Integrative genomic and transcriptomic profiling of pulmonary sarcomatoid carcinoma identifies molecular subtypes associated with distinct immune features and clinical outcomes.

Background: Pulmonary sarcomatoid carcinoma (PSC) is a rare and aggressive subtype of non-small cell lung cancer (NSCLC), characterized by the presence of epithelial and sarcoma-like components. The molecular and immune landscape of PSC has not been well defined. Methods: Multiomics profiling of 21 pairs of PSCs with matched normal lung tissues was performed through targeted high-depth DNA panel, whole-exome, and RNA sequencing. We describe molecular and immune features that define subgroups of PSC with disparate genomic and immunogenic features as well as distinct clinical outcomes. Results: In total, 27 canonical cancer gene mutations were identified, with TP53 the most frequently mutated gene, followed by KRAS. Interestingly, most TP53 and KRAS mutations were earlier genomic events mapped to the trunks of the tumors, suggesting branching evolution in most PSC tumors. We identified two distinct molecular subtypes of PSC, driven primarily by immune infiltration and signaling. The Immune High (IM-H) subtype was associated with superior survival, highlighting the impact of immune infiltration on the biological and clinical features of localized PSCs. Conclusions: We provided detailed insight into the mutational landscape of PSC and identified two molecular subtypes associated with prognosis. IM-H tumors were associated with favorable recurrence-free survival and overall survival, highlighting the importance of tumor immune infiltration in the biological and clinical features of PSCs.

Safety and short-term outcomes of esophagectomy after neoadjuvant immunotherapy combined with chemotherapy or chemoradiotherapy for locally advanced esophageal squamous cell cancer: analysis of two phase-II clinical trials.

Background: Preoperative chemotherapy (CT) or chemoradiotherapy (CRT) show survival benefits in patients with locally advanced esophageal squamous cell carcinoma (ESCC); however, ESCC patients still have a dismal prognosis. We conducted two phase-II, single-armed clinical trials to assess the potential benefits, efficacy, feasibility, and safety of esophagectomy after combining preoperative CT or CRT and neoadjuvant programmed cell death protein 1 (PD-1) inhibitors in the treatment of ESCC. Methods: Patients were included with histologically confirmed ESCC (clinical stage II-IVA according to the American Joint Committee on Cancer 8th staging system) from two phase-II, single-arm trials (NCT04506138 and NCT03940001). Patients underwent two doses of intravenous PD-1 inhibitor (either camrelizumab or sintilimab) every 3 weeks, combined with two cycles of either CT or CRT. The primary endpoint of the study was the safety and short-term outcomes of esophagectomy as measured by the risk of developing complications within 30 days, after the combination of preoperative PD-1 inhibitor and CT or CRT Secondary endpoint was to evaluate the pCR rates (pT0N0), primary tumor pCR rates (pT0), operation time, postoperative stay, and 30-day mortality rate between both groups. Results between both groups were compared using a multivariable log-binomial regression model to obtain the adjusted relative risk ratios (RRs). Results: Between May 2019 and June 2022, 55 patients were included. All patients completed neoadjuvant therapy. Age, sex, performance status, clinical stage, histologic subtype, procedure type, operative time, and blood loss volume were similar between the two groups. The primary tumor pCR rates were 52.9% in the nICRT group and 21.6% in the nICT group (P=0.03), while the postoperative pCR rates were 41.2% in the nICRT group and 21.6% in the nICT group (P=0.19). The minimally invasive surgery rates were 89.2% (33/37) in the nICT group and 94.1% (16/17) in the nICRT group. The risk of developing pulmonary, anastomotic, or other complications were similar between the two groups. Conclusions: Esophagectomy was safe after the addition of the PD-1 inhibitor to preoperative CT or CRT in ESCC neoadjuvant therapies. Follow-up and the exploratory endpoints, including biomarkers analyses, are ongoing.

Optimizing Intermediate Adsorption on Pt Sites via Triple-Phase Interface Electronic Exchange for Methanol Oxidation.

For the most commonly applied platinum-based catalysts of direct methanol fuel cells, the adsorption ability toward reaction intermediates, including CO and OH, plays a vital role in their catalytic activity and antipoisoning in anodic methanol oxidation reaction (MOR). Herein, guided by a theoretical mechanism study, a favorable modulation of the electronic structure and intermediate adsorption energetics for Pt active sites is achieved by constructing the triple-phase interfacial structure between tin oxide (SnO2), platinum (Pt), and nitrogen-doped graphene (NG). From the strong electronic exchange at the triple-phase interface, the adsorption ability toward MOR reaction intermediates on Pt sites could be efficiently optimized, which not only inhibits the adsorption of CO* on active sites but also facilitates the adsorption of OH* to strip the poisoning species from the catalyst surface. Accordingly, the resulting catalyst delivers excellent catalytic activity and antipoisoning ability for MOR catalysis. The mass activity reaches 1098 mA mg-1Pt, 3.23 times of commercial Pt/C. Meanwhile, the initial potentials and main peak for CO oxidation are also located at a much lower potential (0.51 and 0.74 V) against commercial Pt/C (0.83 and 0.89 V).

Controllable Electronic Transfer Tailoring d-band Center via Cobalt-Oxygen-Bridged Ru/Fe Dual-sites for Boosted Oxygen Evolution.

Rational tailoring of the electronic structure at the defined active center of reconstructed metal (oxy)hydroxides (MOOH) during oxygen evolution reaction (OER) remains a challenge. With the guidance of density functional theory (DFT), herein a dual-site regulatory strategy is reported to tailor the d-band center of the Co site in CoOOH via the controlled electronic transfer at the Ru─O─Co─O─Fe bonding structure. Through the bridged O2- site, electrons are vastly flowed from the t2g-orbital of the Ru site to the low-spin orbital of the Co site in the Ru-O-Co coordination and further transfer from the strong electron-electron repulsion of the Co site to the Fe site by the Co-O-Fe coordination, which balancing the electronic configuration of Co sites to weaken the over-strong adsorption energy barrier of OH* and O*, respectively. Benefiting from the highly active of the Co site, the constructed (Ru2Fe2Co6)OOH provide an extremely low overpotential of 248 mV and a Tafel slope of 32.5 mV dec-1 at 10 mA cm-2 accompanied by long durability in alkaline OER, far superior over the pristine and Co-O-Fe bridged CoOOH catalysts. This work provides guidance for the rational design and in-depth analysis of the optimized role of metal dual-sites.

Co/CoS2 Heterojunction Embedded in N, S-Doped Hollow Nanocage for Enhanced Polysulfides Conversion in High-Performance Lithium-Sulfur Batteries.

Modulating the electronic configuration of the substrate to achieve the optimal chemisorption toward polysulfides (LiPSs) for boosting polysulfide conversion is a promising way to the efficient Li-S batteries but filled with challenges. Herein, a Co/CoS2 heterostructure is elaborately built to tuning d-orbital electronic structure of CoS2 for a high-performance electrocatalyst. Theoretical simulations first evidence that Co metal as the electron donator can form a built-in electric field with CoS2 and downshift the d-band center, leading to the well-optimized adsorption strength for lithium polysulfides on CoS2 , thus contributing a favorable way for expediting the redox reaction kinetics of LiPSs. As verification of prediction, a Co/CoS2 heterostructure implanted in porous hollow N, S co-doped carbon nanocage (Co/CoS2 @NSC) is designed to realize the electronic configuration regulation and promote the electrochemical performance. Consequently, the batteries assembled with Co/CoS2 @NSC cathode display an outstanding specific capacity and an admirable cycling property as well as a salient property of 8.25 mAh cm-2 under 8.18 mg cm-2 . The DFT calculation also reveals the synergistic effect of N, S co-doping for enhancing polysulfide adsorption as well as the detriment of excessive sulfur doping.

Directed Dual Charge Pumping Tunes the d-Orbital Configuration of Pt Cluster Boosting Hydrogen Evolution Kinetic.

Achieving high catalytic activity with a minimum amount of platinum (Pt) is crucial for accelerating the cathodic hydrogen evolution reaction (HER) in proton exchange membrane (PEM) water electrolysis, yet it remains a significant challenge. Herein, a directed dual-charge pumping strategy to tune the d-orbital electronic distribution of Pt nanoclusters for efficient HER catalysis is proposed. Theoretical analysis reveals that the ligand effect and electronic metal-support interactions (EMSI) create an effective directional electron transfer channel for the d-orbital electrons of Pt, which in turn optimizes the binding strength to H*, thereby significantly enhancing HER efficiency of the Pt site. Experimentally, this directed dual-charge pumping strategy is validated by elaborating Sb-doped SnO2 (ATO) supported Fe-doped PtSn heterostructure catalysts (Fe-PtSn/ATO). The synthesized 3%Fe-PtSn/ATO catalysts exhibit lower overpotential (requiring only 10.5 mV to reach a current density of 10 mA cm- 2), higher mass activity (28.6 times higher than commercial 20 wt.% Pt/C), and stability in the HER process in acidic media. This innovative strategy presents a promising pathway for the development of highly efficient HER catalysts with low Pt loading.

Treatment options for stage III-N2 pulmonary lymphoepithelioma-like carcinoma: A retrospective cohort study.

BACKGROUND AND PURPOSE: Pulmonary lymphoepithelioma-like carcinoma (PLELC) is a rare form of non-small cell lung carcinoma (NSCLC) that shares similarities with nasopharyngeal carcinoma. The optimal treatment for stage III-N2 PLELC remains controversial. METHODS AND MATERIALS: We conducted a retrospective analysis from stage III-N2 PLELC patients between 2009 and 2022 in our center. The patients were categorized into three groups: Group 1 (G1, definitive chemoradiotherapy), Group 2 (G2, radical surgery plus adjuvant chemoradiotherapy), and Group 3 (G3, radical surgery plus adjuvant chemotherapy). RESULTS: A total of 103 patients were included in the study, with 34, 25, and 44 patients in G1, G2, and G3, respectively. The median follow-up time was 47.4 months. The overall median PFS was 66.6 months, with 3-year PFS and 3-year OS rates of 66.0% and 92.4%, respectively, for all patients. Multivariate analysis revealed no significant difference in PFS between G1 and G2 (p = 0.354), while both groups exhibited significantly longer PFS than G3 (p < 0.001; p = 0.039). Similarly, no significant difference in OS was observed between G1 and G2 (p = 0.649), but both tended to demonstrate improved OS compared to G3 (p = 0.081; p = 0.092). Only one case of grade 3 radiation esophagitis was observed in G1, and no grade 3 or higher radiation pneumonitis were reported. CONCLUSIONS: Patients with stage III-N2 PLELC have a favorable prognosis, with radiotherapy playing a crucial role in treatment. Both definitive chemoradiotherapy and radical surgery followed by chemoradiotherapy demonstrate favorable efficacy and manageable toxicity.

A novel statistical method for decontaminating T-cell receptor sequencing data.

The T-cell receptor (TCR) repertoire is highly diverse among the population and plays an essential role in initiating multiple immune processes. TCR sequencing (TCR-seq) has been developed to profile the T cell repertoire. Similar to other high-throughput experiments, contamination can happen during several steps of TCR-seq, including sample collection, preparation and sequencing. Such contamination creates artifacts in the data, leading to inaccurate or even biased results. Most existing methods assume 'clean' TCR-seq data as the starting point with no ability to handle data contamination. Here, we develop a novel statistical model to systematically detect and remove contamination in TCR-seq data. We summarize the observed contamination into two sources, pairwise and cross-cohort. For both sources, we provide visualizations and summary statistics to help users assess the severity of the contamination. Incorporating prior information from 14 existing TCR-seq datasets with minimum contamination, we develop a straightforward Bayesian model to statistically identify contaminated samples. We further provide strategies for removing the impacted sequences to allow for downstream analysis, thus avoiding any need to repeat experiments. Our proposed model shows robustness in contamination detection compared with a few off-the-shelf detection methods in simulation studies. We illustrate the use of our proposed method on two TCR-seq datasets generated locally.

Tailored Lattice Compressive Strain of Pt-Skins by the L12 -Pt3 M Intermetallic Core for Highly Efficient Oxygen Reduction.

The sluggish kinetics of oxygen reduction reaction (ORR) and unsatisfactory durability of Pt-based catalysts are severely hindering the commercialization of proton-exchange-membrane fuel cells (PEMFCs). In this work, the lattice compressive strain of Pt-skins imposed by Pt-based intermetallic cores is tailored for highly effective ORR through the confinement effect of the activated nitrogen-doped porous carbon (a-NPC). The modulated pores of a-NPC not only promote Pt-based intermetallics with ultrasmall size (average size of <4 nm), but also efficiently stabilizes intermetallic nanoparticles and sufficient exposure of active sites during the ORR process. The optimized catalyst (L12 -Pt3 Co@ML-Pt/NPC10 ) achieves excellent mass activity (1.72 A mgPt -1 ) and specific activity (3.49 mA cmPt -2 ), which are 11- and 15-fold that of commercial Pt/C, respectively. Besides, owing to the confinement effect of a-NPC and protection of Pt-skins, L12 -Pt3 Co@ML-Pt/NPC10 retains 98.1% mass activity after 30 000 cycles, and even 95% for 100 000 cycles, while Pt/C retains only 51.2% for 30 000 cycles. Rationalized by density functional theory, compared with other metals (Cr, Mn, Fe, and Zn), L12 -Pt3 Co closer to the top of "volcano" induces a more suitable compressive strain and electronic structure on Pt-skin, leading to an optimal oxygen adsorption energy and a remarkable ORR performance.

Dual roles of sub-nanometer NiO in alkaline hydrogen evolution reaction: breaking the Volmer limitation and optimizing d-orbital electronic configuration.

Pt-based nanoclusters toward the hydrogen evolution reaction (HER) remain the most promising electrocatalysts. However, the sluggish alkaline Volmer-step kinetics and the high-cost have hampered progress in developing high-performance HER catalysts. Herein, we propose to construct sub-nanometer NiO to tune the d-orbital electronic structure of nanocluster-level Pt for breaking the Volmer-step limitation and reducing the Pt-loading. Theoretical simulations firstly suggest that electron transfer from NiO to Pt nanoclusters could downshift the Ed-band of Pt and result in the well-optimized adsorption/desorption strength of the hydrogen intermediate (H*), therefore accelerating the hydrogen generation rate. NiO and Pt nanoclusters confined into the inherent pores of N-doped carbon derived from ZIF-8 (Pt/NiO/NPC) were designed to realize the structure of computational prediction and boost the alkaline hydrogen evolution. The optimal 1.5%Pt/NiO/NPC exhibited an excellent HER performance and stability with a low Tafel slope (only 22.5 mv dec-1) and an overpotential of 25.2 mV at 10 mA cm-2. Importantly, the 1.5%Pt/NiO/NPC possesses a mass activity of 17.37 A mg-1 at the overpotential of 20 mV, over 54 times higher than the benchmark 20 wt% Pt/C. Furthermore, DFT calculations illustrate that the Volmer-step could be accelerated owing to the high OH- attraction of NiO nanoclusters, leading to the Pt nanoclusters exhibiting a balance of H* adsorption and desorption (ΔGH* = -0.082 eV). Our findings provide new insights into breaking the water dissociation limit of Pt-based catalysts by coupling with a metal oxide.

Prognostic value of the immunohistochemical score based on four markers in head and neck squamous cell carcinoma.

Purpose: Head and neck squamous cell carcinoma (HNSCC) ranks sixth among all cancers globally regarding morbidity, and it has a poor prognosis, high mortality, and highly aggressive properties. In this study, we established a model for predicting prognosis based on immunohistochemical (IHC) scores. Methods: Data on 402 HNSCC cases were collected, the glmnet Cox proportional hazards model was used, risk factors were analyzed for predicting the prognosis of survival, and the IHC score was established. We used the IHC score to predict disease-free survival (DFS) using training and independent validation cohorts, including 264 cases in total. Additionally, the accuracy of the IHC score and the TNM system (8th edition) was compared. A DFS prediction nomogram was established by combining the prognostic factors. Results: The IHC scores included CK, Ki-67, p16, and p40 staining intensity. The concordance index and the Kaplan-Meier survival analysis showed that the IHC scores had high predictive power for HNSCC. Our results showed that the IHC score is an independent factor that can predict prognosis in a multivariate Cox regression analysis. When predicting DFS, the IHC score had a significantly higher value for the area under the ROC curve (AUC) than that of the TNM system. A nomogram was established and included the IHC score, age, tumor location, and the TNM stage. The calibration curves exhibited high consistency between the prognosis predicted by our nomogram and the actual prognosis. Conclusions: The IHC score was more accurate than the eighth edition of the TNM system in predicting HNSCC prognosis. Therefore, combining the two methods can facilitate individualized patient consultation and care.

Comparison of stereotactic body radiation therapy versus surgery for multiple primary lung cancers after prior radical resection: A multicenter retrospective study.

Background: Patients who previously underwent surgical resection of initial primary lung cancer are at a high risk of developing multiple primary lung cancers (MPLCs). The purpose of this study was to compare the efficacy and safety between stereotactic body radiation therapy (SBRT) and surgery for MPLCs patients after prior radical resection for the first lung cancers. Methods: In this multicenter retrospective study, eligible MPLC patients with tumor diameter of 5.0 cm or less at N0M0 who underwent SBRT or reoperation between January 2013 and August 2020 were enrolled. The primary endpoint was the 3-year locoregional recurrence and treatment-related toxicity. Kaplan-Meier method was used to calculate survival rates. The χ2 test was adapted to assess the difference of categorical variables between the two subgroup patients. Results: A total of 203 (73 in the SBRT group and 130 in the surgery group) patients from three academic cancer centers were evaluated with a median follow-up of 38.3 months. The cumulative 1-, 2-, and 3-year incidences of locoregional recurrence were 5.6 %, 7.0 % and 13.1 % in the SBRT group versus 3.2 %, 4.8 % and 7.4 % in the surgery group, respectively [hazard ratio (HR), 1.97; 95 % confidence interval (CI), 0.74-5.24; P = 0.14]. The cancer-specific survival rates were 95.9 %, 94.5 % and 88.1 % versus 96.9 %, 94.6 % and 93.8 % in the SBRT and surgery groups respectively (HR, 1.72; 95 % CI, 0.67-4.44; P = 0.23). In the SBRT group, two patients (2.7 %) suffered from grade 3 radiation pneumonitis, while in the surgery group, grade 3 complications occurred in four (3.1 %) patients, and four cases were expired due to pneumonia or pulmonary heart disease within 90 days after surgery. Conclusions: SBRT is an effective therapeutic option with limited toxicity compared to surgery for patients with MPLCs after prior radical surgical resection, and it could be considered as an alternative treatment for those patients.

Optimizing d-Orbital Electronic Configuration via Metal-Metal Oxide Core-Shell Charge Donation for Boosting Reversible Oxygen Electrocatalysis.

Tuning the d-orbital electronic configuration of active sites to achieve well-optimized adsorption strength of oxygen-containing intermediates toward reversible oxygen electrocatalysis is desirable for efficient rechargeable Zn-Air batteries but extremely challenging. Herein, this work proposes to construct a Co@Co3 O4 core-shell structure to regulate the d-orbital electronic configuration of Co3 O4 for the enhanced bifunctional oxygen electrocatalysis. Theoretical calculations first evidence that electron donation from Co core to Co3 O4 shell could downshift the d-band center and simultaneously weak spin state of Co3 O4 , result in the well-optimized adsorption strength of oxygen-containing intermediates on Co3 O4 , thus contributing a favor way for oxygen reduction/evolution reaction (ORR/OER) bifunctional catalysis. As a proof-of-concept, the Co@Co3 O4 embedded in Co, N co-doped porous carbon derived from thickness controlled 2D metal-organic-framework is designed to realize the structure of computational prediction and further improve the performance. The optimized 15Co@Co3 O4 /PNC catalyst exhibits the superior bifunctional oxygen electrocatalytic activity with a small potential gap of 0.69 V and a peak power density of 158.5 mW cm-2 in ZABs. Moreover, DFT calculations shows that the more oxygen vacancies on Co3 O4 contribute too strong adsorption of oxygen intermediates which limit the bifunctional electrocatalysis, while electron donation in the core-shell structure can alleviate the negative effect and maintain superior bifunctional overpotential.

Analysis of Immune Intratumor Heterogeneity Highlights Immunoregulatory and Coinhibitory Lymphocytes as Hallmarks of Recurrence in Stage I Non-Small Cell Lung Cancer.

Our understanding of the molecular mechanisms underlying postsurgical recurrence of non-small cell lung cancer (NSCLC) is rudimentary. Molecular and T cell repertoire intratumor heterogeneity (ITH) have been reported to be associated with postsurgical relapse; however, how ITH at the cellular level impacts survival is largely unknown. Here we report the analysis of 2880 multispectral images representing 14.2% to 27% of tumor areas from 33 patients with stage I NSCLC, including 17 cases (relapsed within 3 years after surgery) and 16 controls (without recurrence ≥5 years after surgery) using multiplex immunofluorescence. Spatial analysis was conducted to quantify the minimum distance between different cell types and immune cell infiltration around malignant cells. Immune ITH was defined as the variance of immune cells from 3 intratumor regions. We found that tumors from patients having relapsed display different immune biology compared with nonrecurrent tumors, with a higher percentage of tumor cells and macrophages expressing PD-L1 (P =.031 and P =.024, respectively), along with an increase in regulatory T cells (Treg) (P =.018), antigen-experienced T cells (P =.025), and effector-memory T cells (P =.041). Spatial analysis revealed that a higher level of infiltration of PD-L1+ macrophages (CD68+PD-L1+) or antigen-experienced cytotoxic T cells (CD3+CD8+PD-1+) in the tumor was associated with poor overall survival (P =.021 and P =.006, respectively). A higher degree of Treg ITH was associated with inferior recurrence-free survival regardless of tumor mutational burden (P =.022), neoantigen burden (P =.021), genomic ITH (P =.012) and T cell repertoire ITH (P =.001). Using multiregion multiplex immunofluorescence, we characterized ITH at the immune cell level along with whole exome and T cell repertoire sequencing from the same tumor regions. This approach highlights the role of immunoregulatory and coinhibitory signals as well as their spatial distribution and ITH that define the hallmarks of tumor relapse of stage I NSCLC.

Derived Neutrophil-Lymphocyte Ratio and C-Reactive Protein as Prognostic Factors for Early-Stage Non-Small Cell Lung Cancer Treated with Stereotactic Body Radiation Therapy.

Objectives: To explore the relationship between peripheral blood inflammation parameters and overall survival (OS) and progression-free survival (PFS) of early-stage non-small cell lung cancer patients who underwent stereotactic body radiotherapy (SBRT). Patients and methods: In this study, eligible patients treated with SBRT from 2013 to 2018, and both serum complete blood count and blood biochemical results were available prior to (within 60 days) radiotherapy were included. Results: A review of hospital registries identified 148 patients, and the 5-year OS and PFS of the entire cohort were 69.8% and 65.6%, respectively, with the median follow-up time was 52.8 months. Multivariable analysis showed that derived neutrophil-lymphocyte ratio (dNLR) ≥1.4 and C-reactive protein (CRP) ≥2.9 were statistically and independently associated with worse OS (HR = 4.62, 95% CI 1.89-11.27, p = 0.001; HR = 2.92, 95% CI 1.49-5.70, p = 0.002, respectively). The 5-year OS for patients with dNLR below and equal to or above the 1.4 were 85.3% and 62.9% (p = 0.002), respectively, and 76.7% for the low CRP group versus 58.5% for the high CRP group (p = 0.030). Higher serum level of post-treatment CRP also independent parameters for inferior PFS (HR = 4.83, 95% CI 1.28-18.25, p = 0.020). Conclusions: Our results demonstrate that dNLR and CRP are associated with the outcomes of early-stage NSCLC patients treated with SBRT, which may assist in selecting optimal nursing care and therapeutic scheme for every individual.

Analysis of genomic and immune intratumor heterogeneity in linitis plastica via multiregional exome and T-cell receptor sequencing.

The molecular landscape and the intratumor heterogeneity (ITH) architecture of gastric linitis plastica (LP) are poorly understood. We performed whole-exome sequencing (WES) and T-cell receptor (TCR) sequencing on 40 tumor regions from four LP patients. The landscape and ITH at the genomic and immunological levels in LP tumors were compared with multiple cancers that have previously been reported. The lymphocyte infiltration was further assessed by immunohistochemistry (IHC) in LP tumors. In total, we identified 6339 non-silent mutations from multi-samples, with a median tumor mutation burden (TMB) of 3.30 mutations per Mb, comparable to gastric adenocarcinoma from the Cancer Genome Atlas (TCGA) cohort (P = 0.53). An extremely high level of genomic ITH was observed, with only 12.42%, 5.37%, 5.35%, and 30.67% of mutations detectable across 10 regions within the same tumors of each patient, respectively. TCR sequencing revealed that TCR clonality was substantially lower in LP than in multi-cancers. IHC using antibodies against CD4, CD8, and PD-L1 demonstrated scant T-cell infiltration in the four LP tumors. Furthermore, profound TCR ITH was observed in all LP tumors, with no T-cell clones shared across tumor regions in any of the patients, while over 94% of T-cell clones were restricted to individual tumor regions. The Morisita overlap index (MOI) ranged from 0.21 to 0.66 among multi-regions within the same tumors, significantly lower than that of lung cancer (P = 0.002). Our results show that LP harbored extremely high genomic and TCR ITH and suppressed T-cell infiltration, suggesting a potential contribution to the frequent recurrence and poor therapeutic response of this adenocarcinoma.

Immunogenomic profiling of lung adenocarcinoma reveals poorly differentiated tumors are associated with an immunogenic tumor microenvironment.

OBJECTIVES: Pathologists have routinely observed distinct histologic patterns of growth in early-stage lung adenocarcinoma (LUAD), which have been suggested to be associated with prognosis. Herein, we investigated the relationship between LUAD patterns of growth, as defined by the updated international association for the study of lung cancer (IASLC) grading criteria, and differences in the tumor immune microenvironment to identify predictors of response to immunotherapy. METHODS: 174 resected stage I-III LUAD tumors were classified by histologic pattern of growth (i.e. solid, micropapillary, acinar, papillary, and lepidic) and then grouped as well differentiated, moderately differentiated, and poorly differentiated. Comprehensive multiplatform analysis including whole exome sequencing, gene expression profiling, immunohistochemistry, CIBERSORT, and T-cell receptor sequencing was performed and groups were compared for differences in genomic drivers, immune cell infiltrate, clonality, and survival. Finally, multivariate analysis was performed adjusting for pathologic stage and smoking status. RESULTS: Poorly differentiated tumors demonstrated a strong association with smoking relative to moderately differentiated or well differentiated tumors. However, unlike in prior reports, poorly differentiated tumors were not associated with a worse survival after curative-intent resection. Genomic analysis revealed that poorly differentiated tumors are associated with high tumor mutation burden but showed no association with oncogenic drivers. Immune analyses revealed that poorly differentiated tumors are associated with increased T-cell clonality, expression of PD-L1, and infiltration by cytotoxic CD8 T-cells, activated CD4 T-cells, and pro-inflammatory (M1) macrophages. Finally, multivariate analysis controlling for stage and smoking status confirmed independence of immune differences between IASLC grade groups. CONCLUSIONS: Poorly differentiated tumors, as defined by the updated IASLC grading criteria, are associated with a distinct immunogenic tumor microenvironment that predicts for therapeutic response to immune agents, including checkpoint inhibitors, and should be included in the clinical trial design of immunotherapy studies in early-stage lung adenocarcinoma.

Immunogenomic intertumor heterogeneity across primary and metastatic sites in a patient with lung adenocarcinoma.

BACKGROUND: Lung cancer is the leading cause of cancer death, partially owing to its extensive heterogeneity. The analysis of intertumor heterogeneity has been limited by an inability to concurrently obtain tissue from synchronous metastases unaltered by multiple prior lines of therapy. METHODS: In order to study the relationship between genomic, epigenomic and T cell repertoire heterogeneity in a rare autopsy case from a 32-year-old female never-smoker with left lung primary late-stage lung adenocarcinoma (LUAD), we did whole-exome sequencing (WES), DNA methylation and T cell receptor (TCR) sequencing to characterize the immunogenomic landscape of one primary and 19 synchronous metastatic tumors. RESULTS: We observed heterogeneous mutation, methylation, and T cell patterns across distinct metastases. Only TP53 mutation was detected in all tumors suggesting an early event while other cancer gene mutations were later events which may have followed subclonal diversification. A set of prevalent T cell clonotypes were completely excluded from left-side thoracic tumors indicating distinct T cell repertoire profiles between left-side and non left-side thoracic tumors. Though a limited number of predicted neoantigens were shared, these were associated with homology of the T cell repertoire across metastases. Lastly, ratio of methylated neoantigen coding mutations was negatively associated with T-cell density, richness and clonality, suggesting neoantigen methylation may partially drive immunosuppression. CONCLUSIONS: Our study demonstrates heterogeneous genomic and T cell profiles across synchronous metastases and how restriction of unique T cell clonotypes within an individual may differentially shape the genomic and epigenomic landscapes of synchronous lung metastases.

Cold and heterogeneous T cell repertoire is associated with copy number aberrations and loss of immune genes in small-cell lung cancer.

Small-cell lung cancer (SCLC) is speculated to harbor complex genomic intratumor heterogeneity (ITH) associated with high recurrence rate and suboptimal response to immunotherapy. Here, using multi-region whole exome/T cell receptor (TCR) sequencing as well as immunohistochemistry, we reveal a rather homogeneous mutational landscape but extremely cold and heterogeneous TCR repertoire in limited-stage SCLC tumors (LS-SCLCs). Compared to localized non-small cell lung cancers, LS-SCLCs have similar predicted neoantigen burden and genomic ITH, but significantly colder and more heterogeneous TCR repertoire associated with higher chromosomal copy number aberration (CNA) burden. Furthermore, copy number loss of IFN-γ pathway genes is frequently observed and positively correlates with CNA burden. Higher mutational burden, higher T cell infiltration and positive PD-L1 expression are associated with longer overall survival (OS), while higher CNA burden is associated with shorter OS in patients with LS-SCLC.