Matched Tumor Research Articles

Abstract 5580: Circulating tumor DNA (ctDNA) identifies genomic alterations associated with resistance to Nivolumab in combination with other agents in metastatic castration-resistant prostate cancer from the CheckMate 9KD trial

Abstract Introduction: Metastatic castration-resistant prostate cancer (mCRPC) is characterized by an immunosuppressive tumor microenvironment resulting in resistance to single agent immunotherapy, and several combination strategies are being clinically evaluated to address this resistance. CheckMate 9KD (NCT03338790) was a nonrandomized, open-label, multicohort, phase 2 trial of nivolumab combined with rucaparib, docetaxel, or enzalutamide for mCRPC, which showed encouraging clinical activity for the nivolumab plus docetaxel combination. To identify genetic factors potentially associated with response or resistance in this trial, we conducted a retrospective analysis of the tumor genomic alteration landscape utilizing circulating tumor DNA (ctDNA) from plasma samples. Methods: We performed integrated analyses of sequence and structural alterations identified through comprehensive genomic profiling of cell-free DNA (cfDNA) obtained from plasma at baseline using the GuardantOMNI™ assay (500 genes). The analysis was performed on 253 unique samples across all cohorts for which both clinical and OMNI datasets were available. Variant prevalence in ctDNA was compared to that of matched tumor tissue using the FoundationONE® assay (395 genes). Hazard ratios with corresponding two-sided 95% CI were estimated via unstratified multivariable Cox modeling adjusted by subject age and homologous recombination repair deficiency (HRD) status. Odds ratios with corresponding two-sided 95% CI were estimated via unstratified logistic regression modeling adjusted by subject age and HRD status. Results: Most patients (239/253; 94.5%) were ctDNA(+), with a substantially higher prevalence of most gene variants detected in cfDNA compared to patient-matched tumor tissue. Mutations in the AR, TERT, DNMT3A, HNF1A, and TP53 genes had the highest frequency. Amplifications in a number of genes detected in ctDNA including the androgen receptor (AR), PI3K/Akt pathway regulators (PIK3CA, PIK3CB, PREX2), and epigenetic regulators (DNMT3A, EZH2, KDM6A), were positively associated with poorer clinical outcomes (rPFS and/or OS) in the nivolumab + docetaxel arm. Conclusions: This investigation highlights the utility of liquid biopsy for evaluating tumor genomic alterations in late-stage mCRPC trials and provides translational insights into potential resistance mechanisms to inform patient selection and combination strategies for future clinical development. Acknowledgements: We acknowledge the patients and families, clinical study teams, and investigators who made the CheckMate 9KD study possible, and acknowledge Guardant Health and Foundation Medicine for the collaborative development and validation of the GuardantOMNI™ and FoundationOne®CDx assays, respectively. Citation Format: Yu Wang, Jun Li, Jonathan Baden, Saurabh Gupta, Justin M. David. Circulating tumor DNA (ctDNA) identifies genomic alterations associated with resistance to Nivolumab in combination with other agents in metastatic castration-resistant prostate cancer from the CheckMate 9KD trial. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5580.

Abstract 6667: Pan-cancer assessment of tumour and peripheral T-cell receptor repertoire dynamics in patients treated with immune checkpoint inhibitors

Abstract Introduction: Clinical benefit from Immune Checkpoint Blockade (ICB) is a function of local T-cell specificity for tumor-associated antigens. However, overcoming local T-cell dysfunction necessitates systemic immunity engagement. Therefore, studying the dynamics of both local and peripheral T-cell repertoires in response to ICB is required to identify features of T-cell repertoires associated with pathological response. Methods: We conducted TCRβ-sequencing on tumor-residing T-cells (n=59), Peripheral Blood Mononuclear Cells (PBMCs) (n=306) and cell-free DNA (cfDNA) (n=73) from pre- and multiple on-ICB timepoints collected from patients enrolled in the pan-cancer INvestigator-initiated Phase II Study of Pembrolizumab Immunological Response Evaluation (INSPIRE; NCT02644369) trial. To assess specificity-agnostic shifts in TCR repertoires, we first compared TCR diversity and clonal expansion in longitudinal tumor and PBMC samples. Then, to temporally track the specificity-associated features of local and systemic TCR repertoires, we leveraged a Graph Neural Network (GNN) model that took in unique TCRβ chains as nodes. The connectivity between the nodes was defined by multi-relational edges that represented VJ-gene usage and GLIPHII-identified (Grouping Lymphocyte Interactions by Paratope Hotspots) specificities derived from a compendium of TCR sequences with empirically confirmed specificities. Results: While absolute diversity and clonal expansion values in baseline tumor (n=33) were not associated with response to ICB, changes in these values were informative between pre- and on-ICB tumors. All patients (n=4) with low baseline tumor TCR diversity and lack of clonotypic re-structuring in tumor TCR repertoire on-ICB had either progressive or short-term stable disease. Furthermore, pairwise comparison of pre- and on-ICB tumors for each patient (n=17) revealed that all the patients, irrespective of their pathological response, experienced emergence of new TCR clonotypes (i.e., clonal replacement) in response to ICB, suggesting only a minority of these TCRs might consist of tumor-associated clonotypes. Patients with clinical benefit also had higher degree of GLIPHII-identified clustering at baseline tumor, highlighting the role of both specificity-agnostic and specificity-centric TCR analysis in determining the response to ICB. Analysis of TCR sequences in blood plasma found cfDNA contains a small number of TCR sequences (median 32, range 12-89) enriched for TCRs found in matched tumor tissues, suggesting that cfDNA TCR repertoire may provide an indirect measurement of tumor-residing T-cells. Conclusions: TCR diversity and functional clonal annotation are emerging biomarkers of ICB response and cfDNA TCR repertoire can potentially be exploited for clinical diagnostics and monitoring. Citation Format: Shirin Soleimani, Ben X. Wang, Stephanie Pedersen, Jenna Eagles, Jacob Brick, Marcus O. Butler, Scott V. Bratman, Lillian L. Siu, Pamela S. Ohashi, Trevor J. Pugh. Pan-cancer assessment of tumour and peripheral T-cell receptor repertoire dynamics in patients treated with immune checkpoint inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6667.

Abstract 2374: Squamous cell carcinoma antigen regulates macrophage polarization, contributing to inhibition of T cell activity in cervical cancer chemo-radiotherapy

Abstract Chemoradiation therapy (CRT) is the standard treatment for locally advanced cervical cancer. Anti-tumor T cell response is critical for immunogenic cell death and tumor regression enabled by CRT. Squamous cell carcinoma antigen (SCCA) is highly expressed in cervical tumors and passively released from tumor cells. Patients with elevated serum SCCA often showed radioresistance and recurrence. Despite its prognostic value, little is known about the function of extracellular SCCA. We analyzed SCCA-associated immune landscape using RNAseq from 20 cervical matched tumor biopsy pairs collected prior to (pre-) and 3 weeks into (mid-) CRT. Patients with low pretreatment SCCA (<6 ng/ml, SCCA/L) and high SCCA (≥6ng/ml, SCCA/H) showed decreased CD4/CD8 T cells at mid-CRT, with a more significant decrease in SCCA/H patients. This corresponded to significantly reduced expression of T-cell trafficking chemokine CXCL9/10 during CRT, particularly in SCCA/H patients. Interestingly, granzyme B (GZMB) and interferon-γ (IFNγ), associated with T-cell cytotoxicity, were increased in 6 of the 10 SCCA/L patients, compared to 1 and 2 of the 10 SCCA/H patients with increased GZMB and IFNγ respectively. Another RNAseq cohort of 66 pre-CRT tumor biopsies also showed significantly higher LAG3 and CTLA4 expression in SCCA/H than SCCA/L patients. In vitro stimulation of human PBMC with CD3/28 antibody in the presence of SCCA1 protein resulted in inhibition of T cell proliferation and decreased cytotoxicity. However, when SCCA1 was incubated with purified CD3 T cells, no inhibition in T cell activity was observed, suggesting the involvement of myeloid cells in SCCA1 mediated T cell activity. To investigate the effect of SCCA1 on myeloid cells, we isolated human CD14+ monocytes, incubated with SCCA1, and found improved survival of CD14+ HLADRlo/neg monocytes. THP1 monocytes, possessed polarizing ability, were differentiated into M1/M2 macrophage with the supplement of SCCA1 during the polarization. The result showed that SCCA1 promoted M2 macrophage phenotypes, including increased M2 marker (CD209), PD-L1 expression, M2-associated cytokines (IL10, CCL18), and M2 polarizing signaling (STAT3 phosphorylation and Myc expression). Macrophages isolated from murine tumors with high SCCA1 expression demonstrated increased suppression on T cell activity in co-culture functional assays. Furthermore, tissue microarray from cervical cancer patients showed that high SCCA was associated with increased infiltration of CD11b+ myeloid cells and CD68+ macrophages in tumors. Overall, we concluded that SCCA promoted M2 polarization and macrophage infiltration, which may contribute to T cell exhaustion, leading to poor survival. Thus, therapeutic targeting of extracellular SCCA should be considered to improve treatment outcomes. Citation Format: Liyun Chen, Victoria Shi, Matthew Inkman, Jin Zhang, Pippa Cosper, Julie K. Schwarz, Stephanie Markovina. Squamous cell carcinoma antigen regulates macrophage polarization, contributing to inhibition of T cell activity in cervical cancer chemo-radiotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2374.

Abstract 3134: Calling somatic variants from UG100 data using deep learning

Abstract UG100 is a novel next-generation sequencing platform that combines high throughput with significantly lower sequencing cost. Previous studies have demonstrated broad applicability of UG100 data for whole-genome germline variant calling, single cell transcriptomics and whole-genome methylation analysis, as well as for recalling cancer signatures from cfDNA at very low fraction of circulating tumor DNA. Somatic variant calling is a natural application for this platform as it can benefit from lower sequencing cost to enable deeper sequencing coverage. Here, we describe the implementation and evaluation of a somatic calling pipeline from UG100 whole genome sequence data. Since deep-learning-based variant calling methods currently outperform statistical variant calling methods for germline variant calling on UG100 data, we cast somatic variant calling as a classification problem. Specifically, we trained a classifier to distinguish if a candidate at a particular location is a somatic variant or a sequencing error. We used a version of DeepVariant optimized for UG100 data to train the deep-learning classifier in three scenarios: tumor only, tumor with an unmatched background sample and matched tumor-normal samples. The labeled truth set for training was generated by mixing whole genome sequenced samples from the genome-in-a-bottle project in a wide range of proportions (0-100% mixing ratio) to simulate various allele frequencies, with an average genome coverage of 100x. The tumor/normal model was the best-performing of the three models with a recall of >98% for SNPs and 90% for Indels at allele fraction > 10%. Notably, the model also showed high specificity as well with 16 false positive SNPs and 19 false positive indels at AF over 10% called on the chromosome that was not part of the training (chr20). We then applied the model for calling from the WGS data on three well characterized pairs of matched tumor and normal cell lines: HCC1143, COLO829 and HCC1395. We evaluated the performance on the pre-defined UG-HCR (Ultima Genomics - High Confidence Region), which includes 95% of the human genome. DeepVariant models performed very well on calling SNPs (>92% recall at allele frequencies above 10%) and indels (>90% recall). The calls were also highly specific, with less than 1/Mb variants absent in the ground truth across the UG-HCR. Lastly, we applied the models to 8 unpaired cell lines with known driver mutations and observed that we call 34/34 driver mutations of length <=20 bp that appear in COSMIC (100% recall). We expect the UG100 sequencer to become an important tool for somatic genome analysis and to enable deep whole-genome sequencing to become a routine assay in clinical oncology. Citation Format: Maya Levy, Doron Shem-Tov, Hila Benjamin, Sima Benjamin, Ilya Soifer, Shlomit Gilad, Danit Lebanony, Nika Iremadze, Eti Meiri, Doron Lipson, Omer Barad. Calling somatic variants from UG100 data using deep learning [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3134.

Abstract 6663: Immunostimulatory gene therapy targeting CD40/4-1BB in combination with chemotherapy induces an inflammatory gene profile in tumors from patients with advanced disease

Abstract In the LOKON002 phase I/II clinical trial (NCT03225989), therapy with LOAd703 (delolimogene mupadenorepvec) is investigated in combination with gemcitabine-based chemotherapy in patients with advanced cancer. LOAd703 is an immunostimulatory gene therapy utilizing an oncolytic adenovirus that is engineered to express two transgenes (trimerized membrane-bound CD40L (TMZ-CD40L) and 4-1BBL), which are key players in the induction of an anti-tumor immune response. Herein, we present the preliminary immunological evaluation of the first 27 patients enrolled in the trial. The primary tumor was pancreatic cancer (n=16), colorectal cancer (n=5), ovarian cancer (n=3) or biliary cancer (n=3). Patients received a maximum of eight intratumoral LOAd703 treatments, given biweekly, and chemotherapy was administered at the same time according to standard protocol. Matched tumor biopsies from the injected tumor lesion were taken at baseline and after six LOAd703 treatments, and analyzed for gene expression with nCounter® PanCancer Immune Profiling Panel from NanoString (n=12; 7 patients analyzed so far). Blood samples were collected for isolation of serum samples and peripheral blood mononuclear cells, and these were analyzed with multiplex assays (Meso Scale Diagnostics) (n=15) and flow cytometry (n=27), respectively. Preliminary results indicate that after treatment, most tumors displayed a strong inflammatory profile with an upregulation of gene profiles, which have been shown to predict responses to immune checkpoint inhibitor therapy (T cell inflamed profile (Ayers et al.) & T effector and IFNγ associated profile (Fehrenbacher et al.)). We also noted an upregulation of genes connected to dendritic cell activation and antigen presentation (MHC class I and II, CD80, CD86, TAP1/2), as well as adenoviral-response genes. Moreover, we observed systemic treatment effects after three LOAd703 treatments, as shown by an increase in serum levels of pro-inflammatory cytokines and chemokines (IFNγ, IL-15, CXCL10, CCL2, IL-8, IL-6), as well as an increased percentage of CD8+ effector memory T cells (CD45RA-CCR7-) and PD-1+ CD8+ T cells in the blood. The fractions of natural killer (NK) cells (CD14-CD3-CD56+CD16+) and M2-like macrophages (CD11b+CD163+) were reduced in the blood at that time point. In conclusion, LOAd703 therapy in combination with chemotherapy generated an inflamed tumor microenvironment in tumors that are normally seen as immunologically “cold”. Hence, LOAd703 may be able to prime tumors for immune checkpoint inhibitors or other immunotherapies, such as adoptive T or NK cell transfer. Citation Format: Jessica Wenthe, Emma Eriksson, Sedigheh Naseri, Linda Sandin, Amanda Hahn, Sandra Irenaeus, Anders Sundin, Justyna Leja-Jarblad, Gustav Ullenhag, Tanja Lövgren, Angelica Loskog. Immunostimulatory gene therapy targeting CD40/4-1BB in combination with chemotherapy induces an inflammatory gene profile in tumors from patients with advanced disease [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6663.

Abstract 6545: Investigating secondary findings in a pediatric cancer cohort: preliminary findings

Abstract Purpose: An expected outcome following germline genome sequencing in oncology is the discovery of ‘secondary findings’ (SFs). SFs comprise pathogenic(P)/likely P (LP) germline variants in cancer genes not typically associated with the presenting cancer, in addition to germline variants of uncertain significance (VUS) to the patient’s cancer. Due to the rarity of childhood cancers and a dearth of studies analyzing SFs, many pediatric SFs are categorized as VUS without clinical interpretation. Interpreting SFs poses significant challenges: VUSs and other SFs are frequently not included in clinical molecular reports, and even when reported (often through research), their clinical utility and long-term impact on patient health are unclear. However, we know VUSs can have clinical importance because some VUSs, when investigated thoroughly, have been reclassified as pathogenic predictors of significant health conditions in children. We hypothesize that an in-depth characterization of the landscape of germline SFs/VUSs across a diverse pediatric cancer cohort will reveal new roles of these genes and mutations in pediatric cancers. Methods: To explore germline SFs in pediatric cancer patients, we analyzed germline whole-genome sequencing (WGS) data for patients with rare, relapsed, refractory, and metastatic childhood cancers enrolled in the SickKids Cancer Sequencing Program (KiCS). We developed a custom analysis pipeline to identify germline single-nucleotide variants and indels deemed SFs, auto-classify their pathogenicity (ex. P, LP, or VUS) using CharGer, filter for PanCanAtlas-indicated cancer predisposition genes, and sort the remaining variants by cancer and non-cancer associations. Results: The KiCS cohort (n = 511) encompassed over 133 different tumor types; the median age of participants was 14 years (SD = 10.27) and 55% of patients were male. Ongoing work in our lab will catalogue the frequency and distribution of SFs in KiCS and analyze germline variants by subgroup (gene, tumor subtype, stage, demographics, gene function). We will also compare SF prevalence in KiCS to the general population using the gnomAD dataset. Results from preliminary analyses of this cohort will be presented. Significance: SFs/VUSs are under-utilized in cancer management. This work advances the holistic understanding of germline genomics in pediatric oncology and the roles of SFs in disease. Future studies will evaluate SFs by patient ancestry and validate cancer associations through the evaluation of allelic imbalance/loss of heterozygosity in matched tumor genomes. Citation Format: Safa Majeed, Stephenie Prokopec, Brianne Laverty, Vallijah Subasri, Michael Taylor, Yvonne Bombard, Trevor Pugh, Adam Shlien, Anita Villani, David Malkin. Investigating secondary findings in a pediatric cancer cohort: preliminary findings. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6545.

PD25-07 PROTEOMIC PROFILING OF MUSCLE INVASIVE BLADDER CANCER TREATED WITH NEOADJUVANT CHEMOTHERAPY REVEALS UNIQUE BIOLOGIC CLUSTERS WITH CLINICAL RELEVANCE

You have accessJournal of UrologyCME1 Apr 2023PD25-07 PROTEOMIC PROFILING OF MUSCLE INVASIVE BLADDER CANCER TREATED WITH NEOADJUVANT CHEMOTHERAPY REVEALS UNIQUE BIOLOGIC CLUSTERS WITH CLINICAL RELEVANCE Alberto Contreras-Sanz, Moritz J. Reike, Gian L. Negri, Htoo Zarni Oo, Sandra Spencer Miko, Karina Nielsen, Morgan E. Roberts, Joshua Scurll, Kenichiro Ikeda, Gang Wang, Roland Seiler, Gregg B. Morin, and Peter C. Black Alberto Contreras-SanzAlberto Contreras-Sanz More articles by this author , Moritz J. ReikeMoritz J. Reike More articles by this author , Gian L. NegriGian L. Negri More articles by this author , Htoo Zarni OoHtoo Zarni Oo More articles by this author , Sandra Spencer MikoSandra Spencer Miko More articles by this author , Karina NielsenKarina Nielsen More articles by this author , Morgan E. RobertsMorgan E. Roberts More articles by this author , Joshua ScurllJoshua Scurll More articles by this author , Kenichiro IkedaKenichiro Ikeda More articles by this author , Gang WangGang Wang More articles by this author , Roland SeilerRoland Seiler More articles by this author , Gregg B. MorinGregg B. Morin More articles by this author , and Peter C. BlackPeter C. Black More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000003303.07AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: Neoadjuvant chemotherapy (NAC) followed by radical cystectomy (RC) is recommended for muscle invasive bladder cancer (MIBC). However, only ∼40% of patients show an objective response. While DNA alterations and RNA classifiers may predict response to NAC in retrospective studies, the proteome has not been evaluated in this context. Here we profile the MIBC proteome in a NAC-treated cohort to identify markers of response and to elucidate mechanisms of resistance to NAC. METHODS: Pre-NAC tissue was included from 107 MIBC patients who received NAC followed by RC. Residual tumor (≥ypT1N0-3M0-1) in the RC specimen was present in 62% of patients after NAC, and was profiled for 55 of those patients (51%). Multiregional sampling was conducted in 37/107 pre-NAC and 15/55 post-NAC samples. Benign ureter was used as control. SP3-Clinical Tissue Proteomics (SP3-CTP) and bioinformatic analysis using formalin-fixed paraffin-embedded tissue (FFPE) were performed. Immunohistochemistry (IHC) validation was conducted on matched tissues. RESULTS: We quantified 9769 proteins across all samples. Unsupervised clustering of pre NAC tissue established 4 clusters based on biology and survival outcomes, but no difference in response by pathologic stage. Clusters were confirmed by IHC, and consisted of: Cluster 1 (CC1), with high metabolic activity and a luminal profile; Cluster 2 (CC2) with high nuclear activity; Cluster 3 (CC3) with high immune infiltration and basal profile; and Cluster (CC4) with high immune infiltration and stromal signature. CC3 showed worse survival outcomes (p<0.01). Multivariable analysis identified novel favorable (MAPK9 and MTIF3) and unfavorable (DVL2 and NES) biomarkers. Matched analysis of pre- and post-NAC tissue showed markers (AZGP1 and ORM1) and pathways indicative of NAC resistance. In post-NAC (i.e. resistant) tumors we identified 2 clusters: Post-NAC Cluster 1 was enriched for nuclear processes and had worse outcomes, whereas Post-NAC Cluster 2 was enriched for immune pathways. Multiregional analysis of pre- and post-NAC matched tumors revealed clonal heterogeneity suggestive of important chemoresistance mechanisms. CONCLUSIONS: Here we describe 4 pre-NAC and 2 post-NAC proteomic clusters with distinct biology and survival outcomes, alongside novel prognostic biomarkers. Future work includes IHC validation of clusters in larger independent MIBC cohorts. A non-NAC cohort using pre-RC biopsy tissue will be used to confirm the prognostic vs. predictive relevance of these findings. Source of Funding: Bladder Cancer Canada, Deutsche Forschungsgemeinschaft © 2023 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 209Issue Supplement 4April 2023Page: e731 Advertisement Copyright & Permissions© 2023 by American Urological Association Education and Research, Inc.MetricsAuthor Information Alberto Contreras-Sanz More articles by this author Moritz J. Reike More articles by this author Gian L. Negri More articles by this author Htoo Zarni Oo More articles by this author Sandra Spencer Miko More articles by this author Karina Nielsen More articles by this author Morgan E. Roberts More articles by this author Joshua Scurll More articles by this author Kenichiro Ikeda More articles by this author Gang Wang More articles by this author Roland Seiler More articles by this author Gregg B. Morin More articles by this author Peter C. Black More articles by this author Expand All Advertisement PDF downloadLoading ...

Establishment of papillary thyroid cancer organoid lines from clinical specimens.

Papillary thyroid cancer (PTC) is a common malignancy of the endocrine system, and its morbidity and mortality are increasing year by year. Traditional two-dimensional culture of cell lines lacks tissue structure and is difficult to reflect the heterogeneity of tumors. The construction of mouse models is inefficient and time-consuming, which is difficult to be applied to individualized treatment on a large scale. Clinically relevant models that recapitulate the biology of their corresponding parental tumors are urgently needed. Based on clinical specimens of PTC, we have successfully established patient-derived organoids by exploring and optimizing the organoid culture system. These organoids have been cultured stably for more than 5 passages and successfully cryopreserved and retried. Histopathological and genome analysis revealed a high consistency of the histological architectures as well as mutational landscapes between the matched tumors and organoids. Here, we present a fully detailed method to derive PTC organoids from clinical specimens. Using this approach, we have developed PTC organoid lines from thyroid cancer samples with a success rate of 77.6% (38/49) until now.

Somatic mutation landscape in a cohort of meningiomas that have undergone grade progression

BackgroundA subset of meningiomas progress in histopathological grade but drivers of progression are poorly understood. We aimed to identify somatic mutations and copy number alterations (CNAs) associated with grade progression in a unique matched tumour dataset.MethodsUtilising a prospective database, we identified 10 patients with meningiomas that had undergone grade progression and for whom matched pre- and post-progression tissue (n = 50 samples) was available for targeted next-generation sequencing.ResultsMutations in NF2 were identified in 4/10 patients, of these 94% were non-skull base tumours. In one patient, three different NF2 mutations were identified in four tumours. NF2 mutated tumours showed large-scale CNAs, with highly recurrent losses in 1p, 10, 22q, and frequent CNAs on chromosomes 2, 3 and 4. There was a correlation between grade and CNAs in two patients. Two patients with tumours without detected NF2 mutations showed a combination of loss and high gain on chromosome 17q. Mutations in SETD2, TP53, TERT promoter and NF2 were not uniform across recurrent tumours, however did not correspond with the onset of grade progression.ConclusionMeningiomas that progress in grade generally have a mutational profile already detectable in the pre-progressed tumour, suggesting an aggressive phenotype. CNA profiling shows frequent alterations in NF2 mutated tumours compared to non NF2 mutated tumours. The pattern of CNAs may be associated with grade progression in a subset of cases.

Next-generation sequencing (NGS) profiling of matched tumor and circulating tumor DNA (ctDNA) in head and neck squamous cell carcinoma (HNSCC)

ObjectivesThe aim of this pilot study was to evaluate the presence of somatic mutations in matched tumor and circulating DNA (ctDNA) samples from patients with primary head and neck squamous cell carcinoma (HNSCC) and assess the association of changes in ctDNA levels with survival. Materials and methodsOur study included 62 patients with stage I-IVB HNSCC treated with surgery or radical chemoradiotherapy with curative intent. Plasma samples were obtained at baseline, at the end of treatment (EOT), and at disease progression. Tumor DNA was extracted from plasma (ctDNA) and tumor tissue (tDNA). The Safe Sequencing System was used assess the presence of pathogenic variants in four genes (TP53, CDKN2A, HRAS and PI3KCA) in both ctDNA and tDNA. ResultsForty-five patients had available tissue and plasma samples. Concordance of genotyping results between tDNA and ctDNA at baseline was 53.3%. TP53 mutations were most commonly identified at baseline in both ctDNA (32.6%) and tDNA (40%). The presence of mutations in this restricted set of 4 genes in tissue samples at baseline was associated with decreased overall survival (OS) [median 58.3 months for patients with mutations vs. 89 months for patients without mutations, p < 0.013]. Similarly, patients presenting with mutations in ctDNA had shorter OS [median 53.8 vs. 78.6 months, p < 0.037]. CtDNA clearance at EOT did not show any association with PFS or OS. ConclusionsLiquid biopsy enables real-time molecular characterization of HNSCC and might predict survival. Larger studies are needed to validate the utility of ctDNA as a biomarker in HNSCC.

Genomic characteristics and clinical significance of CD56+ circulating tumor cells in small cell lung cancer

Circulating tumor cells (CTC) have been studied in various solid tumors but clinical utility of CTC in small cell lung cancer (SCLC) remains unclear. The aim of the CTC-CPC study was to develop an EpCAM-independent CTC isolation method allowing isolation of a broader range of living CTC from SCLC and decipher their genomic and biological characteristics. CTC-CPC is a monocentric prospective non-interventional study including treatment-naïve newly diagnosed SCLC. CD56+ CTC were isolated from whole blood samples, at diagnosis and relapse after first-line treatment and submitted to whole-exome-sequencing (WES). Phenotypic study confirms tumor lineage and tumorigenic properties of isolated cells for the 4 patients analyzed with WES. WES of CD56+ CTC and matched tumor biopsy reveal genomic alteration frequently impaired in SCLC. At diagnosis CD56+ CTC were characterized by a high mutation load, a distinct mutational profile and a unique genomic signature, compared to match tumors biopsies. In addition to classical pathways altered in SCLC, we found new biological processes specifically affected in CD56+ CTC at diagnosis. High numeration of CD56+ CTC (> 7/ml) at diagnosis was associated with ES-SCLC. Comparing CD56+ CTC isolated at diagnosis and relapse, we identify differentially altered oncogenic pathways (e.g. DLL3 or MAPK pathway). We report a versatile method of CD56+ CTC detection in SCLC. Numeration of CD56+ CTC at diagnosis is correlated with disease extension. Isolated CD56+ CTC are tumorigenic and show a distinct mutational profile. We report a minimal gene set as a unique signature of CD56+ CTC and identify new affected biological pathways enriched in EpCAM-independent isolated CTC in SCLC.

Abstract P6-04-14: Comparison of next-generation sequencing and real-time PCR for PIK3CA testing in hormone receptor-positive/HER2-negative breast cancer on metastatic and matched primary tumor samples

Abstract Introduction: Based on the SOLAR-1 study, the PI3Kα-specific inhibitor alpelisib has been approved in combination with fulvestrant for postmenopausal women, and men, with HR+/HER2-, PIK3CA-mutated, advanced or metastatic breast cancer (BC). Despite PIK3CA mutations occurring in ⁓40% of HR+/HER2- BC, PIK3CA molecular testing is a new task to be carried out in clinical practice. Adopting the most appropriate testing strategy (RT-PCR vs. NGS) on the most appropriate biological sample is of capital significance in oncologic pathology. Here, we sought to assess the concordance rate for PIK3CA molecular analysis between different technical platforms in both metastatic and matched primary tumors. Methods: From our Institutional registry, n=16 HR+/HER2- metastatic BC, which were found to harbor PIK3CA mutations via next-generation sequencing (NGS) assays [custom panel and Oncomine Comprehensive Assay (OCA) v3 (Thermo Fisher Scientific, Waltham, MA, USA)], were selected. In half of the cases (n=8), matched primary tumors were available and were subjected to PIK3CA testing with NGS. The analytical performance between NGS and a semi-closed RT-PCR (EasyPGX®, Diatech Pharmacogenetics, Italy) was assessed in 13/16 (81.3%) metastatic samples for which archival slides and blocks and/or residual extracted DNA were available, and all the primary tumors. Results: Overall, upfront testing of PIK3CA mutational status with NGS detected genetic alterations in exons 7, 9, and 20. A concordance rate of 100.0% was observed between primary and metastatic tumors. On the other hand, the analysis of primary tumors (n=8) and 13/16 (81.3%) metastatic samples with RT-PCR revealed a concordance of 42.9%. Analytical performance comparison showed that the two technologies were concordant in 7/13 metastatic cases (53.8%). In two of the discordant cases (15.4%), RT-PCR did not identify the PIK3CA mutations due to their absence from its reference range. Interestingly, visual inspection of the RT-PCR raw data increased the concordance to 76.9%. In primary tumors, consensus between the two testing methods was observed in 5 (62.5%) cases. Discussion: The concordance rate analysis shows that upfront PIK3CA molecular testing with NGS appears to be more efficacious compared with RT-PCR. Our data suggest that primary tissues reflect the PIK3CA mutational status when tested with NGS. RT-PCR is simpler with a shorter turnaround time, and less expensive than NGS approaches, however, trained personnel are required for accurate results interpretation. In addition, the limited reference range of this testing method should be taken into account for potential false negative results. Conclusion: In terms of PIK3CA molecular testing, NGS should be the preferred method in comparison with RT-PCR. Primary tumors represent a valid biospecimen to be used for this analysis in the absence of the metastatic sample. Citation Format: Konstantinos Venetis, Francesco Pepe, Elham Sajjadi, Giuseppina Bonizzi, Mariia Ivanova, Davide Vacirca, Alessandra Rappa, Massimo Barberis, Giuseppe Viale, Elena Guerini-Rocco, Elisabetta Munzone, Umberto Malapelle, Nicola Fusco. Comparison of next-generation sequencing and real-time PCR for PIK3CA testing in hormone receptor-positive/HER2-negative breast cancer on metastatic and matched primary tumor samples [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P6-04-14.

Abstract PD2-09: Characterization of the lymphovascular invasion microenvironment reveals immune response dichotomy

Abstract Background: Metastasis is the leading cause of cancer related deaths in breast cancer patients. Lymphovascular invasion represents one of the earliest stages of metastasis wherein the cells are introduced to a very different and distinct microenvironment. Methods: We leveraged spatial techniques developed for limited specimens in archival tissue to study patient matched cross-sectional tumor samples from different stages of breast neoplasia including normal breast, ductal carcinoma in situ (DCIS), primary invasive carcinoma (IBC), lymphovascular invasion (LVI) and regional lymph node metastasis. We selected a set of 21 patients with ER+ breast cancer to generate cross-sectional samples of each of these stages, for a total of 331 samples. The areas of LVI were identified by a combination of H&amp;E review and immunohistochemistry for podoplanin. We performed smart-3SEQ for gene expression profiling and light pass whole genome sequencing for DNA copy number alterations. Results: We profiled the spectrum of neoplasia for transcriptome-wide gene expression. Principal component analysis of all 252 DCIS, LVI, IBC, or metastasis samples using the top 500 genes with the highest variance demonstrated that clustering was roughly based on the diagnostic stage (i.e. DCIS, LVI, IBC, or metastasis). Differential gene expression profiling identified thousands of genes increased or decreased in expression across the transitional stages with the largest change in gene expression being the transition from normal breast to DCIS, dominated by gene expression down regulation. We next performed NMF clustering on 62 samples of LVI from 18 cases and identified two patterns of gene expression which define two subgroups. Gene ontology analysis revealed that one cluster was associated with increased proliferation and metabolism, whereas the second cluster was dominated by an immune response. When we analyzed the immune and proliferative LVI subgroups separately, we found that the immune profiles in the patient matched IBC and LVI samples from the LVI Immune cluster were similar, whereas the immune profiles in the patient matched IBC and LVI samples from the Proliferative cluster were significantly different. At the LVI stage, all immune cell populations estimated by CibersortX were decreased in the Proliferative LVI cluster. These changes were validated using immunofluorescence for proliferation (Ki67), T cells (CD3) and macrophages (CD68) on the same samples. Using the LVI centroids, we built a model that could predict the same clusters in the METABRIC IBC. Kaplan-Meier analysis showed a significant difference between groups, with the Proliferative-like IBC group having a worse prognosis than the Immune-like IBC group. Conclusions: We observed a dichotomy at the LVI stage with a more proliferative cluster that may escape the immune response and an immune cluster which has a microenvironment with a similar pattern to its primary IBC. The recognition of two groups of LVI, differing in immune association and proliferation, raises the possibility that the risk of metastasis could be different in these two groups, leading to different biological pathways of progression. Citation Format: Belén Rivero-Gutiérrez, Diego Mallo, Almudena Espín-Pérez, Sujay Vennam, Chunfang Zhu, Sushama Varma, Greg Scott, Joseph Foley, E Shelley Hwang, Carlo Maley, Robert West. Characterization of the lymphovascular invasion microenvironment reveals immune response dichotomy [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD2-09.

Abstract HER2-10: HER2-10 Dynamics of HER2-low expression in triple-negative breast cancer

Abstract Background: With the development of novel antibody drug conjugates (ADC), it is increasingly important to understand the changes that occur in cell-surface targets over time from early-stage to metastatic breast cancer. Discordance in HER2 expression per immunohistochemistry (IHC) has been reported between primary and metastatic tumors in patients (pts) with HER2-negative breast cancer defined per ASCO/CAP guidelines, with both gain and loss of expression described. Representation of HR-negative (TNBC) tumors has been limited in these studies, and HER2 status at multiple time points in TNBC has not been described. Here we report changes in HER2 IHC in patients diagnosed with TNBC, using a collection of matched tumor samples over time. Methods: Pts were identified from two sources: 1) an institutional database including all consecutive pts who underwent surgery for stage I-III breast cancer at Dana-Farber/Brigham Cancer Center between 2015-2018, and 2) a prospective research biopsy protocol for pts with known or suspected metastatic breast cancer. Pts were included in the present analysis if they received neoadjuvant chemotherapy (NAC) for stage I-III TNBC (eTNBC), or if they were diagnosed with any stage TNBC and ultimately developed metastatic TNBC (mTNBC). Clinical pathology records were reviewed for HER2 IHC results of samples collected at: initial diagnosis (DX); residual disease (RD) post-NAC, if applicable; and at recurrence (M). HER2 IHC was classified as HER2-0 if HER2 IHC 0, and HER2-low if 1+ or 2+ (and ISH non-amplified). For matched comparisons, if IHC was performed in more than one DX sample (e.g., breast, node), only the breast was considered; if more than one M sample, only the first M biopsy with available IHC was considered. Results: Among 110 pts in this cohort, 101 were initially diagnosed with eTNBC (79 received NAC; 22 underwent surgery as first intervention) and 9 with de novo mTNBC. Median age was 48.7 years (range 19.8-71.6). Among all pts, a total of 292 samples (136 DX, 53 RD, 103 M) had available HER2 IHC scores. When restricting to one sample per time point, HER2-low prevalence was 49/102 (48.0%) in DX breast tumors, 21/53 (39.6%) in RD, and 13/58 (22.4%) in first M samples (with all remaining samples HER2-0, except one HER2 3+ sample). In eTNBC pts, HER2 IHC scores were available for 50 paired DX and RD, and 48 paired DX and M samples. Among 50 pts with paired DX and RD, HER2 IHC was discordant in 56% (28/50) (Table 1). Of the 21 HER2-0 DX tumors, 23.8% (5/21) became HER2-low at RD. Of the 29 HER2-low DX tumors, 51.7% (15/29) became HER2-0 at RD. Among 48 eTNBC pts who recurred and had paired DX and M samples, HER2 IHC was discordant in 50% (24/48) (Table 1). Change from HER2-0 to low was 12.5% (3/24), and from HER2-low to HER2-0 was 66.7% (16/24). Among 9 de novo mTNBC pts, 5 had HER2 IHC available in paired DX breast and M prior to starting therapy; 3 were concordant (IHC 0, n=2; IHC 1+, n=1), one had IHC 0 in DX breast and IHC 2+ in M (liver), one had IHC 1+ in DX breast and IHC 0 in M (node). Conclusions: HER2 IHC classification was discordant in about half of the TNBC cases we examined, with more frequent rates of conversion from HER2-low to HER2-0 in both paired DX/RD post-NAC, and paired DX/M samples. Additional analyses will be presented exploring HER2 IHC changes among multiple metastases per patient. Genomic and molecular analysis, including whole exome sequencing, RNA sequencing, and methylation profiling, are underway in these samples to further elucidate HER2 evolutionary dynamics. Citation Format: Ana C. Garrido-Castro, Lan D. Ngo, Edward T. Richardson, Allison Frangieh, Ayesha Mohammed-Abreu, Melissa E. Hughes, Jorge Gomez Tejada Zanudo, John Navarro, Paolo Tarantino, Elizabeth A. Mittendorf, Sara Tolaney, Tari King, Eric Winer, Nancy U. Lin, Nikhil Wagle. HER2-10 Dynamics of HER2-low expression in triple-negative breast cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr HER2-10.

Phosphoproteomics Reveals the Wolframin-Calcium Axis as an Important Pathogenic Signaling Node in Primary Aldosteronism.

Aldosterone-producing adenoma (APA) is a benign adrenal tumor with autonomous aldosterone production which causes hypertension and excess cardiovascular risk. Protein phosphorylation regulates aldosterone secretion from adrenal cortical cells, but how signaling networks are remodeled in APA remains unknown. We performed an integrated proteomic and phosphoproteomic profiling of 15 APA and 10 matched nonfunctioning adrenocortical tumors (NFAT) based on the 4-dimensional label-free technique. We further validated our main findings in enlarged APA samples, mice, and adrenocortical cell line. The proteomic and phosphoproteomic profiling of APA and NFAT quantified 5989 proteins and 9011 phosphopeptides. We highlighted differentially expressed and phosphorylated proteins which modulated aldosterone synthesis and secretion from APA. As intracellular calcium is the central signal for aldosterone synthesis, our integrated calcium signaling network implicated wolframin in the control of calcium influx and CYP11B2 (aldosterone synthase) activation in APA (ratio of wolframin expression in APA to NFAT: 6.411, P<0.001). Among 97 APA cases for validation, a higher expression level of wolframin was associated with a higher plasma aldosterone concentration postcaptopril challenge test and a higher systolic blood pressure. In vitro, the secretion of aldosterone was enhanced by wolframin overexpression, while aldosterone secretion in response to potassium or angiotensin II was inhibited by the knockdown of wolframin. Further in vivo and in vitro data demonstrated the wolframin-calcium axis as an important regulator of CYP11B2 expression and aldosterone production. Wolframin is a regulatory protein in aldosterone hypersecretion. Remodeled calcium transportation and mitochondrial function are involved in wolframin-related aldosterone secretion.

Combined low-pass whole genome and targeted sequencing in liquid biopsies for pediatric solid tumors

We designed a liquid biopsy (LB) platform employing low-pass whole genome sequencing (LP-WGS) and targeted sequencing of cell-free (cf) DNA from plasma to detect genome-wide copy number alterations (CNAs) and gene fusions in pediatric solid tumors. A total of 143 plasma samples were analyzed from 19 controls and 73 patients, including 44 bone or soft-tissue sarcomas and 12 renal, 10 germ cell, five hepatic, and two thyroid tumors. cfDNA was isolated from plasma collected at diagnosis, during and after therapy, and/or at relapse. Twenty-six of 37 (70%) patients enrolled at diagnosis without prior therapy (radiation, surgery, or chemotherapy) had circulating tumor DNA (ctDNA), based on the detection of CNAs from LP-WGS, including 18 of 27 (67%) patients with localized disease and eight of 10 (80%) patients with metastatic disease. None of the controls had detectable somatic CNAs. There was a high concordance of CNAs identified by LP-WGS to CNAs detected by chromosomal microarray analysis in the matching tumors. Mutations identified in tumor samples with our next-generation sequencing (NGS) panel, OncoKids®, were also detected by LP-WGS of ctDNA in 14 of 26 plasma samples. Finally, we developed a hybridization-based capture panel to target EWSR1 and FOXO1 fusions from patients with Ewing sarcoma or alveolar rhabdomyosarcoma (ARMS), respectively. Fusions were detected in the plasma from 10 of 12 patients with Ewing sarcoma and in two of two patients with ARMS. Combined, these data demonstrate the clinical applicability of our LB platform to evaluate pediatric patients with a variety of solid tumors.

Impact of Whole Genome Doubling on Detection of Circulating Tumor DNA in Colorectal Cancer

Circulating tumor DNA (ctDNA) is a candidate biomarker of cancer with practice-changing potential in the detection of both early and residual disease. Disease stage and tumor size affect the probability of ctDNA detection, whereas little is known about the influence of other tumor characteristics on ctDNA detection. This study investigates the impact of tumor cell whole-genome doubling (WGD) on the detection of ctDNA in plasma collected preoperatively from newly diagnosed colorectal cancer (CRC) patients. WGD was estimated from copy numbers derived from whole-exome sequencing (WES) data of matched tumor and normal DNA from 833 Danish CRC patients. To explore if tumor WGD status impacts ctDNA detection, we applied tumor-informed ctDNA analysis to preoperative plasma samples from all patients. Patients with WGD+ tumors had 53% increased odds of being ctDNA positive (OR = 1.53, 95%CI: 1.12-2.09). After stratification for UICC stage, the association persisted for Stage I (OR = 2.44, 95%CI: 1.22-5.03) and Stage II (OR = 1.76, 95%CI: 1.11-2.81) but not for Stage III (OR = 0.83, 95%CI: 0.44-1.53) patients. The presence of WGD significantly increases the probability of detecting ctDNA, particularly for early-stage disease. In patients with more advanced disease, the benefit of WGD on ctDNA detection is less pronounced, consistent with increased DNA shedding from these tumors, making ctDNA detection less dependent on the amount of ctDNA released per tumor cell.

Insights into the Peritumoural Brain Zone of Glioblastoma: CDK4 and EXT2 May Be Potential Drivers of Malignancy.

Despite the efforts made in recent decades, glioblastoma is still the deadliest primary brain cancer without cure. The potential role in tumour maintenance and progression of the peritumoural brain zone (PBZ), the apparently normal area surrounding the tumour, has emerged. Little is known about this area due to a lack of common definition and due to difficult sampling related to the functional role of peritumoural healthy brain. The aim of this work was to better characterize the PBZ and to identify genes that may have role in its malignant transformation. Starting from our previous study on the comparison of the genomic profiles of matched tumour core and PBZ biopsies, we selected CDK4 and EXT2 as putative malignant drivers of PBZ. The gene expression analysis confirmed their over-expression in PBZ, similarly to what happens in low-grade glioma and glioblastoma, and CDK4 high levels seem to negatively influence patient overall survival. The prognostic role of CDK4 and EXT2 was further confirmed by analysing the TCGA cohort and bioinformatics prediction on their gene networks and protein-protein interactions. These preliminary data constitute a good premise for future investigations on the possible role of CDK4 and EXT2 in the malignant transformation of PBZ.

Phase II/III study of circulating tumor DNA as a predictive biomarker in adjuvant chemotherapy in patients with stage II colon cancer: NRG-GI005 (COBRA).

TPS259 Background: Detection of circulating tumor DNA (ctDNA) shed into the bloodstream represents a highly specific and sensitive approach for identifying microscopic or residual tumor cells after surgical resection. For patients (pts) with colon cancer (CC), the detection of ctDNA is associated with persistent disease after resection and outperforms traditional clinical and pathological features in prognosticating risk for recurrence. However, for pts with stage II CC, there are currently no validated biomarkers predicting benefit in identifying pts whose residual disease cancer be cleared by adjuvant chemotherapy. We hypothesize that for pts whose stage II colon cancer has been resected and who have no traditional high-risk features, a positive ctDNA status may identify those who will benefit from adjuvant chemotherapy. Methods: In this prospective phase II/III clinical trial, pts (N=1,408) with resected stage II CC without traditional high-risk features and whom the evaluating oncologist deems suitable for active surveillance (i.e., not needing adjuvant chemotherapy) will be randomized 1:1 into 2 arms: standard-of-care/observation (Arm A), or prospective testing for ctDNA (Arm B). Postoperative blood will be analyzed for ctDNA with the Guardant Reveal assay, covering CC-relevant mutations and CC-specific methylation profiling. Pts in Arm B with ctDNA detected will be treated with 6 months of adjuvant (FOLFOX) chemotherapy. For all pts in Arm A, ctDNA status will be analyzed retrospectively at the time of endpoint analysis. The primary endpoints are clearance of ctDNA with adjuvant chemotherapy (phase II) and recurrence-free survival (RFS) for “ctDNA-detected” pts treated with or without adjuvant chemotherapy (phase III). Secondary endpoints will include time-to-event outcomes (OS, RFS, TTR) by ctDNA marker status and treatment, prevalence of detectable ctDNA in stage II CC, and rates of compliance with assigned intervention. Archived normal and matched tumor and blood samples will be collected for exploratory correlative research. Enrollment continues across North America to the 540-patient phase II endpoint. Support: U10CA180868, -180822; UG1CA189867; GuardantHealth. Clinical trial information: NCT04068103 .

Identification of HER2+ malignant cells in gastric tumors from single-cell RNAseq data.

417 Background: Gastric cancer is the 4th leading cause of cancer death worldwide with high incidence in East Asia. Despite recent developments in treatment options, gastric cancer survival rate remains low, partially attribute to tumor heterogeneity. Here we performed a comprehensive single cell analysis of malignant cells from gastric tumor samples. In addition to characterizing heterogenous transcriptional patterns, we developed a framework to identify HER2+ malignant cells, which may complement standard diagnostics for treatment decisions. Methods: Published and in-house generated 10x Genomics single cell RNAseq data in tumor and normal samples from gastric cancer patients were aggregated, including 64 tumor samples and 27 pre-cancerous samples and 12 adjacent normal samples. The R package Seurat (version 4.0) was applied for data QC and downstream analysis. High quality cells were clustered using highly variable genes and cell types were annotated by curated marker genes. To identify malignant epithelial cells, a gastric cancer signature was derived using matched tumor and normal samples from TCGA gastric cancer patients. Gastric tumor samples were also leveraged to develop a HER2 signature and TCGA breast tumor samples were used to validate the signature. HER2+ malignant cells were identified by re-clustering malignant epithelial cells using the HER2 signature. Results: 345,361 high-quality single cells were profiled, representing major cell types within tumor microenvironment. Among 59,861 epithelial cells, 22,770 malignant cells were identified with high expression of a gastric cancer signature. Copy number alterations (aneuploid) were highly enriched in inferred malignant cells compared with non-malignant cells (48.6% vs 1.4%, p&lt;2.2×10-16, Fisher’s exact test). Further clustering analysis identified 10 subclusters with divergent expression of cancer oncogenic pathways, highlighting the vast heterogeneity of tumor origin. A Her2 amplification signature was derived using TCGA gastric cancer cohort (AUC=0.99) and validated in breast cancer cohort (AUC=0.93). Applying this signature to malignant cells, HER2+ cells were identified in a majority of tumors, with various proportions. In an independent data set, the percentage of HER2+ malignant cells is highly concordant with clinical HER2+ status, indicating the potential use of single cell data to supplement HER2+ clinical testing for treatment selection. Conclusions: This meta-analysis of single cell RNAseq data provides a comprehensive snapshot of tumor heterogeneity in gastric cancers, with aberrance in multiple oncogenic pathways observed in patients. The HER2+ cell classifier developed here holds the potential to complement standard clinical testing and enable personalized medicine, warranting further validation.