Lung Squamous Cell Research Articles

Multi-resolution deep learning characterizes tertiary lymphoid structures and their prognostic relevance in solid tumors

BackgroundTertiary lymphoid structures (TLSs) are dense accumulations of lymphocytes in inflamed peripheral tissues, including cancer, and are associated with improved survival and response to immunotherapy in various solid tumors. Histological TLS quantification has been proposed as a novel predictive and prognostic biomarker, but lack of standardized methods of TLS characterization hampers assessment of TLS densities across different patients, diseases, and clinical centers.MethodsWe introduce an approach based on HookNet-TLS, a multi-resolution deep learning model, for automated and unbiased TLS quantification and identification of germinal centers in routine hematoxylin and eosin stained digital pathology slides. We developed HookNet-TLS using n = 1019 manually annotated TCGA slides from clear cell renal cell carcinoma, muscle-invasive bladder cancer, and lung squamous cell carcinoma.ResultsHere we show that HookNet-TLS automates TLS quantification across multiple cancer types achieving human-level performance and demonstrates prognostic associations similar to visual assessment.ConclusionsHookNet-TLS has the potential to be used as a tool for objective quantification of TLS in routine H&E digital pathology slides. We make HookNet-TLS publicly available to promote its use in research.

Gene co-expression analysis uncovers the different effects of cathelicidin in lung squamous cell and in invasive breast carcinomas

Antimicrobial peptides are multi-functional peptides that possess a broad range of mechanisms of action. They have been investigated as novel therapeutic options in the field of infectious diseases, but an increasing number of publications suggest that they also play an important role in the pathology of cancer.Here, using an in silico approach, we investigated the pathways associated with LL-37, the only human member of the cathelicidin family of antimicrobial peptides, in lung squamous cell and in invasive breast carcinomas.We found that LL-37 is implicated in different and even opposing cell responses, depending on the type of cancer, and participates in intriguing molecular processes, such as platelets activity, coagulation and extracellular matrix organization.

Retraction of "Altered Treg and IL-1A Expression in the Immune Microenvironment of Lung Squamous-cell Cancer after EGFR Blockade. Zhongguo Feiai Zazhi, 2017, 20(3): 143-148."

This corrects the article DOI: 10.3779/j.issn.1009-3419.2017.03.01.

The developmental gene Chordin is amplified and expressed in human cancers

ABSTRACT Chordin (CHRD) is a secreted protein important in early development, yet a role for CHRD in human disease has not been identified. In this study we investigated CHRD in cancer and normal adult tissues using the wealth of genome-wide data available in public databases. We found that Chordin is amplified in the DNA of specific cancers such as lung squamous cell and others, although copy number variation did not strictly correlate with higher mRNA expression. In some cancers, such as renal and stomach carcinomas, increased CHRD expression significantly correlated with poor survival. In normal adult human tissues, CHRD mRNA was highest in hepatocytes. Crossveinless-2/BMPER, a component of the Chordin morphogenetic pathway expressed at the opposite side in embryos, was expressed in liver stellate cells. This raises the intriguing possibility that a BMP gradient might be established in the extracellular matrix of the space of Disse that surrounds portal sinusoid capillaries.

Abstract 2386: Investigating cyclopamine tartrate as a potential suppressor of lung adenocarcinoma and squamous cell carcinoma

Abstract Lung cancer is the leading cause of death by cancer, and non-small cell lung cancer comprises of 85-90% of lung cancer cases. Previous studies have demonstrated the importance of heme in mitochondrial metabolism and OXPHOS. Heme is an essential molecule in the oxidative phosphorylation pathway especially since Complex II-IV all contain heme. During lung tumorigenesis there is a marked increase in heme synthesis and uptake; other protein and enzymes relating to heme were also upregulated. Heme-sequestration proteins (HeSPs) have shown high effectiveness in suppressing the development and progression of lung adenocarcinoma and squamous cell carcinoma, therefore targeting heme using CycT should yield similar results. Previous studies have indicated that cyclopamine tartrate (CycT) can effectively arrest lung tumor growth and progression. CycT does this by inhibiting the levels of proteins and enzymes involved in heme uptake, synthesis, as well as reducing heme synthesis and degradation in adenocarcinoma. We therefore aim to examine the effectiveness of CycT in both, adenocarcinoma and squamous cell carcinoma.In vitro experiments using NSCLC adenocarcinoma cell line A549 and squamous cell carcinoma HCC15 are in progression with initial results supporting the hypothesis. Cell proliferation assays have shown a marked decrease in CycT-treated groups in both cell lines. Based on colony formation assays, results indicate that CycT inhibits colony formation. Heme synthesis and degradation have also shown the effectiveness of CycT in suppressing tumorigenesis in both cell types. Oxygen consumption rates of both cell types were examined with CycT inhibiting oxygen consumption. Overall, in vitro experiments support the idea that CycT can suppress or arrest lung adenocarcinoma and squamous cell carcinoma. Citation Format: Eranda Berisha, Adnin Ashrafi, Maria Del Carmen Chacon Castro, Li Zhang. Investigating cyclopamine tartrate as a potential suppressor of lung adenocarcinoma and squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2386.

Abstract 845: Pan-cancer proteogenomic signatures associated with HRD, MSI, APOBEC, and smoking

Abstract The increased quality and data availability of large-scale transcriptomic, genomic, and proteomic studies require a pan-cancer integrated proteogenomic approach to define tumor molecular signatures accurately and identify new therapeutic targets. We comprehensively investigate more than 1000 samples across 12 cancer types from the Clinical Proteomics Tumor Analysis Consortium (CPTAC) and the International Cancer Proteogenome Consortium (ICPC). The types are comprised of breast (BR), colorectal (CO), and ovarian (OV) cancers, clear cell renal cell (ccRCC), head and neck squamous cell (HNSCC), lung squamous cell (LSCC), hepatitis B virus (HBV)-related hepatocellular (HCC), and endometrial (EC) carcinomas, lung adenocarcinoma (LUAD), pancreatic ductal adenocarcinoma (PDAC), and glioblastoma (GBM). In particular, we examine 8 Tumor Signature Associated Phenotypes (TSAPs), namely aristolochic acid (AA), aging, microsatellite instability (MSI), homologous recombination deficiency (HRD), POLE, APOBEC, smoking, and ultraviolet (UV) light exposure. This study is the first to report proteomic markers associated with these TSAPs on a pan-cancer level. In addition to genetic alterations and mutational signatures, we utilize multi-omics data of high-resolution proteome, phosphoproteome, acetylome, and gene expression to infer expression signatures of TSAPs by defining the most critical changes in the transcriptome and proteome accompanying the transitions to these TSAPs, especially markers that were uniquely found in proteomic data. We consolidated multi-omic data and calculated the novel quantitative Tumor Signature Associated Phenotypes (TSAPs) score to predict the TSAP status. For example, the use of proteomic markers for MSI-TSAP scoring can improve clinical testing of MSI status. We further study environmental exposure-related tumor proteogenomic signatures, immune proteogenomic signatures, and the association between the immune subtypes and TSAPs. Smoking strongly influences the tumor immune microenvironment and disease prognosis. We show that expression signatures can facilitate the prediction of TSAPs and help to uncover their underlying molecular mechanisms. By connecting these findings with druggable databases, we provide a link to actionable therapies, identify putative TSAP-related targets, and offer novel cues to optimize therapeutic options for patients, such as how additional targeting of genes up-regulated in PARP1 inhibitor-treated HRD tumors may overcome resistance. This will promote the identification not only of unique druggable targets, but also to determine putative novel therapeutic targets using integrated approaches. Citation Format: Yize Li, Nadezhda V. Terekhanova, Daniel Cui Zhou, Kelly V. Ruggles, Samuel H. Payne, Michael Wendl, David Fenyő, Li Ding. Pan-cancer proteogenomic signatures associated with HRD, MSI, APOBEC, and smoking [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 845.

Abstract 5415: Glypican-3 immunohistochemistry precision, validation, and prevalence in selected solid tumors to identify target populations for CAR T cell therapy

Abstract Background: Glypican-3 (GPC3) is an oncofetal tumor antigen that is an attractive target for chimeric antigen receptor (CAR) T cell therapy due to its highly restricted expression on normal tissue and high prevalence in several adult and pediatric solid tumors. Aberrant GPC3 expression is implicated in tumorigenesis, and GPC3+ cancers are characterized by a highly immunosuppressive landscape which induces exhaustion in tumor-resident T cells. We sought to assess the validity of a GPC3 antibody clone in immunohistochemistry (IHC) and then measure GPC3+ prevalence in selected solid tumors. Methods: We evaluated GPC3 transcripts in human normal and tumor tissue specimens from The Cancer Genome Atlas (TCGA) and the Genome-Tissue Expression Project. GPC3 IHC was performed on formalin fixed paraffin embedded tumor tissues: hepatocellular (HCC), squamous cell lung (SCC), colorectal (CRC), serous ovarian (OC), Merkel cell carcinomas (MCC) and liposarcoma (LS) using antibody clone GC33 and scored using H-score (range 0-300), with appropriate positive and negative controls. Accuracy and precision of GPC3 antibody clone GC33 were tested in GPC3+ high prevalence tumor types compared to a validated anti-GPC3 clone (1G12). GPC3+ cutoff was set as H-score ≥ 30 (GC33) compared to >20 (1G12). The prevalence of GPC3 expression measured by IHC was also used to calculate the theoretical mRNA cutoff value from the TCGA data for GPC3+ indications represented in the database. Results: GPC3 mRNA was expressed at low levels predominantly in lung, adipose, tibial nerve, kidney and breast. GPC3 IHC of normal tissue showed predominantly faint, cytoplasmic staining in a few tissues including heart, kidney and stomach and no expression in lung or breast. HCC, SCC, LS, CRC, and OC showed high and varying levels of GPC3 mRNA expression in TCGA samples. The theoretical mRNA expression cutoff value based on IHC were HCC=1396 RSEM, SCC= 2675 RSEM, Sarcoma= 4126 RSEM; and OC 4486 RSEM; respectively. A cutoff for CRC could not be determined because the prevalence of GPC3 by IHC was <10%. GPC3 IHC using GC33 showed a higher prevalence of positive cases in myxoid/round cell LS (MRCLS) relative to other LS subtypes (15/45 vs. 8/75). HCC (n=110), SCC (n=73), MRCLS (n=45), and MCC (n=20) had a prevalence of 69%, 33%, 33%, and 70%; respectively. However, <10% of CRC (n=80) or OC (n=31) were GPC3+. GPC3 IHC assay using clone GC33 was fully validated for use as a lab-developed test by assessing accuracy, sensitivity, specificity, and precision in SCC, HCC, MCC and LS specimens. Conclusions: GPC3 has a high prevalence in selected tumors with low level expression in some normal tissues, making it an attractive target for CAR T cell therapy. The GC33 clone performs similarly to 1G12 and could be used for IHC screening for CAR T cell therapy. MRCLS has higher prevalence of GPC3+ expression relative to other LS subtypes. Citation Format: Glen J. Weiss, Amy Jensen-Smith, Sujatha Muralidharan. Glypican-3 immunohistochemistry precision, validation, and prevalence in selected solid tumors to identify target populations for CAR T cell therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5415.

Abstract 5762: Genomic correlates of response to immune checkpoint blockade in Epstein-Barr virus-associated pulmonary lymphoepithelioma-like carcinoma

Abstract Introduction: Pulmonary lymphoepithelioma-like carcinoma (PLELC) is a rare and distinct subtype of non-small cell lung cancer (NSCLC). The use of immune checkpoint inhibitors (ICIs) for advanced PLELC and tumor genomic features underlying varied treatment responses remains poorly investigated. Methods: The study involved 33 PLELC patients with clinically annotated outcomes to ICIs. Targeted sequencing covering 520 cancer related genes were performed in 22 patients to identify single nucleotide variations (SNVs), copy number variations (CNVs), tumor mutation burden (TMB) and microsatellite instability. Mutation profiles of PLELC were compared with other NSCLC subtypes including lung adenocarcinoma (LUAD) and squamous cell lung carcinoma (LUSC) as well as EBV (Epstein-Barr virus) positive nasopharyngeal carcinoma (NPC) in public databases. Associations between PLELC mutation profiles and treatment responses to ICIs were analyzed. An external dataset of ICI-treated melanoma was used in further analysis of B2M. Results: The objective response rate (ORR), disease control rate (DCR), durable clinical benefit (DCB) rate, and median PFS was 18.2%, 60.6%, 45.5%, and 4.5 months respectively. Genetic alterations were frequently identified in B2M (9 of 22, 41%), CDKN1B (7 of 22, 32%), TP53 (6 of 22, 27%), SGK1 (5 of 22, 23%), NFKBIA (4 of 22, 18%) and TNFAIP3 (4 of 22, 18%). CNVs were comprehensively presented in PLELC while SVNs were less common. In our study, 8 of 9 tumors with B2M mutations and all tumors with CDKN1B, SGK1, TNFAIP3 mutations harbored copy number amplifications. Mutation profiles of PLELC were largely different from those of LUAD and LUSC but were similar to NPC. The median TMB was 2.99 mutations/Mb. All tumors were microsatellite stable (MSS). Patients with higher TMB showed improved DCR (p=0.029), PFS (p=0.056) and overall survival (p=0.038) than those with lower TMB. Patients with lower baseline plasma EBV DNA level also had longer PFS (p<0.001). The presence of B2M amplifications was significant associated with higher TMB level (p=0.022). The PFS of 7 patients with high TMB and amplified B2M were significantly longer than that of other patients (p=0.046). In the external dataset, higher expression of B2M was associated with better ICI responses for melanoma (p<0.05). Pathways involving anti-tumor immune responses such as NK cell-mediated cytotoxicity, antigen processing and presentation were correlated with high B2M expression while Wnt, TGF-beta and MAPK pathways that define poor response to ICI were correlated with low B2M expression. Conclusion: Our study observed comprehensive CNVs in PLELC patients which is a unique molecular feature compared with other NSCLC subtypes and EBV-positive NPC. Higher TMB level and amplifications of B2M in PLELC patients may be used as potential biomarkers to indicate better treatment responses to ICIs. Citation Format: Li-na He, Xuanye Zhang, Xinze Lv, Yuxi Zhou, Min Li, Ting Hou, Wenjie Sun, Li Zhang, ShaoDong Hong. Genomic correlates of response to immune checkpoint blockade in Epstein-Barr virus-associated pulmonary lymphoepithelioma-like carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5762.

Abstract 2378: Methylmalonic acid is elevated in non-small cell lung cancer and promotes drug resistance

Abstract Lung cancer is the leading cause of cancer-related deaths in the United States. Identifying new factors that promote drug resistance is critical to restoring drug sensitivity and improving patient outcomes. Methylmalonic acid (MMA) is a dicarboxylic acid by-product of propionate metabolism. MMA levels rise in the serum with age and are associated with cancer-related mortality (the higher the MMA, the worse the mortality). We recently asked whether this metabolite had a functional impact and showed that treating non-small cell lung cancer (NSCLC) cells with MMA in vitro promotes drug resistance through triggering epithelial-to-mesenchymal transition (EMT). However, whether MMA is elevated in lung cancer is not known, and how MMA levels are regulated is poorly understood. To determine if MMA is elevated in NSCLC, we performed targeted metabolomics on 20 resected lung adenocarcinomas and squamous cell carcinomas with matched normal lung tissue. We found that MMA was 2.5 fold elevated in tumors compared to controls (p<0.001, paired t-test). To our knowledge, this is the first report of MMA being elevated in any cancer. MMAB is one of the key MMA regulatory genes. When MMAB is inactivated or underexpressed, MMA cannot be metabolized and its intracellular levels increase. We hypothesized that loss of MMAB expression may explain elevated MMA levels in lung cancer. To test this, we analyzed publicly available mRNA expression data sets and found that MMAB is underexpressed in NSCLC (suggesting high levels of MMA). Moreover, MMAB expression correlates with survival. The lower the MMAB expression (suggesting higher MMA), the worse the survival (Hazard Ratio 0.36, p<0.001). We thus asked if suppressing MMAB expression had a functional impact on cell lines. Using shRNA constructs, we knocked down MMAB in the A549 and H1975 NSCLC cell lines. Targeted metabolomics confirmed that knockdown of MMAB increased MMA levels. Moreover, knockdown of MMAB decreased cellular proliferation and increased resistance to carboplatin, pemetrexed, and osimertinib. RNA-seq analysis showed that suppressing MMAB induced EMT and senescence expression signatures. Furthermore, we found that hypoxia and nutrient stress downregulate MMAB expression at the mRNA and protein level. Collectively, our data suggest that loss of MMAB expression through hypoxia or nutrient stress can increase MMA levels, triggering EMT and resistance to chemotherapy and targeted therapy in NSCLC. Our results indicate that dysregulation of MMA plays an important role in lung cancer. Citation Format: Bobak Parang, Zhongchi Li, Vivien Low, Jennifer Endress, Murtaza Malbari, Ashish Saxena, Nasser Altorki, John Blenis. Methylmalonic acid is elevated in non-small cell lung cancer and promotes drug resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2378.

Abstract 3776: Frequent alteration of mitochondria functional pathways in lung cancer

Abstract Lung cancer killed 1.8 million people globally in 2020. In the United States, there will be over 235,760 cases of lung cancer with an estimated death of 131,880 individuals in 2021. Despite significant improvement in multimodal therapeutic approaches, overall 5-year survival rate is only 21.7%. Lung cancer appears to be mitochondria enriched cancer, however, alteration pattern of hallmark molecular pathways associated with diverse mitochondrial functions remain largely unknown in lung tumorigenesis. Utilizing high-throughput genomic profiling, we identified altered copy number of a panel of 40 mitochondria targeted molecules in primary lung cancer patients and their histologically normal appearing follow up mucosal biopsies. These altered molecules are critical components of the mitochondrial protein carrier, OXPHOS, stress response, amino acid metabolism and apoptosis pathways. This finding suggests for clonal genetic relationship between multifocal lesions and potential role of these alterations in the evolution of second primary tumors, which is an existing problem among lung cancer patients. The Human Cancer Genome Atlas database was utilized to further assess the mRNA expression pattern of these 40 molecules and determine their clinico-pathological correlations. Immunohistochemistry and digital pathology system based evaluations were performed to validate expression pattern of key altered molecules. We identified overexpression of various critical mitochondria pathway molecules including AARS2, AGMAT, SDHA, NDUFB7, LONP1, DGUOK, MRM1 and GCAT in both lung adenocarcinomas (LUAD) and squamous cell carcinomas (LUSC), predicting poor prognosis. Significant loss of expression of ACSF2, ACSS1, MTCH1, SLC25A4, ACAD8 and NAGS was evident in both adenocarcinoma and squamous cell carcinoma subtypes. Molecular characterization of both LUAD and LUSC tumor subtypes identified significant association of various key molecules including ACAD8, AGMAT, DGUOK and NDUFAB1 with proximal-inflammatory, proximal-proliferative and terminal respiratory unit pathways in LUAD; and an association of DGUOK, MDH2, MRM1 and MRPL10 with basal, classical, primitive and secretory pathways in LUSC. Significant loss of SLC25A4 protein expression was evident in lung cancer tissues, which predicted poor survival of the lung cancer patients. Capturing the compendium of hallmark mitochondrial alterations in lung tumorigenesis may open up novel avenues for therapeutic and biomarker interventions to improve the overall survival of the lung cancer patients. Citation Format: Kate L. Hertweck, Brian Persing, Pranitha Prodduturvar, Seema Singh, Ajay Singh, Santanu Dasgupta. Frequent alteration of mitochondria functional pathways in lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3776.

Abstract 5710: Identification of convergent gene repression mechanisms through integrative genomic and DNA methylation analysis in TRACERx

Abstract Introduction: Lung TRACERx is a prominent study employing multi-region and longitudinal multi-omics sequencing to unravel the evolutionary trajectories of lung cancer. Aberrant DNA methylation patterns have been widely described in nearly all human cancers, yet their interplay with DNA mutations in lung cancer is not well understood. Incorporating the contribution of epigenetic modifications to cancer evolution trajectories within TRACERx could improve our understanding of the intricate relationship between genetic and epigenetic changes in non-small cell lung cancer (NSCLC) evolution. Methods: Multi-region sampling from 38 TRACERx patients including 112 tumor regions and 37 matched normal adjacent tissue samples was performed. Reduced representation bisulfite sequencing (RRBS) was performed to assess DNA methylation and the CAMDAC (Larose-Cadieux et al, 2020) was applied to estimate purified tumor methylation rates and correct for copy number changes. Whole exome sequencing and somatic copy number alterations (SCNAs) were inferred using the ASCAT tool (Van Loo et al, 2010) and Methsig (Pan et al, 2021) was performed to discover new methylation driver genes. Results: Using multi-region sequencing, we identified ubiquitous hypermethylation of 29 known driver genes in both lung adenocarcinoma (LUAD) and squamous cell lung cancer (LUSC), together with an additional 9 and 27 genes exclusive to LUSC and LUAD, respectively. We also identified 13 and 7 driver genes non-ubiquitously hypermethylated exclusively in LUSC and LUAD, respectively. Using a differential methylation based approach, we describe a method to determine the extent of intra-tumor methylation heterogeneity akin to established ITH scores based on genomics data. In addition, we report the identification of novel subtype-specific methylation driver genes enriched in HOX family members which are related to cancer progression. Through integration of DNA methylation and genomic sequencing data, we identify parallel mechanisms contributing towards ubiquitous tumor suppressor gene alterations. At the patient level, multiple driver genes such as NSD1, GATA3 and MGA were subject to repression by both copy number loss and DNA hypermethylation. Finally, we describe dosage-compensation of genes such as the Notch ligands JAG2 and DLK1 that are proximal to amplified oncogenes and hypermethylated during tumor evolution. Conclusion: We describe the contribution of DNA methylation and genomic alterations to altering the landscape of NSCLC. Leveraging DNA methylation, we can determine the extent of convergent repression mechanisms in different regions of the same tumor, assess DNA methylation heterogeneity, and discover DNA methylation-based driver genes in NSCLC. Citation Format: Francisco Gimeno-Valiente, Carla Castignani, Elizabeth Larose-Cadieux, Kezhong Chen, Nana Mensah, Olga Chervova, Thomas Watkins, Pawan Dhami, Heli Vaikkinen, Andrew Feber, TRACERx Consortium, Jonas Demeulemeester, Miljana Tanic, Stephan Beck, Peter Van Loo, Charles Swanton, Nnennaya Kanu. Identification of convergent gene repression mechanisms through integrative genomic and DNA methylation analysis in TRACERx [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5710.

Abstract 3626: Genomic evolutionary patterns in matched pre-invasive and invasive lung disease in TRACERx

Abstract Introduction: The genomic landscape of pre-invasive lung disease, including AAH/AIS/MIA (atypical adenomatous hyperplasia, adenocarcinoma in situ, minimally invasive carcinoma) and squamous CIS (carcinoma in situ) which are considered to be precursors to lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC), has been profiled to a limited degree, due to the lack of matched samples within the same patient. Using TRACERx study we investigated the phylogenetic evolutionary patterns between matched pre-invasive and invasive lesions. Methods: Post-operative pathology reports for 746 primary invasive tumors collected within TRACERx were screened to identify pre-invasive lesions that had been resected at the time of primary surgery. 50 pre-invasive lesions (21 AAH, 7 AIS, 6 MIA, 16 CIS) from 36 pts were subjected to whole exome sequencing with 119 matched tumor regions from 22 LUAD, 13 LUSC and 1 pleomorphic carcinoma. Phylogenetic relationships between pre-invasive and invasive lesions, timing of clonal divergence, mutational processes were investigated. Results: Two major types of phylogenetic relationships were identified based on whether pre-invasive and invasive lesions shared a somatic common ancestor (SCA group; 7/22 LUAD, 11/13 LUSC) or not (non-SCA group; 15/22 LUAD, 2/13 LUSC, 1/1 pleomorphic carcinoma). Within SCA group, two evolutionary patterns were identified based on whether only clonal mutations or clonal and subclonal mutations were shared between pre-invasive and invasive lesions. 3/16 SCA pre-invasive lesions from ex-smokers were found to diverge from the invasive tumor years prior to diagnosis. Compared with non-SCA, SCA pre-invasive lesions harbored elevated mutational burden, APOBEC mutagenesis, chromosomal instability featured by increased loss of heterozygosity and somatic copy number alterations (SCNAs). Whole genome doubling was only detected in SCA pre-invasive lesions. In SCA LUAD, 3/7 exhibited clonal TP53 mutations, 3/7 exhibited clonal co-mutations of KEAP1 and STK11. In 5/15 non-SCA LUADs harboring a KRAS mutation, convergent KRAS mutation was detected in 4 matched pre-invasive and invasive lesions. Clonal focal gains on 3q21-29 (containing PIK3CA, ATR, SOX2) were detected in 10/11 SCA LUSC, suggesting that 3q gains may represent early events in tumor initiation. In the non-SCA group, convergent SCNAs encompassing oncogenes (PIK3CA, SOX2, FGFR3) or tumor suppressor genes (STK11, KEAP1, MGA) were detected. Conclusions: We demonstrate that matched pre-invasive and invasive lesions fall in two distinct phylogenetic evolutionary groups: those that have a shared somatic common ancestor and those that do not. SCA pre-invasive lesions exhibit elevated APOBEC mutagenesis and chromosomal instability, shedding some light on the process of malignant transformation. Citation Format: Haoran Zhai, Clare Puttick, David A. Moore, Michelle Dietzen, Sophia Ward, Maise Al Bakir, Thomas Watkins, Andrew Rowan, Selvaraju Veeriah, Robert Hynds, Oriol Pich, Nnennaya Kanu, TRACERx Consortium, Nicholas McGranahan, Charles Swanton, Mariam Jamal-Hanjani. Genomic evolutionary patterns in matched pre-invasive and invasive lung disease in TRACERx [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3626.

Image analysis reveals molecularly distinct patterns of TILs in NSCLC associated with treatment outcome

Despite known histological, biological, and clinical differences between lung adenocarcinoma (LUAD) and squamous cell carcinoma (LUSC), relatively little is known about the spatial differences in their corresponding immune contextures. Our study of over 1000 LUAD and LUSC tumors revealed that computationally derived patterns of tumor-infiltrating lymphocytes (TILs) on H&E images were different between LUAD (N = 421) and LUSC (N = 438), with TIL density being prognostic of overall survival in LUAD and spatial arrangement being more prognostically relevant in LUSC. In addition, the LUAD-specific TIL signature was associated with OS in an external validation set of 100 NSCLC treated with more than six different neoadjuvant chemotherapy regimens, and predictive of response to therapy in the clinical trial CA209-057 (n = 303). In LUAD, the prognostic TIL signature was primarily comprised of CD4+ T and CD8+ T cells, whereas in LUSC, the immune patterns were comprised of CD4+ T, CD8+ T, and CD20+ B cells. In both subtypes, prognostic TIL features were associated with transcriptomics-derived immune scores and biological pathways implicated in immune recognition, response, and evasion. Our results suggest the need for histologic subtype-specific TIL-based models for stratifying survival risk and predicting response to therapy. Our findings suggest that predictive models for response to therapy will need to account for the unique morphologic and molecular immune patterns as a function of histologic subtype of NSCLC.

Phase 1 study of SGN-B7H4V, a novel, investigational vedotin antibody–drug conjugate directed to B7-H4, in patients with advanced solid tumors (SGNB7H4V-001, trial in progress).

TPS3155 Background: B7-H4, a B7 immune checkpoint ligand, is expressed at low levels in normal tissue and negatively regulates T-cell function by inhibiting T-cell proliferation and cytokine production. B7-H4 expression is elevated in solid tumors, including breast, ovarian, and endometrial cancers. Targeting B7-H4–expressing tumor cells may relieve B7-H4–mediated T-cell inhibition. SGN-B7H4V is a novel, investigational vedotin antibody–drug conjugate directed to B7-H4 with proposed mechanisms of action including monomethyl auristatin E (MMAE)-directed cytotoxicity, bystander effect, antibody-dependent cellular cytotoxicity, and antibody-dependent cellular phagocytosis. SGN-B7H4V elicited antitumor activity in cell line-derived xenograft models of triple-negative breast cancer (TNBC) and patient-derived xenograft models of TNBC and ovarian cancer (Gray et al 2021), providing a rationale to evaluate SGN-B7H4V in patients (pts) with advanced solid tumors. Methods: SGNB7H4V-001 (NCT05194072) is a phase 1, first-in-human, multicenter, open-label trial evaluating the safety, tolerability, pharmacokinetics (PK), and antitumor activity of SGN-B7H4V in pts with advanced solid tumors. This study includes 3 parts: dose escalation (Part A), dose and schedule optimization (Part B), and dose expansion in disease-specific cohorts and a biology cohort (Part C). Adult pts (≥18 years) with histologically/cytologically confirmed locally advanced unresectable or metastatic solid tumors including high-grade serous epithelial ovarian cancer, primary peritoneal cancer, fallopian tube cancer, human epidermal growth factor receptor 2-negative and hormone receptor-positive breast cancer, TNBC, endometrial carcinoma, squamous non-small cell lung cancer, cholangiocarcinoma, or gallbladder carcinoma, are eligible. Pts must have ECOG PS 0–1 and relapsed/refractory disease or be intolerant to standard-of-care therapies. Prior treatment with an MMAE-containing agent or a B7-H4–targeted agent is not permitted. Primary endpoints include the rate of adverse events, laboratory abnormalities, dose-limiting toxicities, and cumulative dose-level safety. Secondary endpoints are objective response rate (ORR), complete response rate, duration of objective response (DOR), progression-free survival (PFS), overall survival (OS), PK, and incidence of antidrug antibodies. Exploratory endpoints include pharmacodynamic (PD) analyses, PD and PK exposure measurements, B7-H4 characterization on malignant cells, and biomarker analyses. Safety and antitumor activity endpoints will be assessed using descriptive statistics. ORR will be analyzed by tumor type and dose. DOR, PFS, and OS will be estimated using the Kaplan–Meier method. Enrollment for Part A is ongoing in North America and is planned in Europe. Clinical trial information: NCT05194072.

InnovaTV 207: New combination dosing cohorts in the open label phase 2 study of tisotumab vedotin in solid tumors.

TPS6100 Background: Tisotumab vedotin (TV; TIVDAK) is a tissue factor (TF)-directed antibody-drug conjugate that has been granted accelerated approval in the US for treatment of adults with recurrent/metastatic (r/m) cervical cancer with disease progression on or after chemotherapy. TV remains investigational in other tumor types including squamous cell carcinoma of the head and neck (HNSCC) and squamous non-small cell lung cancer (sqNSCLC). This abstract presents the addition of Part D to innovaTV 207 (NCT03485209), a global, open label, multicenter phase 2 trial investigating the safety, tolerability, and activity of TV in solid tumors. Untreated patients (pts) with r/m HNSCC or sqNSCLC enrolled in Part D will receive either TV in combination with pembrolizumab (pembro) or TV + pembro and a platinum agent. Based on encouraging preliminary safety and efficacy results with 2.0 mg/kg TV once every 3 weeks (Q3W) in combination with pembro or carboplatin (carbo) in innovaTV 205 cervical cancer study cohorts, TV is being evaluated at 2.0 mg/kg Q3W in combination with pembro or pembro + carbo (or cisplatin). Methods: Up to 140 treatment-naive pts with r/m HNSCC or sqNSCLC will be enrolled in Part D of innovaTV 207. First, the All-Comers cohorts for HNSCC and sqNSCLC will each enroll up to 30 pts, regardless of PD-L1 expression, for Q3W dosing with 2.0 mg/kg TV in combination with 200 mg pembro and AUC 5 carbo. After enrollment in the HNSCC All-Comers Cohort is complete, up to 20 pts with HNSCC will be enrolled into a Cisplatin Safety Cohort for dosing with 2.0 mg/kg TV in combination with 200 mg pembro and 100 mg/m2 cisplatin. Completion of enrollment in the All-Comers Cohort for each tumor type will also be followed by enrollment of up to 30 pts with HNSCC (CPS ≥1) and 30 pts with sqNSCLC (TPS ≥1%) into PD-L1 Selected cohorts for dosing with TV in combination with 200 mg pembro. Response will be assessed every 6 weeks for the first 6 months, every 12 weeks for the next 6 months, and then every 6 months after that. Pts with HNSCC must have had no previous systemic therapy for metastatic disease (exception is systemic therapy given as part of multimodal treatment for locally advanced disease completed > 6 months prior). Pts with NSCLC must have histologically or cytologically documented squamous cell NSCLC and must not have had any previous systemic therapy for metastatic disease or radiation therapy to the lung that is > 30 Gy within 6 months of the first dose of study drug. The primary endpoint is investigator-determined confirmed ORR per RECIST v1.1. Secondary endpoints include confirmed and unconfirmed ORR per RECIST v1.1, disease control rate, duration of response, time to response, PFS, OS, safety and tolerability, pharmacokinetics, and immunogenicity. The trial opened in June 2018 and was amended to add Part D in November 2021. Part D enrollment will begin in early 2022; updates will be provided at the meeting. Clinical trial information: NCT03485209.

Novel use of clinical pathways to identify poor prognosis lung cancer patients: Implementation and outcomes.

1589 Background: Cancer patients in the last year of life have different clinical needs and evolving goals of care. Using our oncology decision-support pathways to help clinicians consistently identify such patients in a systematic and prospective fashion, at a discrete moment in the care trajectory, may be an important step towards matching the care of these patients with their stated goals. Methods: Medical oncologists from each disease group at the Dana-Farber Cancer Institute (DFCI) were tasked with identifying clinical settings in each oncology care pathway associated with an expected median survival of < 12 months. This information was embedded into the underlying data model of the pathways platform, allowing us to determine how often clinicians navigated through each poor prognosis node. Results: From 3/1/20 – 6/30/21, there were 264 navigations in 205 unique lung cancer patients receiving standard of care (i.e., not on clinical trial) for a clinical condition associated with poor prognosis. Overall, the median overall survival from the time of a patient’s first navigation through a poor prognosis node during the defined study period was 6.4 months. Table lists outcomes for each specific setting. Patients with squamous or small cell lung cancer being treated in or beyond the third-line setting had notably poor outcomes, with less than a third of these patients surviving 6 months from the time of navigation. Conclusions: A clinical pathways platform can be a key tool in designating clinical scenarios associated with poor prognosis and identifying patients who may be particularly at risk. Pathways analytics provide real-world evidence corroborating the expected poor prognosis based on published studies and can identify specific clinical subsets for whom specific resources are warranted. By embedding this into the pathways data model, we aim to alert physicians to conduct goals of care conversations, offer supportive care resources, and match patients to appropriate treatment options and clinical trials. [Table: see text]

Cytokine storm promoting T cell exhaustion in severe COVID-19 revealed by single cell sequencing data analysis.

BackgroundEvidence has suggested that cytokine storms may be associated with T cell exhaustion (TEX) in COVID-19. However, the interaction mechanism between cytokine storms and TEX remains unclear.MethodsWith the aim of dissecting the molecular relationship of cytokine storms and TEX through single-cell RNA sequencing data analysis, we identified 14 cell types from bronchoalveolar lavage fluid of COVID-19 patients and healthy people. We observed a novel subset of severely exhausted CD8 T cells (Exh T_CD8) that co-expressed multiple inhibitory receptors, and two macrophage subclasses that were the main source of cytokine storms in bronchoalveolar.ResultsCorrelation analysis between cytokine storm level and TEX level suggested that cytokine storms likely promoted TEX in severe COVID-19. Cell–cell communication analysis indicated that cytokines (e.g. CXCL10, CXCL11, CXCL2, CCL2, and CCL3) released by macrophages acted as ligands and significantly interacted with inhibitory receptors (e.g. CXCR3, DPP4, CCR1, CCR2, and CCR5) expressed by Exh T_CD8. These interactions formed the cytokine–receptor axes, which were also verified to be significantly correlated with cytokine storms and TEX in lung squamous cell carcinoma.ConclusionsCytokine storms may promote TEX through cytokine-receptor axes and be associated with poor prognosis in COVID-19. Blocking cytokine-receptor axes may reverse TEX. Our finding provides novel insights into TEX in COVID-19 and new clues for cytokine-targeted immunotherapy development.

Increased PPARD Expression May Play a Protective Role in Human Lung Adenocarcinoma and Squamous Cell Carcinoma.

Peroxisome proliferator-activated receptor-δ, encoded by gene PPARD, is overexpressed in a majority of human lung cancer subtypes, but its role in the tumor progression remains poorly understood. We have analyzed the expression of PPARD in lung adenocarcinoma (LA) and squamous cell carcinoma (LSCC) datasets. The potential roles of PPARD in the pathological development of LA and LSCC were explored through literature-based pathway analysis and pathway enrichment analysis. In all LA datasets (N = 11) and in seven out of nine LSCC studies, the levels of PPARD were increased as compared to control tissues (log-fold changes were 0.37 ± 0.20 and 0.10 ± 0.37 for LA and LSCC, respectively). On average, the expression levels of PPARD in LA were higher than those in LSCC (p = 0.036). Pathway analysis showed that the overexpression of PPARD might play both positive and negative roles in the development of both LA and LSCC. Specifically, PPARD inhibits seven LSCC promoters and seven LA promoters and activates one LSCC inhibitor and another LA inhibitor. However, PPARD also activates six and one promoters of LA and LSCC, respectively, which would facilitate the development of LA/LSCC. Our results suggested a mixed role of PPARD in LA/LSCC, which may add new insights into the understanding of the PPARD-lung cancer relationship.

MiR-139-3p Targets CHEK1 Modulating DNA Repair and Cell Viability in Lung Squamous Carcinoma Cells.

Non-small-cell lung carcinoma (NSCLC) can be classified into several subtypes, where lung squamous carcinoma (LUSC) is one common subtype. Though miR-139-3p has been reported to be implicated in the development of various cancers, its mechanisms and functions remain unclear in LUSC. In this study, miR-139-3p was screened as one of the significantly down-regulated miRNAs in LUSC by an "edgeR" differential analysis based on TCGA database, which was verified by qRT-PCR in LUSC cell lines as well. The viability and cell cycle of the LUSC cells were examined by CCK-8 and flow cytometry, respectively, exhibiting that upregulating miR-139-3p restrained cell viability and thus accelerating the cell cycle. To explain this phenomenon, we further explored the downstream target gene through miRTarBase and starBase databases, where CHEK1 was predicted as one candidate. The targeting relationship was verified by a dual luciferase assay, identifying that CHEK1 could be targeted by miR-139-3p. Then, qRT-PCR and western blot analyses were performed to detect the expression of CHEK1 mRNA and proteins under the alteration of miR-139-3p expression. Rescue experiments were conducted to confirm the impacts of miR-139-3p/CHEK1 axis on the cell viability and cell cycle of LUSC. The results indicated that the effects of miR-139-3p on the LUSC cell phenotypes could be blocked by overexpressing CHEK1. In conclusion, our study provides a novel insight into the regulatory role of miR-139-3p in the development of LUSC.

Positron Emission Tomography/Magnetic Resonance Imaging Radiomics in Predicting Lung Adenocarcinoma and Squamous Cell Carcinoma.

ObjectiveTo investigate the diagnostic value of positron emission tomography (PET)/magnetic resonance imaging (MRI) radiomics in predicting the histological classification of lung adenocarcinoma and lung squamous cell carcinoma.MethodsPET/MRI radiomics and clinical data were retrospectively collected from 61 patients with lung cancer. According to the pathological results of surgery or fiberscope, patients were divided into two groups, lung adenocarcinoma and squamous cell carcinoma group, which were set as positive for adenocarcinoma (40 cases) and negative for squamous cell carcinoma (21 cases). The radiomics characteristics most related to lung cancer classification were calculated and selected using radiomics software, and the two lung cancer groups were randomly assigned into a training set (70%) and a test set (30%). Maximum relevance and minimum redundancy (mRMR) and least absolute shrinkage and selection operator (LASSO) methods in the uAI Research Portal software (United Imaging Intelligence, China) were used to select the desired characteristics from 2600 features extracted from MRI and PET. Eight optimal features were finally retained through 5-fold cross-validation, and a PET/MRI fusion model was constructed. The predictive ability of this model was evaluated by the difference in area under the curve (AUC) obtained from the receiver operating characteristic (ROC) curve.ResultsAUC of PET/MRI model for the training group and test group were 0.886 (0.787-0.985) and 0.847 (0.648-1.000), respectively. PET/MRI radiomics features revealed different degrees of correlation with the classification of lung adenocarcinoma and squamous cell carcinoma, with significant differences.ConclusionThe prediction model constructed based on PET/MRI radiomics features can predict the preoperative histological classification of lung adenocarcinoma and squamous cell carcinoma without seminality and repeatability. It can also provide an objective basis for accurate clinical diagnosis and individualized treatment, thus having important guiding significance for clinical treatment.