Distinct tumor-infiltrating lymphocyte landscapes are associated with clinical outcomes in localized non-small-cell lung cancer

BACKGROUND

Despite the importance of tumor-infiltrating T lymphocytes (TILs) in cancer biology, the relationship between TIL phenotypes and their prognostic relevance for localized non-small-cell lung cancer (NSCLC) has not been well established.

PATIENTS AND METHODS

Fresh tumor and normal adjacent tissue was prospectively collected from 150 patients with localized NSCLC. Tissue was comprehensively characterized by high-dimensional flow cytometry of TILs integrated with immunogenomic data from multiplex immunofluorescence, T-cell receptor sequencing, exome sequencing, RNA sequencing, targeted proteomics, and clinicopathologic features.

RESULTS

While neither the magnitude of TIL infiltration nor specific TIL subsets were significantly prognostic alone, the integration of high-dimensional flow cytometry data identified two major immunotypes (IM1 and IM2) that were predictive of recurrence-free survival independent of clinical characteristics. IM2 was associated with poor prognosis and characterized by the presence of proliferating TILs expressing cluster of differentiation 103, programmed cell death protein 1, T-cell immunoglobulin and mucin-domain containing protein 3, and inducible T-cell costimulator. Conversely, IM1 was associated with good prognosis and differentiated by an abundance of CD8⁺ T cells expressing cytolytic enzymes, CD4⁺ T cells lacking the expression of inhibitory receptors, and increased levels of B-cell infiltrates and tertiary lymphoid structures. While increased B-cell infiltration was associated with good prognosis, the best prognosis was observed in patients with tumors exhibiting high levels of both B cells and T cells. These findings were validated in patient tumors from The Cancer Genome Atlas.

CONCLUSIONS

Our study suggests that although the number of infiltrating T cells is not associated with patient survival, the nature of the infiltrating T cells, resolved in distinct TIL immunotypes, is prognostically relevant in NSCLC and may inform therapeutic approaches to clinical care.

Mutation profiles in early-stage lung squamous cell carcinoma with clinical follow-up and correlation with markers of immune function

Background

Lung squamous cell carcinoma (LUSC) accounts for 20–30% of non-small cell lung cancers (NSCLCs). There are limited treatment strategies for LUSC in part due to our inadequate understanding of the molecular underpinnings of the disease. We performed whole-exome sequencing (WES) and comprehensive immune profiling of a unique set of clinically annotated early-stage LUSCs to increase our understanding of the pathobiology of this malignancy.

Methods

Matched pairs of surgically resected stage I-III LUSCs and normal lung tissues (n = 108) were analyzed by WES. Immunohistochemistry and image analysis-based profiling of 10 immune markers were done on a subset of LUSCs (n = 91). Associations among mutations, immune markers and clinicopathological variables were statistically examined using analysis of variance and Fisher’s exact test. Cox proportional hazards regression models were used for statistical analysis of clinical outcome.

Results

This early-stage LUSC cohort displayed an average of 209 exonic mutations per tumor. Fourteen genes exhibited significant enrichment for somatic mutation: TP53, MLL2, PIK3CA, NFE2L2, CDH8, KEAP1, PTEN, ADCY8, PTPRT, CALCR, GRM8, FBXW7, RB1 and CDKN2A. Among mutated genes associated with poor recurrence-free survival, MLL2 mutations predicted poor prognosis in both TP53 mutant and wild-type LUSCs. We also found that in treated patients, FBXW7 and KEAP1 mutations were associated with poor response to adjuvant therapy, particularly in TP53-mutant tumors. Analysis of mutations with immune markers revealed that ADCY8 and PIK3CA mutations were associated with markedly decreased tumoral PD-L1 expression, LUSCs with PIK3CA mutations exhibited elevated CD45ro levels and CDKN2A-mutant tumors displayed an up-regulated immune response.

Conclusion(s)

Our findings pinpoint mutated genes that may impact clinical outcome as well as personalized strategies for targeted immunotherapies in early-stage LUSC.

Whole-exome sequencing and immune profiling of early-stage lung adenocarcinoma with fully annotated clinical follow-up

Background

Lung adenocarcinomas (LUADs) lead to the majority of deaths attributable to lung cancer. We performed whole-exome sequencing (WES) and immune profiling analyses of a unique set of clinically annotated early-stage LUADs to better understand the pathogenesis of this disease and identify clinically relevant molecular markers.

Methods

We performed WES of 108 paired stage I-III LUADs and normal lung tissues using the Illumina HiSeq 2000 platform. Ten immune markers (PD-L1, PD-1, CD3, CD4, CD8, CD45ro, CD57, CD68, FOXP3 and Granzyme B) were profiled by imaging-based immunohistochemistry (IHC) in a subset of LUADs (n = 92). Associations among mutations, immune markers and clinicopathological variables were analyzed using ANOVA and Fisher's exact test. Cox proportional hazards regression models were used for multivariate analysis of clinical outcome.

Results

LUADs in this cohort exhibited an average of 243 coding mutations. We identified 28 genes with significant enrichment for mutation. SETD2-mutated LUADs exhibited relatively poor recurrence- free survival (RFS) and mutations in STK11 and ATM were associated with poor RFS among KRAS-mutant tumors. EGFR, KEAP1 and PIK3CA mutations were predictive of poor response to adjuvant therapy. Immune marker analysis revealed that LUADs in smokers and with relatively high mutation burdens exhibited increased levels of immune markers. Analysis of immunophenotypes revealed that LUADs with STK11 mutations exhibited relatively low levels of infiltrating CD4+/CD8+ T-cells indicative of a muted immune response. Tumoral PD-L1 was significantly elevated in TP53 mutant LUADs whereas PIK3CA mutant LUADs exhibited markedly down-regulated PD-L1 expression. LUADs with TP53 or KEAP1 mutations displayed relatively increased CD57 and Granzyme B levels indicative of augmented natural killer (NK) cell infiltration.

Conclusion(s)

Our study highlights molecular and immune phenotypes that warrant further analysis for their roles in clinical outcomes and personalized immune-based therapy of LUAD.

The International Association for the Study of Lung Cancer Lung Cancer Staging Project: Proposals for the Revision of the Clinical and Pathologic Staging of Small Cell Lung Cancer in the Forthcoming Eighth Edition of the TNM Classification for Lung Cancer

INTRODUCTION

Small cell lung cancer (SCLC) is commonly classified as either limited or extensive, but the Union for International Cancer Control TNM Classification of Malignant Tumours seventh edition (2009) recommended tumor, node, and metastasis (TNM) staging based on analysis of the International Association for the Study of Lung Cancer (IASLC) database.

METHODS

Survival analyses were performed for clinically and pathologically staged patients presenting with SCLC from 1999 through 2010. Prognosis was compared in relation to the TNM seventh edition staging to serve as validation and analyzed in relation to proposed changes to the T descriptors found in the eighth edition.

RESULTS

There were 5002 patients: 4848 patients with clinical and 582 with pathological stages. Among these, 428 had both. Survival differences were confirmed for T and N categories and maintained in relation to proposed revisions to T descriptors for seventh edition TNM categories and proposed changes in the eighth edition. There were also survival differences, notably at 12 months, in patients with brain-only single-site metastasis (SSM) compared to SSM at other sites, and SSM without a pleural effusion showed a better prognosis than other patients in the M1b category.

CONCLUSION

We confirm the prognostic value of clinical and pathological TNM staging in patients with SCLC, and recommend continued usage for SCLC in relation to proposed changes to T, N, and M descriptors for NSCLC in the eighth edition. However, for M descriptors, it remains uncertain whether survival differences in patients with SSM in the brain simply reflect better treatment options rather than better survival based on anatomic extent of disease.

Open-lung biopsy in patients with undiagnosed lung lesions referred at a tertiary cancer center is safe and reveals noncancerous, noninfectious entities as the most common diagnoses

We evaluated the diagnostic yield of open-lung biopsies (OLBs) in a large tertiary cancer center to determine the role of infectious diseases as causes of undiagnosed pulmonary lesions. All consecutive adult patients with either single or multiple pulmonary nodules or masses who underwent a diagnostic OLB over a period of 10 years (1998-2007) were retrospectively identified. Their risk factors for malignancy and clinical and radiological characteristics were reviewed, and their postoperative complications were assessed. We evaluated 155 patients with a median age of 57 years (range, 19-83 years). We identified infectious etiologies in 29 patients (19 %). The most common diagnosis in this group was histoplasmosis (12 [41 %]), followed by nontuberculous mycobacterial infection (7 [24 %]) and aspergillosis (4 [14 %]). The majority of the 126 remaining patients had nonmalignant diagnoses, the most prevalent being nonspecific granuloma (26 %), whereas only 17 % had malignant diagnoses. We observed no significant differences among the patients with infectious, malignant, or both noninfectious and nonmalignant final diagnoses regarding their demographic, laboratory, and clinical characteristics. Six percent of the patients had at least one post-OLB complication, and the post-OLB mortality rate was 1 %. OLB is a safe diagnostic procedure which frequently identifies a wide variety of infectious and inflammatory diseases.

Minimally invasive esophagectomy versus open esophagectomy, a symptom assessment study

Minimally invasive esophagectomy (MIE) is used with hope to decrease the morbidity associated with an open esophagectomy. Reflux and dumping syndromes are the most important functional complaints in patients after esophagectomy. This study compares the functional benefits of MIE with open esophagectomy. The study enrolled patients who underwent either minimally invasive or open esophagectomy for cancer between 2004 and 2009. No patients in the MIE group had a pyloroplasty or myotomy. Each patient in the MIE group was paired to a patient in the open esophagectomy group via propensity matching. Matching variables included age, race, gender, preoperative treatment, history of prior cancer, American Society of Anesthesiologists Risk Scale, performance status, clinical stage, body mass index, histology, level of anastomosis, and time elapsed since surgery. The patients were asked to answer 26 questions about their reflux and dumping using validated questionnaires. A total of 181 patients were included in the study. From this group, 44 pairs of patients were created and used for the analysis. The median follow-up was 12.1 months for the MIE group and 18.3 months for the open group. The reflux score was slightly worse in the MIE group (5.5 versus 3.5, P= 0.021). There was no difference in the dumping symptoms between the two groups. The most common complaints seen in the dumping questionnaire in almost one-third of all patients were early satiety, abdominal discomfort, nausea, and diarrhea. Of the patients, 77% were satisfied or very satisfied with their condition in the MIE group compared with 93% in the open group (P= 0.287). Reflux, dumping, and overall satisfaction after MIE without pyloroplasty are comparable with those obtained after open esophagectomy with a pyloric drainage procedure.

Phase I trial of neoadjuvant dasatinib in patients with resectable malignant pleural mesothelioma

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Background: The optimal multi-modality treatment for resectable malignant pleural mesothelioma (MPM) remains unknown. We designed a biomarker-based neoadjuvant trial from our preclinical studies showing that dasatinib, a multi-targeted Src kinase inhibitor, has activity against MPM and target specificity to Src Tyr419. Methods: Untreated MPM patients underwent extended surgical staging (ESS) with multiple biopsies to account for tumor heterogeneity, lymph node status and to rule out sarcomatoid features. If deemed a surgical candidate for either pleurectomy/decortication (P/D) or extrapleural pneumonectomy (EPP), patients received 4 weeks of oral dasatinib (70 mg BID) followed by P/D or EPP. If either a radiographic or molecular response (de-phosphorylation of Src Tyr419 in tumor) is achieved, an additional 2 years of dasatinib maintenance after adjuvant radiotherapy and systemic chemotherapy is given. The primary endpoint of this trial was biomarker modulation of Src Tyr419. Secondary endpoints included response, survival, safety/toxicity, and biomarker modulation in tumor/serum/platelets/pleural effusion. The total planned sample size is 24 to detect a 50% reduction in positive p-Src Tyr419 expression with 80% power, one-sided 10% type I error rate, and 10% inevaluable rate. Results: To date, ten patients have registered on the trial (4/08 - 12/08); six have successfully completed the ESS, neoadjuvant dasatinib, and P/D (n=3) or EPP (n=3). Two patients are still receiving neoadjuvant dasatinib; and 2 patients were deemed to not be surgical candidates due to a rapid decline in PS and one was found to have bilateral mesothelioma. The main side effects to dasatinib were grade 1–2: anemia, nausea, vomiting, anorexia, electrolyte abnormalities, fatigue, and anxiety. Grade 3 toxicities included hyperkalemia (1), infection - pneumonia (1), and hypoxia (1). There were no grade 4–5 toxicities. Post-surgical grade 3 toxicity included anemia, electrolyte abnormalities, arrhythmia, HTN, and pleural effusion; one grade 4 episode of hyperglycemia was seen. Conclusions: This study demonstrates that biomarker-based neoadjuvant MPM trials with novel agents are feasible. Updated clinical and translational correlative results will be presented.

No significant financial relationships to disclose.

3p and 10q deletions detected by fluorescence in situ hybridization (FISH): A potential new tool for early detection of non-small cell lung cancer (NSCLC)

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Objectives: To study the feasibility of detecting chromosomal deletions at the 3p and 10q regions in bronchoscopic brush biopsies and touch preparations by FISH and to study their distribution in different areas of the airway in patients with NSCLC. Methods: Bronchoscopic brush biopsies from the mainstem bronchus on the normal side contralateral to the tumor (NBB) and normal mainstem bronchus on the tumor side (TBB) were obtained from 120 patients who underwent surgical resection. Touch preparations from the tumor (TTP) and normal lung parenchyma from the involved lung (NTP) and from bronchi adjacent to the tumor (TAB) were also obtained. Two FISH assays using probes complementary to 3p22.1 and 10q22.3 were used for evaluation of chromosomal deletions at each site. The ratios of the percentage of deletions detected at different anatomical sites were compared using the Wilcoxon signed rank test. Correlations between deletions at TTP and other sites were estimated with a Spearman coefficient. Results: Contralateral normal bronchial tissue (NBB) showed a relatively low deletion rate of 3p and 10q compared to TTP (p<0.0001). FISH on brush biopsies at TBB showed a significantly higher rate of deletions compared to NBB (p<0.05) for both 3p and 10q. A significantly higher deletion rate was seen at TTP compared to NTP at both the 3p (p<0.0001) and 10 q regions (p<0.0001). Significant correlations were seen between the rate of deletions between TTP and TBB at 3p (ρ=0.61, p<0.0001) and between TTP and TAB at 10q (ρ=0.64, p<0.0001). Conclusions: Chromosomal deletions of the 3p and 10q regions can be reliably detected by FISH in bronchoscopic biopsies and touch preparations. As one progresses from the contralateral normal bronchus to the bronchus on the side of tumor and the tumor itself, the percentage of chromosomal deletions increases in a statistically significant fashion,supporting an etiological role of these changes. Deletions at the bronchoscopically normal main and adjacent bronchus on the side of the tumor correlate with an increased deletion rate in the tumor itself. This suggests that FISH analysis of bronchoscopic brushes may be useful for identifying patients at high risk for developing NSCLC.

No significant financial relationships to disclose.

Genetic deletion of PKR abrogates TNF-induced activation of IkappaBalpha kinase, JNK, Akt and cell proliferation but potentiates p44/p42 MAPK and p38 MAPK activation

Double-stranded RNA-dependent protein kinase (PKR), a ubiquitously expressed serine/threonine kinase, has been implicated in the regulation or modulation of cell growth through multiple signaling pathways, but how PKR regulates tumor necrosis factor (TNF)-induced signaling pathways is poorly understood. In the present study, we used fibroblasts derived from PKR gene-deleted mice to investigate the role of PKR in TNF-induced activation of nuclear factor-kappaB (NF-kappaB), mitogen-activated protein kinases (MAPKs) and growth modulation. We found that in wild-type mouse embryonic fibroblast (MEF), TNF induced NF-kappaB activation as measured by DNA binding but deletion of PKR abolished this activation. This inhibition was associated with suppression of inhibitory subunit of NF-kappaB (IkappaB)alpha kinase (IKK) activation, IkappaBalpha phosphorylation and degradation, p65 phosphorylation and nuclear translocation, and NF-kappaB-dependent reporter gene transcription. TNF-induced Akt activation needed for IKK activation was also abolished by deletion of PKR. NF-kappaB activation was diminished in PKR-deleted cells transfected with TNF receptor (TNFR) 1, TNFR-associated death domain and TRAF2 plasmids; NF-kappaB activated by NF-kappaB-inducing kinase, IKK or p65, however, was minimally affected. Among the MAPKs, it was interesting that whereas TNF-induced c-Jun N-terminal kinase (JNK) activation was abolished, activation of p44/p42 MAPK and p38 MAPK was potentiated in PKR-deleted cells. TNF induced the expression of NF-kappaB-regulated gene products cyclin D1, c-Myc, matrix metalloproteinase-9, survivin, X-linked inhibitor-of-apoptosis protein (IAP), IAP1, Bcl-x(L), A1/Bfl-1 and Fas-associated death domain protein-like IL-1beta-converting enzyme-inhibitory protein in wild-type MEF but not in PKR-/- cells. Similarly, TNF induced the proliferation of wild-type cells, but this proliferation was completely suppressed in PKR-deleted cells. Overall, our results indicate that PKR differentially regulates TNF signaling; IKK, Akt and JNK were positively regulated, whereas p44/p42 MAPK and p38 MAPK were negatively regulated.

Treatment outcomes of patients (pts) with primary mediastinal germ cell tumors (PMGCT): The M. D. Anderson Cancer Center (MDACC) experience

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Background: PMGCT are uncommon germ cell malignancies. Mediastinal nonseminomatous germ cell tumors (NSGCT) have a poor prognosis, whereas pure seminoma (Sem) has a good or intermediate prognosis irrespective of mediastinal presentation. Methods: We retrospectively identified 19 male pts with PMGCT seen at MDACC between October 1998 and September 2004 from a clinical database. Pts with resectable NSGCT were offered surgery upon plateau of their chemotherapy response. Prior to referral, 1 pt had primary surgical resection without preoperative (preop) chemotherapy. Results: There were 14 pts with NSGCT and 5 with good prognosis Sem. The median age was 29.5 (20–60). Seven pts with NSGCT had mixed or undifferentiated histology, and the remainder had pure yolk sac (5 pts) or choriocarcinoma (2 pts). The estimated median survival (Kaplan-Meier) for all patients (Sem + NSGCT) was 21 months. All pts with Sem were alive and disease-free at last follow-up (median 12 months, range 7–34). All pts with Sem received 4 courses of etoposide and cisplatin (EP); one also received bleomycin (BEP); one received radiotherapy consolidation; none received surgery. Of the pts with NSGCT, 9 (64%) have died, including 1 who refused surgery. Five pts with NSGCT were alive at last follow-up and 3 (21%) were disease-free (15+, 27+ and 35+ months). Four pts with NSGCT (29%) reached beyond 2 years survival (27+, 28, 35+, and 63+ months) including 3 with lung metastases and one with elevated preop alpha-fetoprotein (28,022 ng/ml). Each of these pts received 6–10 courses of multiple-regimen preop chemotherapy, and 2 received initially 4 courses of BEP without marker normalization. Conclusions: Mediastinal Sem treated with 4 courses EP had an excellent outcome without surgery. Pts with mediastinal NSGCT had a 64% mortality rate despite aggressive treatment. Several pts with mediastinal NSGCT did achieve long-term survival following aggressive chemotherapy and surgery, even with lung metastases and failure to normalize markers. A phase III trial of BEP versus dose-dense chemotherapy for poor-prognosis NSGCT is now in progress at MDACC.

No significant financial relationships to disclose.