bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 56: MSK-ACCESS Heme: A cell-free DNA next-generation sequencing assay to identify somatic alterations in patients with lymphoma
Authors: DiNapoli Sara E. , Spence Coleman , Gedvilaite Erika , Bowman Anita , Diosdado Monica , Razumova Anna , Tsui Dana , Salles Gilles A. , Batlevi Connie , von Keudell Gottfried , Ptashkin Ryan , Zehir Ahmet , Berger Michael , Brannon A Rose , Benayed Ryma , Arcila Maria
Published: June 2022

Next-generation sequencing of cell-free DNA (cfDNA) can be used to noninvasively assess and monitor patients with lymphoma. Here, we describe the preliminary validation of MSK-ACCESS Heme (Memorial Sloan Kettering-Analysis of Circulating cfDNA to Examine Somatic Status), a cfDNA assay that employs unique molecular indexing and ultra-deep sequencing to detect somatic alterations in 117 genes related to hematologic malignancies. To our knowledge, this is the first report of a clinical-grade cfDNA assay developed specifically for hematologic malignancies.

Overall assay performance was assessed using 53 validation samples (26 normal samples and 27 cfDNA samples with somatic variants). Initial accuracy studies showed excellent correlation with the reference next-generation sequencing method (MSK-ACCESS Solid), detecting 32/32 (100%) of expected variants with a variant allele frequency over 1%. The limit of detection was assessed using standard samples, with detection of variants down to 0.5% variant allele frequency. Results were highly concordant in both inter- and intra-assay reproducibility studies.

Overall, these data indicate that MSK-ACCESS Heme is a robust cfDNA-based assay that can be used to detect variants at low frequency with high reproducibility. Future work sequencing additional samples will be performed to further assess the performance of the panel.

Citation Format: Sara E. DiNapoli, Coleman Spence, Erika Gedvilaite, Anita Bowman, Monica Diosdado, Anna Razumova, Dana Tsui, Gilles A. Salles, Connie Batlevi, Gottfried von Keudell, Ryan Ptashkin, Ahmet Zehir, Michael Berger, A Rose Brannon, Ryma Benayed, Maria Arcila. MSK-ACCESS Heme: A cell-free DNA next-generation sequencing assay to identify somatic alterations in patients with lymphoma [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 56.
Abstract 5620: CD34+humanized huHSC-NCG mice engrafted with hematological malignancies models for preclinical study of anti-human CD19 therapeutic antibodies
Authors: Yu Weiwei , Ju Cunxiang , Sun Hongyan , Zhang Mingkun , Bao Honghong , Li Shuai , Ju Chao , Zhao Jing , Gao Xiang
Published: June 2022

CD19, has become a vital immune and cellular therapeutic target to treat B-cell malignancies, as anti CD19 antibodies has produced remarkable clinical outcomes. Due to the lack of functional murine T cells, as well as B and NK cells, NCG mice engrafted with CDX or PDX models are well suited for evaluating CAR-T anti-tumor efficacy, but do not meet the needs of evaluating in vivo anti-tumor efficacy of anti-human CD19 bispecific or tri-specific antibodies that require functional human T cells.huHSC-NCG mice were established by the engraftment of CD34+ hematopoietic stem cells (HSC) into irradiated NCG mice. Among multi-lineages of human immune cells, the level of reconstituted human CD3+ T cells gradually increased in huHSC-NCG mice from 10 weeks after engraftment for long-term efficacy evaluation study. Both CD8+ cytotoxic and CD4+ helper T lymophocytes were detected by FACS in blood circulation. In this study, we established mice engrafted with Raji-Luciferase lymphoma and orthotopically engrafted with Nalm6-Luciferase leukemia cells. Both Blinatumomab and tri-specific antibodies displayed a pharmacological effect by reducing the proportion and total counts of B cells in circulation, showed significant tumor growth inhibition and prolonged the survival of xenograft huHSC-NCG mice. Taken together, huHSC-NCG mice is an ideal mouse model for preclinical study of bi-specific or tri-specific T cell engager therapeutic antibodies.

Citation Format: Weiwei Yu, Cunxiang Ju, Hongyan Sun, Mingkun Zhang, Honghong Bao, Shuai Li, Chao Ju, Jing Zhao, Xiang Gao. CD34+humanized huHSC-NCG mice engrafted with hematological malignancies models for preclinical study of anti-human CD19 therapeutic antibodies [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 5620.
Abstract 5626: Acquisition of lymphatic phenotype in bone marrow endothelial progenitors is regulated by immunosuppressive Th2 cytokines
Authors: Gonzalez Maria Espinoza , Volk-Draper Lisa , Bhattarai Nihit , Ran Sophia
Published: June 2022

Introduction: Myeloid-lymphatic endothelial progenitors (M-LECPs) significantly contribute to expansion of tumor lymphatics and metastasis to lymph nodes. Bone marrow (BM) generated M-LECPs are a subset of M2-type of tumor-associated macrophages (TAMs) that heavily infiltrate breast and other human cancers. The M2-type of TAMs is primarily induced by immunosuppressive Th2 cytokines IL-4, IL-13, and IL-10. The goal of this study was to determine whether Th2 factors also promote the lymphatic phenotype in precursors of M-LECPs.

Methods: Mouse BM cells were differentiated into M-LECPs by priming with CSF-1 followed by activation of LPS-TLR4 pathway. Transcripts of IL-4, IL-13, and IL-10 were measured by qPCR, and their proteins secreted into conditioned medium were detected by ELISA. The levels of receptors for Th2 cytokines IL-4, IL-13, and IL-10 as well as for stem cells (CD117, Sca-1), M2-TAMs (CD204, CD206) and lymphatic endothelial cells (Lyve-1, podoplanin, integrin-9a, collectin-12 and stabilin-1) were quantified by qPCR and flow cytometry. Impact of TLR4 induced autocrine IL-10 pathway was determined by analyzing the surface markers and gene profiles of differentiated M-LECPs in the presence of IL-10 blocking or control antibodies. Tumor levels of Th2 cytokines and expression of Th2 receptors in Lyve-1+ progenitors were detected by ELISA and immunofluorescence, respectively.

Results: More than 95% of myeloid precursors treated with CSF-1 and LPS upregulated all three Th2 receptors and IL-10 but not IL-4 or IL-13 ligands. All receptors were functional as indicated by upregulation of M2, immunosuppressive, lymphatic and stem markers in cells co-treated with exogenous Th2 ligands as compared with CSF-1 alone. Blocking autocrine IL-10 significantly suppressed both M2-specific and pro-lymphatic differentiation. Tumor-infiltrating M-LECPs expressed Th2 receptors as well as all corresponding ligands including IL-4 and IL-13 that were absent in the BM cells.

Conclusion: These data present a novel evidence that activation of immunosuppressive Th2 pathways in BM myeloid precursors induces both the M2-type and lymphatic phenotype. Expansion of lymphatics can enhance tumor immunosuppression by physical removal of immunostimulatory cells. These findings suggest that targeting Th2 pathways can simultaneously relieve immunosuppression and inhibit differentiation of pro-lymphatic progenitors that promote metastasis.

Citation Format: Maria Espinoza Gonzalez, Lisa Volk-Draper, Nihit Bhattarai, Sophia Ran. Acquisition of lymphatic phenotype in bone marrow endothelial progenitors is regulated by immunosuppressive Th2 cytokines [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 5626.
Abstract 5635: Combined MEK and mitophagy inhibition promotes mtDNA-mediated innate immunity in KRAS-mutant cancer
Authors: Tanaka Kosuke , Morita Tomoko Yamamori , Hakozaki Yumi , Yoshiya Miyuki , Mashima Chiaki , Liu Jie , Kageyama Shun-ichiro , Ohashi Akihiro , Kobayashi Susumu
Published: June 2022

Although mitochondrial DNA (mtDNA) can stimulate innate immune response that potentiates the efficacy of cancer immunotherapy, how to maximize this innate immune system in certain cancer subtypes remains unknown. Here we show that mtDNA is enriched in KRAS-mutant tumor where the dsDNA-sensor machinery cGAS-STING signaling is autonomously activated at the baseline. Intriguingly, MEK inhibitor induces cytosolic mtDNA release to potently activate cGAS-STING pathway, that is counteracted by PRKN-mediated mitophagy to eliminate mtDNA within damaged mitochondria in KRAS-mutant tumor. Combined MEK and mitophagy inhibitors synergistically boost type I IFNs through mitochondrial stress and promote lymphocyte infiltration into the TME in a mtDNA efflux-dependent manner. Moreover, this combination enhances the efficacy of PD-1 blockade in KRAS-mutant tumor. PRKN clinically associates with KRAS/LKB1-mutant subtype, lower antigen-presenting signature, and ICB resistance. Together, targeting mtDNA renders promising strategy to enable cancer immunotherapy in KRAS-mutant cancers.

Citation Format: Kosuke Tanaka, Tomoko Yamamori Morita, Yumi Hakozaki, Miyuki Yoshiya, Chiaki Mashima, Jie Liu, Shun-ichiro Kageyama, Akihiro Ohashi, Susumu Kobayashi. Combined MEK and mitophagy inhibition promotes mtDNA-mediated innate immunity in KRAS-mutant 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 5635.
Abstract 5657: Anti-hypertensive drugs increase TRAIL sensitivity-induced surface DR5 via autophagy inhibition pathway in prostate cancer cells
Authors: park sang-youel , Kim Jong-Hun , Hong Jeong-Min , Seol Jae-Won
Published: June 2022

Angiotensin II type 1 receptor blockers(ARB) are used as antihypertensive agents, The cohort study found that among people with prostate cancer, thus taking Angiotensin II type 1 receptor blockers had reduced risk ratio. This study investigated that can ARB treatment enhance the TRAIL-mediated prostate cancer cell apoptosis, and the detailed molecular mechanisms. The results showed that ARB treatment increased the TRAIL-mediated prostate cancer cell apoptosis. In the mechanism study, ARB treatment increased DR5 protein expression level, surface DR5 protein amount, and DR5 protein stability. Furthermore, the Regulation of DR5 expression was mediated by autophagy flux inhibition followed by ARB treatment. Taken together, the results demonstrated that ARB treatment sensitized prostate cancer cells to TRAIL-induced apoptosis via autophagy inhibition and DR5 protein stabilization, and also suggest that the prostate cancer cells of ARB taken-patient may be sensitized to TRAIL-mediated apoptosis, and may support the mechanism of cohort study which showed reduction of prostate cancer risk ratio in patient taking angiotensin II type 1 receptor blockers.

Citation Format: sang-youel park, Jong-Hun Kim, Jeong-Min Hong, Jae-Won Seol. Anti-hypertensive drugs increase TRAIL sensitivity-induced surface DR5 via autophagy inhibition pathway in prostate cancer cells [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 5657.
Abstract 5674: A developmentally prometastatic niche to hepatoblastoma in neonatal liver mediated by the Cxcl1/Cxcr2 axis
Authors: Fan Li , Pan Qingfei , Yang Wentao , Koo Selene C. , Tian Cheng , Li Liyuan , Lu Meifen , Brown Anthony , Ju Bensheng , Easton John , Ranganathan Sarangarajan , Shin Soona , Bondoc Alexander , Yang Jun J. , Yu Jiyang , Zhu Liqin
Published: June 2022

Background and Rationale: Hepatoblastoma (HB) is the most common pediatric liver cancer. Its predominant occurrence in very young children led us to investigating whether the neonatal liver provides a protumorigenic niche to HB development.

Methods: HB development was compared between orthotopic transplantation models established in postnatal day 5 and 60 mice (P5Tx and P60Tx models). Single-cell RNA-sequencing was performed using tumor and liver tissues from both models and the top candidate cell types and genes identified are investigated for their roles in HB cell growth, migration, and survival.

Results: We found that various HB cell lines including HepG2 cells were consistently and considerably more tumorigenic and metastatic in the P5Tx model than in the P60Tx models. Sc-RNAseq of the P5Tx and P60Tx HepG2 models revealed that the P5Tx tumor was more hypoxic and had a larger number of activated hepatic stellate cells (aHSCs) in the tumor-surrounding liver which express significantly higher levels of Cxcl1 than those from the P60Tx model. We found these differences were developmentally present in normal P5 and P60 liver. We showed that the Cxcl1/Cxcr2 axis mediated HB cell migration and was critical to HB cell survival under hypoxia. Treating HepG2 P60Tx model with recombinant CXCL1 protein induced intrahepatic and pulmonary metastasis and CXCR2 knockout in HepG2 cells abolished their metastatic potential in the P5Tx model. Lastly, we showed that in metastatic HB patient tumors there was a similar larger population of aHSCs in the tumor-surrounding liver than in localized tumors, and tumor hypoxia was uniquely associated with HB patient prognosis among pediatric cancers.

Conclusion: We demonstrated that the neonatal liver provides a prometastatic niche to HB development via the Cxcl1/Cxcr2 axis.

Citation Format: Li Fan, Qingfei Pan, Wentao Yang, Selene C. Koo, Cheng Tian, Liyuan Li, Meifen Lu, Anthony Brown, Bensheng Ju, John Easton, Sarangarajan Ranganathan, Soona Shin, Alexander Bondoc, Jun J. Yang, Jiyang Yu, Liqin Zhu. A developmentally prometastatic niche to hepatoblastoma in neonatal liver mediated by the Cxcl1/Cxcr2 axis [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 5674.
Abstract 5724: Loss of SWI/SNF chromatin remodeling alters NRF2 signaling in human cancers
Authors: Nguyen Vinh , Shranck Travis , Hamad Samera , Weissman Bernard
Published: June 2022

Next-generation sequencing studies of lung cancer has shown a significant number of mutations in two previously unrecognized regulatory pathways. Activating mutations, the NF-E2-related factor 2 (NFE2L2, NRF2) transcription factor induces constitutive expression of cytoprotective and redox maintenance genes. Inactivating mutations in members of the SWI/SNF chromatin-remodeling complex, especially SMARCA4 (BRG1) and ARID1A, lead to changes in nucleosome positioning and gene expression. Here, we show that loss of SWI/SNF complex function activated a subset of NRF2-mediated transcriptional targets. Using a series of isogenic NSCLC lines with reduced or depleted BRG1 and/or BRM expression, we observed significantly increased expression and protein levels of the NRF2-target genes HMOX1 and GSTM4. RNA sequencing of BRG1-proficient and -deficient cell lines confirmed changes in KEAP1-NRF2 target gene expression as well as identified novel targets of the SWI/SNF complex. Importantly, low BRG1 expression levels in primary human NSCLC tumors correlated with increased NRF2-target gene expression. In addition to BRG1 levels, we examined loss of ARID1A across primary human tumors and found ARID1A deficiency was associated with altered NRF2 signaling. The tumors with the highest frequency of altered NRF2 signaling were lung squamous (LUSC) and head and neck squamous (HNSCC), cancers strongly associated with environmental toxicants. Interestingly ARID1A loss depressed NRF2 signaling in LUSC while amplifying it in HNSCC, an observation we are exploring mechanistically in cell line knock out models. Our data demonstrate that loss of SWI/SNF in lung cancer results in activation of the NRF2/KEAP1 pathway and increased expression of a subset of its downstream targets. These data provide an additional molecular explanation for why patients harboring SWI/SNF mutations show a poor prognosis. Our results also potentially link mutations in SWI/SNF complex components, that occur in >20% of human cancers, with exposure to environmental toxicants. A better understanding of these mechanism may yield novel insights into the design of targeted treatment modalities for human lung cancers.

Citation Format: Vinh Nguyen, Travis Shranck, Samera Hamad, Bernard Weissman. Loss of SWI/SNF chromatin remodeling alters NRF2 signaling in human cancers [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 5724.
Abstract 5734: The effect of PRAME on retinoid response and cell proliferation in cutaneous and head and neck squamous cell carcinoma
Authors: Ramchatesingh Brandon Liam , Litvinov Ivan
Published: June 2022

As cells undergo terminal differentiation, they adopt their tissue-specific functions and permanently exit the cell cycle. Inducing differentiation of premalignant cells and malignant cells are proposed strategies for cancer prevention and treatment, respectively. Retinoids, compounds related to retinol, drive terminal differentiation of numerous cell types. These compounds exhibit efficacy for the prevention of cutaneous squamous cell carcinomas (cSCC) and head and neck squamous cell carcinomas (HNSCCs), and their incorporation into treatment plans for these cancers is supported by laboratory and clinical studies. Preferentially Expressed Antigen in Melanoma (PRAME) is a cancer-testis antigen that represses retinoid signaling, and is associated with adverse outcomes in a plethora of malignancies. Although PRAME is known to be expressed in subsets of cutaneous SCC (cSCC) and head and neck SCC (HNSCC) tumors, its functions, prognostic and therapeutic significance have never been investigated in these cancers. We hypothesize that PRAME expression in SCC cells confers resistance to the anti-neoplastic effects of retinoids and supports cell proliferation. PRAME expression was evaluated in human cSCC tumors, and in cSCC and HNSCC cell lines by immunoblotting and qRT-PCR. PRAME-overexpressing immortalized keratinocyte, cSCC and HNSCC cell lines were generated. shRNA-mediated knockdown of PRAME was performed in a cSCC and a HNSCC cell line. Cells were treated with all-trans retinoic acid (ATRA) for 24, 48 or 72 hours. Expression of differentiation markers was assessed by immunoblotting and qRT-PCR of markers of differentiation. Cell counting assays, immunoblot analysis of cell cycle genes and Ki67 immunofluorescence staining were used to assess proliferation. PRAME expression is detected in subsets of cSCC tumors and in select SCC cell lines. Overexpression of PRAME in HNSCC cells enhanced cell proliferation compared to control cells. Treatment with ATRA did not promote differentiation of PRAME-expressing cells. Furthermore, PRAME overexpression attenuated the anti-proliferative effect of ATRA in HNSCC cells. We conclude that PRAME enhances proliferation of malignant keratinocytes in vitro and may confer resistance to retinoid-induced differentiation and proliferation arrest. Investigations to assess the prognostic and therapeutic significance of PRAME expression in SCCs are warranted.

Citation Format: Brandon Liam Ramchatesingh, Ivan Litvinov. The effect of PRAME on retinoid response and cell proliferation in cutaneous and head and neck squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5734.
Abstract 5739: Genetic characteristics of the early stage Chinese NSCLC patients
Authors: Mao Naiquan , Yao Weishen , Su Liufu , Huang Xiaochun , Huang mengli
Published: June 2022

Background: Lung Cancer, predominantly non-small-cell lung cancer (NSCLC), is the leading cause of cancer-related death in China. Although precision therapies for patients with advanced or metastatic NSCLC have developed over the past two decades, the 5-year survival rate remains low at 0%-26%. Thus, recurrence monitoring and treatment at an early stage are of great significance for improving survival benefits. Here, we explored the genetic characteristics of early stage NSCLC patients to provide additional values to predict recurrence risk and treatment strategies.

Methods: Tumor or plasma samples were collected from 146 Chinese NSCLC patients in stage I-III (127 LUAD, 5 LUSC, 2 LUASC, 12 unknown pathology). 733 cancer-related genes were sequenced on NGS platform for variants analysis. Tumor mutation burden (TMB) was defined by all somatic mutation counts in coding region per megabase. Immunohistochemistry (IHC) was performed using antibodies (clone 22C3 or SP263) to analyze PD-L1 expression. PD-L1 positivity was defined as TPS ≥1%. Online databases, such as cBioPortal, TIMER2.0 and Kaplan-Meier Plotter, were also used for analysis. Statistical analysis was performed using the R Software (v 4.0.5).

Results: Of 146 NSCLC patients, commonly mutated genes were detected, including EGFR (68%), TP53 (40%), KMT2D (10%), MSH3 (9%), RBM10 (9%), ZFHX3 (9%). Six pathogenic or likely pathogenic fusion variants harbored in common driver genes like EGFR, ALK and ROS1 were identified for the first time. EGFR was more frequently mutated in female patients (P < 0.01), while CDH10 mutations occurred more often in male patients (P < 0.05). Correlation analysis showed RBM10, ZFHX3 and CTNNB1 mutations were respectively co-occurrent with CARD11, ARHGAP5 and APC, reflecting the distinct profile of our cohort when compared to cBioPortal. Patients with TP53mut, MSH3mut or LRP1Bmut had significantly higher TMB (P < 0.05). Compared to PD-L1- group, TP53, TIMELESS, FBXW7 were remarkably mutated in PD-L1+ group. In LUAD, SPTA1mut and TIMELESSmut were noticeably related to CD8+T and B cell infiltration, while FBXW7mut and ZFHX3mut with more M1 macrophages infiltration. Prognostic analysis showed that LUAD patients harboring MSH3mut (P < 0.001) and SPENmut (P = 0.0005) at stage II exhibited significantly shorter RFS. Moreover, we found that cases carried somatic mutations in TP53 signaling pathway had more lymph node metastasis.

Conclusion: These findings expanded our understanding of the early stage Chinese NSCLC, hopefully providing valuable guidance for recurrence risk prediction and treatment strategies.

Citation Format: Naiquan Mao, Weishen Yao, Liufu Su, Xiaochun Huang, mengli Huang. Genetic characteristics of the early stage Chinese NSCLC patients [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 5739.
Abstract 5741: Characterizing isoform switching events in esophageal adenocarcinoma
Authors: Zhang Yun , Weh Katherine M. , Howard Connor L. , Riethoven Jean-Jack , Clarke Jennifer L. , Lagisetty Kiran H. , Lin Jules , Reddy Rishindra M. , Chang Andrew C. , Beer David G. , Kresty Laura A.
Published: June 2022

Esophageal adenocarcinoma (EAC), the major subtype of esophageal cancer in the US, is characterized by increasing incidence rates and high mortality due to ineffective screening, late-stage diagnosis, and poor treatment efficacy. The only known precursor to EAC is Barrett’s Esophagus (BE), but the precise mechanisms and molecular events leading to disease progression are still being unraveled. In recent years, analysis of TCGA data revealed that isoform switching events with predicted functional consequences are common in many cancers, but the characterization of switching events in esophageal adenocarcinoma (EAC) is lacking. Next-generation sequencing was utilized to detect levels of RNA transcripts and specific isoforms in 66 treatment naïve esophageal tissues from 41 patients. Tissues ranged from premalignant Barrett’s esophagus (BE), BE with low or high-grade dysplasia (LGD or HGD) to EAC. Samples were stratified by histopathology, p53 mutation status, and significant isoform switching events with predicted functional consequences, followed by enrichment analysis. Barrett’s with high-grade dysplasia increased risk for EAC progression. Comparing BE with LGD and BE with HGD, isoform switching events were identified in 75 genes including KRAS, APC, RNF-128 and WRAP53. Stratification based on p53 status increased the number of significant isoform switches to 135 suggesting switching events impact cellular functions based on tissue histopathology, as well as p53 status. Analysis of isoforms agnostic to mutant p53, exclusive to mutant p53, and shared between the two groups revealed unique signatures including demethylation, lipid and retinoic acid metabolism, and glucuronidation, respectively. About 25% of isoform switching events were identified without significant alteration of gene-level expression. Importantly, two p53-interacting isoforms, RNF128 and WRAP53, were significantly linked to patient survival. Analysis of global isoform switching consequences and alternative splicing events also revealed significant changes in the fraction of coding transcripts, complete open-reading-frames, signal peptides, alternative 5’ donor sites, and alternative transcription start sites. Thus, analysis of isoform switching events may provide new insight for the identification of prognostic markers and inform new potential therapeutic targets for EAC treatment or prevention.

Citation Format: Yun Zhang, Katherine M. Weh, Connor L. Howard, Jean-Jack Riethoven, Jennifer L. Clarke, Kiran H. Lagisetty, Jules Lin, Rishindra M. Reddy, Andrew C. Chang, David G. Beer, Laura A. Kresty. Characterizing isoform switching events in esophageal adenocarcinoma [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 5741.
Abstract 5754: The molecular characteristics of EGFR co-mutations in lung adenocarcinoma
Authors: Shang Yanhong , Zhang Hao , Zang Aiming , Yuan Shaohua , Li Xiaofang , Zhang Wenpan , Huo Ran , Fang Guotao , Dou Zhengyue , Liu Weiwei , Han Xiao , Zhao Qi , Xi Chenglin
Published: June 2022

Background: With the development of sensitive next-generation sequencing (NGS) techniques that go beyond the genotyping of specific mutations, detection rates for uncommon mutations have risen clinically. Given this rise in mutation identification, discoveries regarding isolation or coexistent mutations with the EGFR mutation (termed a “complex” mutation) are in “uncharted territory” in terms of their biological impacts on oncogenic pathways and their sensitivity or resistance, to EGFR TKIs.

Methods: Targeted NGS for 450 genes was performed in OrigiMed (Shanghai, China), a College of American Pathologists (CAP) accredited and Clinical Laboratory Improvement Amendments (CLIA) certified laboratory.

Results: A cohort of 262 Chinese lung adenocarcinoma patients were recruited. The most common mutated gene was EGFR (63%, 165/262), and followed by TP53 gene (59.2%, 155/262). Beyond single genetic lesions, we found that enriched co-mutations in lung adenocarcinoma were significantly different for TP53 (p < 0.001) and RTK-RAS (p = 0.0012) signaling pathways between the EGFR-positive and EGFR-negative groups. In all EGFR co-mutated patients, the frequency of co-mutation for EGFR/TP53 and the classical EGFR mutation was 106 (64.2%) and 144 (87.3%), respectively. EGFR-only mutations occurred in 50 (30.3%) patients, while co-mutation of EGFR and at least one tumor suppressor gene (TSG) occurred in 84 (50.9%) patients. Patients with EGFR-only mutation had a lower tumor mutational burden (p = 0.026) as compared to patients with only a TSG mutation. Patients with co-mutations of EGFR and at least one TSG also displayed a lower tumor mutational burden, although only a slight difference (p = 0.062) was determined.

Conclusions: Profiles of EGFR co-mutational TSGs should be regarded as a unique subgroup for predictive insights in treatments for patients with co-occurrence of somatic EGFR and TSG mutations. To improve predictions related to drug sensitivity in targeted therapies for oncogenes with diverse mutations, our future studies will include publications dedicated to this topic.

Citation Format: Yanhong Shang, Hao Zhang, Aiming Zang, Shaohua Yuan, Xiaofang Li, Wenpan Zhang, Ran Huo, Guotao Fang, Zhengyue Dou, Weiwei Liu, Xiao Han, Qi Zhao, Chenglin Xi. The molecular characteristics of EGFR co-mutations in lung adenocarcinoma [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 5754.
Abstract 5756: Next-generation sequencing (NGS) reveals different molecular profiles of pediatric sarcoma in children and adults
Authors: Cai Weisong , Liu Fang , Liu Xuejiao , Wang Xiaojuan , Wang Chunyang , Ma Tonghui , Li Shu
Published: June 2022

Background: Pediatric sarcomas represent approximately 12% of all pediatric cancers with over 100 subtypes. Although some molecular detection techniques can be used to assist the diagnosis and treatment of pediatric sarcoma, it still remains challenging due to overlapping morphological features and limited biopsy specimens. Here we performed next generation sequencing (NGS) to analyze the molecular profiles of pediatric and adult sarcomas in China.

Methods: A total of 700 Chinese patients with sarcoma were collected. The tumor tissue and matching blood specimens were tested by the integrative DNA and RNA sequencing panel Onco Panscan plus࣪ at Genetronhealth.

Results: Of the 700 sarcoma patients, there were 224 children (32%) and 476 adults (68%). Difference from the almost same ratio of men to women in adults, there were more males (n = 134) than females (n = 90) in children. Rhabdomyosarcoma was the most common soft tissue tumor in children, accounting for 24.1% (n = 54), followed by Ewing's sarcoma (9.8%, n = 22) and Osteosarcoma (8.5%, n = 34), while Angiosarcoma (3.8%, n = 18) and Fibrosarcoma (3.6%, n = 17) were the most common in adults. Based on mutation types, the frequent alterations were missense mutations (n = 326, 51.2%), fusions (n = 129, 20.3%) and copy number variants (n = 66, 10.4%) in children with a mean of 3 mutations per patient, and missense mutations (n = 1438, 66.8%), fusions (n = 221, 10.3%) and truncating mutations (n = 215, 10.0%) in adults with an average 5 mutations. TP53 (12.9%, n = 29), EWSR1 (8.9%, n = 20) and ALK mutations (6.7%, n = 15) were common in children, which was distinct from TP53 (29.4%, n = 140), NF1 (4.8%, n = 23), CTNNB1 (4.2%, n = 20) and RB1 (4.2%, n = 20) in adults. Based on NGS results, pathological subtypes could be confirmed in 40.2% (90/224) and 48.1% (229/476) of children and of adults sarcoma patients, respectively. In addition, we identified a total of 72 drug-targeted gene mutations in the 57 children patients, of which 35 (48.6%) gene mutations could be targeted by FDA-approved drugs. In adults, 256 drug-targeted gene mutations were detected and the proportion of actionable mutations was up to 78.9% (n = 202).

Conclusion: The genomic landscape of pediatric sarcomas is different from that of adults. NGS aids in the subtype classification and clinical guidance of pediatric sarcomas, providing evidence for personalized treatments with clinical benefit.

Citation Format: Weisong Cai, Fang Liu, Xuejiao Liu, Xiaojuan Wang, Chunyang Wang, Tonghui Ma, Shu Li. Next-generation sequencing (NGS) reveals different molecular profiles of pediatric sarcoma in children and adults [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 5756.
Abstract 576: Shark VNAR single domain-based CAR T cells targeting PD-L1 for cancer therapy
Authors: Li Dan , English Hejiao , Hong Jessica , Liang Tianyuzhou , Merlino Glenn , Day Chi-Ping , Ho Mitchell
Published: June 2022

Background: Chimeric antigen receptor (CAR)-T therapy shows great potency against hematological malignancies, whereas it is difficult to transfer CAR T into solid tumors due to lack of appropriate antigenic targets and immunosuppressive tumor microenvironment. Checkpoint molecule PD-L1 is widely overexpressed on multiple tumor types, and PD-1/PD-L1 interaction is a primary mediator of immunosuppression in the TME. Here, we generated anti-PD-L1-specific shark single domain VNAR-based CAR T cell strategy and explored its anti-tumor efficacy in xenograft mouse models.

Methods: We isolated anti-PD-L1 single domain antibodies from semi-synthetic shark VNAR phage display libraries. The binding of isolated VNARs was validated by ELISA, flow cytometry, and Octet. A peptide library based on human PD-L1 was synthesized to predict the epitope of select VNARs. Anti-tumor efficacy of CAR T cells was determined via cell luciferase-based cell assay as well as xenograft mouse models. Two tumor models, MDA-MB-231 (triple-negative breast cancer) and Hep3B (hepatocellular carcinoma or HCC) were used in the present study. Glypican-3 (GPC3) is a tumor-specific target in the Hep3B model.

Results: We identified three anti-PD-L1 phage binders, B2, A11, and F5 from our shark phage libraries. All three binders showed cross-activity to human, mouse, and canine antigens, whereas only B2 functionally blocked the interaction of human PD-1 to PD-L1. Moreover, CAR (B2) T cells specifically lysed both MDA-MB-231 and Hep3B tumor cells by targeting constitutive and inducible expression of PD-L1. Importantly, the combination of anti-GPC3 CAR (hYP7) T cells with CAR (B2) T cells regress Hep3B tumors synergistically in mice.

Conclusions: PD-L1-targeted shark VNAR single domain-based CAR T cell therapy is a novel strategy to treat breast cancer and liver cancer. This work provides a rationale for a potential use of anti-PD-L1 CAR T cells as a monotherapy or combination with a tumor-specific therapy in clinical studies for solid tumors.

Citation Format: Dan Li, Hejiao English, Jessica Hong, Tianyuzhou Liang, Glenn Merlino, Chi-Ping Day, Mitchell Ho. Shark VNAR single domain-based CAR T cells targeting PD-L1 for cancer therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 576.
Abstract 5764: Genomic profiling of cutaneous, acral and mucosal melanomas in Chinese populations
Authors: Chen Jing , Ye Ting , Fan Li , Zhang Jieying , Cao Rubo , Liu Yanshen
Published: June 2022

Background: Targeted therapies and immunotherapies have significantly improved the survival of patients with cutaneous melanoma. Nevertheless, patients with acral and mucosal melanomas show limited benefit. The proportion of acral and mucosal subtypes are much higher in Chinese populations than Caucasians. Therefore, it is of great interest to detail the genomic features of acral and mucosal melanomas and compare these with cutaneous melanoma.

Methods: A total of 111 Chinese patients with melanoma treated in Union Hospital, Tongji Medical College, Huazhong University of Science and Technology were enrolled in this study, comprising 32 cutaneous(28.8%), 41 acral(36.9%) and 26 mucosal(23.4%) subtypes. NGS-based genomic profiling of major cancer-related genes was performed on formalin-fixed, paraffin-embedded (FFPE) tumor tissue specimens with matched blood samples. Tumor mutational burden (TMB) was calculated based on somatic nonsynonymous missense mutations.

Results: The most commonly mutated genes of cutaneous melanoma include BRAF(48%), CDKN2A(41%), CDKN2B(41%), NRAS(22%) and PTEN(22%). In acral melanoma patients, the mutation rate of BRAF was 10% while NRAS(31%), CDKN2A(21%), EMSY(21%), KIT(18%), CCND1(18%)) and NF1(18%) were frequently mutated. Mucosal melanomas were found most commonly to have mutations in CDKN2A(36%), KIT(32%), CDKN2B(28%), PDGFRA(24%), KDR(20%) and BRAF(16%). In acral and mucosal subtypes, the overall mutation rates of BRAF were significantly lower while the relative proportions of non-V600 mutations were higher as compared to cutaneous subtype. These may explain the less significant survival benefit of BRAFi+/-MEKi in acral and mucosal melanomas. In contrast, KIT mutations including SNVs and amplification, were enriched in acral and mucosal melanomas. Acral melanomas had lower mutation load than mucosal melanomas(2.42 Muts/Mb vs 4.84 Muts/Mb, p=0.0002), while cutaneous melanomas(4.03 Muts/Mb) did not differ from other subtypes in mutation burden. Additionally, patients with TERT, APC and FAT1 gene mutations had a significantly higher TMB than patients with wild-type genes respectively, indicating more activated anti-tumor immune profiles and suggesting therapeutic benefit from immune checkpoint inhibitors.

Conclusions: We conducted a direction comparison of comprehensive genomic profiles of different melanoma subtypes among Chinese patients. The genomic alterations identified in our study may provide reference to discover potential strategies for targeted therapy and immunotherapy in acral and mucosal melanomas.

Citation Format: Jing Chen, Ting Ye, Li Fan, Jieying Zhang, Rubo Cao, Yanshen Liu. Genomic profiling of cutaneous, acral and mucosal melanomas in Chinese populations [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 5764.
Abstract 5769: Comprehensive analysis of genomic alteration in histologic components of myxoid liposarcoma
Authors: Chae Jee Hoon , Kim Sun il , Kim Do Hee , Kim Sangkyum , Choi Junjeong
Published: June 2022

Purpose: Myxoid liposarcoma (MLS) is the most common type of liposarcoma in humans. Tumor with round cell component shows poor clinical prognosis. Currently, specific target therapies for this tumor type have not been developed. We performed next-generation sequencing (NGS) analysis of paired samples to investigate genomic alteration in MLS with two histologic features.

Methods: Whole exome sequencing (WES) and transcriptome sequencing data were acquired from formalin-fixed paraffin-embedded samples of 10 patients. We performed differential gene expression analysis and pathway analysis between the conventional myxoid liposarcoma area lesion and that of round cell component using transcriptome sequencing data. In addition, we analyzed characteristics of mutational signatures in the two histologic features of MLS using WES data.

Results: CD37 showed the most significant expression in round cell components of myxoid liposarcoma (RMLS) compared to conventional MLS. The immune response pathway was significantly enriched in the conventional lesion. The pathway involving cell mitotic and metabolic processes were represented considerably in with RMLS. FUS-DDIT3/EWSR1-DDIT3 fusion oncogene was detected in these RMLS samples more frequently than MLS. Some patients showed mutational signatures related to oxidative stress.

Conclusion: The expression of CD37 was highly expressed in almost all the RMLS. We identified smoking profile signature characteristics in these two samples, but no significant mutational difference was placed between the RMLS and MLS samples. In RMLS, the fusion oncogene and other overexpression oncogenes that occur in the cell cycle affect lipid metabolism due to oxidative stress such as ROS. Finally, we observed CD37 expression by performing IHC only in RMLS samples. The above data suggest that CD37 and other markers can be a promising biomarker target in myxoid liposarcoma with unfavorable histological features.

Citation Format: Jee Hoon Chae, Sun il Kim, Do Hee Kim, Sangkyum Kim, Junjeong Choi. Comprehensive analysis of genomic alteration in histologic components of myxoid liposarcoma [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 5769.
Abstract 5771: The refined stratification of receptor tyrosine kinase fusions in lung cancer
Authors: Liang Chaoyang , Li Lin , Liu Xiaofang , Liu Qiuhua , Wang Baoming , Wang Chunyang , Ma Tonghui , Meng Fanlu
Published: June 2022

Background: The overall survival of patients with the actionable receptor tyrosine kinase (TRK) fusions can be significantly prolonged after taking targeted kinase inhibitors. However, the outcomes are variable due to the different fusion types of the same driver gene.

Method: Formalin fixed paraffin embedded tissues from patients with lung cancer between March 2018 and September 2021 were performed by using next generation sequencing (NGS) at Genetronhealth, a laboratory accredited by College of American Pathologists and Clinical Laboratory Improvement Amendments.

Results: In a large cohort of 3768 patients with lung cancer, 348 cases harboring the actionable TKR fusions, including ALK, ROS1, RET, EGFR, MET, BRAF, NTRK1/2/3. TRK fusions can be divided into three types based on the breakpoints, partners and fusion models: single 3’ fusions, nonreciprocal fusions with the intact tyrosine kinase domain (TKD); single 5’ fusions, reciprocal fusions with the incomplete TKD; complex fusions, nonreciprocal/reciprocal fusions or nonreciprocal fusions with different partners. At the gene level, 58% (203 of 348) of TRK fusions were ALK, among which 71% of single 3’ ALK (144 of 203), 3% of single 5’ ALK (6 of 203) and 26% of complex fusions (53 of 203) were included. ROS1 fusions accounted for 14% (50 of 348) of all TRK fusions, and the proportions of single 3’ fusions, single 5’ fusions and complex fusions were 60% (30 of 50), 6% (3 of 50) and 34% (17 of 50), respectively. RET captured 19% (66 of 348) TRK fusions with 70% of single 3’ RET (46 of 66), 5% of single 5’ RET (3 of 66) and 26% of the complex fusions (17 of 66). EGFR owned 3% (9 of 348) with 33% of single 3’ EGFR (3 of 9), 33% of single 5’ EGFR (3 of 9) and 33% of the complex (3 of 9). MET, BRAF and NTRK1/2/3 shared the rest 5% of total fusions without complex type.

Conclusion: Our research shows different types of TRK fusions in Chinese lung cancer patients, which can help guide the precise treatment in clinical.

Citation Format: Chaoyang Liang, Lin Li, Xiaofang Liu, Qiuhua Liu, Baoming Wang, Chunyang Wang, Tonghui Ma, Fanlu Meng. The refined stratification of receptor tyrosine kinase fusions 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 5771.
Abstract 5772: Differences in clinical actionability by comparing mutational landscape of young and old breast cancer patients
Authors: Liu Jiaqi , Jia Ziqi , Liu Gang , Wang Xiang , Meng Qi , Wang Sha , Shao Yang
Published: June 2022

Background: Early-onset breast cancer (BC) is associated with poor prognosis, which is also characterized by high recurrence risk, distant metastases and advanced stages at the time of diagnosis. While germline mutations in BRCA1/2 are known to underlie a subset of early-onset BC cases, the clinical and genetic characteristics in other young BC patients remain to be explored.

Method: We profiled primary lesions from 440 Chinese female BC patients by using a 425-cancer-gene panel. The population was sub-divided into young (≤40 years old) and old (>40 years old) BC patients according to ages at diagnosis. Young and old BC patients were compared for their associations with genomic aberrations, with focus on existing BC targetable alterations, including those in the ERBB2 gene and PI3K and homologous recombination repair (HRR) pathways.

Results: 137 (31.1%) patients presented with BC at a young age (median age=35 [18-40]) and 303 (68.9%) with BC diagnosed at an older age (median age=53 [41-82]) in our study cohort. TP53 (young, 61.3%; old, 67%), PIK3CA (33.6% and 41.3%), and GATA3 (9.5% and 8.3%) were among the top frequently altered genes in both subgroups. A total of 70 patients carried pathogenic germline mutations. Of these, 57.3% were alterations in the HRR pathway genes, including BRCA1/2, WRN, BLM, and PALB2, etc, with comparable frequencies in young and old patients. Germline BRCA1/2 mutations were detected in nine (6.6%) and 23 (7.6%) of the young and old patients, respectively. Somatic BRCA1/2 mutational frequencies were also comparable between young (8.8%) and old (9.9%) patients. Overall, somatic alterations in HRR pathway genes were detected in 32.1% young and 40.6% old BC patients. While similar frequencies of ERBB2 amplification (14.6% vs. 18.2%; P= 0.41) were detected in young and old BC patients, older patients carried more ERBB2 mutations (1.5% vs. 7.3%, P= 0.01). Interestingly, the highest rate of ERBB2 amplification was observed in the 20-30 years age group. Alterations in NF1 (10.6% vs. 3.6%, P=0.02) and PKHD1 (6.9% vs. 2.2%, P=0.04) were more frequent in older patients. Alterations in the PI3K pathway genes were more enriched in the older BC patients with overall mutational frequencies of 55.5% and 68.6% (P=0.01) in young and old subgroups, respectively. Finally, we observed an age-dependent increase in tumor mutational burden.

Conclusion: BC in young and old patients exhibited different genomic characteristics that could be taken into consideration for treatment recommendations.

Citation Format: Jiaqi Liu, Ziqi Jia, Gang Liu, Xiang Wang, Qi Meng, Sha Wang, Yang Shao. Differences in clinical actionability by comparing mutational landscape of young and old breast cancer patients [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 5772.
Abstract 5789: Multi-omic artificial intelligence outcome modeling of ovarian cancer, phase I: Whole exome and whole transcriptome data
Authors: Orr Brian , Edwards Robert P. , Radolec Mackenzy
Published: June 2022

Background: Over a decade ago, the Cancer Genome Atlas (TCGA) provided the initial genomic characterization of ovarian cancer with targeted exome capture and sequencing. Unlike other TCGA analysis, they were unable to identify prognostic mutational profiles outside of BRCA status. There has been limited characterization of the ovarian cancer genomic profile since. Our objective presented here was to perform whole exome and whole transcriptome analysis of 241 ovarian cancer samples and compare to the TCGA dataset. This is the first phase of a muti-step ongoing analysis wherein we will input and correlate the complete genomic profile, complete patient outcome data, and immunohistochemical staining into a multi-omic artificial intelligence (AI) machine learning model with the aim of improved individualized outcome prediction.

Methods: Tumor samples from 2000-2016 were obtained at time of surgery under approved University of Pittsburgh approved IRB consent. Whole exome and whole transcriptome sequencing were performed in collaboration with Helomics Corporation. Sequencing analysis was compared to TCGA data.

Results: 241 patient samples underwent sequencing analysis. Similar to TCGA, most mutations were missense. I am having a difficulty interpreting the magee vs tcga comparison graphs, how to discuss the TP53 and BRCA comparison without using the lollipop charts and highlighting the rna-seq data into written form. Please add.

Conclusions: We present our findings of one of the largest molecular characterizations of ovarian cancer. Similar to the TCGA, there is noted heterogeneity to the genomic profile of ovarian cancer. Multi-omic AI outcome modeling has the potential to overcome the gap defining prognostic sub-groups so that we can tailor therapies to the individual

Citation Format: Brian Orr, Robert P. Edwards, Mackenzy Radolec. Multi-omic artificial intelligence outcome modeling of ovarian cancer, phase I: Whole exome and whole transcriptome data [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 5789.