Subtype Of Adenocarcinoma Research Articles

Histopathologic Basis for a Chest CT Deep Learning Survival Prediction Model in Patients with Lung Adenocarcinoma.

Background A preoperative CT-based deep learning (DL) prediction model was proposed to estimate disease-free survival in patients with resected lung adenocarcinoma. However, the black-box nature of DL hinders interpretation of its results. Purpose To provide histopathologic evidence underpinning the DL survival prediction model and to demonstrate the feasibility of the model in identifying patients with histopathologic risk factors through unsupervised clustering and a series of regression analyses. Materials and Methods For this retrospective study, data from patients who underwent curative resection for lung adenocarcinoma without neoadjuvant therapy from January 2016 to September 2020 were collected from a tertiary care center. Seven histopathologic risk factors for the resected adenocarcinoma were documented: the aggressive adenocarcinoma subtype (cribriform, morular, solid, or micropapillary-predominant subtype); mediastinal nodal metastasis (pN2); presence of lymphatic, venous, and perineural invasion; visceral pleural invasion (VPI); and EGFR mutation status. Unsupervised clustering using 80 DL model-driven CT features was performed, and associations between the patient clusters and the histopathologic features were analyzed. Multivariable regression analyses were performed to investigate the added value of the DL model output to the semantic CT features (clinical T category and radiologic nodule type [ie, solid or subsolid]) for histopathologic associations. Results A total of 1667 patients (median age, 64 years [IQR, 57-71 years]; 975 women) were evaluated. Unsupervised patient clusters 3 and 4 were associated with all histopathologic risk factors (P < .01) except for EGFR mutation status (P = .30 for cluster 3). After multivariable adjustment, model output was associated with the aggressive adenocarcinoma subtype (odds ratio [OR], 1.03; 95% CI: 1.002, 1.05; P = .03), venous invasion (OR, 1.03; 95% CI: 1.004, 1.06; P = .02), and VPI (OR, 1.08; 95% CI: 1.06, 1.10; P < .001), independently of the semantic CT features. Conclusion The deep learning model extracted CT imaging surrogates for the histopathologic profiles of lung adenocarcinoma. © RSNA, 2022 Online supplemental material is available for this article. See also the editorial by Yanagawa in this issue.

Solid Attenuation Components Attention Deep Learning Model to Predict Micropapillary and Solid Patterns in Lung Adenocarcinomas on Computed Tomography.

High-grade adenocarcinoma subtypes (micropapillary and solid) treated with sublobar resection have an unfavorable prognosis compared with those treated with lobectomy. We investigated the potential of incorporating solid attenuation component masks with deep learning in the prediction of high-grade components to optimize surgical strategy preoperatively. A total of 502 patients with pathologically confirmed high-grade adenocarcinomas were retrospectively enrolled between 2016 and 2020. The SACs attention DL model was developed to apply solid-attenuation-component-like subregion masks (tumor area ≥ - 190 HU) to guide the DL model for predicting high-grade subtypes. The SACA-DL was assessed using 5-fold cross-validation and external validation in the training and testing sets, respectively. The performance, which was evaluated using the area under the curve (AUC), was compared between SACA-DL and the DL model without SACs attention (DLwoSACs), the prior radiomics model, or the model based on the consolidation/tumor (C/T) diameter ratio. We classified 313 and 189 patients into training and testing cohorts, respectively. The SACA-DL achieved an AUC of 0.91 for the cross-validation, which was significantly superior to those of the DLwoSACs (AUC = 0.88; P = 0.02), prior radiomics model (AUC = 0.85; P = 0.004), and C/T ratio (AUC = 0.84; P = 0.002). An AUC of 0.93 was achieved for external validation in the SACA-DL and was significantly better than those of the DLwoSACs (AUC = 0.89; P = 0.04), prior radiomics model (AUC = 0.85; P < 0.001), and C/T ratio (AUC = 0.85; P < 0.001). The combination of solid-attenuation-component-like subregion masks with the DL model is a promising approach for the preoperative prediction of high-grade adenocarcinoma subtypes.

Survival benefits from neoadjuvant treatment in gastric cancer: a systematic review and meta-analysis

BackgroundSurgery is the main treatment option for patients with local gastric cancer. However, surgery alone is usually not sufficient for stomach cancer patients, and combined therapies are recommended for these patients. In recent studies, some preoperative treatments have shown benefits. However, the treatment selection is still uncertain because previous studies failed to obtain a statistically significant difference between preoperative chemotherapy and preoperative chemoradiotherapy. Therefore, we plan to perform a systematic review and meta-analysis to compare the benefits among these preoperative treatments.Methods/designThis review includes randomized controlled trials with or without blinding as well as published studies, high-quality unpublished studies, full articles and meeting abstracts with an English context if sufficient results were provided for analysis. Data sources include the Cochrane Central Register of Controlled Trials, Embase, MEDLINE, major relevant international conferences and manual screening of references. Patients with a diagnosis of resectable primary gastric or EGJ adenocarcinoma (stage II or higher) who underwent surgery alone or preoperative treatment followed by surgery and who were pathologically confirmed as proposed by the AJCC 2017 guidelines without age, sex, race, subtypes of adenocarcinoma and molecular pathology limitations will be included. The following three interventions will be included: surgery alone, neoadjuvant chemistry followed by surgery and neoadjuvant chemoradiotherapy followed by surgery. All-cause mortality, overall survival (OS, the time interval from diagnosis to death) and/or progression-free survival (PFS, the time interval from diagnosis to disease progression or death from any cause) will be defined as major results of concern. The clinical and pathological response rate (according to RECIST and tumour regression score), R0 resection rate, quality of life and grade 3 or above adverse events (according to the National Cancer Institute Common Terminology Criteria for Adverse Events, NCI-CTCAE) will be defined as the secondary outcomes.DiscussionThe aim of this systematic review is to compare the benefits of different preoperative treatments for patients with locoregional stomach cancer. This systematic review will improve the understanding of the relative efficacy of these treatment options by providing the latest evidence on the efficacy of various treatment options in the management of gastric cancer patients and may guide clinical practice.Systematic review registrationPROSPERO CRD4202123718

Differential Infiltration of Immune Cells Driven by Tumor Heterogeneity Reveals Two Immune Subtypes in Lung Adenocarcinoma.

Intra-tumoral heterogeneity (ITH) is a critical factor leading to aggressive progression and response to immunotherapy in lung adenocarcinoma (LUAD). However, the relationship between ITH and immune cells in the tumor microenvironment (TME) has not been systematically elucidated. In the present study, we evaluated the ITH status of LUAD samples based on the mutational data obtained from The Cancer Genome Atlas database. First, we identified five key immune pathways with a significantly continuous downtrend among normal, low-heterogeneous, and high-heterogeneous samples and further excavated nine key immune cells related to the key immune pathways and tumor heterogeneity. Then, two immune subtypes were defined by a consensus clustering algorithm based on the infiltration of these immune cells. Differences between these two immune subtypes were remarkable, including alterations of tumor mutation burden and DNA copy number variation at the genomic level, various metabolic pathways, and the different clinical outcome, which was also validated in two independent Gene Expression Omnibus datasets. The results revealed that ITH was significantly associated with prognosis and infiltrating immune cells in the TME. Our study provides novel insights in understanding the relationship between ITH and immune cells and contributes to the immunotherapy of LUAD patients.

Adenocarcinoma Nasossinusal- a Relevância da História Ocupacional

Introduction Nasosinusal Adenocarcinomas are rare neoplasms that account for less than 5% of head and neck cancers. Occupational risk factors that have been linked to a higher incidence of Nasosinusal Adenocarcinomas include chronic exposure to wood dust and/or leather, nickel and chromium compounds, formaldehyde and other solvents, and polycyclic aromatic hydrocarbons. Occupations with exposure to dense wood dust are particularly associated with the intestinal subtype of adenocarcinoma, the most frequent location of which occurs in the ethmoid sinus and upper nasal cavity. The report of this clinical case aims to raise awareness among health professionals for the surveillance and early diagnosis of these occupational cancers. Description of the Clinical Case The authors present the case of an 81-year-old man who worked for 56 years as a joiner in the furniture industry. In his occupational history he denied the use of Personal Protective Equipment, namely respiratory protection. In a surveillance consultation with his family physician, he reported epistaxis and occasional nasal obstruction of the right nostril with an evolution of about three months. During the evaluation, a neoformative lesion was diagnosed in the right nasal fossa and the patient was immediately referred to Otorhinolaryngology consultation. A biopsy of the lesion revealed “morphological aspects of intestinal adenocarcinoma”. After evaluation in group consultation, he was proposed for endoscopic sinus surgery and adjuvant radiotherapy. Discussion/Conclusion Occupational exposure to wood dust should lower the physician’s threshold of suspicion for symptoms suggestive of occupational cancer. The long latency period for the development of adenocarcinoma and the higher survival of people treated in the early stages of the disease make periodic medical surveillance in the early detection of nasal adenocarcinoma necessary. Keywords: Nasosinusal Adenocarcinoma, Wood Dust, Occupational Disease, Ocupational Medicine, General and Family Medicine.

The correlation between metabolic parameters in (18)F-FDG PET-CT and solid and micropapillary histological subtypes in lung adenocarcinoma

Objective: Solid and micropapillary pattern are highly invasive histologic subtypes in lung adenocarcinoma and are associated with poor prognosis while the biopsy sample is not enough for the accurate histological diagnosis. This study aims to assess the correlation and predictive efficacy between metabolic parameters in (18)F-fluorodeoxy glucose positron emission tomography/computed tomography ((18)F-FDG PET-CT), including the maximum SUV (SUV(max)), metabolic tumor volume (MTV), total lesion glycolysis (TLG) and solid and micropapillary histological subtypes in lung adenocarcinoma. Methods: A total of 145 resected lung adenocarcinomas were included. The clinical data and preoperative (18)F-FDG PET-CT data were retrospectively analyzed. Mann-Whitney U test was used for the comparison of the metabolic parameters between solid and micropapillary subtype group and other subtypes group. Receiver operating characteristic (ROC) curve and areas under curve (AUC) were used for evaluating the prediction efficacy of metabolic parameters for solid or micropapillary patterns. Univariate and multivariate analyses were conducted to determine the prediction factors of the presence of solid or micropapillary subtypes. Results: Median SUV(max) and TLG in solid and papillary predominant subtypes group (15.07 and 34.98, respectively) were significantly higher than those in other subtypes predominant group (6.03 and 10.16, respectively, P<0.05). ROC curve revealed that SUV(max) and TLG had good efficacy for prediction of solid and micropapillary predominant subtypes [AUC=0.811(95% CI: 0.715~0.907) and 0.725(95% CI: 0.610~0.840), P<0.05]. Median SUV(max) and TLG in lung adenocarcinoma with the solid or micropapillary patterns (11.58 and 22.81, respectively) were significantly higher than those in tumors without solid and micropapillary patterns (4.27 and 6.33, respectively, P<0.05). ROC curve revealed that SUV(max) and TLG had good efficacy for predicting the presence of solid or micropapillary patterns [AUC=0.757(95% CI: 0.679~0.834) and 0.681(95% CI: 0.595~0.768), P<0.005]. Multivariate logistic analysis showed that the clinical stage (Stage Ⅲ-Ⅳ), SUV(max) ≥10.27 and TLG≥7.12 were the independent predictive factors of the presence of solid or micropapillary patterns (P<0.05). Conclusions: Preoperative SUV(max) and TLG of lung adenocarcinoma have good prediction efficacy for the presence of solid or micropapillary patterns, especially for the solid and micropapillary predominant subtypes and are independent factors of the presence of solid or micropapillary patterns.

Diverse contributions of the visceral fat area to the etiology of two distinct subtypes of esophago-gastric junctional adenocarcinoma

Background There are two distinct etiologies of esophago-gastric junctional adenocarcinomas (EGJACs): one associated with extensive gastric mucosal atrophy (GA), resembling non-cardiac gastric cancers; and the other related to gastro-esophageal reflux disease, resembling esophageal adenocarcinoma. In this study, we investigated the associations between the visceral fat area (VFA) and EGJACs separately in the two subtypes of EGJACs, depending on the extent of background GA. Methods Sixty-four consecutive patients with EGJACs (Siewert type 2) were enrolled from a population-based database in Akita Prefecture, Japan, between 2014 and 2019. Two age- and sex-matched healthy controls were randomly assigned to each EGJAC case. The extents of GA were evaluated endoscopically, and the VFA values were measured based on computed tomography images. Logistic regression analyses were performed to investigate the associations between EGJACs and the VFA. Results Study subjects were classified into 2 subgroups depending on the extent of endoscopic GA: 29 (45.3%) without and 35 (54.7%) with extensive GA. Multivariable regression analyses revealed that a VFA of ≥100 cm2 was significantly associated with EGJACs in subjects without extensive GA [odds ratio (95% confidence interval): 2.65 (1.08–6.54)], while there was no such association in subjects with extensive GA [odds ratio (95% confidence interval): 1.52 (0.60–3.83)]. Conclusions The contribution of the VFA to the etiology of EGJACs seems to differ depending on the extent of background GA, with the VFA more prominently associated with EGJACs in subjects without extensive GA than in those with it, providing further rationale concerning the heterogeneous nature of EGJAC etiology.

Single-cell RNA-seq reveals the genesis and heterogeneity of tumor microenvironment in pancreatic undifferentiated carcinoma with osteoclast-like giant-cells

BackgroundUndifferentiated carcinoma with osteoclast-like giant cells (OGCs) of pancreas (UCOGCP) is a rare subtype of pancreatic ductal adenocarcinoma (PDAC), which had poorly described histopathological and clinical features.MethodsIn this study, single-cell RNA sequencing (scRNA-seq) was used to profile the distinct tumor microenvironment of UCOGCP using samples obtained from one UCOGCP patient and three PDAC patients. Bioinformatic analysis was carried out and immunohistochemical (IHC) staining was used to support the findings of bioinformatic analysis. After quality control of the raw data, a total of 18,376 cells were obtained from these four samples for subsequent analysis. These cells were divided into ten main cell types following the Seurat analysis pipeline. Among them, the UCOGCP sample displayed distinct distribution patterns from the rest samples in the epithelial cell, myeloid cell, fibroblast, and endothelial cell clusters. Further analysis supported that the OGCs were generated from stem-cell-like mesenchymal epithelial cells (SMECs).ResultsFunctional analysis showed that the OGCs cluster was enriched in antigen presentation, immune response, and stem cell differentiation. Gene markers such as LOX, SPERINE1, CD44, and TGFBI were highly expressed in this SMECs cluster which signified poor prognosis. Interestingly, in myeloid cell, fibroblasts, and endothelial cell clusters, UCOGCP contained higher percentage of these cells and unique subclusters, compared with the rest of PDAC samples.ConclusionsAnalysis of cell communication depicted that CD74 plays important roles in the formation of the microenvironment of UCOGCP. Our findings illustrated the genesis and function of OGCs, and the tumor microenvironment (TME) of UCOGCP, providing insights for prognosis and treatment strategy for this rare type of pancreatic cancer.

Abstract 472: PACpAInt: A deep learning approach to identify molecular subtypes of pancreatic adenocarcinoma on histology slides

Abstract Introduction: Pancreatic adenocarcinoma (PAC) is highly heterogeneous, resulting in overall ineffectiveness of most anti-tumor treatments. Two tumor subtypes (Classical and Basal) and two stromal subtypes (“active” and “inactive”) have been described. The Basal and the active stroma have worse prognosis. These subtypes could also be predictive of the response to different chemotherapies. To date, molecular subtype classification or phenotype quantification can only be defined by RNAseq, a complex technique sensitive to the quantity and quality of samples, requiring a timescale limiting its routine application. We propose a deep learning approach (PACpAInt) to predict molecular subtypes in PAC on routine histological slides. Patients and Methods: 424 digitalized HES slides of 202 resected PAC from 3 centers with clinical and transcriptomic data were used as training cohort. 3 validation cohorts were used (i) 250 resected PAC from a 4th center including 97 cases with an exact HES/RNAseq spatial match and all tumor slides digitalized (n = 891); (ii) 126 resected PAC from the TCGA (HES + RNAseq); (iii) 25 liver biopsies from metastatic PAC (HES + RNAseq). A multi-step deep learning model was developed to recognize tumor tissue, tumor from stroma cells, and then predicts their transcriptomic molecular subtypes, either at the level of an entire slide, or at the tile level (squares of 112 μm) allowing to study intratumor heterogeneity. Results: PACpAInt correctly predicted the tumor subtype at the whole slide level (AUC = 0.86 and 0.81 in 2 validation cohorts) and improved for samples with unambiguous molecular subtype (AUC = 0.91 and 0.88) confirming the limit of a binary approach. Similar results were obtained on liver biopsies (AUC = 0.85 and 0.92 on unambiguous cases). PACpAInt independently predicted progression-free and overall survival (PFS HR=1.37 [1.16 - 1.62] and OS HR=1.27 [1.08 - 1.49]). Analysis of all tumor slides from 77 Classical cases showed that 39% were heterogeneous with a Basal contingent. These cases had shorter PFS (15 vs. 47 months, p= 0.001) and OS (31 vs. 64 months, p= 5e-5).The analysis of intratumoral heterogeneity using PACpAInt predicted the molecular subtype of tumor and stroma cells of each tile within a slide (&amp;gt; 6 million tiles analyzed). 61% of cases had a main subtype either Classical (42%) or Basal (19%). 39% of the cases were ambiguous could be considered either hybrid (10%) with coexistence of Basal and Classical cells, or intermediate (29%) corresponding to homogeneous tumors but of intermediate differentiation. This classification had a strong prognostic impact (OS: 45.1 vs 33.0 vs 23.4 vs 13.6 months, resp. Classical, intermediate, hybrid, Basal; p &amp;lt;e-12). Conclusion: This study provides the first PAC subtyping tool widely usable in clinical practice, opening the possibility of molecular classification useful for routine care and clinical trials. Citation Format: Charlie Saillard, Flore Delecourt, Benoit Schmauch, Olivier Moindrot, Magali Svrcek, Armelle Bardier-Dupas, Jean Francois Emile, Mira Ayadi, Vinciane Rebours, Louis De Mestier, Pascal Hammel, Cindy Neuzillet, Jean Baptiste Bachet, Juan Iovanna, Nelson Dusetti, Yuna Blum, Magali Richard, Yasmina Kermezli, Valerie Paradis, Mikhail Zaslavskiy, Pierre Courtiol, Aurelie Kamoun, Remy Nicolle, Jerome Cros. PACpAInt: A deep learning approach to identify molecular subtypes of pancreatic adenocarcinoma on histology slides [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 472.

Abstract 615: Tim-3 as an immune therapy target, mechanism and action, and prognostic values with its ligands in patient stratification

Abstract BACKGROUND: Immune checkpoint inhibitors (ICIs) have revolutionized the cancer therapy landscape in recent years. Despite the success of the checkpoint blockade strategies targeting cytotoxic T lymphocyte antigen 4 (CTLA-4) and programmed death receptor 1 (PD-1), many cancer patients cannot benefit from these therapies. T cell immunoglobulin and mucin domain 3 (TIM-3) has emerged as one of the next generation ICI targets, with potentially lower toxicity and higher safety compared to CTLA-4 and PD-1 blockades. TIM-3 is widely expressed in different immune lineages playing various roles such as mediating immune tolerance and regulating innate immune response. However, the mechanism of action of TIM-3 inhibition in different malignancies is not completely understood. Whether the expression and genomic status of TIM-3 and its ligands, Ceacam-1, galectin-9, HMGB1 and phosphatidyl serine (PtdSer) are associated with clinical outcome or any indication would be essential for patient selection for TIM-3 targeting therapies. METHODS: Human PD-1/TIM-3 double-knock-in mice (PD-1/TIM-3 dKI HuGEMM™) engrafted with CT26.WT tumor model were used to test human PD-1 antibody (Keytruda) and TIM-3 antibody (MBG453). Immune phenotyping of blood, tumor draining lymph node (TDLN) and spleen tissues were assessed by flow cytometry at different time points after dosing. Cytokine levels in serum were measured by MSD assays at 48 hours post the 3rd dose and at study termination. Patient genomic and clinical data for various cancer types such as colorectal adenocarcinoma and pancreatic adenocarcinoma were collected for prognostic biomarker analysis. RESULTS: In the in vivo efficacy study of single and combination treatment with Keytruda and MBG453, we observed that NK cells were induced by anti-TIM-3 treatment, alone and in combination, in both blood and TDLN. This indicates TIM-3 blockade may lead to NK cell proliferation in the TME to enhance tumor killing. Transcriptomic analysis on thousands of patients from TCGA showed that high expression of TIM-3 was highly associated with MSI-H and MSI/CIMP subtypes of colorectal adenocarcinoma, suggesting the potential of Tim-3 target therapy in combination with PD-1 blockade in colorectal cancers. By survival analysis, we observe that one of the TIM-3 ligands, HMGB1, expression is associated with patient OS and PFS with pancreatic adenocarcinoma, but not in colorectal cancers. Furthermore, TIM-3 expression was associated with many immune cell signatures, including macrophages, dendritic cells, CD8+ memory T cells, CD4+ memory T cells and Tregs in both colorectal and pancreatic adenocarcinoma. CONCLUSIONS: Evaluation in preclinical model demonstrated that TIM-3 blockade may cause NK cell proliferation to enhance anti-tumor immunity. In addition, the expression and genomic alteration of TIM-3 and its ligand have prognostic values for certain cancers. Citation Format: Jia Xue, Yu Zhang, Xianfei He, Henry Q. Li, Sheng Guo. Tim-3 as an immune therapy target, mechanism and action, and prognostic values with its ligands in patient stratification [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 615.

Abstract 3474: Molecular subtypes characterize appendiceal adenocarcinoma genomic evolution and disease behavior

Abstract Appendiceal adenocarcinoma (AC) are rare gastrointestinal tumors that exhibit a heterogeneous spectrum of tumor histology and differentiation patterns. Personalized AC treatments are limited by the lack of robust histopathological or genomic predictors of disease behavior. We utilized the MSK IMPACT sequencing panel to profile genomic signature patterns in somatic mutations, copy number alterations, and germline mutations in a large curated dataset of patients with AC. We evaluated co-occurrence and clonality patterns between frequently altered genes in AC (RAS, GNAS, TP53) to establish five molecular subtypes of mucinous appendiceal adenocarcinoma (MAAP): RAS mutated-only, GNAS mutated, TP53 &amp; KRAS mutated, TP53 mutated-only, and none (all wild-type). In multivariable Cox regression models, patients with RAS mutated-only tumors exhibit a nearly non-lethal disease course compared to other molecular subtypes, including TP53 mutated-only tumors (hazard ratio for death: 75.6, p&amp;lt;0.001). Inclusion of tumor molecular subtype in conventional multivariable models improves model prognostic strength. In addition, MAAP-derived molecular subtypes prognosticate patient survival in a separate cohort of 248 patients with right-sided, mismatch-repair-proficient metastatic colorectal cancer. Molecular characterization of AC also reveals differences in tumor biology and behavior. In addition to an improved prognosis, RAS mutated-only MAAP tumors exhibit significantly lower tumor mutational quantity and aneuploidy compared to other subtypes in multivariable models (p&amp;lt;0.001). Together with clonality patterns, this suggests that RAS mutated-only tumors exhibit a relatively younger molecular age. In a subset of patients with MAAP who underwent cytoreductive surgery, patients with RAS-only tumors demonstrate significantly lower intra-operative assessed peritoneal cancer indices (PCI) compared to patients with other molecular subtypes (p=0.049). Microscopic assessment of surgical samples reveals that RAS mutated-only tumors are significantly less likely (p&amp;lt;0.001) to exhibit destructive metastatic stromal invasion compared to GNAS and TP53 mutated subtypes. Molecular subtype is also a significant independent predictor of both radiographic and biochemical response to first line chemotherapy for patients with AC. Overall, through a comprehensive profiling of the AC mutational landscape we introduce a unique disease entity of RAS-only mutated MAAP that exhibits dramatically low lethality, low peritoneal spread, and decreased tissue invasiveness despite high-risk histological characteristics. The behavior of this clinically-metastatic, but molecularly-young subtype introduces a new characterization of metastatic pathogenesis and risk that may apply to other premalignant and malignant diseases. Citation Format: Michael B. Foote, Henry Walch, Walid Chatila, Efsevia Vakiani, Chris Chandler, Felix Steinrucke, Garrett Nash, Zsofia Stadler, Sebastian Chung, Yelena Kemel, Anna Maio, Margaret Sheehan, Nikolaus Shultz, Luis A. Diaz, Andrea Cercek. Molecular subtypes characterize appendiceal adenocarcinoma genomic evolution and disease behavior [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 3474.

Abstract 1036: Targeting bone morphogenetic protein 6 as a therapeutic target for LKB1-inactivated lung cancer

Abstract Lung cancer is among the most commonly diagnosed cancers and the leading cause of cancer-related death globally, with approximately 85% of all lung cancers having non-small cell lung cancer (NSCLC). The protein kinase LKB1 is the 3rd most frequently mutated gene in lung adenocarcinoma, and serves as a master regulator of cell metabolism and growth. LKB1-inactivating mutations have a significant impact on NSCLC development. Although KRAS mutation is most frequently co-mutated with the tumor suppressor p53, the strongest cooperation was seen with homozygous inactivation of LKB1. Loss of LKB1 on a KRAS-mutant (KL) background leads to increased tumor burden, shortened survival time and increased metastasis compared to loss of TP53 (KP). Furthermore, inactivation or loss of LKB1 correlated with poor prognosis, where tumors are typically aggressive and chemoresistant. To discover therapeutic vulnerabilities for this aggressive genetic subtype of lung adenocarcinoma, we evaluated the contribution of multiple single- and double-genetic alterations (KRAS G12D (K), LKB1 knockdown (L), and p53 knockdown (P)) to 3D invasion phenotypes using immortalized human bronchial epithelial cells (HBEC3-KT) and conducted RNA transcriptome profiling of the invading HBEC3-KT 3D spheroids. We found that bone morphogenetic protein 6 (BMP-6) is upregulated in invasive KL spheroids only compared to K and KP, suggesting that the loss of both KL drives increased BMP6 expression. Consistent with this finding, the iron regulator hepcidin, which is regulated by BMP6 is also upregulated in KL spheroids. Both BMP-6 and hepcidin expression can be repressed by restoring exogenous LKB1 in KL spheroids suggesting that LKB1 loss is at least in part responsible for the overexpression of the BMP6/hepcidin pathway. In addition, inhibition of BMP-6 signaling via BMP type I receptor ALK2 using small molecule inhibitor LDN214117 suppressed of cell invasion in 3D culture and decreased tumor growth in a KL syngeneic mouse model. Collectively, our findings show that upregulation of hepcidin via BMP6 signaling and followed by iron sequestration in tumor cells is part of the metastatic invasion strategy of LKB1 inactivated NSCLC. Therefore, current clinical strategies targeting BMP6 signaling could improve outcomes for LKB1-mutant lung cancer patients. Citation Format: Junghui Koo, Chang-Soo Seong, Bhakti Dwivedi, Carol Tucker-Burden, Adam I. Marcus, Melissa Gilbert-Ross. Targeting bone morphogenetic protein 6 as a therapeutic target for LKB1-inactivated 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 1036.

Abstract 6377: Developing combination therapy with SHP2 inhibition for CIN-type gastroesophageal adenocarcinoma with KRAS amplification

Abstract Recent studies from the cancer genome atlas (TCGA. Nature. 2014) (TCGA. Nature. 2017) and other groups showed that a molecular subtype with chromosomal instability (CIN) is the most common subtype of gastroesophageal adenocarcinoma (GEA) and is characterized by aneuploidy without somatic hypermutation. The oncogene KRAS is frequently amplified in CIN type gastric cancer (14.3%) and esophageal adenocarcinoma (10.4%). SHP2 is a phosphatase which is a part of a machinery activating KRAS from GDP-bound inactive status to GTP-bound active status, and our group previously reported that KRAS-amplified gastric tumors are relatively resistant to MEK inhibition but sensitive to MEK/SHP2 co-inhibition. While the combination of MEK and SHP2 inhibitors showed efficacy in pre-clinical models, the translation of this combination has been challenging, in part due to on-target toxicity from inhibitors of the MAPK pathway (Auliac, et al. Cancers. 2020). Therefore, we sought better combination strategy with SHP2 inhibition, using genome-wide CRISPR screen. We conducted primary CRISPR screening with two GEA cell lines (KE-39 and HUG1-N) and CRISPR-KO lentivirus library (Brunello CRISPR knockout pooled library, 77,741 sgRNAs/19,114 genes, Broad Institute Genomic Perturbation Platform) and identified candidate targets both within the MAPK pathway and among upstream tyrosine kinases that may enhance the efficacy of a SHP2 inhibitor in KRAS-amplified GEA. Prior to detailed analyses of potential hits from the screen, we performed the secondary screen with additional KRAS-amplified and -mutant cell lines (CAT12, YCC-1, and GSU) using a custom CRISPR-Cas9 sgRNA library targeting 509 genes of interest including top hits in each cell line data set, and confirmed that knockout of KRAS upstream and downstream genes have additive cytotoxicity to SHP2 inhibition. Given our focus on finding targets that could be readily translated into therapeutics, we focused our analysis on those of most ready translational relevance and specifically chose ERBBs, FAK, SRC, RAFs, ERK1/2, and CDK4/6 as candidate targets. Further analyses showed the potent cytotoxicity of SHP2 inhibition with a pan-ERBB kinase inhibitior (Afatinib) and with a CDK4/6 inhibitor (Ribociclib), with greater efficacy of this combination in KRAS-amplified tumors compared to KRAS-mutant tumors, both in vitro and in vivo experiments. Overall, these results suggest co-inhibition of SHP2 and upstream/downstream of KRAS as a promising treatment strategy against KRAS-amplified CIN-type GEA. Citation Format: Osamu Kikuchi, Tianxia Li, Jin Zhou, Yichen Wang, Klavdija Bastl, Prafulla C. Gokhale, Aine Knott, Yanxi Zhang, John G. Doench, Zandra Ho, Daniel V. Catenacci, Adam J. Bass. Developing combination therapy with SHP2 inhibition for CIN-type gastroesophageal adenocarcinoma with KRAS amplification [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 6377.

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 2555: Immunophenotyping early stage lung adenocarcinomas (LUAD) by histologic subtype

Abstract The immune microenvironment is thought to influence Lung Adenocarcinoma (LUAD) subtype formation, disease progression, and thus patient outcome. Despite recent advancements in screening, immunotherapy, and targeted therapy, the biology of aggressive LUAD is still poorly understood, and in-depth characterization associated with LUAD histologic subtypes and progression are needed. In this study, we sought to measure the immune environment associated with different LUAD subtypes using Imaging Mass Cytometry (IMC). IMC has emerged as a powerful new tool that enables the multiplex imaging of more than 50 markers simultaneously, quantify multiple protein expressions at a single cell level, and preserve tissue spatial information. We stained a tissue microarray of early stage LUAD patient samples, representing different LUAD subtypes, with a panel of 21 antibodies. These antibodies are designed to phenotype immune cell subsets, as well as using Ki67 to stain for highly proliferative epithelial cells. This will allow us to better understand how different immune cells are interacting with each other, as well as how they interact with highly proliferating epithelial cells. The resulting ablated samples generate images containing antibody intensity and coordinates, which we then perform cell segmentation to generate single cell data. The marker expression is then quantified, and single cell data analyzed using HistoCAT. Cell neighborhood interactions are analyzed based on spatial relationships, and similarly interacting cells are grouped into phenoclusters. Our results suggest that a Ki67 high phenocluster within solid LUAD subtypes have fewer macrophages (CD68, CD163) and T cell populations (CD8, CD4, FOXP3), however, are enriched for plasma B cells (CD20) and immune suppressive populations (PD1, PDL1). In contrast, a Ki67 high cluster within lepidic subtypes are enriched for of macrophage (CD68) and T cell populations (CD8, CD4, FOXP3). Using IMC, we have begun to identify immune subset shifts in LUAD. This early analysis of LUAD using IMC begins to shed light on the immune regulation that may indicate progression and/or guide intervention approaches. Citation Format: Zhanhao Xi, Roxana Pfefferkorn, Eric Burks, Jennifer Beane, Sarah Mazzilli. Immunophenotyping early stage lung adenocarcinomas (LUAD) by histologic subtype [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 2555.

Abstract 2151: Identification and proteogenomic characterization of novel lung adenocarcinoma subtypes with therapeutic relevance

Abstract Lung adenocarcinoma (LUAD) is one of the most common cancer types with various available treatment modalities. However, better biomarkers of response are still needed for further improving precision medicine. Therefore, a robust LUAD subtyping can substantially aid in determining the most effective therapies that target subtype-specific vulnerabilities. In this study, we integrated multiple datasets: (i) the full 509 LUAD patient cohort from The Cancer Genome Atlas (TCGA) project, (ii) cancer vulnerability data in LUAD cell lines from the Broad Institute’s DependencyMap, and (iii) proteomic data from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) LUAD patients. Using these datasets, we identified 5 expression subtypes (S1-S5) with unique proteogenomic and dependency profiles that increased the resolution of previously defined subtypes (Proximal Inflammatory [PI]; Proximal Proliferative [PP]; and Terminal Respiratory Unit [TRU]). S4-associated cell lines exhibited specific vulnerability to CDK6 and CDK6-cyclin D3 complex gene, CCND3. S3 was characterized by dependency on CDK4, immune-related expression patterns, and altered MET signaling. Experimental validation showed that S3-associated cell lines responded to MET inhibitors, which also led to increased PD-L1 expression. Finally, we identified a small set of biomarkers for S3 and S4 that could be used in the clinic to classify patients into our therapeutically relevant subtypes. Overall, our lung adenocarcinoma expression subtypes, especially S3 that represents 20% of LUAD patients and S4 that represents 25% of LUAD patients, and their biomarkers could help identify patients likely to respond to CDK4/6, MET, or PD-L1 inhibitors, potentially improving patient outcome. Citation Format: Whijae Roh, Yifat Geffen, Mendy Miller, Shankara Anand, Jaegil Kim, David Heiman, Matthew Meyerson, Peter Laird, Andrew Cherniack, NCI CCG Tumor Molecular Pathology (TMP) Analysis Working Group, Gad Getz. Identification and proteogenomic characterization of novel lung adenocarcinoma subtypes with therapeutic relevance [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 2151.

The role of histone chaperone spty2d1 in human colorectal cancer

Colorectal cancer (CRC) remains a major public health concern, associated with a high rate of morbidity and mortality. Several factors have been implicated in its occurrence and development, which includes histone chaperones. The role of spty2d1 (spt2)—a novel histone chaperone protein—has rarely been investigated in CRC. Therefore, we demonstrated in this study that spt2 undergoes different genetic alterations in colorectal adenocarcinoma datasets and that it was associated with the proliferation of colon carcinoma. Spt2 silencing can reduce the ability of proliferation and increase the rate of apoptosis of LoVo cells. Regarding the overall survival associated with spt2, only the quartile disease-free survival of colon adenocarcinoma (COAD) was found to be statistically significant, while that of rectum adenocarcinoma (READ) was not. The positive (+++) expression of spt2 was correlated with a deeper invasion depth in colorectal adenocarcinoma, and this effect was more pronounced in COAD. These data collectively suggest that spt2 can influence the progression and prognosis in some subtypes of colorectal adenocarcinoma. Therefore, we propose spt2 as a potential target for application in enhancing the overall therapeutic efficacy in some specific subtypes of colorectal adenocarcinoma.

COUGH, FEVER, AND BILATERAL INFILTRATES ON IMAGING: WHAT CAN IT BE?

TYPE: Case Report TOPIC: Lung Cancer INTRODUCTION: Lepidic-predominant adenocarcinoma (LPA), is a subtype of invasive adenocarcinoma, histologically characterized by bland pneumocytic-type neoplastic cells with growth along with normal structures. Radiologic pattern is variable; most typical appearance being part-solid nodule or mass. However, it can also present as segmental or lobar consolidation, with a multifocal or diffuse pattern. We present a case of LPA which was being treated as recurrent pneumonia due to its clinical and radiologic presentation. CASE PRESENTATION: 67-year-old non-smoker male, without medical comorbidities presented with worsening cough, wheezing, shortness of breath that initially started a year ago. He stated having intermittent episodes of low-grade fever with night sweats. Patient was treated with multiple courses of antibiotics and steroids throughout the year which would provide intermittent symptomatic relief. He denied hemoptysis, leg swelling or any other associated symptoms. Patient used to work in cotton fields and denied having birds or pets. Computed tomographic imaging of chest showed bilateral infiltrates with air bronchograms, consolidations with minimal ground glass opacities and nodular infiltrates with some showing evidence of cavitation. Laboratory data and bronchoscopic cultures were non-diagnostic. Open lung biopsy revealed lepidic-predominant adenocarcinoma. DISCUSSION: Diagnosing LPA might be challenging due to its varied and non-specific symptomatology. Suspicion should be high in patients with recurrent, ongoing symptoms that fail to resolve with multiple courses of antibiotics and steroids. Timely diagnosis is the key to successful therapy and thereby, early biopsy should be considered. CONCLUSIONS: LPA may mimic pneumonia radiologically and symptomatically. Early biopsy is the key to establish timely diagnosis in such patients. DISCLOSURE: Nothing to declare. KEYWORD: Lepidic-predominant adenocarcinoma

The pattern of KRAS mutations in non-small cell lung cancer (NSCLC): A retrospective study from south-eastern Georgia.

e15110 Background: Carcinogenic Kirsten rat sarcoma viral oncogene homolog (KRAS) mutation is a common oncogenic mutation found in lung cancer. It is a gain-of-function mutation that is the most commonly mutated oncogene in NSCLC; occurs in about 30% of all lung adenocarcinomas. A lot of progress has been made in targeted therapies against other oncogenic drivers, such as EGFR, HER2, MET, BRAF mutations. However, KRAS mutant lung cancer is still very difficult to manage and options are limited. Most recently, K-ras G12C has a newly approved novel targeted therapy. Different KRAS mutations may also represent different outcomes. Multiple studies have been looking into mutant KRAS and investigating it in the clinical relevance in lung cancer. Here we characterize a cohort of KRAS subtypes in all tumor types of lung cancer from south-eastern Georgia. Methods: This is a retrospective study that evaluated patients with K-ras mutant lung cancer from Augusta, Georgia geographical area. Samples were obtained from May 15th, 2015 to January 4th, 2022 and patients with KRAS mutant lung cancers were identified via Guardant platform. Results: In our cohort of patients, a total of 622 patients were evaluated in which 531 patients had a lung cancer diagnoses. Of those 531 patients, 383 had lung adenocarcinoma, 109 lung squamous cell, 34 NSCLC, 3 small cell, 1 lung carcinoid, and 1 large cell lung carcinoma. Of the 531 lung cancer patients, 14 (2.6%) patients expressed KRAS mutation with 12 (3.1%) patients expressing KRAS with lung adenocarcinoma. NRAS was expressed separately in 2 patients and HRAS was expressed separately in 1 patient. Our cohort of patients with K-ras mutant NSCLC had TP53 co-mutation in 78 (14%), MSI-High mutation in 60 (11%) patients, and EGFR mutation in 23 (4.3%) patients. The most common KRAS subtype in lung adenocarcinoma was G12V (42%), G12C (42%), and Y64D (8.3%). Two patients were unable to identify the type of the K-ras mutation. In addition, 92% of the carriers for KRAS mutation in lung adenocarcinoma were males. Its been noted that G12C mutation is the most common; however, in south-east Georgia, G12V is as common as G12C. Conclusions: KRAS mutation subtypes have distinct genomic landscape which requires further assessment to guide future therapeutic development. In the geographical area of Augusta, Georgia, KRAS subtype G12V is as common as G12C.

Combined Radiomic and Visual Assessment for Improved Detection of Lung Adenocarcinoma Invasiveness on Computed Tomography Scans: A Multi-Institutional Study

ObjectiveThe timing and nature of surgical intervention for semisolid abnormalities are dependent upon distinguishing between adenocarcinoma-in-situ (AIS), minimally invasive adenocarcinoma (MIA), and invasive adenocarcinoma (INV). We sought to develop and evaluate a quantitative imaging method to determine invasiveness of small, ground-glass lesions on computed tomography (CT) chest scans.MethodsThe study comprised 268 patients from 4 institutions with resected (<=3 cm) semisolid lesions with confirmed histopathological diagnosis of MIA/AIS or INV. A total of 248 radiomic texture features from within the tumor nodule (intratumoral) and adjacent to the nodule (peritumoral) were extracted from manually annotated lung nodules of chest CT scans. The datasets were randomly divided, with 40% of patients used for training and 60% used for testing the machine classifier (Training DTrain, N=106; Testing, DTest, N=162).ResultsThe top five radiomic stable features included four intratumoral (Laws and Haralick feature families) and one peritumoral feature within 3 to 6 mm of the nodule (CoLlAGe feature family), which successfully differentiated INV from MIA/AIS nodules with an AUC of 0.917 [0.867-0.967] on DTrain and 0.863 [0.79-0.931] on DTest. The radiomics model successfully differentiated INV from MIA cases (<1 cm AUC: 0.76 [0.53-0.98], 1-2 cm AUC: 0.92 [0.85-0.98], 2-3 cm AUC: 0.95 [0.88-1]). The final integrated model combining the classifier with the radiologists’ score gave the best AUC on DTest (AUC=0.909, p<0.001).ConclusionsAddition of advanced image analysis via radiomics to the routine visual assessment of CT scans help better differentiate adenocarcinoma subtypes and can aid in clinical decision making. Further prospective validation in this direction is warranted.