclusion, lethal co-expression intolerance underlies the mutual exclusivity between these pioneer TFs, ASCL1 and NEUROD1, in an SCLC cell. Further investigation is warranted to enable therapeutic targeting of this vulnerability.

Targeting FOXP1 phase separation in small cell lung cancer mechanisms of chemotherapy resistance

Our study elucidates the role of FOXP1 in chemoresistance in small cell lung cancer(SCLC). FOXP1 enhances chemoresistance by regulating SP8 expression through its super-enhancer (SP8-SE), with SP8 mediating resistance via the homologous recombination repair (HRR) pathway. We also discovered that FOXP1 forms punctate nuclear structures indicative of liquid-liquid phase separation, crucial for its transcriptional regulation. Targeting the FOXP1-SP8-HR axis with BRD4 and PARP inhibitors showed synergistic effects in reducing tumor growth in vitro and in patient-derived xenograft models. These findings identify FOXP1 as a critical mediator and marker of chemoresistance in SCLC, providing a foundation for developing targeted therapies to overcome this resistance.

Integrative spatial analysis reveals tumor heterogeneity and immune colony niche related to clinical outcomes in small cell lung cancer

Recent advances have shed light on the molecular heterogeneity of small cell lung cancer (SCLC), yet the spatial organizations and cellular interactions in tumor immune microenvironment remain to be elucidated. Here, we employ co-detection by indexing (CODEX) and multi-omics profiling to delineate the spatial landscape for 165 SCLC patients, generating 267 high-dimensional images encompassing over 9.3 million cells. Integrating CODEX and genomic data reveals a multi-positive tumor cell neighborhood within ASCL1+ (SCLC-A) subtype, characterized by high SLFN11 expression and associated with poor prognosis. We further develop a cell colony detection algorithm (ColonyMap) and reveal a spatially assembled immune niche consisting of antitumoral macrophages, CD8+ T cells and natural killer T cells (MT2) which highly correlates with superior survival and predicts improving immunotherapy response in an independent cohort. This study serves as a valuable resource to study SCLC spatial heterogeneity and offers insights into potential patient stratification and personalized treatments.

Noninvasive molecular imaging using anti-Trop-2 aptamer for targeted therapy of small cell lung cancer

Recent advancements in antibody-drug conjugates (ADCs) targeting trophoblast surface cell antigen 2 (Trop-2) have brought important progress in the field of targeted therapy. This progress also holds promise for the treatment of small cell lung cancer (SCLC) as anti-Trop-2 therapy appears to have a safe and effective clinical activity in metastatic SCLC patients. However, effective treatments of anti-Trop-2 ADCs rely on the comprehensive assessment of Trop-2 expression at the tumor sites, SCLC exhibits intratumoral heterogeneity, making the accurate acquisition of histological biopsies a challenge. To address this issue, we herein report the development of an anti-Trop-2 aptamer consisting of 76 bases is specifically bind to Trop-2-overexpressing SCLC cells. Further truncated anti-Trop-2 aptamer with 46 nucleotides also possesses excellent in vitro and in vivo binding affinity with Trop-2 antigens. After radiolabeling with gallium-68 radionuclide, an aptamer-based molecular imaging probe was successfully fabricated named [68Ga]Ga-NOTA-TRP-c. This imaging probe demonstrated effective and precise differentiation of Trop-2-positive tumors in both murine- and human-derived animal models, exhibiting favorable metabolic profiles. Furthermore, Trop-2-positive SCLC tumors recognized by anti-Trop-2 aptamer can be treated with anti-Trop-2 ADC sacituzumab govitecan (SG), either in vitro or in vivo. Importantly, SG induces DNA damage and cell apoptosis without affecting the expression of Trop-2 on the cell surface, which makes it possible to use anti-Trop-2 aptamer to monitor the expression of Trop-2 in SCLC. This study highlights the potential of aptamer-based molecular imaging and imaging-guided SG treatment as a promising option for targeted therapy in SCLC.

Small cell lung cancer unveiled: Exploring the untapped resource of circulating tumor cells-derived organoids

Small cell lung cancer (SCLC) remains a challenge in oncology due to its aggressive behavior and dismal prognosis. Despite advances in treatments, novel strategies are urgently needed. Enter liquid biopsy-a game-changer in SCLC management. This revolutionary non-invasive approach allows for the analysis of circulating tumor cells (CTCs), offering insights into tumor behavior and treatment responses. Our review focuses on a groundbreaking frontier: harnessing CTCs to create three-dimensional (3D) organoid models. These models, derived from CTCs that break away from the primary tumor or metastatic locations, hold immense potential for revolutionizing cancer research, especially in SCLC. We explore the essential conditions for successfully establishing CTC-derived organoids-a transformative approach with profound implications for personalized medicine. Our evaluation spans diverse isolation techniques, shedding light on their advantages and limitations. Furthermore, we uncover the critical factors governing the cultivation of 3D organoids from CTCs, meticulously mimicking the tumor microenvironment. This review comprehensively elucidates the molecular characterization of these organoids, showcasing their potential in identifying treatment targets and predicting responses. In essence, our review amalgamates cutting-edge methodologies for isolating CTCs, establishing transformative CTC-derived organoids, and characterizing their molecular landscape. This represents a promising frontier for advancing personalized medicine in the complex realm of SCLC management and holds significant implications for translational research.

Whole-section digital analysis of immune profiles in surgically resected small cell lung carcinoma and their associations with molecular subtypes

Background

The molecular subtype-specific features of the tumor immune microenvironment (TIME) in small cell lung carcinoma (SCLC) remain poorly understood. We aimed to analyze the immune profiles in surgically resected SCLC and their associations with molecular subtypes.

Methods

Tumor samples from 83 treatment-naive SCLC patients who underwent surgical resection were analyzed. The protein expression of subtype-defining markers (ASCL1, NEUROD1, POU2F3, and YAP1) and nine immune-related markers were assessed using whole-section immunohistochemistry. Digital image analysis was employed for precise quantification of immune cell infiltrates and distributions. The findings were subsequently correlated with clinicopathological parameters and patient prognoses.

Results

Unsupervised hierarchical clustering categorized the tumors into four molecular subtypes: achaete-scute homologue 1-dominant (ASCL1; SCLC-A, 71.1%, n=59), neuronal differentiation factor 1-dominant (NEUROD1; SCLC-N, 12.1%, n=10), POU class 2 homeobox 3-dominant (POU2F3; SCLC-P, 10.8%, n=9), and quadruple-negative (SCLC-QN, 6.0%, n=5). Expression of major histocompatibility complex class I (MHC I) and class II (MHC II; P=0.02, P=0.02), tumor programmed death-ligand 1 (PD-L1; P=0.006), and an inflamed phenotype characterized by CD8+/CD3+ T cells (P=0.001, P=0.003) were more prominent in SCLC-P tumors compared to other subtypes. Additionally, SCLC-P tumors demonstrated the highest levels of MHC II (P=0.04) and PD-L1 expression on both tumor and stromal cells (P=0.003, P=0.01). The tumor proportion score of PD-L1 positively correlated with tumor expression levels of POU2F3 (rho=0.297, P=0.006) and MHC I (rho=0.239, P=0.03), as well as the combined positive score of PD-L1 (rho=0.222, P=0.04; rho=0.433, P<0.001). Intra-tumoral tertiary lymphoid structures (intra-TLS) and peri-tumoral TLS (peri-TLS) were observed in 60.2% (n=50) and 96.4% (n=80) of patients, respectively. High intra-TLS density was more frequently associated with SCLC-P tumors (P=0.02). Notably, low peri-TLS density and stromal PD-L1 expression were linked to improved overall survival (OS) and progression-free survival (PFS), respectively.

Conclusions

This study highlights the heterogeneity of the TIME across molecular subtypes of SCLC. The SCLC-P subtype and MHC I expression may serve as predictive biomarkers for immunotherapy response, while peri-TLS density and stromal PD-L1 expression might serve as prognostic indicators in resected SCLC.

Deep analysis of the trials and major challenges in the first-line treatment for patients with extensive-stage small cell lung cancer

The median overall survival (OS) is approximately 10 months when chemotherapy alone is the first-line treatment for extensive-stage small cell lung cancer (ES-SCLC). The approval of the two PD-L1 inhibitors, atezolizumab and durvalumab, marked the beginning of the immunotherapy era for ES-SCLC. Serplulimab, as the first PD-1 inhibitor to achieve success in the first-line treatment of ES-SCLC, has not only demonstrated significant improvements in patient survival outcomes but also ushered in a new era for PD-1 inhibitors in the treatment of ES-SCLC. Recently, antiangiogenic agents with chemo-immunotherapy have achieved breakthroughs in first-line ES-SCLC treatment. Improving the clinical benefits of individualized treatment for patients with ES-SCLC remains challenging. Challenges include identifying biomarkers for targeted therapy, exploring new treatments, developing new medicines, and classifying SCLC molecular subtypes. This review provides an in-depth analysis of research on first-line ES-SCLC treatment. Additionally, it discusses advances in ES-SCLC treatment.

Exploring YAP1-related TIME in SCLC: implications for survival and treatment response to immuno-chemotherapy

Aim: Small-cell lung cancer (SCLC) is usually diagnosed as an advanced stage with a poor outcome. SCLC has limited response to immunotherapy due to the absence or lack of immune cell infiltration, so studying its tumor immune microenvironment (TIME) is essential. Methods: The study involved patients with extensive-stage small-cell lung cancer (ES-SCLC) diagnosed at the Guangdong Lung Cancer Institute between January 2018 and April 2022 who had received the atezolizumab/carboplatin/etoposide (ECT) treatment. We used multi-immunohistochemistry (mIHC) to assess the prognostic value of YAP1 and TIME in SCLC, with results confirmed using public data. Results: 15 patients with sufficient baseline biopsy samples were included in this study. The total population of YAP1-positive cells is inversely related to progression-free survival (PFS) and shows a potential negative correlation with overall survival (OS). CD56-positive cells are the primary components of TIME in SCLC tumor parenchyma and stroma. The total population and cell density of YAP1-positive cells are significantly positively correlated with CD4-positive cells. Furthermore, in the tumor parenchyma, both the proportion and the cell density of YAP1-positive cells are positively correlated with that of FOXP3-positive cells. The total population of CD56-positive cells showed a negative correlation trend with YAP1-positive cells but without significant difference. Conclusion: YAP1 has shown prognostic value in SCLC patients receiving ECT regimen treatment. The high expression level of YAP1 seems related to the inhibitory TIME. However, some prospective studies with larger populations are warranted.

Identifying Reproducible Transcription Regulator Coexpression Patterns with Single Cell Transcriptomics

The proliferation of single cell transcriptomics has potentiated our ability to unveil patterns that reflect dynamic cellular processes such as the regulation of gene transcription. In this study, we leverage a broad collection of single cell RNA-seq data to identify the gene partners whose expression is most coordinated with each human and mouse transcription regulator (TR). We assembled 120 human and 103 mouse scRNA-seq datasets from the literature (>28 million cells), constructing a single cell coexpression network for each. We aimed to understand the consistency of TR coexpression profiles across a broad sampling of biological contexts, rather than examine the preservation of context-specific signals. Our workflow therefore explicitly prioritizes the patterns that are most reproducible across cell types. Towards this goal, we characterize the similarity of each TR's coexpression within and across species. We create single cell coexpression rankings for each TR, demonstrating that this aggregated information recovers literature curated targets on par with ChIP-seq data. We then combine the coexpression and ChIP-seq information to identify candidate regulatory interactions supported across methods and species. Finally, we highlight interactions for the important neural TR ASCL1 to demonstrate how our compiled information can be adopted for community use.

Heterogeneity of molecular subtyping and therapy-related marker expression in primary tumors and paired lymph node metastases of small cell lung cancer

The classification of molecular subtypes and the identification of targetable molecules have been proposed for small cell lung cancer (SCLC) patients. Our aim was to investigate whether the expression of these markers evaluated using lymph node (LN) metastases represents that of primary tumors. We enrolled 46 surgically resected SCLC patients' primary tumors and paired mediastinal LN metastases. The protein expression of subtype-defining markers (ASCL1, NEUROD1, POU2F3, and YAP1) and therapeutic markers (DLL3, MYC, PD-L1, and MHC I) was examined by immunohistochemistry and was correlated with clinicopathological parameters and prognoses. In primary and metastatic tumors, the expression of these markers was 78.3% and 87.0%, 50.0% and 63.0%, 13.0% and 6.5%, 17.4% and 15.2%, 84.8% and 87.0%, 17.4% and 6.5%, 50.0% and 34.8%, and 60.9% and 37.0%, respectively. Positive tumor PD-L1 expression was less present in LN metastases (p = 0.015), and the same was true for MHC I expression (p = 0.036). NEUROD1 and DLL3 expression levels in metastatic tumors were stronger (p < 0.001 and p = 0.002, respectively); conversely, POU2F3, MYC, PD-L1, and MHC I expression levels were weaker (p = 0.018, p = 0.019, p = 0.001, and p < 0.001, respectively). In 15 (32.6%) patients, we observed a change in the molecular subtyping pattern, and a higher number of neuroendocrine (NE)-high phenotype patients were diagnosed when using the LN specimens (91.3% vs. 84.8%). TNM stage and postoperative chemotherapy were independent prognostic factors in surgically resected SCLC patients, and no prognostic differences were found among molecular subtypes. This study highlights the discordance of subtype-specific proteins and therapeutic markers between SCLC primary tumors and LN metastases. Additionally, our findings have therapeutic and prognostic implications and warrant further clinical investigation.

ATAD2 is a potential immunotherapy target for patients with small cell lung cancer harboring HLA-A∗0201

BACKGROUND

Small cell lung cancer (SCLC) represents a highly aggressive neuroendocrine tumour with a dismal prognosis. Currently, the identification of a specific tumour antigen that can facilitate immune-based therapies for SCLC remains elusive.

METHODS

We employed liquid chromatography-tandem mass spectrometry (LC-MS/MS) to analyse cancer/testis antigens (CTAs) in SCLC cell lines and human tumour specimens. Immunohistochemistry of clinical specimens was performed to compare protein expression in SCLC, non-small cell lung cancer (NSCLC), and matched normal-adjacent tissues. Additionally, publicly available RNA sequencing databases were interrogated to identify gene expression patterns in different SCLC subtypes and in different disease stages.

FINDINGS

Distinct numbers and types of CTAs were identified across SCLC subtypes, with significantly higher expression levels of ATPase family AAA domain-containing protein 2 (ATAD2) observed in SCLC compared to normal adjacent tissues and NSCLC tissues. A dynamic expression pattern of ATAD2 was found throughout the clinical course of SCLC and exhibited a positive correlation with achaete-scute family bHLH transcription factor 1 (ASCL1) expression in SCLC. Immunopeptidomics analysis identified the YSDDDVPSV sequence derived from the HLA-A∗02:01 restriction epitope of ATAD2 as a highly promising tumour antigen candidate for potential immunotherapy applications. YSDDDVPSV immunopeptides were confirmed to be present in SCLC-A and SCLC-N with HLA-A∗02:01 restriction. Notably, HLA-A∗02:01 T cells exhibited a robust response upon stimulation with YSDDDVPSV immunopeptide pulsed by T2 cells.

INTERPRETATION

Our findings highlight the potential of targeting the ATAD2 YSDDDVPSV immunopeptide for SCLC immunotherapy, thereby offering a promising avenue for the development of adoptive T cell therapies to effectively treat ASCL1-positive or NEUROD1-positive SCLC carrying HLA-A∗02:01.

FUNDING

This study was supported by the National key R&D program of China (2022YFC2505000); National Natural Science Foundation of China (NSFC) general program (82272796) NSFC special program (82241229); CAMS Innovation Fund for Medical Sciences (CIFMS 2022-I2M-1-009); CAMS Key Laboratory of Translational Research on Lung Cancer (2018PT31035); Aiyou foundation (KY201701). National key R&D program of China (2022YFC2505004). NSFC general program (81972905). Medical Oncology Key Foundation of Cancer Hospital Chinese Academy of Medical Sciences (CICAMS-MOCP2022012).

Phase I/II Investigator-Initiated Study of Olaparib and Temozolomide in SCLC: Final Analysis and CNS Outcomes

PURPOSE

Temozolomide plus PARP inhibition has shown promise in small cell lung cancer (SCLC). We previously reported outcomes from the first 50 patients (cohort 1) of a phase I/II trial of olaparib/temozolomide in recurrent SCLC. In this study, we report a final analysis of this trial, including a second cohort with an alternate dosing strategy and an exploratory analysis of central nervous system (CNS)-specific outcomes.

PATIENTS AND METHODS

This was an open-label phase I/II trial testing the combination of olaparib and temozolomide in relapsed SCLC. The primary endpoint was objective response rate (ORR). Secondary endpoints were safety, progression-free survival, and overall survival. We tested escalating doses of olaparib/temozolomide across two cohorts, both of which had temozolomide dosed on days 1 to 7 of each 21-day cycle. In previously published cohort 1, olaparib was dosed on days 1 to 7; in cohort 2, olaparib was dosed continuously.

RESULTS

Sixty-six patients were enrolled across the two cohorts: 50 in cohort 1 and 16 in cohort 2. The confirmed ORR of cohort 1 was 41.7% (20/48 evaluable), and the confirmed ORR of cohort 2 was 7% (1/14 evaluable; closed after dose escalation to enrollment for lack of observed efficacy). Among 15/66 patients (22.7%) with untreated brain metastases at enrollment, the best overall intracranial response was complete response in 6/15 patients, partial response in 4/15 patients, and stable disease in 3/15 patients for a CNS disease control rate of 87% (95% confidence interval, 59.5%-98.3%).

CONCLUSIONS

Olaparib/temozolomide may be effective in relapsed SCLC, especially for patients with CNS disease. Ongoing analyses with regard to optimal dosing schedule will inform potential for future use of this combination in SCLC.

Comparison of molecular subtype composition between independent sets of primary and brain metastatic small cell lung carcinoma and matched samples

INTRODUCTION

Recent advances in the subclassification of small cell lung carcinomas (SCLCs) may help to overcome the unmet need for targeted therapies and improve survival. However, limited information is available on how the expression of the subtype markers changes during tumour progression. Our study aimed to compare the expression of these markers in primary and brain metastatic SCLCs.

MATERIALS AND METHODS

Immunohistochemical analysis of the subtype markers was performed on 120 SCLCs (including 10 matched samples) and SCLC xenografts.

RESULTS

Compared to primary SCLCs, there was a significant increase in the proportion of mixed subtypes in brain metastases, with a rate of ASCL1high/NeuroD1high and ASCL1high/NeuroD1high/YAP1high subtypes increasing to 48 % and 18 %, respectively. The subtype of the paired samples matched in only one-third of the cases. Although we did not observe a significant change after chemotherapy, a continuous decrease in ASCL1 expression coupled with an increase in the NeuroD1 expression was detected in the xenografts in a long-term experiment.

DISCUSSION

Our results indicate that the expression of subtype markers frequently changes during disease progression, and subtype analysis of the primary SCLC may not provide accurate information about the characteristics of the recurrent or metastatic tumour. Therefore, repeated sampling and subtyping may be necessary for subtype-specific targeted therapy.

Molecular subtypes, predictive markers and prognosis in small-cell lung carcinoma

AIMS

A new molecular subtype classification was proposed for small-cell lung carcinoma (SCLC). We aimed to further validate the classification in various SCLC patient samples using immunohistochemistry (IHC) to highlight its clinical significance.

METHODS

We analysed the protein expression of four subtype (achaete-scute family BHLH transcription factor 1 (ASCL1), neuronal differentiation 1 (NEUROD1), POU class 2 homeobox 3 (POU2F3) and Yes1-associated transcriptional regulator (YAP1)) and two predictive markers (delta-like ligand 3 (DLL3) and MYC) using IHC in 216 specimens from 195 SCLC patients, including 21 pairs of resected biopsy tumours. Associations among molecular subtypes, clinicopathological features and prognostic implications were also explored.

RESULTS

The ASCL1, NEUROD1, POU2F3, YAP1, DLL3 and MYC-positive expression rates were 70.3%, 56.9%, 14.9%, 19.0%, 75.4% and 22.6%, respectively. DLL3 expression had positive and negative associations with that of ASCL1 and POU2F3/YAP1, respectively, whereas MYC had the opposite effect. Strong associations of ASCL1 (Ρ=0.8603, p<0.0001), NEUROD1 (Ρ=0.8326, p<0.0001), POU2F3 (Ρ=0.6950, p<0.0001) and YAP1 (Ρ=0.7466, p<0.0001) expressions were detected between paired resected biopsy tumours. In addition to SCLC-A (ASCL1-dominant), SCLC-N (NEUROD1-dominant) and SCLC-P (POU2F3-dominant), unsupervised hierarchical cluster analyses identified a fourth, quadruple-negative SCLC subtype (SCLC-QN) characterised by the low expression of all four subtype-specific proteins, and 55.4% (n=108), 27.2% (n=53), 11.8% (n=23) and 5.6% (n=11) were categorised as SCLC-A, SCLC-N, SCLC-P and SCLC-QN, respectively. Significant enrichment of SCLC-P in the combined SCLC cohort was observed, and adenocarcinoma was more prevalent in SCLC-A, while large-cell neuroendocrine carcinoma was more commonly seen in SCLC-P. No survival difference was found among molecular subtypes.

CONCLUSIONS

Our results provide clinical insights into the diagnostic, prognostic and predictive significance of SCLC molecular subtype classifications.

The molecular subtypes of small cell lung cancer defined by key transcription factors and their clinical significance

BACKGROUND

Lung cancer, a prevalent and deadly malignancy, is classified into small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC). SCLC is further subdivided into four molecular subtypes-SCLC-A, SCLC-N, SCLC-P, and SCLC-I-based on key transcription factor expression.

METHODS

Immunohistochemistry (IHC) was used to assess ASCL1, NEUROD1, and POU2F3 expression in tumor tissues. The H-Score quantified these results. Clinical characteristics, overall survival (OS), progression-free survival (PFS), and treatment responses were analyzed by subtype, and sensitivity to different treatments was assessed. Risk factors were identified through univariate and multivariate analyses.

RESULTS

IHC and H-Score analysis showed that POU2F3 expression was mutually exclusive with ASCL1 or NEUROD1. Subtype distribution was as follows: SCLC-A (40 %), SCLC-N (33 %), SCLC-P (7 %), and SCLC-I (20 %). There were no significant differences in baseline characteristics, OS (p = 0.829), or PFS (p = 0.924) among subtypes. However, the SCLC-I subtype showed a trend toward improved outcomes with platinum-based doublet chemotherapy plus immune checkpoint inhibitors. Multivariate COX regression identified M stage (HR: 1.72, 95 % CI: 1.13-2.63, p = 0.012) and bone metastasis at diagnosis (HR: 1.58, 95 % CI: 1.02-2.43, p = 0.040) as independent risk factors.

CONCLUSION

This study confirmed the SCLC subtyping based on key transcription factors. While no significant differences in OS and PFS among subtypes were found, the SCLC-I subtype showed potential benefit from platinum-based chemotherapy combined with immune checkpoint inhibitors. M stage and bone metastasis at diagnosis were identified as independent risk factors for SCLC.

Stimulation of cGAS-STING pathway as a challenge in the treatment of small cell lung cancer: a feasible strategy?

Lung cancer has a significant incidence among the population and, unfortunately, has an unfavourable prognosis in most cases. The World Health Organization (WHO) classifies lung tumours into two subtypes based on their phenotype: the Non-Small Cell Lung Cancer (NSCLC) and the Small Cell Lung Cancer (SCLC). SCLC treatment, despite advances in chemotherapy and radiotherapy, is often unsuccessful for cancer recurrence highlighting the need to develop novel therapeutic strategies. In this review, we describe the genetic landscape and tumour microenvironment that characterize the pathological processes of SCLC and how they are responsible for tumour immune evasion. The immunosuppressive mechanisms engaged in SCLC are critical factors to understand the failure of immunotherapy in SCLC and, conversely, suggest that new signalling pathways, such as cGAS/STING, should be investigated as possible targets to stimulate an innate immune response in this subtype of lung cancer. The full comprehension of the innate immunity of cancer cells is thus crucial to open new challenges for successful immunotherapy in treating SCLC and improving patient outcomes.

Unveiling the Molecular Features of SCLC With a Clinical RNA Expression Panel

Introduction

The translation of gene expression profiles of SCLC to clinical testing remains relatively unexplored. In this study, gene expression variations in SCLC were evaluated to identify potential biomarkers.

Methods

RNA expression profiling was performed on 44 tumor samples from 35 patients diagnosed with SCLC using the clinically validated RNA Salah Targeted Expression Panel (RNA STEP). RNA sequencing (RNA-Seq) and immunohistochemistry were performed on two different SCLC cohorts, and correlation analyses were performed for the ASCL1, NEUROD1, POU2F3, and YAP1 genes and their corresponding proteins. RNA STEP and RNA-Seq results were evaluated for gene expression profiles and heterogeneity between SCLC primary and metastatic sites. RNA STEP gene expression profiles of independent SCLC samples (n = 35) were compared with lung adenocarcinoma (n = 160) and squamous cell carcinoma results (n = 25).

Results

The RNA STEP results were highly correlated with RNA-Seq and immunohistochemistry results. The dominant transcription regulator by RNA STEP was ASCL1 in 74.2% of the samples, NEUROD1 in 20%, and POU2F3 in 2.9%. The ASCL1, NEUROD1, and POU2F3 gene expression profiles were heterogeneous between primary and metastatic sites. SCLCs displayed markedly high expression for targetable genes DLL3, EZH2, TERT, and RET. SCLCs were found to have relatively colder immune profiles than lung adenocarcinomas and squamous cell carcinomas, characterized by lower expression of HLA genes, immune cell, and immune checkpoint genes, except the LAG3 gene.

Conclusions

Clinical-grade SCLC RNA expression profiling has value for SCLC subtyping, design of clinical trials, and identification of patients for trials and potential targeted therapy.

Neuroendocrine transdifferentiation in human cancer: molecular mechanisms and therapeutic targets

Neuroendocrine transdifferentiation (NEtD), also commonly referred to as lineage plasticity, emerges as an acquired resistance mechanism to molecular targeted therapies in multiple cancer types, predominately occurs in metastatic epidermal growth factor receptor (EGFR)-mutant non-small cell lung cancer treated with EGFR tyrosine kinase inhibitors and metastatic castration-resistant prostate cancer treated with androgen receptor targeting therapies. NEtD tumors are the lethal cancer histologic subtype with unfavorable prognosis and limited treatment. A comprehensive understanding of molecular mechanism underlying targeted-induced plasticity could greatly facilitate the development of novel therapies. In the past few years, increasingly elegant studies indicated that NEtD tumors share key the convergent genomic and phenotypic characteristics irrespective of their site of origin, but also embrace distinct change and function of molecular mechanisms. In this review, we provide a comprehensive overview of the current understanding of molecular mechanism in regulating the NEtD, including genetic alterations, DNA methylation, histone modifications, dysregulated noncoding RNA, lineage-specific transcription factors regulation, and other proteomic alterations. We also provide the current management of targeted therapies in clinical and preclinical practice.

Small cell lung cancer profiling: an updated synthesis of subtypes, vulnerabilities, and plasticity

Small cell lung cancer (SCLC) is a devastating disease with high proliferative and metastatic capacity. SCLC has been classified into molecular subtypes based on differential expression of lineage-defining transcription factors. Recent studies have proposed new subtypes that are based on both tumor-intrinsic and -extrinsic factors. SCLC demonstrates substantial intratumoral subtype heterogeneity characterized by highly plastic transcriptional states, indicating that the initially dominant subtype can shift during disease progression and in association with resistance to therapy. Strategies to promote or constrain plasticity and cell fate transitions have nominated novel targets that could prompt the development of more durably effective therapies for patients with SCLC. In this review, we describe the latest advances in SCLC subtype classification and their biological and clinical implications.

Molecular subtypes and prognostic factors of lung large cell neuroendocrine carcinoma

Background

Lung large cell neuroendocrine carcinoma (LCNEC) is an aggressive disease with poor prognosis and short-term survival, which lacks effective prognostic indicators. The study aims to investigate the molecular subtypes and prognostic markers of lung LCNEC.

Methods

Patients diagnosed with lung LCNEC at Sun Yat-sen University Cancer Center (SYSUCC) between November 2007 and January 2021 were screened. Baseline clinical data were collected and routine blood indexes including lymphocyte-to-monocyte ratio (LMR), neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR) and systemic immune-inflammation index (SII) were calculated. Immunohistochemistry (IHC) of ASCL1, NEUROD1, POU2F3, YAP1 were done to perform molecular subtyping, while CD56, Syn, CgA, CD3, CD8, CD20, CD68, and CD163 were also stained on tissue samples. Then prognostic factors of lung LCNEC were explored.

Results

One hundred and fifty-one lung LCNEC patients were identified, 103 of whom had complete clinical information, available routine blood and biochemical indexes were eventually included in the present study. Tumor tissue specimens were available from 64 patients. Positive expression rates of ASCL1, NEUROD1, and YAP1 were 82.8%, 50.0%, and 28.1%, respectively. No POU2F3+ cases were detected. Forty (62.5%) patients co-expressed with two or three markers. High LMR (>3.3) was an independent predictor of favorable prognosis of disease-free survival (DFS) [hazard ratio (HR), 0.391; 95% confidence interval (CI): 0.161-0.948; P=0.04] and overall survival (OS) (HR, 0.201; 95% CI: 0.071-0.574; P=0.003). Notably, high LMR was correlated with higher intra-tumoral CD3+ (P=0.004), CD8+ (P=0.01), and CD68+ (P<0.001) immune cell infiltration compared to low LMR in lung LCNEC.

Conclusions

Our study validated molecular subtypes by IHC in lung LCNEC, and co-expression was found among different subtypes, with no prognostic effect. High blood LMR level was associated with a favorable prognosis in lung LCNEC, which might partly reflect a hot tumor tissue immune microenvironment. Our findings may benefit clinical practice, and further studies are warranted.

Single-cell and spatial proteo-transcriptomic profiling reveals immune infiltration heterogeneity associated with neuroendocrine features in small cell lung cancer

Small cell lung cancer (SCLC) is an aggressive pulmonary neuroendocrine malignancy featured by cold tumor immune microenvironment (TIME), limited benefit from immunotherapy, and poor survival. The spatial heterogeneity of TIME significantly associated with anti-tumor immunity has not been systemically studied in SCLC. We performed ultra-high-plex Digital Spatial Profiling on 132 tissue microarray cores from 44 treatment-naive limited-stage SCLC tumors. Incorporating single-cell RNA-sequencing data from a local cohort and published SCLC data, we established a spatial proteo-transcriptomic landscape covering over 18,000 genes and 60 key immuno-oncology proteins that participate in signaling pathways affecting tumorigenesis, immune regulation, and cancer metabolism across 3 pathologically defined spatial compartments (pan-CK-positive tumor nest; CD45/CD3-positive tumor stroma; para-tumor). Our study depicted the spatial transcriptomic and proteomic TIME architecture of SCLC, indicating clear intra-tumor heterogeneity dictated via canonical neuroendocrine subtyping markers; revealed the enrichment of innate immune cells and functionally impaired B cells in tumor nest and suggested potentially important immunoregulatory roles of monocytes/macrophages. We identified RE1 silencing factor (REST) as a potential biomarker for SCLC associated with low neuroendocrine features, more active anti-tumor immunity, and prolonged survival.

[Molecular Subtype of Small Cell Lung Cancer: Challenge for Transforming into Clinical Practice]

Small cell lung cancer (SCLC), one of the histological subtypes of lung cancer, is characterized by high proliferation, early metastasis, susceptibility to drug resistance and recurrence. For several years, SCLC has always been regarded as a homogeneous disease, treated with a unified radiotherapy and chemotherapy strategy. Despite significant early therapeutic effects, drug resistance and recurrence occur quickly, and there is a lack of satisfactory treatment results, which may be due to insufficient understanding of the tumor heterogeneity of SCLC at present. Recently, the concept of SCLC molecular subtype based on the definition of relatively high expression of lineage transcription factors has been proposed in preclinical studies. This article mainly elaborates on the current status and latest findings of SCLC molecular subtype, emphasizing the potential problems that molecular typing may encounter in clinical practice, aiming to promote understanding of the research progress of molecular subtype in SCLC.
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Emerging advances in defining the molecular and therapeutic landscape of small-cell lung cancer

Small-cell lung cancer (SCLC) has traditionally been considered a recalcitrant cancer with a dismal prognosis, with only modest advances in therapeutic strategies over the past several decades. Comprehensive genomic assessments of SCLC have revealed that most of these tumours harbour deletions of the tumour-suppressor genes TP53 and RB1 but, in contrast to non-small-cell lung cancer, have failed to identify targetable alterations. The expression status of four transcription factors with key roles in SCLC pathogenesis defines distinct molecular subtypes of the disease, potentially enabling specific therapeutic approaches. Overexpression and amplification of MYC paralogues also affect the biology and therapeutic vulnerabilities of SCLC. Several other attractive targets have emerged in the past few years, including inhibitors of DNA-damage-response pathways, epigenetic modifiers, antibody-drug conjugates and chimeric antigen receptor T cells. However, the rapid development of therapeutic resistance and lack of biomarkers for effective selection of patients with SCLC are ongoing challenges. Emerging single-cell RNA sequencing data are providing insights into the plasticity and intratumoural and intertumoural heterogeneity of SCLC that might be associated with therapeutic resistance. In this Review, we provide a comprehensive overview of the latest advances in genomic and transcriptomic characterization of SCLC with a particular focus on opportunities for translation into new therapeutic approaches to improve patient outcomes.

Genome-Wide Analysis Identifies Nuclear Factor 1C as a Novel Transcription Factor and Potential Therapeutic Target in SCLC

INTRODUCTION

Recent insights regarding mechanisms mediating stemness, heterogeneity, and metastatic potential of lung cancers have yet to be fully translated to effective regimens for the treatment of these malignancies. This study sought to identify novel targets for lung cancer therapy.

METHODS

Transcriptomes and DNA methylomes of 14 SCLC and 10 NSCLC lines were compared with normal human small airway epithelial cells (SAECs) and induced pluripotent stem cell (iPSC) clones derived from SAEC. SCLC lines, lung iPSC (Lu-iPSC), and SAEC were further evaluated by DNase I hypersensitive site sequencing (DHS-seq). Changes in chromatin accessibility and depths of transcription factor (TF) footprints were quantified using Bivariate analysis of Genomic Footprint. Standard techniques were used to evaluate growth, tumorigenicity, and changes in transcriptomes and glucose metabolism of SCLC cells after NFIC knockdown and to evaluate NFIC expression in SCLC cells after exposure to BET inhibitors.

RESULTS

Considerable commonality of transcriptomes and DNA methylomes was observed between Lu-iPSC and SCLC; however, this analysis was uninformative regarding pathways unique to lung cancer. Linking results of DHS-seq to RNA sequencing enabled identification of networks not previously associated with SCLC. When combined with footprint depth, NFIC, a transcription factor not previously associated with SCLC, had the highest score of occupancy at open chromatin sites. Knockdown of NFIC impaired glucose metabolism, decreased stemness, and inhibited growth of SCLC cells in vitro and in vivo. ChIP-seq analysis identified numerous sites occupied by BRD4 in the NFIC promoter region. Knockdown of BRD4 or treatment with Bromodomain and extra-terminal domain (BET) inhibitors (BETis) markedly reduced NFIC expression in SCLC cells and SCLC PDX models. Approximately 8% of genes down-regulated by BETi treatment were repressed by NFIC knockdown in SCLC, whereas 34% of genes repressed after NFIC knockdown were also down-regulated in SCLC cells after BETi treatment.

CONCLUSIONS

NFIC is a key TF and possible mediator of transcriptional regulation by BET family proteins in SCLC. Our findings highlight the potential of genome-wide chromatin accessibility analysis for elucidating mechanisms of pulmonary carcinogenesis and identifying novel targets for lung cancer therapy.

Spatially Preserved Multi-Region Transcriptomic Subtyping and Biomarkers of Chemoimmunotherapy Outcome in Extensive-Stage Small Cell Lung Cancer

PURPOSE

Transcriptomic subtyping holds promise for personalized therapy in extensive-stage small cell lung cancer (ES-SCLC). In this study, we aimed to assess intratumoral transcriptomic subtype diversity and to identify biomarkers of long-term chemoimmunotherapy benefit in human ES-SCLC.

EXPERIMENTAL DESIGN

We analyzed tumor samples from 58 patients with ES-SCLC enrolled in two multicenter single-arm phase IIIb studies evaluating frontline chemoimmunotherapy in Spain: n = 32 from the IMfirst trial and n = 26 from the CANTABRICO trial. We used the GeoMx Digital Spatial Profiler system to perform multi-region transcriptomic analysis. For subtype classification, we performed hierarchical clustering using the relative expression of ASCL1 (SCLC-A), NEUROD1 (SCLC-N), POU2F3 (SCLC-P), and YAP1 (SCLC-Y).

RESULTS

Subtype distribution was found to be similar between bothcohorts, except for SCLC-P, which was not identified in the CANTABRICO_DSP cohort. A total of 44% of the patients in both cohorts had tumors with multiple coexisting transcriptional subtypes. Transcriptional subtypes or subtype heterogeneity was not associated with outcomes. Most potential targets did not show subtype-specific expression. Consistently in both cohorts, tumors from patients with long-term benefit (time to progression ≥12 months) contained an IFNγ-dominated mRNA profile, including enhanced capacity for antigen presentation. Hypoxia and glycolytic pathways were associated with resistance to chemoimmunotherapy.

CONCLUSIONS

This work suggests that intratumoral heterogeneity, inconsistent association with outcome, and unclear subtype-specific target expression might be significant challenges for subtype-based precision oncology in SCLC. Preexisting IFNγ-driven immunity and mitochondrial metabolism seem to be correlates of long-term efficacy in this study, although the absence of a chemotherapy control arm precludes concluding that these are predictive features specific for immunotherapy.

Circulating tumor cells: advancing personalized therapy in small cell lung cancer patients

Small cell lung cancer (SCLC) is a highly aggressive cancer with a dismal 5-year survival of < 7%, despite the addition of immunotherapy to first-line chemotherapy. Specific tumor biomarkers, such as delta-like ligand 3 (DLL3) and schlafen11 (SLFN11), may enable the selection of more efficacious, novel immunomodulating targeted treatments like bispecific T-cell engaging monoclonal antibodies (tarlatamab) and chemotherapy with PARP inhibitors. However, obtaining a tissue biopsy sample can be challenging in SCLC. Circulating tumor cells (CTCs) have the potential to provide molecular insights into a patient's cancer through a "simple" blood test. CTCs have been studied for their prognostic ability in SCLC; however, their value in guiding treatment decisions is yet to be elucidated. This review explores novel and promising targeted therapies in SCLC, summarizes current knowledge of CTCs in SCLC, and discusses how CTCs can be utilized for precision medicine.

The emerging role of Schlafen-11 (SLFN11) in predicting response to anticancer treatments: Focus on small cell lung cancer

Small cell lung cancer (SCLC) is characterized by a dismal prognosis. Many efforts have been made so far for identifying novel biomarkers for a personalized treatment for SCLC patients. Schlafen 11 (SLFN11) is a protein differently expressed in many cancers and recently emerged as a new potential biomarker. Lower expression of SLFN11 correlates with a worse prognosis in SCLC and other tumors. SLFN11 has a role in tumorigenesis, inducing replication arrest in the presence of DNA damage through the block of the replication fork. SLFN11 interacts also with chromatin accessibility, proteotoxic stress and mammalian target of rapamycin signalling pathway. The expression of SLFN11 is regulated by epigenetic mechanisms, including promoter methylation, histone deacetylation, and the histone methylation. The downregulation of SLFN11 correlates with a worse response to topoisomerase I and II inhibitors, alkylating agents, and poly ADP-ribose polymerase inhibitors in different cancer types. Some studies exploring strategies for overcoming drug resistance in tumors with low levels of SLFN11 showed promising results. One of these strategies includes the interaction with the Ataxia Telangiectasia and Rad3-related pathway, constitutively activated and leading to cell survival and tumor growth in the presence of low levels of SLFN11. Furthermore, the expression of SLFN11 is dynamic through time and different anticancer therapy and liquid biopsy seems to be an attractive tool for catching SLFN11 different expressions. Despite this, further investigations exploring SLFN11 as a predictive biomarker, its longitudinal changes, and new strategies to overcome drug resistances are needed.

Microenvironment shapes small-cell lung cancer neuroendocrine states and presents therapeutic opportunities

Small-cell lung cancer (SCLC) is the most fatal form of lung cancer. Intratumoral heterogeneity, marked by neuroendocrine (NE) and non-neuroendocrine (non-NE) cell states, defines SCLC, but the cell-extrinsic drivers of SCLC plasticity are poorly understood. To map the landscape of SCLC tumor microenvironment (TME), we apply spatially resolved transcriptomics and quantitative mass spectrometry-based proteomics to metastatic SCLC tumors obtained via rapid autopsy. The phenotype and overall composition of non-malignant cells in the TME exhibit substantial variability, closely mirroring the tumor phenotype, suggesting TME-driven reprogramming of NE cell states. We identify cancer-associated fibroblasts (CAFs) as a crucial element of SCLC TME heterogeneity, contributing to immune exclusion, and predicting exceptionally poor prognosis. Our work provides a comprehensive map of SCLC tumor and TME ecosystems, emphasizing their pivotal role in SCLC's adaptable nature, opening possibilities for reprogramming the TME-tumor communications that shape SCLC tumor states.

Extracellular vesicles from non-neuroendocrine SCLC cells promote adhesion and survival of neuroendocrine SCLC cells

Small cell lung cancer (SCLC) tumors are made up of distinct cell subpopulations, including neuroendocrine (NE) and non-neuroendocrine (non-NE) cells. While secreted factors from non-NE SCLC cells have been shown to support the growth of the NE cells, the underlying molecular factors are not well understood. Here, we show that exosome-type small extracellular vesicles (SEVs) secreted from non-NE SCLC cells promote adhesion and survival of NE SCLC cells. Proteomic analysis of purified SEVs revealed that extracellular matrix (ECM) proteins and integrins are highly enriched in SEVs of non-NE cells whereas nucleic acid-binding proteins are enriched in SEVs purified from NE cells. Addition of select purified ECM proteins identified in purified extracellular vesicles (EVs), specifically fibronectin, laminin 411, and laminin 511, were able to substitute for the role of non-NE-derived SEVs in promoting adhesion and survival of NE SCLC cells. Those same proteins were differentially expressed by human SCLC subtypes. These data suggest that ECM-carrying SEVs secreted by non-NE cells play a key role in supporting the growth and survival of NE SCLC cells.

Molecular classification and biomarkers of outcome with immunotherapy in extensive-stage small-cell lung cancer: analyses of the CASPIAN phase 3 study

BACKGROUND

We explored potential predictive biomarkers of immunotherapy response in patients with extensive-stage small-cell lung cancer (ES-SCLC) treated with durvalumab (D) + tremelimumab (T) + etoposide-platinum (EP), D + EP, or EP in the randomized phase 3 CASPIAN trial.

METHODS

805 treatment-naïve patients with ES-SCLC were randomized (1:1:1) to receive D + T + EP, D + EP, or EP. The primary endpoint was overall survival (OS). Patients were required to provide an archived tumor tissue block (or ≥ 15 newly cut unstained slides) at screening, if these samples existed. After assessment for programmed cell death ligand-1 expression and tissue tumor mutational burden, residual tissue was used for additional molecular profiling including by RNA sequencing and immunohistochemistry.

RESULTS

In 182 patients with transcriptional molecular subtyping, OS with D ± T + EP was numerically highest in the SCLC-inflamed subtype (n = 10, median 24.0 months). Patients derived benefit from immunotherapy across subtypes; thus, additional biomarkers were investigated. OS benefit with D ± T + EP versus EP was greater with high versus low CD8A expression/CD8 cell density by immunohistochemistry, but with no additional benefit with D + T + EP versus D + EP. OS benefit with D + T + EP versus D + EP was associated with high expression of CD4 (median 25.9 vs. 11.4 months) and antigen-presenting and processing machinery (25.9 vs. 14.6 months) and MHC I and II (23.6 vs. 17.3 months) gene signatures, and with higher MHC I expression by immunohistochemistry.

CONCLUSIONS

These findings demonstrate the tumor microenvironment is important in mediating better outcomes with D ± T + EP in ES-SCLC, with canonical immune markers associated with hypothesized immunotherapy mechanisms of action defining patient subsets that respond to D ± T.

TRIAL REGISTRATION

ClinicalTrials.gov, NCT03043872.

The Evolving Scenario of ES-SCLC Management: From Biology to New Cancer Therapeutics

Small cell lung cancer (SCLC) is an aggressive neuroendocrine carcinoma accounting for 15% of lung cancers with dismal survival outcomes. Minimal changes in therapy and prognosis have occurred in SCLC for the past four decades. Recent progress in the treatment of extensive-stage disease (ES-SCLC) has been marked by incorporating immune checkpoint inhibitors (ICIs) into platinum-based chemotherapy, leading to modest improvements. Moreover, few second-line-and-beyond treatment options are currently available. The main limitation for the molecular study of SCLC has been the scarcity of samples, because only very early diseases are treated with surgery and biopsies are not performed when the disease progresses. Despite all these difficulties, in recent years we have come to understand that SCLC is not a homogeneous disease. At the molecular level, in addition to the universal loss of retinoblastoma (RB) and TP53 genes, a recent large molecular study has identified other mutations that could serve as targets for therapy development or patient selection. In recent years, there has also been the identification of new genetic subtypes which have shown us how intertumor heterogeneity exists. Moreover, SCLC can also develop intratumoral heterogeneity linked mainly to the concept of cellular plasticity, mostly due to the development of resistance to therapies. The aim of this review is to quickly present the current standard of care of ES-SCLC, to focus on the molecular landscapes and subtypes of SCLC, subsequently present the most promising therapeutic strategies under investigation, and finally recap the future directions of ongoing clinical trials for this aggressive disease which still remains a challenge.

Molecular pathology of small cell lung cancer: Overview from studies on neuroendocrine differentiation regulated by ASCL1 and Notch signaling

Pulmonary neuroendocrine (NE) cells are rare airway epithelial cells. The balance between Achaete-scute complex homolog 1 (ASCL1) and hairy and enhancer of split 1, one of the target molecules of the Notch signaling pathway, is crucial for NE differentiation. Small cell lung cancer (SCLC) is a highly aggressive lung tumor, characterized by rapid cell proliferation, a high metastatic potential, and the acquisition of resistance to treatment. The subtypes of SCLC are defined by the expression status of NE cell-lineage transcription factors, such as ASCL1, which roles are supported by SRY-box 2, insulinoma-associated protein 1, NK2 homeobox 1, and wingless-related integration site signaling. This network reinforces NE differentiation and may induce the characteristic morphology and chemosensitivity of SCLC. Notch signaling mediates cell-fate decisions, resulting in an NE to non-NE fate switch. The suppression of NE differentiation may change the histological type of SCLC to a non-SCLC morphology. In SCLC with NE differentiation, Notch signaling is typically inactive and genetically or epigenetically regulated. However, Notch signaling may be activated after chemotherapy, and, in concert with Yes-associated protein signaling and RE1-silencing transcription factor, suppresses NE differentiation, producing intratumor heterogeneity and chemoresistance. Accumulated information on the molecular mechanisms of SCLC will contribute to further advances in the control of this recalcitrant cancer.

Molecular and Pathologic Characterization of YAP1-Expressing Small Cell Lung Cancer Cell Lines Leads to Reclassification as SMARCA4-Deficient Malignancies

PURPOSE

The classification of small cell lung cancer (SCLC) into distinct molecular subtypes defined by ASCL1, NEUROD1, POU2F3, or YAP1 (SCLC-A, -N, -P, or -Y) expression, paves the way for a personalized treatment approach. However, the existence of a distinct YAP1-expressing SCLC subtype remains controversial.

EXPERIMENTAL DESIGN

To better understand YAP1-expressing SCLC, the mutational landscape of human SCLC cell lines was interrogated to identify pathogenic alterations unique to SCLC-Y. Xenograft tumors, generated from cell lines representing the four SCLC molecular subtypes, were evaluated by a panel of pathologists who routinely diagnose thoracic malignancies. Diagnoses were complemented by transcriptomic analysis of primary tumors and human cell line datasets. Protein expression profiles were validated in patient tumor tissue.

RESULTS

Unexpectedly, pathogenic mutations in SMARCA4 were identified in six of eight SCLC-Y cell lines and correlated with reduced SMARCA4 mRNA and protein expression. Pathologist evaluations revealed that SMARCA4-deficient SCLC-Y tumors exhibited features consistent with thoracic SMARCA4-deficient undifferentiated tumors (SMARCA4-UT). Similarly, the transcriptional profile SMARCA4-mutant SCLC-Y lines more closely resembled primary SMARCA4-UT, or SMARCA4-deficient non-small cell carcinoma, than SCLC. Furthermore, SMARCA4-UT patient samples were associated with a YAP1 transcriptional signature and exhibited strong YAP1 protein expression. Together, we found little evidence to support a diagnosis of SCLC for any of the YAP1-expressing cell lines originally used to define the SCLC-Y subtype.

CONCLUSIONS

SMARCA4-mutant SCLC-Y cell lines exhibit characteristics consistent with SMARCA4-deficient malignancies rather than SCLC. Our findings suggest that, unlike ASCL1, NEUROD1, and POU2F3, YAP1 is not a subtype defining transcription factor in SCLC. See related commentary by Rekhtman, p. 1708.

Applied models and molecular characteristics of small cell lung cancer

Small cell lung cancer (SCLC) is a highly aggressive type of cancer frequently diagnosed with metastatic spread, rendering it surgically unresectable for the majority of patients. Although initial responses to platinum-based therapies are often observed, SCLC invariably relapses within months, frequently developing drug-resistance ultimately contributing to short overall survival rates. Recently, SCLC research aimed to elucidate the dynamic changes in the genetic and epigenetic landscape. These have revealed distinct subtypes of SCLC, each characterized by unique molecular signatures. The recent understanding of the molecular heterogeneity of SCLC has opened up potential avenues for precision medicine, enabling the development of targeted therapeutic strategies. In this review, we delve into the applied models and computational approaches that have been instrumental in the identification of promising drug candidates. We also explore the emerging molecular diagnostic tools that hold the potential to transform clinical practice and patient care.

Pathogenic role of super-enhancers as potential therapeutic targets in lung cancer

Lung cancer is still one of the deadliest malignancies today, and most patients with advanced lung cancer pass away from disease progression that is uncontrollable by medications. Super-enhancers (SEs) are large clusters of enhancers in the genome's non-coding sequences that actively trigger transcription. Although SEs have just been identified over the past 10 years, their intricate structure and crucial role in determining cell identity and promoting tumorigenesis and progression are increasingly coming to light. Here, we review the structural composition of SEs, the auto-regulatory circuits, the control mechanisms of downstream genes and pathways, and the characterization of subgroups classified according to SEs in lung cancer. Additionally, we discuss the therapeutic targets, several small-molecule inhibitors, and available treatment options for SEs in lung cancer. Combination therapies have demonstrated considerable advantages in preclinical models, and we anticipate that these drugs will soon enter clinical studies and benefit patients.

Molecular phenotyping of small cell lung cancer using targeted cfDNA profiling of transcriptional regulatory regions

We report an approach for cancer phenotyping based on targeted sequencing of cell-free DNA (cfDNA) for small cell lung cancer (SCLC). In SCLC, differential activation of transcription factors (TFs), such as ASCL1, NEUROD1, POU2F3, and REST defines molecular subtypes. We designed a targeted capture panel that identifies chromatin organization signatures at 1535 TF binding sites and 13,240 gene transcription start sites and detects exonic mutations in 842 genes. Sequencing of cfDNA from SCLC patient-derived xenograft models captured TF activity and gene expression and revealed individual highly informative loci. Prediction models of ASCL1 and NEUROD1 activity using informative loci achieved areas under the receiver operating characteristic curve (AUCs) from 0.84 to 0.88 in patients with SCLC. As non-SCLC (NSCLC) often transforms to SCLC following targeted therapy, we applied our framework to distinguish NSCLC from SCLC and achieved an AUC of 0.99. Our approach shows promising utility for SCLC subtyping and transformation monitoring, with potential applicability to diverse tumor types.