bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 6697: Deep learning algorithm for cancer detection using multimodal characteristics of whole methylome sequencing of cf-DNA
Authors: Park Juntae , Kim Minjung , Park Sook Ryun , Song Ki-Byung , Jun Eunsung , Oh Dongryul , Lee Jeong-Won , Park Young Sik , Song Ki-Won , Byeon Jeong-Sik , Kim Bo Hyun , Ki Chang-Seok , Cho Eunhae
Published: April 2023

Background Various cell-free DNA (cfDNA) features including methylation and genomic profiles have been investigated for their potential use in early cancer detection. We developed deep learning models based the data generated by the enzymatic conversion based whole methylome sequencing of cfDNA.

Methods Cell-free whole genome Enzymatic Methyl sequencing(cfWEMseq) data were generated from 198 cancer patients (stage I: 11%, II: 17%, III: 22%, IV: 20%, unknown: 31%) and 69 healthy controls. The cancer types were consisted of breast (n=31), liver (n=24), esophageal (n=38), pancreatic (n=30), colon (n=34), ovarian (n=18), and lung (n=23). Sequence data was produced on average of 200 million reads using Novaseq 6000 (Illumina). For model training and evaluation, data partitioning was stratified by cancer type, and 5-fold cross validation was used. Coverage and methylation beta values ​​were calculated by binning at fixed size of 100K, 1M, and 5M base and variable size from Topologically Associated Domains (TAD). Genome Coverage (GC), Genome Methylation Beta values ​​(GMB), and Mutation Signature (MS) features were trained using a one-dimensional convolutional neural network (1D-CNN). The performance of the model was evaluated by measuring the average value of the results measured in each test set of 5 fold.

Results We tested the cancer detection performance of various feature combinations using all data from cfWEMseq (n=267). Regardless of the bin size, the GMB single model achieved higher performance than the GC single model. The best-performing model is the ensemble model of GMB (100k bin) and MS. The cancer detection performance of this ensemble model reached an accuracy 96% (CI: 93.6% to 98.1%), AUC 0.99 (CI: 0.97 to 1.0) and sensitivity 98.0% (CI: 92.4% to 99.5%) with a specificity of 90%.

Conclusions These results provide an opportunity for higher accuracies by integrating methylation information and genomic data using cfWEMseq. This research was supported through the National Research Foundation (NRF) funded by the Ministry of Science and ICT (2020M2D9A3094213).

Citation Format: Juntae Park, Minjung Kim, Sook Ryun Park, Ki-Byung Song, Eunsung Jun, Dongryul Oh, Jeong-Won Lee, Young Sik Park, Ki-Won Song, Jeong-Sik Byeon, Bo Hyun Kim, Chang-Seok Ki, Eunhae Cho. Deep learning algorithm for cancer detection using multimodal characteristics of whole methylome sequencing of cf-DNA. [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 6697.
Abstract 670: Sex differences in the innate immune response to lung cancer
Authors: May Lauren A. , Landry Joseph W. , Martin Rebecca , Li Howard Y. , Koblinski Jennifer , Bos Paula D.
Published: April 2023

Lung cancer is the second most diagnosed cancer. Lung cancer exhibits a sex difference, though the exact mechanisms behind this difference are not well understood. Men have a higher lifetime risk of developing lung cancer and often have more severe disease than women. There are thought to be multiple factors that contribute to this difference, including the environment, lifestyle, sex hormones, and differing immune responses. Mouse tumor models of lung, breast, colon, melanoma and kidney were used in immune competent or immune compromised mouse models treated with the chemotherapy ABT-263. The study of the immune response to lung tumors utilized ex vivo killing assays, multicolor flow cytometry, and clonogenic survival, as well as humanized mice and patient-derived xenografts. We observe a sex difference in two models of lung cancer in immunocompetent mice, but not in models of breast, colon, kidney, or melanoma. This difference is dependent on the innate immune system, specifically through natural killer cells and macrophages. This sex difference is lost in ovariectomized mice. Multicolor flow cytometry shows differences in innate immune cell populations in tumors and spleens in males and females. Preliminary data suggests the pro-apoptotic ligand TRAIL secreted from innate immune cells is more effective on cells exposed to female compared to ovariectomized female mouse serum. Reduced tumor growth in female mice can be further enhanced with ABT-263, and this effect requires NK cells. Patient-derived xenografts transplanted into female humanized mice grow more slowly than those transplanted into non-humanized mice, confirming the role of the immune system in modulating tumor growth. This research opens the potential for immune stimulating therapies, combined with ABT-263, as a novel treatment approach.

Citation Format: Lauren A. May, Joseph W. Landry, Rebecca Martin, Howard Y. Li, Jennifer Koblinski, Paula D. Bos. Sex differences in the innate immune response to lung cancer [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 670.
Abstract 792: SARS-CoV-2 spike S1 mediated lung tumor regression in a mouse model
Authors: Sheinin Monica , Pahan Kalipada , Paidi Ramesh K.
Published: April 2023

Lung cancer is the leading cause of cancer related deaths worldwide, with a relatively low 5-year survival rate. Although there are some therapies against lung cancer, new effective treatment options are urgently required. Recently during the COVID-19 pandemic, we have seen that SARS-CoV-2 binds to its receptor angiotensin-converting enzyme 2 (ACE2) via spike S1 to enter the cells. This study underlines the importance of SARS-CoV-2 spike S1 in inducing death in human lung cancer cells. Interestingly, we have seen that recombinant spike S1 treatment at very low doses led to death of human A549 lung cancer cells. On the other hand, boiled recombinant SARS-CoV-2 spike S1 remained unable to induce death, suggesting that the induction of cell death in A549 cells was due to native SARS-CoV-2 spike S1 protein. SARS-CoV-2 spike S1-induced A549 cell death was also inhibited by neutralizing antibodies against spike S1 and ACE2. Moreover, our newly designed wild type ACE2-interacting domain of SARS-CoV-2 (wtAIDS), but not mAIDS, peptide also attenuated SARS-CoV-2 spike S1-induced cell death, suggesting that SARS-CoV-2 spike S1-induced death in lung cancer cells depends on its interaction with ACE2 receptor. Similarly, recombinant spike S1 treatment also led to death of H1299 and H358 human lung cancer cells. Finally, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) intoxication led to the formation tumors in lungs of A/J mice and alternate day intranasal treatment with low dose of recombinant SARS-CoV-2 spike S1 from 22-weeks of NNK insult (late stage) led to induced apoptosis and tumor regression in the lungs. These studies indicate that recombinant SARS-CoV-2 Spike S1 protein may have implications in the treatment of lung cancer.

Citation Format: Monica Sheinin, Kalipada Pahan, Ramesh K. Paidi. SARS-CoV-2 spike S1 mediated lung tumor regression in a mouse model [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 792.
Abstract 821: Targeting metastatic prostate cancer using planetary ball-milled (PBM) nanoparticles
Authors: Singh Santosh K. , Lillard James W. , Singh Rajesh
Published: April 2023

Men are most likely to develop prostate cancer (PCa), which has a high morbidity and fatality rate. Chemotherapy, the most recommended therapeutic strategy to combat PCa, has shown adverse effects on patients and develops drug-resistant PCa resulting in overall restricted survival of the patients. Many studies have demonstrated that natural compound-mediated therapy can be an effective option for treating PCa. Among the natural compounds, Thymoquinone (TQ), a derivative of Nigella sativa, has shown anti-proliferative, antioxidant, and anti-cancer effects. However, issues remain regarding its bioavailability, safety, and effective delivery system to cancer cells in vivo. In this study, we developed TQ nanoparticles (NPs) alone or in combination with DTX-encapsulated planetary ball-milled nanoparticles (PBM-NPs), formulated with starch (natural polysaccharides) inner core and biodegradable co-polymers poly (ε-caprolactone)/poly (ethylene glycol), functionalized with a prostate-specific membrane antigen (PSMA) aptamer (A10) to target the metastatic niche in PCa metastasis pre-clinical (patient-derived xenograft (PDX) and intra-tibial metastatic (LNCaP, PC-3 cells were injected directly into the tibia of SCID mice.) models. To determine the minimum effective dose (MED), efficacy, and safety of PBM-NPs, mice were treated intravenously with dose levels of vehicle control (empty-PBM-NPs), DTX alone (5 mg/kg, weekly), TQ alone (10 mg/kg, weekly), and a combination of TQ and DTX (25-fold less than maximum tolerance dose) using PBM-NPs, respectively for five weeks. Blood serum chemistry for toxicity and immunohistochemistry were performed to characterize these metastatic models. Our results showed TQ+DTX PBM NPs suppressed p-EGFR, ERK1/2, ABCB1, and Caspase3-expression, which are regulated by the EGFR-dependent pathway. We detected OPG, RANKL, PTHrP, and ET-1 immunoreactivity in all xenografts in the bone. In conclusion, sustained-release of combination PBM NPs demonstrated more significant anti-tumor activity following their conjugation to a prostate cancer cell-specific ligand, the toxicity of the drug can be reduced, and effective concentrations of the drug can be maintained locally for prolonged periods and prevention of PCa bone metastasis.

Citation Format: Santosh K. Singh, James W. Lillard, Rajesh Singh. Targeting metastatic prostate cancer using planetary ball-milled (PBM) nanoparticles [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 821.
Abstract 854: A pharmaco-pheno-multiomic integration analysis of pancreatic cancer: A highly predictive biomarker model of biomarkers of Gemcitabine/Abraxane sensitivity and resistance
Authors: Silberberg Gilad , Killick-Cole Clare , Mosesson Yaron , Khoury Haia , Ren Xuan , Gilardi Mara , Ciznadija Daniel , Schiavini Paolo , Zipeto Marianna , Ritchie Michael
Published: April 2023

The overall survival of patients diagnosed with Pancreatic Cancer remains low. Initial responses to current therapeutic interventions are below 50%, leading to a high mortality rate shortly after diagnosis. To date, only a companion diagnostic, non-specific for pancreatic cancer, has been approved for this indication. A better understanding of the tumor cell biology and resistance mechanisms may shed light onto novel therapeutic targets that improve long-term outcome and improved patient stratification. In this study, we performed an exhaustive analysis to identify predictive biomarkers for gemcitabine/abraxane sensitivity using multiomics datasets. These datasets were integrated in a pharmaco-phenotypic-multiomic (PPMO) model predictive of therapeutic sensitivity or resistance, using sparse partial least squares (sPLS). Our results reveal major cellular discriminants in genomic variants, transcriptomics, and most pronouncedly in proteomics data. Tumors exhibiting Gemcitabine/Abraxane resistance associate with increased TPRV6 RNA expression, MUC13 protein expression, and USP42 mutation among others. Prospective application of the PPMO integration model was able to accurately predict Gemcitabine/Abraxane response profiles for 4/5 additional Pancreatic samples, therefore suggesting a potential application as a predictive diagnostic tool.

Citation Format: Gilad Silberberg, Clare Killick-Cole, Yaron Mosesson, Haia Khoury, Xuan Ren, Mara Gilardi, Daniel Ciznadija, Paolo Schiavini, Marianna Zipeto, Michael Ritchie. A pharmaco-pheno-multiomic integration analysis of pancreatic cancer: A highly predictive biomarker model of biomarkers of Gemcitabine/Abraxane sensitivity and resistance [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 854.
Abstract 869: Molecular genetic positioning of small intestine and papilla of Vater carcinomas including clinicopathological classification
Authors: Okamura Yukiyasu , Nakamura Masanori
Published: April 2023

Purpose: Small intestine carcinoma (SIC) cases in Japan have recently been treated with chemotherapy according to colorectal carcinoma classification, while papilla of Vater carcinoma (PVC) cases according to cholangiocarcinoma (CHC) classification. However, few research reports support the molecular genetic validity of these therapeutic choices. Here, we investigated the clinicopathological and molecular genetic factors of SIC and PVC.

Patients and Methods: We used the data from the Japanese version of The Cancer Genome Atlas (JCGA). Additionally, molecular genetic data on gastric adenocarcinoma (GAD), colorectal adenocarcinoma (CRAD), pancreatic ductal adenocarcinoma (PDAC), and CHC were also referred to.

Results: This study consisted of tumor specimens from 12 cases of SIC and three cases of PVC treated from January 2014 to March 2019. Among them, six cases had pancreatic invasion. t-Distributed Stochastic Neighbor Embedding analysis showed that the gene expression pattern of SIC was similar not only to those of GAD and CRAD, but also to that of PDAC in the pancreatic invasion cases. In addition, PVC resembled the GAD, CRAD, and PDAC, rather than the CHC. The molecular genetic characteristics of the six patients with pancreatic invasion were: one had high microsatellite instability (MSI-High), two had a TP53 driver mutation, and three had tumor mutation burden values < 1 mutation/Mb with no driver mutation.

Conclusions: The molecular genetics of SIC and PVC suggested that they may be similar to GAD, CRAD, and PDAC. In addition, the data demonstrate that pancreatic invasive cases may be classified into several subtypes using molecular genetic factors.

Citation Format: Yukiyasu Okamura, Masanori Nakamura. Molecular genetic positioning of small intestine and papilla of Vater carcinomas including clinicopathological classification [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 869.
Abstract 899: Deciphering the benefits of variable delivery routes and molecular armoring to enhance efficacy of MUC1-CAR T-cells in targeting triple-negative breast cancer
Authors: Erler Piril , Cho Hana , Skinner Jordan , Poirot Laurent , Aranda-Orgilles Beatriz
Published: April 2023

As immune-therapies continue to develop for solid tumors, the tumor microenviroment (TME) poses many challenges that CAR T-cells need to overcome for efficient tumor cell clearance. Tumor immune evasion mechanisms, presence of immunosuppressive factors and cellular resistance to tumor infiltration are key mechanisms that the TME uses to reduce efficacy of T-cells against the tumor. Therapeutic options for triple negative breast cancer (TNBC) remain limited to date despite it being the most aggressive subtype of breast cancers and carrying the poorest prognosis. Tumor-associated MUC1 antigen is overexpressed in a large number of TNBC patients offering an effective discriminatory target for CAR T-cell therapy. Here, we present innovative strategies exploring alternative delivery routes and purposeful armoring of CAR T-cells to boost efficiency while preserving safety. To maintain anti-tumor CAR T-cell cytotoxic and proliferation in the hostile TME of solid tumors, we developed state-of-the-art multiplexed gene editing using high precision TALEN® technology. With that aim, we armored allogeneic CAR T-cells with specific attributes to release immune inflammatory cytokines and protect from inhibitory effects of the TGFB1 and PD1 pathways. A combination of strategies using allogeneic CAR T-cells with diverse attributes were evaluated against TNBC tumors in various in vivo pre-clinical models. Local CAR T-delivery resulted in effective control of tumor growth and robust antigen specific recognition. Furthermore, we assessed how the delivery route contributes to CAR-T cell distribution. CAR T-cell activity could also be increased systemically upon tumor-specific release of immunostimulatory cytokines without compromising safety. Our results demonstrate not only superior activity of armored MUC1-CAR T-cells resulting in tumor clearance but also in the recovery of normal glands. Thus, innovative strategies can be used to allow CAR T-cell efficiency in the hostile tumor microenvironment while preserving safety. Overall, our pre-clinical results underline the capability of armored allogenic MUC1-CAR T-cells to excel in the immune suppressive tumor micro-environment, suggesting that allogenic MUC1-CAR T-cell therapy could be an effective option in treating relapsed/refractory TNBC patients with limited therapeutic options.

Citation Format: Piril Erler, Hana Cho, Jordan Skinner, Laurent Poirot, Beatriz Aranda-Orgilles. Deciphering the benefits of variable delivery routes and molecular armoring to enhance efficacy of MUC1-CAR T-cells in targeting triple-negative breast cancer [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 899.
Abstract 905: A novel bioluminescent bioassay platform for the discovery and development of engineered T cell therapies for cancer
Authors: Grailer Jamison , Slater Michael , Hartnett Jim , Fan Frank , Cong Mei
Published: April 2023

Adoptive transfer of T cells genetically modified to express antigen receptor transgenes has shown promise for the treatment of cancer. Both chimeric antigen receptors (CARs) and transgenic T cell receptors (TCRs) have been used to redirect T cells in preclinical and clinical studies. TCR Therapy (TCR-T) can target essentially any tumor antigen via the major histocompatibility (MHC) system. However, the development of novel tumor antigen specific TCRs is hampered by the lack of easy-to-use model systems and sensitive readouts to facilitate candidate screening and development. Particularly, determination of transgenic TCR activation in primary and immortalized T cells is confounded by the presence of endogenous TCR expression which results in mixed alpha/beta TCR pairings and compression of assay readouts. Herein, we describe the development of a novel cell-based TCR knockout (TCR-KO) reporter assay platform for the development and characterization of novel TCR candidates. CRISPR/Cas9 was used to knockout the endogenous TCR chains in a T cell line that stably expresses a luciferase reporter gene responsive to TCR activation. Reintroduction of a transgenic TCR into the TCR-KO reporter cells results in robust antigen-specific reporter activation compared to parental reporter cells. The further development of CD4/CD8 double-positive and double-negative versions enable low and functional high avidity TCR screening with or without MHC bias. Furthermore, stable TCR-expressing reporter cells generated from TCR-KO reporter cells exhibit sufficient sensitivity and robustness for safety and specificity studies of lead TCR candidates. Together, our data demonstrate that TCR-KO reporter cells can be a useful tool for the discovery, characterization, and deployment of T cell immunotherapy.

Citation Format: Jamison Grailer, Michael Slater, Jim Hartnett, Frank Fan, Mei Cong. A novel bioluminescent bioassay platform for the discovery and development of engineered T cell therapies for cancer [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 905.
Abstract 958: Signal transduction pathway activity of TGF-β and Hedgehog as possible response predictors to checkpoint inhibition in patients with advanced melanoma; a retrospective cohort study
Authors: vanRavensteijn Stefan G. , Taurello Daniele V. , Amir Avital , Wesseling Yvonne J. , vanBrussel Anne G. , Keizer Diederick M. , Verheul Henk M. , Bol Kalijn F.
Published: April 2023

Introduction: Although immunotherapy is highly effective in patients with melanoma, not all patients respond equally well to immune checkpoint inhibition (ICI). Preclinical data indicate that TGF-β pathway activity mediates immune evasion by tumor T cell exclusion and may therefore be predictive for response. Recently, a new mRNA-based methodology has been developed to measure and quantify signal transduction pathway (STP) activities in tissue. This study was initiated to characterize the STPs in advanced melanoma samples to better understand the role of STPs in immune check point efficacy.

Method: The OncoSIGNal pathway activity profiling PCR test (InnoSIGN) was used to measure the activity of 8 different STPs (AR, PI3K, MAPK, Hedgehog (HH), TGF-β, Notch, NFkB and JAK-STAT1/2) in biopsies (FFPE) from patients with advanced melanoma (n=34) and expressed on a scale from 0 -100. A biopsy of a metastatic site was obtained prior start of ICI therapy (nivolumab or pembrolizumab). These samples were analyzed for STP activity and related to progression-free survival (PFS). Also, STP activities were compared between responders (n=15; partial or complete response) and non-responders (n=19; defined as progression within 6 months).

Results: The mean HH score of responders versus non-responders was 35.7 + 6.1 vs 41.6 + 8.7 (p=0.038), while TGF-β scores were 53.9 + 6.2 vs 56.8 + 8.2 (p=0.265), respectively. Cox regression analysis showed a hazard ratio of 1-1.1 for PFS of both HH and TGF-β (HH: p=0.032) (TGF-β: p=0.071). Kaplan Meier curves indicated a better PFS for lower HH activity at a threshold of 46 (p< 0.001) and lower MAPK activity at a threshold of 47.3 (p= 0.041). No relation with PFS was detected for TGF-β activity. No statistically significant differences were observed in STP activity between different metastatic locations ((sub)cutaneous, lymph node or visceral metastases).

Conclusion: Signal transduction pathway activity of metastatic samples, taken prior start of ICI therapy, from patients with advanced melanoma, suggest that TGF-β did not correlate with response nor PFS but increased HH and MAPK STP activity may relate towards a worse PFS from ICI therapy.

Citation Format: Stefan G. vanRavensteijn, Daniele V. Taurello, Avital Amir, Yvonne J. Wesseling, Anne G. vanBrussel, Diederick M. Keizer, Henk M. Verheul, Kalijn F. Bol. Signal transduction pathway activity of TGF-β and Hedgehog as possible response predictors to checkpoint inhibition in patients with advanced melanoma; a retrospective cohort study [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 958.
Supplementary Figure 1 from RETRACTED: Minocycline Targets the NF-κB Nexus through Suppression of TGF-β1-TAK1-IκB Signaling in Ovarian Cancer
Authors: Ataie-Kachoie Parvin , Badar Samina , Morris David L. , Pourgholami Mohammad H.
Published: April 2023

PDF file - 1416K, Minocycline ablated TAK-1-induced activation of NF-кB.
Supplementary Data from KRAS Activation in Gastric Adenocarcinoma Stimulates Epithelial-to-Mesenchymal Transition to Cancer Stem–Like Cells and Promotes Metastasis
Authors: Yoon Changhwan , Till Jacob , Cho Soo-Jeong , Chang Kevin K. , Lin Jian-xian , Huang Chang-ming , Ryeom Sandra , Yoon Sam S.
Published: April 2023

Supplementary Table 1. Clinicopathologic characteristics of patients whose tumor samples were included in the tissue microarray (Figure 2).
FigureS5 from Adipokine Apelin/APJ Pathway Promotes Peritoneal Dissemination of Ovarian Cancer Cells by Regulating Lipid Metabolism
Authors: Dogra Samrita , Neelakantan Deepika , Patel Maulin M. , Griesel Beth , Olson Ann , Woo Sukyung
Published: April 2023

Fatty acid oxidation in APJ knockdown cells
Supplementary Tables 1-3 and Supplemental Figures 1-7 from A TGFβ-Dependent Stromal Subset Underlies Immune Checkpoint Inhibitor Efficacy in DNA Mismatch Repair–Deficient/Microsatellite Instability-High Colorectal Cancer
Authors: Endo Eisei , Okayama Hirokazu , Saito Katsuharu , Nakajima Shotaro , Yamada Leo , Ujiie Daisuke , Kase Koji , Fujita Shotaro , Endo Hisahito , Sakamoto Wataru , Saito Motonobu , Saze Zenichiro , Momma Tomoyuki , Ohki Shinji , Mimura Kosaku , Kono Koji
Published: April 2023

Table S1. Clinical Characteristics of multiple cohorts Table S2. Association of MSI-H subtypes with clinical and genomic characteristics in multiple cohorts Table S3. Association of dMMR subtypes with clinical characteristics in Cohort 4 Supplementary Figure S1. Prognostic significance of MSI/MMR status in patients with colorectal cancer. Supplementary Figure S2. Prognostic significance of TGFB expression in patients with MSI-H colorectal cancer. Supplementary Figure S3. Expression z-scores for genes encoding immune checkpoint molecules for MSI-H-Stromal, MSI-H-Conventional and MSS tumors in Cohort 1. Supplementary Figure S4. Correlation of TGFβ-stromal signature (TBSS) z-score with stage of disease in Cohort 2 (A) and Cohort 3 (B). Supplementary Figure S5. Expression z-scores for genes encoding transcription factors that regulate Th cell differentiation, including TBX21 (Th1), GATA3 (Th2) and RORC (Th17) for MSI-H-Stromal, MSI-H-Conventional and MSS tumors in Cohort 1 (A), Cohort 2 (B) and Cohort 3 (C). Supplementary Figure S6. Genomic aberrations in 43 TGFβ pathway genes, including TGFβ superfamily ligands, receptors and receptor-associated proteins, SMADs, and adaptor molecules. Supplementary Figure S7. Correlation between RNA-seq-based transcriptomic TBSS and mass spectrometry-based proteomic TBSS in the CPTAC dataset.
Table S1 from AXL Inhibition Induces DNA Damage and Replication Stress in Non–Small Cell Lung Cancer Cells and Promotes Sensitivity to ATR Inhibitors
Authors: Ramkumar Kavya , Stewart C. Allison , Cargill Kasey R. , Della Corte Carminia M. , Wang Qi , Shen Li , Diao Lixia , Cardnell Robert J. , Peng David H. , Rodriguez B. Leticia , Fan You-Hong , Heymach John V. , Wang Jing , Gay Carl M. , Gibbons Don L. , Byers Lauren A.
Published: April 2023

Table S1. Mutations in key oncogenes in lung cancer cell lines tested.
Supplementary Fig. S7 from AXL Inhibition Induces DNA Damage and Replication Stress in Non–Small Cell Lung Cancer Cells and Promotes Sensitivity to ATR Inhibitors
Authors: Ramkumar Kavya , Stewart C. Allison , Cargill Kasey R. , Della Corte Carminia M. , Wang Qi , Shen Li , Diao Lixia , Cardnell Robert J. , Peng David H. , Rodriguez B. Leticia , Fan You-Hong , Heymach John V. , Wang Jing , Gay Carl M. , Gibbons Don L. , Byers Lauren A.
Published: April 2023

Supplementary Fig. S7: Effect of AXL and ATR inhibitor combination on cell cycle progression of NSCLC and LCNEC cells.
Supplementary Data from Chk1 Inhibition Potently Blocks STAT3 Tyrosine705 Phosphorylation, DNA-Binding Activity, and Activation of Downstream Targets in Human Multiple Myeloma Cells
Authors: Zhou Liang , Pei Xinyan , Zhang Yu , Ning Yanxia , Li Lin , Hu Xiaoyan , Chalasani Sri Lakshmi , Sharma Kanika , Nkwocha Jewel , Yu Jonathan , Bandyopadhyay Dipankar , Sebti Said M. , Grant Steven
Published: April 2023

Supplementary Data from Chk1 Inhibition Potently Blocks STAT3 Tyrosine705 Phosphorylation, DNA-Binding Activity, and Activation of Downstream Targets in Human Multiple Myeloma Cells
Supplementary Figure from The C-terminus of Gain-of-Function Mutant p53 R273H Is Required for Association with PARP1 and Poly-ADP-Ribose
Authors: Lundine Devon , Annor George K. , Chavez Valery , Maimos Styliana , Syed Zafar , Jiang Shuhong , Ellison Viola , Bargonetti Jill
Published: April 2023

Supplementary Figure from The C-terminus of Gain-of-Function Mutant p53 R273H Is Required for Association with PARP1 and Poly-ADP-Ribose
Supplementary Table from Tumor Microenvironment Acidity Triggers Lipid Accumulation in Liver Cancer via SCD1 Activation
Authors: Ding Ming , Zhang Shuwei , Guo Yajuan , Yao Jingjing , Shen Qinghong , Huang Min , Chen Wenbo , Yu Shaofang , Zheng Yaqiu , Lin Yuefang , Yan Wenxin , Liu Zhongqiu , Su Tao , Lu Linlin
Published: April 2023

Supplementary Table from Tumor Microenvironment Acidity Triggers Lipid Accumulation in Liver Cancer via SCD1 Activation
Supplementary Data from Pan-Cancer HLA Gene-Mediated Tumor Immunogenicity and Immune Evasion
Authors: Gong Xutong , Karchin Rachel
Published: April 2023

Supplementary Data from Pan-Cancer HLA Gene-Mediated Tumor Immunogenicity and Immune Evasion
Supplementary Table 2 from XIAP and PHB1 Regulate Anoikis through Competitive Binding to TRAF6
Authors: Yang Bo , Lou Chao , Chen Shengkai , Zhang Zhiyuan , Xu Qin
Published: April 2023

Table S2. The binding sites between TRAF6 and PHB1 were predicted by the docking algorithm Cluspro.
Supplementary Figure 6 from XIAP and PHB1 Regulate Anoikis through Competitive Binding to TRAF6
Authors: Yang Bo , Lou Chao , Chen Shengkai , Zhang Zhiyuan , Xu Qin
Published: April 2023

S6. Quantitative analysis of protein expression.
Supplementary Figure S8 from Sox2 Is an Oncogenic Driver of Small-Cell Lung Cancer and Promotes the Classic Neuroendocrine Subtype
Authors: Voigt Ellen , Wallenburg Madeline , Wollenzien Hannah , Thompson Ethan , Kumar Kirtana , Feiner Joshua , McNally Moira , Friesen Hunter , Mukherjee Malini , Afeworki Yohannes , Kareta Michael S.
Published: April 2023

SOX2 CRISPR knockdown and NEUROD1 localization in relation to Figure 4
Supplementary Figure 1 from XIAP and PHB1 Regulate Anoikis through Competitive Binding to TRAF6
Authors: Yang Bo , Lou Chao , Chen Shengkai , Zhang Zhiyuan , Xu Qin
Published: April 2023

S1. Testing and validation of siRNA against TRAF6, XIAP and PHB1.
Supplementary Figure S1 from Sox2 Is an Oncogenic Driver of Small-Cell Lung Cancer and Promotes the Classic Neuroendocrine Subtype
Authors: Voigt Ellen , Wallenburg Madeline , Wollenzien Hannah , Thompson Ethan , Kumar Kirtana , Feiner Joshua , McNally Moira , Friesen Hunter , Mukherjee Malini , Afeworki Yohannes , Kareta Michael S.
Published: April 2023

Characterization of SCLC lesions in Figure 1
Supplementary Data from Diurnal Expression of PD-1 on Tumor-Associated Macrophages Underlies the Dosing Time-Dependent Antitumor Effects of the PD-1/PD-L1 Inhibitor BMS-1 in B16/BL6 Melanoma-Bearing Mice
Authors: Tsuruta Akito , Shiiba Yuki , Matsunaga Naoya , Fujimoto Marina , Yoshida Yuya , Koyanagi Satoru , Ohdo Shigehiro
Published: April 2023

Supplementary Data from Diurnal Expression of PD-1 on Tumor-Associated Macrophages Underlies the Dosing Time-Dependent Antitumor Effects of the PD-1/PD-L1 Inhibitor BMS-1 in B16/BL6 Melanoma-Bearing Mice
Supplementary Data from Ecdysoneless Overexpression Drives Mammary Tumorigenesis through Upregulation of C-MYC and Glucose Metabolism
Authors: Mohapatra Bhopal C. , Mirza Sameer , Bele Aditya , Gurumurthy Channabasavaiah B. , Raza Mohsin , Saleem Irfana , Storck Matthew D. , Sarkar Aniruddha , Kollala Sai Sundeep , Shukla Surendra K. , Southekal Siddesh , Wagner Kay-Uwe , Qiu Fang , Lele Subodh M. , Alsaleem Mansour A. , Rakha Emad A. , Guda Chittibabu , Singh Pankaj K. , Cardiff Robert D. , Band Hamid , Band Vimla
Published: April 2023

Supplementary Data from Ecdysoneless Overexpression Drives Mammary Tumorigenesis through Upregulation of C-MYC and Glucose Metabolism
Supplementary Table from Targeting Metabolic Adaptations in the Breast Cancer–Liver Metastatic Niche Using Dietary Approaches to Improve Endocrine Therapy Efficacy
Authors: Zuo Qianying , Mogol Ayca Nazli , Liu Yu-Jeh , Santaliz Casiano Ashlie , Chien Christine , Drnevich Jenny , Imir Ozan Berk , Kulkoyluoglu-Cotul Eylem , Park Nicole Hwajin , Shapiro David J. , Park Ben Ho , Ziegler Yvonne , Katzenellenbogen Benita S. , Aranda Evelyn , O'Neill John D. , Raghavendra Akshara Singareeka , Tripathy Debu , Madak Erdogan Zeynep
Published: April 2023

Supplementary Table from Targeting Metabolic Adaptations in the Breast Cancer–Liver Metastatic Niche Using Dietary Approaches to Improve Endocrine Therapy Efficacy
Data from ARF Regulates the Stability of p16 Protein Via REGγ-Dependent Proteasome Degradation
Authors: Kobayashi Takashi , Wang Jingqiang , Al-Ahmadie Hikmat , Abate-Shen Cory
Published: April 2023

Abstract
The cell-cycle regulatory gene INK4A-ARF (CDKN2A) has two alternative transcripts that produce entirely different proteins, namely p14ARF and p16, which have complementary functions as regulators of p53 and pRB tumor suppressor pathways, respectively. The unusual organization of INK4A-ARF has long led to speculation of a need for coordinated regulation of p14ARF and p16. We now show that p14ARF (ARF) regulates the stability of p16 protein in human cancer cell lines, as well as in mouse embryonic fibroblasts (MEFs). In particular, ARF promotes rapid degradation of p16 protein, which is mediated by the proteasome and, more specifically, by interaction of ARF with one of its subunits, REGγ. Furthermore, this ARF-dependent destabilization of p16 can be abrogated by knockdown of REGγ or by pharmacologic blockade of its nuclear export. Thus, our findings have uncovered a novel crosstalk of 2 key tumor suppressors mediated by a REGγ-dependent mechanism. The ability of ARF to control p16 stability may influence cell-cycle function.

Implications: The ability of ARF to control p16 stability may influence cell cycle function.

Visual Overview: http://mcr.aacrjournals.org/content/11/8/828/F1.large.jpg. Mol Cancer Res; 11(8); 828–33. ©2013 AACR.
Data from C-C Chemokine Receptor 5 on Pulmonary Mesenchymal Cells Promotes Experimental Metastasis via the Induction of Erythroid Differentiation Regulator 1
Authors: Mango Robert L. , Wu Qing Ping , West Michelle , McCook Everett C. , Serody Jonathan S. , van Deventer Hendrik W.
Published: April 2023

Abstract
C-C Chemokine receptor 5 knockout (Ccr5−/−) mice develop fewer experimental pulmonary metastases than wild-type (WT) mice. This phenomenon was explored by applying gene expression profiling to the lungs of mice with these metastases. Consequently, erythroid differentiation regulator 1 (Erdr1) was identified as upregulated in the WT mice. Though commonly associated with bone marrow stroma, Erdr1 was differentially expressed in WT pulmonary mesenchymal cells (PMC) and murine embryonic fibroblasts (MEF). Moreover, the Ccr5 ligand Ccl4 increased its expression by 3.36 ± 0.14–fold. Ccr5 signaling was dependent on the mitogen-activated protein kinase kinase (Map2k) but not the phosphoinositide 3-kinase (Pi3k) pathway because treatment with U0126 inhibited upregulation of Erdr1, but treatment with LY294002 increased the expression by 3.44 ± 0.92–fold (P < 0.05). The effect Erdr1 on B16-F10 melanoma metastasis was verified by the adoptive transfer of WT MEFs into Ccr5−/− mice. In this model, MEFs that had been transduced with Erdr1 short hairpin RNA (shRNA) lowered metastasis by 33% compared with control transduced MEFs. The relevance of ERDR1 on human disease was assessed by coculturing chronic lymphocytic leukemia (CLL) cells with M2-10B4 stromal cells that had been transfected with shRNA or control plasmids. After 96 hours of coculture, the cell counts were higher with control cell lines than with Erdr1 knockdown lines [odds ratio (OR), 1.88 ± 0.27, 2.52 ± 0.66, respectively]. This increase was associated with a decrease in apoptotic cells (OR, 0.69 ± 0.18, 0.58 ± 0.12, respectively).

Implications: Therefore, ERDR1 is a stromal-derived factor that promotes cancer cell survival in vitro and in an experimental metastasis model. Mol Cancer Res; 12(2); 274–82. ©2013 AACR.
Data from Nuclear Expression of β-Catenin Promotes RB Stability and Resistance to TNF-Induced Apoptosis in Colon Cancer Cells
Authors: Han Jinbo , Soletti Rossana C. , Sadarangani Anil , Sridevi Priya , Ramirez Michael E. , Eckmann Lars , Borges Helena L. , Wang Jean Y.J.
Published: April 2023

Abstract
Tumor necrosis factor (TNF)-α promotes tumor development under chronic inflammation. Because TNF also activates caspase-8, selective inhibition of TNF-induced extrinsic apoptosis would be required for inflammation-associated tumor growth. In a mouse model of inflammation-associated colon carcinogenesis, we found nuclear expression of β-catenin in tumors of wild-type, but not mutant, mice that were made resistant to TNF-induced apoptosis by a germline mutation blocking caspase cleavage of the retinoblastoma (RB) protein, despite similar frequencies of β-catenin exon-3 mutations in these two genetic backgrounds. TNF-induced apoptosis was also attenuated in human colon cancer cell lines with genetically activated β-catenin. However, we found that HCT116 cells, which contain an activated allele of β-catenin but do not express nuclear β-catenin, were sensitive to TNF-induced apoptosis. In HCT116 cells, TNF stimulated efficient RB cleavage that preceded chromatin condensation. In contrast, TNF did not induce RB cleavage in colon cancer cells expressing nuclear β-catenin and these cells could be sensitized to basal and/or TNF-induced apoptosis by the knockdown of β-catenin or RB. In the apoptosis-resistant colon cancer cells, knockdown of β-catenin led to a reduction in the RB protein without affecting RB mRNA. Furthermore, ectopic expression of the caspase-resistant, but not the wild-type, RB re-established resistance to TNF-induced caspase activation in colon cancer cells without β-catenin. Together, these results suggest that nuclear β-catenin–dependent RB stabilization suppresses TNF-induced apoptosis in caspase-8–positive colon cancer cells.

Visual Overview: http://mcr.aacrjournals.org/content/11/3/207/F1.large.jpg.

Mol Cancer Res; 11(3); 207–18. ©2012 AACR.
Data from Minocycline Targets the NF-κB Nexus through Suppression of TGF-β1-TAK1-IκB Signaling in Ovarian Cancer
Authors: Ataie-Kachoie Parvin , Badar Samina , Morris David L. , Pourgholami Mohammad H.
Published: April 2023

Abstract
Substantial evidence supports the critical role of NF-κB in ovarian cancer. Minocycline, a tetracycline, has been shown to exhibit beneficial effects in this malignancy through regulation of a cohort of genes that overlap significantly with the NF-κB transcriptome. Here, it was examined whether or not the molecular mechanism could be attributed to modulation of NF-κB signaling using a combination of in vitro and in vivo models. Minocycline suppressed constitutive NF-κB activation in OVCAR-3 and SKOV-3 ovarian carcinoma cells and was correlated with attenuation of IκBα kinase (IKK) activation, IκBα phosphorylation and degradation, and p65 phosphorylation and nuclear translocation. The inhibition of IKK was found to be associated with suppression of TGF-β-activated-kinase-1 (TAK1) activation and its dissociation from TAK1-binding-protein-1 (TAB1), an indispensable functional mediator between TGF-β and TAK1. Further studies demonstrated that minocycline downregulated TGF-β1 expression. Enforced TGF-β1 expression induced NF-κB activity, and minocycline rescued this effect. Consistent with this finding, TGF-β1 knockdown suppressed NF-κB activation and abrogated the inhibitory effect of minocycline on this transcription factor. These results suggest that the minocycline-induced suppression of NF-κB activity is mediated, in part, through inhibition of TGF-β1. Furthermore, the influence of minocycline on NF-κB pathway activation was examined in female nude mice harboring intraperitoneal OVCAR-3 tumors. Both acute and chronic administration of minocycline led to suppression of p65 phosphorylation and nuclear translocation accompanied by downregulation of NF-κB activity and endogenous protein levels of its target gene products. These data reveal the therapeutic potential of minocycline as an agent targeting the pro-oncogenic TGF-β—NF-κB axis in ovarian cancer.

Implications: This preclinical study lends support to the notion that ovarian cancer management would benefit from administration of minocycline. Mol Cancer Res; 11(10); 1279–91. ©2013 AACR.
Data from miR-150 Blocks MLL-AF9–Associated Leukemia through Oncogene Repression
Authors: Bousquet Marina , Zhuang Guoqing , Meng Cong , Ying Wei , Cheruku Patali S. , Shie Andrew T. , Wang Stephanie , Ge Guangtao , Wong Piu , Wang Gang , Safe Stephen , Zhou Beiyan
Published: April 2023

Abstract
The microRNA miR-150, a critical regulator of hematopoiesis, is downregulated in mixed-lineage leukemia (MLL). In this study, miR-150 acts as a potent leukemic tumor suppressor by blocking the oncogenic properties of leukemic cells. By using MLL-AF9–transformed cells, we demonstrate that ectopic expression of miR-150 inhibits blast colony formation, cell growth, and increases apoptosis in vitro. More importantly, ectopic expression of miR-150 in MLL-AF9–transformed cells completely blocked the development of myeloid leukemia in transplanted mice. Furthermore, gene expression profiling revealed that miR-150 altered the expression levels of more than 30 “stem cell signature” genes and many others that are involved in critical cancer pathways. In addition to the known miR-150 target Myb, we also identified Cbl and Egr2 as bona fide targets and shRNA-mediated suppression of these genes recapitulated the pro-apoptotic effects observed in leukemic cells with miR-150 ectopic expression. In conclusion, we demonstrate that miR-150 is a potent leukemic tumor suppressor that regulates multiple oncogenes.

Implications: These data establish new, key players for the development of therapeutic strategies to treat MLL-AF9–related leukemia. Mol Cancer Res; 11(8); 912–22. ©2013 AACR.
Data from A Modified HSP70 Inhibitor Shows Broad Activity as an Anticancer Agent
Authors: Balaburski Gregor M. , Leu Julia I.-Ju , Beeharry Neil , Hayik Seth , Andrake Mark D. , Zhang Gao , Herlyn Meenhard , Villanueva Jessie , Dunbrack Roland L. , Yen Tim , George Donna L. , Murphy Maureen E.
Published: April 2023

Abstract
The stress-induced HSP70 is an ATP-dependent molecular chaperone that plays a key role in refolding misfolded proteins and promoting cell survival following stress. HSP70 is marginally expressed in nontransformed cells, but is greatly overexpressed in tumor cells. Silencing HSP70 is uniformly cytotoxic to tumor but not normal cells; therefore, there has been great interest in the development of HSP70 inhibitors for cancer therapy. Here, we report that the HSP70 inhibitor 2-phenylethynesulfonamide (PES) binds to the substrate-binding domain of HSP70 and requires the C-terminal helical “lid” of this protein (amino acids 573–616) to bind. Using molecular modeling and in silico docking, we have identified a candidate binding site for PES in this region of HSP70, and we identify point mutants that fail to interact with PES. A preliminary structure–activity relationship analysis has revealed a derivative of PES, 2-(3-chlorophenyl) ethynesulfonamide (PES-Cl), which shows increased cytotoxicity and ability to inhibit autophagy, along with significantly improved ability to extend the life of mice with pre-B-cell lymphoma, compared with the parent compound (P = 0.015). Interestingly, we also show that these HSP70 inhibitors impair the activity of the anaphase promoting complex/cyclosome (APC/C) in cell-free extracts, and induce G2–M arrest and genomic instability in cancer cells. PES-Cl is thus a promising new anticancer compound with several notable mechanisms of action. Mol Cancer Res; 11(3); 219–29. ©2013 AACR.
Data from RASSF1A-Mediated Regulation of AREG via the Hippo Pathway in Hepatocellular Carcinoma
Authors: Ahn Ei Yong , Kim Ji Su , Kim Gi Jeong , Park Young Nyun
Published: April 2023

Abstract
Ras association domain family 1 isoform A (RASSF1A) is a tumor suppressor that is methylated in many human cancers, including hepatocellular carcinoma (HCC). RASSF1A has been shown to suppress tumors via activation of the Hippo tumor suppressor pathway, including mammalian STE20-like kinase (MST). Amphiregulin (AREG), a target gene for Yes-associated protein (YAP), is a known oncogenic component of the Hippo pathway; however, the tumor-suppressive effect of RASSF1A on AREG in regard to regulation of the Hippo pathway remains unclear in HCC. Overexpression of RASSF1A in HCC cells, which lack functional RASSF1A, significantly inhibited cell proliferation and induced apoptosis by activating the Hippo pathway. Consequently, overexpression of RASSF1A inhibited the oncogenic functions of YAP, leading to a significant reduction in AREG secretion via regulation of the Hippo pathway. In human specimens, greater expression of RASSF1A was observed in chronic hepatitis/cirrhosis than in HCC, whereas expression of YAP and AREG was higher in 81% and 86% of HCC than in corresponding chronic hepatitis/cirrhosis, respectively. Furthermore, RASSF1A protein gradually decreased as multistep hepatocarcinogenesis progressed from chronic hepatitis/cirrhosis dysplastic nodules toward HCC, whereas the protein expression of YAP and AREG gradually increased. These findings provide mechanistic insight into the regulation of YAP and AREG by RASSF1A in human multistep hepatocarcinogenesis. Mol Cancer Res; 11(7); 748–58. ©2013 AACR.
Data from Tumor-Secreted LOXL2 Activates Fibroblasts through FAK Signaling
Authors: Barker Holly E. , Bird Demelza , Lang Georgina , Erler Janine T.
Published: April 2023

Abstract
Cancer-associated fibroblasts enhance cancer progression when activated by tumor cells through mechanisms not yet fully understood. Blocking mammary tumor cell–derived lysyl oxidase-like 2 (LOXL2) significantly inhibited mammary tumor cell invasion and metastasis in transgenic and orthotopic mouse models. Here, we discovered that tumor-derived LOXL2 directly activated stromal fibroblasts in the tumor microenvironment. Genetic manipulation or antibody inhibition of LOXL2 in orthotopically grown mammary tumors reduced the expression of α-smooth muscle actin (α-SMA). Using a marker for reticular fibroblasts, it was determined that expression of α-SMA was localized to fibroblasts recruited from the host tissue. This marker also revealed that the matrix present in tumors with reduced levels of LOXL2 was more scattered compared with control tumors which exhibited matrices with dense, parallel alignments. Importantly, in vitro assays revealed that tumor-derived LOXL2 and a recombinant LOXL2 protein induced fibroblast branching on collagen matrices, as well as increased fibroblast-mediated collagen contraction and invasion of fibroblasts through extracellular matrix. Moreover, LOXL2 induced the expression of α-SMA in fibroblasts grown on collagen matrices. Mechanistically, it was determined that LOXL2 activated fibroblasts through integrin-mediated focal adhesion kinase activation. These results indicate that inhibition of LOXL2 in tumors not only reduces tumor cell invasion but also attenuates the activation of host cells in the tumor microenvironment.

Implications: These findings reveal new insight into the mechanisms of fibroblast activation, a novel function of LOXL2, and further highlight the importance of generating LOXL2-targeted therapies for the prevention of tumor progression and metastasis. Mol Cancer Res; 11(11); 1425–36. ©2013 AACR.