bluuebunny/crossref_metadata_2025 huggingface dataset:
A perspective on active glassy dynamics in biological systems
Authors: Sadhukhan Souvik , Dey Subhodeep , Karmakar Smarajit , Nandi Saroj Kumar
Published: June 2024

Dynamics is central to living systems. Many experiments in the last two decades have revealed glassy dynamics in diverse biological systems, showing a transition between a solid-like and a fluid-like state. The biological systems have nontrivial characteristics: they are active with novel control parameters and immense complexity. Moreover, glassiness in these systems has many nontrivial features, such as the behavior of dynamical heterogeneity and readily found sub-Arrhenius relaxation dynamics. Theoretical treatments of these systems are generally challenging due to their nonequilibrium nature and large number of control parameters. We first discuss the primary characteristics of a glassy system and then review the experiments that started this field and simulations that have led to a deeper understanding. We also show that despite many challenges in these systems, it has been possible to develop theories that have played a significant role in unifying diverse phenomena and bringing insights. The field is at the interface of physics and biology, freely borrowing tools from both disciplines. We first discuss the known equilibrium scenario and then present the primary changes under activity.
Utility-Oriented Reranking with Counterfactual Context
Authors: Xi Yunjia , Liu Weiwen , Dai Xinyi , Tang Ruiming , Liu Qing , Zhang Weinan , Yu Yong
Published: June 2024

As a critical task for large-scale commercial recommender systems, reranking rearranges items in the initial ranking lists from the previous ranking stage to better meet users’ demands. Foundational work in reranking has shown the potential of improving recommendation results by uncovering mutual influence among items. However, rather than considering the context of initial lists as most existing methods do, an ideal reranking algorithm should consider the
counterfactual context—
the position and the alignment of the items in the
reranked lists
. In this work, we propose a novel pairwise reranking framework, Utility-oriented Reranking with Counterfactual Context (URCC), which maximizes the overall utility after reranking efficiently. Specifically, we first design a utility-oriented evaluator, which applies Bi-LSTM and graph attention mechanism to estimate the listwise utility via the
counterfactual context
modeling. Then, under the guidance of the evaluator, we propose a pairwise reranker model to find the most suitable position for each item by swapping misplaced item pairs. Extensive experiments on two benchmark datasets and a proprietary real-world dataset demonstrate that URCC significantly outperforms the state-of-the-art models in terms of both relevance-based metrics and utility-based metrics.
Early Indicators of the Impact of Using AI in Mammography Screening for Breast Cancer
Authors: Lauritzen Andreas D. , Lillholm Martin , Lynge Elsebeth , Nielsen Mads , Karssemeijer Nico , Vejborg Ilse
Published: June 2024

Full implementation of an artificial intelligence system considerably reduced the workload of breast radiologists while improving screening performance in a regional Danish population-based breast cancer screening program.
Supplementary Figure S6 from A Histone Methylation–MAPK Signaling Axis Drives Durable Epithelial–Mesenchymal Transition in Hypoxic Pancreatic Cancer
Authors: Brown Brooke A. , Myers Paul J. , Adair Sara J. , Pitarresi Jason R. , Sah-Teli Shiv K. , Campbell Logan A. , Hart William S. , Barbeau Michelle C. , Leong Kelsey , Seyler Nicholas , Kane William , Lee Kyoung Eun , Stelow Edward , Jones Marieke , Simon M. Celeste , Koivunen Peppi , Bauer Todd W. , Stanger Ben Z. , Lazzara Matthew J.
Published: June 2024

Supplementary Figure S6
Supplementary Fig. S4 from Whole-Genome DNA Methylation Profiling of Intrahepatic Cholangiocarcinoma Reveals Prognostic Subtypes with Distinct Biological Drivers
Authors: Liao Haotian , Chen Xing , Wang Haichuan , Lin Youpei , Chen Lu , Yuan Kefei , Liao Mingheng , Jiang Hanyu , Peng Jiajie , Wu Zhenru , Huang Jiwei , Li Jiaxin , Zeng Yong
Published: June 2024

Supplementary Fig. S4
Supplementary Fig. S3 from Whole-Genome DNA Methylation Profiling of Intrahepatic Cholangiocarcinoma Reveals Prognostic Subtypes with Distinct Biological Drivers
Authors: Liao Haotian , Chen Xing , Wang Haichuan , Lin Youpei , Chen Lu , Yuan Kefei , Liao Mingheng , Jiang Hanyu , Peng Jiajie , Wu Zhenru , Huang Jiwei , Li Jiaxin , Zeng Yong
Published: June 2024

Supplementary Fig. S3
Supplementary Fig. S14 from Whole-Genome DNA Methylation Profiling of Intrahepatic Cholangiocarcinoma Reveals Prognostic Subtypes with Distinct Biological Drivers
Authors: Liao Haotian , Chen Xing , Wang Haichuan , Lin Youpei , Chen Lu , Yuan Kefei , Liao Mingheng , Jiang Hanyu , Peng Jiajie , Wu Zhenru , Huang Jiwei , Li Jiaxin , Zeng Yong
Published: June 2024

Supplementary Fig. S14
Supplementary Table S1. HCC Patient Data for Organoid Culture from SPARC Stabilizes ApoE to Induce Cholesterol-Dependent Invasion and Sorafenib Resistance in Hepatocellular Carcinoma
Authors: Wan Shan , He Quan-Yao , Yang Yun , Liu Feng , Zhang Xue , Guo Xin , Niu Hui , Wang Yi , Liu Yi-Xuan , Ye Wen-Long , Li Xiu-Ming , ZhuanSun Xue-Mei , Sun Pu , He Xiao-Shun , Hu Guang , Breuhahn Kai , Zhao Hua , Wu Guo-Qiang , Wu Hua
Published: June 2024

Supplementary Table S1.HCC Patient Data for Organoid Culture
Supplementary Figure S7 from Obesogenic High-Fat Diet and MYC Cooperate to Promote Lactate Accumulation and Tumor Microenvironment Remodeling in Prostate Cancer
Authors: Boufaied Nadia , Chetta Paolo , Hallal Tarek , Cacciatore Stefano , Lalli Daniela , Luthold Carole , Homsy Kevin , Imada Eddie L. , Syamala Sudeepa , Photopoulos Cornelia , Di Matteo Anna , de Polo Anna , Storaci Alessandra Maria , Huang Ying , Giunchi Francesca , Sheridan Patricia A. , Michelotti Gregory , Nguyen Quang-De , Zhao Xin , Liu Yang , Davicioni Elai , Spratt Daniel E. , Sabbioneda Simone , Maga Giovanni , Mucci Lorelei A. , Ghigna Claudia , Marchionni Luigi , Butler Lisa M. , Ellis Leigh , Bordeleau François , Loda Massimo , Vaira Valentina , Labbé David P. , Zadra Giorgia
Published: June 2024

Supplementary Figure S7 shows the output of mouse-based deconvolution models ImmuCC and mMCP.
Supplementary Figure 5 from SPARC Stabilizes ApoE to Induce Cholesterol-Dependent Invasion and Sorafenib Resistance in Hepatocellular Carcinoma
Authors: Wan Shan , He Quan-Yao , Yang Yun , Liu Feng , Zhang Xue , Guo Xin , Niu Hui , Wang Yi , Liu Yi-Xuan , Ye Wen-Long , Li Xiu-Ming , ZhuanSun Xue-Mei , Sun Pu , He Xiao-Shun , Hu Guang , Breuhahn Kai , Zhao Hua , Wu Guo-Qiang , Wu Hua
Published: June 2024

SPARC stimulates tumor cell migration in HCC cell lines.
Supplementary Figure 2 from SPARC Stabilizes ApoE to Induce Cholesterol-Dependent Invasion and Sorafenib Resistance in Hepatocellular Carcinoma
Authors: Wan Shan , He Quan-Yao , Yang Yun , Liu Feng , Zhang Xue , Guo Xin , Niu Hui , Wang Yi , Liu Yi-Xuan , Ye Wen-Long , Li Xiu-Ming , ZhuanSun Xue-Mei , Sun Pu , He Xiao-Shun , Hu Guang , Breuhahn Kai , Zhao Hua , Wu Guo-Qiang , Wu Hua
Published: June 2024

SPARC interacts with ApoE in regulating cholesterol in HCC cells.
Supplementary Table S2 from ACSL4-Mediated Membrane Phospholipid Remodeling Induces Integrin β1 Activation to Facilitate Triple-Negative Breast Cancer Metastasis
Authors: Qiu Yuxiang , Wang Xing , Sun Yan , Jin Ting , Tang Rui , Zhou Xinyue , Xu Ming , Gan Yubi , Wang Rui , Luo Haojun , Liu Manran , Tang Xi
Published: June 2024

Supplementary Table S2
Supplementary Table S5 from The Deep Learning Framework iCanTCR Enables Early Cancer Detection Using the T-cell Receptor Repertoire in Peripheral Blood
Authors: Cai Yideng , Luo Meng , Yang Wenyi , Xu Chang , Wang Pingping , Xue Guangfu , Jin Xiyun , Cheng Rui , Que Jinhao , Zhou Wenyang , Pang Boran , Xu Shouping , Li Yu , Jiang Qinghua , Xu Zhaochun
Published: June 2024

Results of iCanTCR, DeepCAT and DeepRC for cancer detection of three cancer types including breast, lung, and melanoma
Supplementary Table S4 from The Deep Learning Framework iCanTCR Enables Early Cancer Detection Using the T-cell Receptor Repertoire in Peripheral Blood
Authors: Cai Yideng , Luo Meng , Yang Wenyi , Xu Chang , Wang Pingping , Xue Guangfu , Jin Xiyun , Cheng Rui , Que Jinhao , Zhou Wenyang , Pang Boran , Xu Shouping , Li Yu , Jiang Qinghua , Xu Zhaochun
Published: June 2024

Details of the original TCR-seq datasets used in this study
Supplementary Figure S9 from Repolarization of Immunosuppressive Macrophages by Targeting SLAMF7-Regulated CCL2 Signaling Sensitizes Hepatocellular Carcinoma to Immunotherapy
Authors: Weng Jialei , Wang Zheng , Hu Zhiqiu , Xu Wenxin , Sun Jia-Lei , Wang Fu , Zhou Qiang , Liu Shaoqing , Xu Min , Xu Minghao , Gao Dongmei , Shen Ying-Hao , Yi Yong , Shi Yi , Dong Qiongzhu , Zhou Chenhao , Ren Ning
Published: June 2024

(A) Immunoblot assays showing the phosphorylated or non-phosphorylated ERK1/2, p38, and JNK proteins in the indicated HCC cells. (B) Flow cytometry analyses of CD80 and CD206 expressions in THP-1-differentiated macrophages cocultured with the indicated HCC cells. (C) Chemotaxis assays showing the effect of supernatants from the indicated coculture systems on the migration abilities of THP-1-differentiated macrophages. Scale bar: 100 μm. (D) qPCR and ELISA analyses of CCL2 transcriptional and secretory levels in the indicated HCC cells. (E) Immunoblot assays of phosphorylated or non-phosphorylated ERK1/2, p38, and JNK proteins in the indicated HCC cells. (F) ChIP-qPCR analyses of ATF2 binding to the CCL2 gene promoter in HCC cell lines with SLAMF7 overexpression and knockdown. (G) Immunoblot assays of SLAMF7, and ATF2 protein levels in the indicated HCC cells. **P<0.01, and ***P<0.001, Student’s t test. Experiments were repeated three time and results were present as the mean ± SD.
Table S8 from Cigarette Smoking and E-cigarette Use Induce Shared DNA Methylation Changes Linked to Carcinogenesis
Authors: Herzog Chiara , Jones Allison , Evans Iona , Raut Janhavi R. , Zikan Michal , Cibula David , Wong Andrew , Brenner Hermann , Richmond Rebecca C. , Widschwendter Martin
Published: June 2024

Supplementary Table 8
Supplementary Information from Cigarette Smoking and E-cigarette Use Induce Shared DNA Methylation Changes Linked to Carcinogenesis
Authors: Herzog Chiara , Jones Allison , Evans Iona , Raut Janhavi R. , Zikan Michal , Cibula David , Wong Andrew , Brenner Hermann , Richmond Rebecca C. , Widschwendter Martin
Published: June 2024

Supplementary Information
Figure S5 from Cigarette Smoking and E-cigarette Use Induce Shared DNA Methylation Changes Linked to Carcinogenesis
Authors: Herzog Chiara , Jones Allison , Evans Iona , Raut Janhavi R. , Zikan Michal , Cibula David , Wong Andrew , Brenner Hermann , Richmond Rebecca C. , Widschwendter Martin
Published: June 2024

Supplementary Figure 5
Figure S4 from Cigarette Smoking and E-cigarette Use Induce Shared DNA Methylation Changes Linked to Carcinogenesis
Authors: Herzog Chiara , Jones Allison , Evans Iona , Raut Janhavi R. , Zikan Michal , Cibula David , Wong Andrew , Brenner Hermann , Richmond Rebecca C. , Widschwendter Martin
Published: June 2024

Supplementary Figure 4
Supplementary Data from Mathematical Model-Driven Deep Learning Enables Personalized Adaptive Therapy
Authors: Gallagher Kit , Strobl Maximilian A.R. , Park Derek S. , Spoendlin Fabian C. , Gatenby Robert A. , Maini Philip K. , Anderson Alexander R.A.
Published: June 2024

Supplementary Information File
Figure S10 from Cigarette Smoking and E-cigarette Use Induce Shared DNA Methylation Changes Linked to Carcinogenesis
Authors: Herzog Chiara , Jones Allison , Evans Iona , Raut Janhavi R. , Zikan Michal , Cibula David , Wong Andrew , Brenner Hermann , Richmond Rebecca C. , Widschwendter Martin
Published: June 2024

Supplementary Figure 10
Figure 5 from Cigarette Smoking and E-cigarette Use Induce Shared DNA Methylation Changes Linked to Carcinogenesis
Authors: Herzog Chiara , Jones Allison , Evans Iona , Raut Janhavi R. , Zikan Michal , Cibula David , Wong Andrew , Brenner Hermann , Richmond Rebecca C. , Widschwendter Martin
Published: June 2024

Mean methylation beta of smoking-associated CpG sets in cancer tissue and progressing versus regressing CIS lesions. A, Mean methylation beta values in each set in TCGA LUAD and LUSC projects. Only samples with matched normal control tissue were included to control for smoking exposure. P values are derived from a paired Wilcoxon test. B and C, AUC plots for mean methylation levels in epithelial hypoM, distal epithelial hyperM, and proximal epithelial hyperM, comparing matched control tissue versus lung cancer tissue in TCGA-LUAD (B) and TCGA-LUSC (C). D, Mean methylation beta values in each set in cervical cancer or matched normal tissue (GSE211668). Only samples with matched normal control tissue were included to control for smoking exposure. P values are derived from a paired Wilcoxon test. E, AUC plots for mean methylation levels in epithelial hypoM, distal epithelial hyperM, and proximal epithelial hyperM, comparing matched control tissue versus cervical cancer tissue (GSE211668). F, Mean methylation beta values in the smoking-associated CpG sets in control lung tissue, regressing CIS lesions, or progressing CIS lesions. P values are derived from paired Wilcoxon tests. G, AUC plots for mean methylation levels in epithelial hypoM, distal epithelial hyperM, and proximal epithelial hyperM, comparing matched regressing CIS versus progressing CIS lesions.
Data from Mathematical Model-Driven Deep Learning Enables Personalized Adaptive Therapy
Authors: Gallagher Kit , Strobl Maximilian A.R. , Park Derek S. , Spoendlin Fabian C. , Gatenby Robert A. , Maini Philip K. , Anderson Alexander R.A.
Published: June 2024

Abstract
Standard-of-care treatment regimens have long been designed for maximal cell killing, yet these strategies often fail when applied to metastatic cancers due to the emergence of drug resistance. Adaptive treatment strategies have been developed as an alternative approach, dynamically adjusting treatment to suppress the growth of treatment-resistant populations and thereby delay, or even prevent, tumor progression. Promising clinical results in prostate cancer indicate the potential to optimize adaptive treatment protocols. Here, we applied deep reinforcement learning (DRL) to guide adaptive drug scheduling and demonstrated that these treatment schedules can outperform the current adaptive protocols in a mathematical model calibrated to prostate cancer dynamics, more than doubling the time to progression. The DRL strategies were robust to patient variability, including both tumor dynamics and clinical monitoring schedules. The DRL framework could produce interpretable, adaptive strategies based on a single tumor burden threshold, replicating and informing optimal treatment strategies. The DRL framework had no knowledge of the underlying mathematical tumor model, demonstrating the capability of DRL to help develop treatment strategies in novel or complex settings. Finally, a proposed five-step pathway, which combined mechanistic modeling with the DRL framework and integrated conventional tools to improve interpretability compared with traditional “black-box” DRL models, could allow translation of this approach to the clinic. Overall, the proposed framework generated personalized treatment schedules that consistently outperformed clinical standard-of-care protocols.
Significance:
Generation of interpretable and personalized adaptive treatment schedules using a deep reinforcement framework that interacts with a virtual patient model overcomes the limitations of standardized strategies caused by heterogeneous treatment responses.
CENP-E Inhibition Induces Chromosomal Instability and Synergizes with Diverse Microtubule-Targeting Agents in Breast Cancer
Authors: Tucker John B. , Carlsen Caleb L. , Scribano Christina M. , Pattaswamy Srishrika M. , Burkard Mark E. , Weaver Beth A.
Published: June 2024

Drugs that perturb microtubules are commonly used to treat breast cancers of all subtypes in both early stage and metastatic disease, but they are effective in only approximately 50% of patients. High concentrations of microtubule-targeting agents can elicit mitotic arrest in cell culture models; however, recent evidence from primary and metastatic breast cancers has revealed that these agents only accumulate at intratumoral levels capable of inducing abnormal multipolar mitotic spindles, not mitotic arrest. Although the maintenance of multipolar spindles can generate cytotoxic rates of chromosomal instability (CIN), focusing of aberrant multipolar spindles into normal bipolar spindles can dramatically reduce CIN and confer resistance to microtubule poisons. Here, we showed that inhibition of the mitotic kinesin centromeric-associated protein-E (CENP-E) overcomes resistance caused by focusing multipolar spindles. Clinically relevant microtubule-targeting agents used a mechanistically conserved pathway to induce multipolar spindles without requiring centrosome amplification. Focusing could occur at any point in mitosis, with earlier focusing conferring greater resistance to antimicrotubule agents. CENP-E inhibition increased CIN on focused spindles by generating chromosomes that remained misaligned at spindle poles during anaphase, which substantially increased death in the resulting daughter cells. CENP-E inhibition synergized with diverse, clinically relevant microtubule poisons to potentiate cell death in cell lines and suppress tumor growth in orthotopic tumor models. These results suggest that primary resistance to microtubule-targeting drugs can be overcome by simultaneous inhibition of CENP-E.

Significance: The increased incidence of polar chromosomes induced by inhibition of the mitotic kinesin CENP-E exacerbates chromosomal instability, reduces daughter cell viability, and improves sensitivity to microtubule-targeting therapies.
Supplementary Figure 7 from Patient-Derived Tumor Xenograft Study with CDK4/6 Inhibitor Plus AKT Inhibitor for the Management of Metastatic Castration-Resistant Prostate Cancer
Authors: Kase Adam M. , Gleba Justyna , Miller James L. , Miller Erin , Petit Joachim , Barrett Michael T. , Zhou Yumei , Parent Ephraim E. , Cai Hancheng , Knight Joshua A. , Orme Jacob , Reynolds Jordan , Durham William F. , Metz Thomas M. , Meurice Nathalie , Edenfield Brandy , Alasonyalilar Demirer Aylin , Bilgili Ahmet , Hickman Peyton G. , Pawlush Matthew L. , Marlow Laura , Wickland Daniel P. , Tan Winston , Copland John A.
Published: June 2024

Supplementary Figure 7
Supplementary Figure 4 from Patient-Derived Tumor Xenograft Study with CDK4/6 Inhibitor Plus AKT Inhibitor for the Management of Metastatic Castration-Resistant Prostate Cancer
Authors: Kase Adam M. , Gleba Justyna , Miller James L. , Miller Erin , Petit Joachim , Barrett Michael T. , Zhou Yumei , Parent Ephraim E. , Cai Hancheng , Knight Joshua A. , Orme Jacob , Reynolds Jordan , Durham William F. , Metz Thomas M. , Meurice Nathalie , Edenfield Brandy , Alasonyalilar Demirer Aylin , Bilgili Ahmet , Hickman Peyton G. , Pawlush Matthew L. , Marlow Laura , Wickland Daniel P. , Tan Winston , Copland John A.
Published: June 2024

Supplementary Figure 4
Supplementary Figure S2 from Discovery of a Long Half-Life AURKA Inhibitor to Treat MYC-Amplified Solid Tumors as a Monotherapy and in Combination with Everolimus
Authors: Chang Chun-Ping , Yeh Teng-Kuang , Chen Chiung-Tong , Wang Wan-Ping , Chen Yen-Ting , Tsai Chia-Hua , Chen Yan-Fu , Ke Yi-Yu , Wang Jing-Ya , Chen Ching-Ping , Hsieh Tsung-Chih , Wu Mine-Hsine , Huang Chen-Lung , Chen Ya-Ping , Zhuang Hong , Chi Ya-Hui
Published: June 2024

Supplementary Figure S2. MYC level in cancer cell lines and its correlation with 6K465 sensitivity. (A) Expression profiles of c-MYC and N-MYC mRNAs in various cancer cell lines retrieved from the cancer cell line encyclopedia (CCLE) repository. A cut-off level at 6.2 was set for c-MYC and, and a cut-off level at 0 was set for N-MYC. (B-C) Summary of genomic and molecular features, half-proliferation inhibition concentration (IC50) of 6K465 and c-MYC/N-MYC protein levels in eleven SCLC (normalized to NCI-H841) and sixteen BC (normalized to HCC1143) cell lines.
Supplementary Figure S1 from Discovery of a Long Half-Life AURKA Inhibitor to Treat MYC-Amplified Solid Tumors as a Monotherapy and in Combination with Everolimus
Authors: Chang Chun-Ping , Yeh Teng-Kuang , Chen Chiung-Tong , Wang Wan-Ping , Chen Yen-Ting , Tsai Chia-Hua , Chen Yan-Fu , Ke Yi-Yu , Wang Jing-Ya , Chen Ching-Ping , Hsieh Tsung-Chih , Wu Mine-Hsine , Huang Chen-Lung , Chen Ya-Ping , Zhuang Hong , Chi Ya-Hui
Published: June 2024

Supplementary Figure S1. Discovery and synthesis of 6K465. (A) Synthesis of pyrimidine derivatives Cmpd-T and 6K465 which possess a six-membered ring amine. (B) Western blot analysis for the expression of c-MYC and N-MYC respectively in NCI-H82 and SK-N-BE(2) cells treated with 1.0 or 5.0 uM of the indicated compounds for 2 hr.
Table S2 from A Novel Dual ATM/DNA-PK Inhibitor, XRD-0394, Potently Radiosensitizes and Potentiates PARP and Topoisomerase I Inhibitors
Authors: Gilmer Tona M. , Lai Chun-Hsiang , Guo Kexiao , Deland Katherine , Ashcraft Kathleen A. , Stewart Amy E. , Wang Yaode , Fu Jianmin , Wood Kris C. , Kirsch David G. , Kastan Michael B.
Published: June 2024

MCF7 clonogenic survival treated with XRD-0394
Table S1 from A Novel Dual ATM/DNA-PK Inhibitor, XRD-0394, Potently Radiosensitizes and Potentiates PARP and Topoisomerase I Inhibitors
Authors: Gilmer Tona M. , Lai Chun-Hsiang , Guo Kexiao , Deland Katherine , Ashcraft Kathleen A. , Stewart Amy E. , Wang Yaode , Fu Jianmin , Wood Kris C. , Kirsch David G. , Kastan Michael B.
Published: June 2024

Clonogenic survival treated with ATMi and DNA-PKi and combination
Figure S7 from A Novel Dual ATM/DNA-PK Inhibitor, XRD-0394, Potently Radiosensitizes and Potentiates PARP and Topoisomerase I Inhibitors
Authors: Gilmer Tona M. , Lai Chun-Hsiang , Guo Kexiao , Deland Katherine , Ashcraft Kathleen A. , Stewart Amy E. , Wang Yaode , Fu Jianmin , Wood Kris C. , Kirsch David G. , Kastan Michael B.
Published: June 2024

Potentiation of SN38
Supplemental Figure S5 from Mitochondrial and Cytosolic One-Carbon Metabolism Is a Targetable Metabolic Vulnerability in Cisplatin-Resistant Ovarian Cancer
Authors: Wallace-Povirk Adrianne , O'Connor Carrie , Dekhne Aamod S. , Bao Xun , Nayeen Md. Junayed , Schneider Mathew , Katinas Jade M. , Wong-Roushar Jennifer , Kim Seongho , Polin Lisa , Li Jing , Back Jessica B. , Dann Charles E. , Gangjee Aleem , Hou Zhanjun , Matherly Larry H.
Published: June 2024

This figure shows purification of the recombinant human thymidylate synthase (TS) and in vitro inhibition by pyrrolo[3,2-d]pyrimidine antifolates.
Supplemental Figure S2 from Mitochondrial and Cytosolic One-Carbon Metabolism Is a Targetable Metabolic Vulnerability in Cisplatin-Resistant Ovarian Cancer
Authors: Wallace-Povirk Adrianne , O'Connor Carrie , Dekhne Aamod S. , Bao Xun , Nayeen Md. Junayed , Schneider Mathew , Katinas Jade M. , Wong-Roushar Jennifer , Kim Seongho , Polin Lisa , Li Jing , Back Jessica B. , Dann Charles E. , Gangjee Aleem , Hou Zhanjun , Matherly Larry H.
Published: June 2024

This figure shows results of apoptosis assays with SKOV3 cells treated with AGF347.
Figure S7 from 89Zr-ImmunoPET for the Specific Detection of EMP2-Positive Tumors
Authors: Chan Ann M. , Olafsen Tove , Tsui Jessica , Salazar Felix B. , Aguirre Brian , Zettlitz Kirstin A. , Condro Michael , Wu Anna M. , Braun Jonathan , Gordon Lynn K. , Ashki Negin , Whitelegge Julian , Xu Shili , Ikotun Oluwatayo , Lee Jason Thanh , Wadehra Madhuri
Published: June 2024

S7. ImmunoPET imaging with 89Zr-DFO- anti-EMP2 mAb of U87MG/EMP2Fluc or sham injected nude mouse in an intracranial model. All mice received the same surgical procedures, but they were injected with either U87MG/EMP2Fluc cells or saline (sham treated). A. Bioluminescence imaging showing the presence of intracranial U87MG/EMP2Fluc cells or no cells in the sham in a representative set of animals. B. Maximum intensity projection (MIP) images were acquired at 24 and 120 hours post-intravenous injection of 89Zr-DFO-anti-EMP2 mAb in a representative animal injected with U87/EMP2Fluc vs sham treated animal. C. In vivo biodistribution of sham mice at 120 hrs indicate that there was no measurable uptake of 89Zr-DFO-anti-EMP2 mAb in the brain. N=2.
Figure S1 from 89Zr-ImmunoPET for the Specific Detection of EMP2-Positive Tumors
Authors: Chan Ann M. , Olafsen Tove , Tsui Jessica , Salazar Felix B. , Aguirre Brian , Zettlitz Kirstin A. , Condro Michael , Wu Anna M. , Braun Jonathan , Gordon Lynn K. , Ashki Negin , Whitelegge Julian , Xu Shili , Ikotun Oluwatayo , Lee Jason Thanh , Wadehra Madhuri
Published: June 2024

S1. Summary of human EMP2 expression. A. HPA-RNAseq data depicting EMP2 mRNA expression in normal tissues. The image is reproduced from (https:www.ncbi.nlm.nih.gov/gene/2013). B. Immunohistochemical staining of representative human tissues using anti-EMP2 antisera. Magnification: 400X.
Figure S7 from Proton FLASH Radiotherapy Ameliorates Radiation-induced Salivary Gland Dysfunction and Oral Mucositis and Increases Survival in a Mouse Model of Head and Neck Cancer
Authors: Chowdhury Priyanka , Velalopoulou Anastasia , Verginadis Ioannis I. , Morcos George , Loo Phoebe E. , Kim Michele M. , Motlagh Seyyedeh Azar Oliaei , Shoniyozov Khayrullo , Diffenderfer Eric S. , Ocampo Emilio A. , Putt Mary , Assenmacher Charles-Antoine , Radaelli Enrico , Lu Jiawei , Qin Ling , Liu Hengxi , Leli Nektaria Maria , Girdhani Swati , Denef Nicolas , Vander Stappen Francois , Cengel Keith A. , Busch Theresa M. , Metz James M. , Dong Lei , Lin Alexander , Koumenis Constantinos
Published: June 2024

Immunofluoresecnce of TUNEL and AQP5 after 10 days post irradiation of PRT.
Figure S1 from Proton FLASH Radiotherapy Ameliorates Radiation-induced Salivary Gland Dysfunction and Oral Mucositis and Increases Survival in a Mouse Model of Head and Neck Cancer
Authors: Chowdhury Priyanka , Velalopoulou Anastasia , Verginadis Ioannis I. , Morcos George , Loo Phoebe E. , Kim Michele M. , Motlagh Seyyedeh Azar Oliaei , Shoniyozov Khayrullo , Diffenderfer Eric S. , Ocampo Emilio A. , Putt Mary , Assenmacher Charles-Antoine , Radaelli Enrico , Lu Jiawei , Qin Ling , Liu Hengxi , Leli Nektaria Maria , Girdhani Swati , Denef Nicolas , Vander Stappen Francois , Cengel Keith A. , Busch Theresa M. , Metz James M. , Dong Lei , Lin Alexander , Koumenis Constantinos
Published: June 2024

The beam profile, as acquired with the film for irradiation with 16 Gy proton.
Supplementary Figure 5 from Thio-2 Inhibits Key Signaling Pathways Required for the Development and Progression of Castration-resistant Prostate Cancer
Authors: Neeb Antje , Figueiredo Ines , Bogdan Denisa , Cato Laura , Stober Jutta , Jiménez-Vacas Juan M. , Gourain Victor , Lee Irene I. , Seeger Rebecca , Muhle-Goll Claudia , Gurel Bora , Welti Jonathan , Nava Rodrigues Daniel , Rekowski Jan , Qiu Xintao , Jiang Yija , Di Micco Patrizio , Mateos Borja , Bielskutė Stasė , Riisnaes Ruth , Ferreira Ana , Miranda Susana , Crespo Mateus , Buroni Lorenzo , Ning Jian , Carreira Suzanne , Bräse Stefan , Jung Nicole , Gräßle Simone , Swain Amanda , Salvatella Xavier , Plymate Stephen R. , Al-Lazikani Bissan , Long Henry W. , Yuan Wei , Brown Myles , Cato Andrew C.B. , de Bono Johann S. , Sharp Adam
Published: June 2024

Development of castration resistant prostate cancer patient derived xenograft organoids.
Supplementary Figure S8 from Structural Basis for Multivalent MUC16 Recognition and Robust Anti-Pancreatic Cancer Activity of Humanized Antibody AR9.6
Authors: Aguilar Eric N. , Sagar Satish , Murray Brandy R. , Rajesh Christabelle , Lei Eric K. , Michaud Sarah A. , Goodlett David R. , Caffrey Thomas C. , Grandgenett Paul M. , Swanson Benjamin , Brooks Teresa M. , Black Adrian R. , van Faassen Henk , Hussack Greg , Henry Kevin A. , Hollingsworth Michael A. , Brooks Cory L. , Radhakrishnan Prakash
Published: June 2024

Figure S8. huAR9.6 induces ADCC and CDC in PDAC cells. (A) Flow cytometry-based assay showing ADCC against CFSE-labeled T3M4, Capan-2 and T3M4-MUC16KO cells via FVD (viability stain) CFSE double positive cells following incubation with peripheral blood mononuclear cells (PBMCs, effector cells) with or without the huAR9.6 antibody (B) Flow cytometry-based assay showing CDC against target T3M4, Capan-2 and T3M4-MUC16KO cells using Annexin-V/PI staining following incubation with human healthy donor derived serum with or without the huAR9.6 antibody.
Supplementary Figure S5 from Structural Basis for Multivalent MUC16 Recognition and Robust Anti-Pancreatic Cancer Activity of Humanized Antibody AR9.6
Authors: Aguilar Eric N. , Sagar Satish , Murray Brandy R. , Rajesh Christabelle , Lei Eric K. , Michaud Sarah A. , Goodlett David R. , Caffrey Thomas C. , Grandgenett Paul M. , Swanson Benjamin , Brooks Teresa M. , Black Adrian R. , van Faassen Henk , Hussack Greg , Henry Kevin A. , Hollingsworth Michael A. , Brooks Cory L. , Radhakrishnan Prakash
Published: June 2024

Fig. S5. RNA sequencing of PDAC cells. (A) Volcano plot showing upregulated (1145) and downregulated (183) genes in T3M4-WT and T3M4-MUC16KO cells (n=3); (B) Gene set enrichment analysis (GSEA) plot showing enrichment of apoptosis in T3M4-MUC16KO cells. (C) Log2FoldChange (Lof2FC) of MUC16KO versus WT and (D) Fragments Per Kilobase of transcript per Million (FPKM) of genes affected in EGF signaling pathway. p < 0.05 was considered as statistically significant.
Supplementary Figure 3 from ATPase Copper Transporting Beta (ATP7B) Is a Novel Target for Improving the Therapeutic Efficacy of Docetaxel by Disulfiram/Copper in Human Prostate Cancer
Authors: Song Liankun , Nguyen Vyvyan , Xie Jun , Jia Shang , Chang Christopher J. , Uchio Edward , Zi Xiaolin
Published: June 2024

Characterization of prostate cancer patient-derived organoids by H&E and immunohistochemistry with anti-ATP7B and androgen receptor antibodies.
Data from Discovery of a Long Half-Life AURKA Inhibitor to Treat MYC-Amplified Solid Tumors as a Monotherapy and in Combination with Everolimus
Authors: Chang Chun-Ping , Yeh Teng-Kuang , Chen Chiung-Tong , Wang Wan-Ping , Chen Yen-Ting , Tsai Chia-Hua , Chen Yan-Fu , Ke Yi-Yu , Wang Jing-Ya , Chen Ching-Ping , Hsieh Tsung-Chih , Wu Mine-Hsine , Huang Chen-Lung , Chen Ya-Ping , Zhuang Hong , Chi Ya-Hui
Published: June 2024

Abstract
Aurora kinase inhibitors, such as alisertib, can destabilize MYC-family oncoproteins and have demonstrated compelling antitumor efficacy. In this study, we report 6K465, a novel pyrimidine-based Aurora A inhibitor, that reduces levels of c-MYC and N-MYC oncoproteins more potently than alisertib. In an analysis of the antiproliferative effect of 6K465, the sensitivities of small cell lung cancer (SCLC) and breast cancer cell lines to 6K465 were strongly associated with the protein levels of c-MYC and/or N-MYC. We also report DBPR728, an acyl-based prodrug of 6K465 bearing fewer hydrogen-bond donors, that exhibited 10-fold improved oral bioavailability. DBPR728 induced durable tumor regression of c-MYC- and/or N-MYC-overexpressing xenografts including SCLC, triple-negative breast cancer, hepatocellular carcinoma, and medulloblastoma using a 5-on-2-off or once-a-week dosing regimen on a 21-day cycle. A single oral dose of DBPR728 at 300 mg/kg induced c-MYC reduction and cell apoptosis in the tumor xenografts for more than 7 days. The inhibitory effect of DBPR728 at a reduced dosing frequency was attributed to its uniquely high tumor/plasma ratio (3.6-fold within 7 days) and the long tumor half-life of active moiety 6K465. Furthermore, DBPR728 was found to synergize with the mTOR inhibitor everolimus to suppress c-MYC- or N-MYC-driven SCLC. Collectively, these results suggest DBPR728 has the potential to treat cancers overexpressing c-MYC and/or N-MYC.
Data from 89Zr-ImmunoPET for the Specific Detection of EMP2-Positive Tumors
Authors: Chan Ann M. , Olafsen Tove , Tsui Jessica , Salazar Felix B. , Aguirre Brian , Zettlitz Kirstin A. , Condro Michael , Wu Anna M. , Braun Jonathan , Gordon Lynn K. , Ashki Negin , Whitelegge Julian , Xu Shili , Ikotun Oluwatayo , Lee Jason Thanh , Wadehra Madhuri
Published: June 2024

Abstract
Epithelial membrane protein-2 (EMP2) is upregulated in a number of tumors and therefore remains a promising target for mAb-based therapy. In the current study, image-guided therapy for an anti-EMP2 mAb was evaluated by PET in both syngeneic and immunodeficient cancer models expressing different levels of EMP2 to enable a better understanding of its tumor uptake and off target accumulation and clearance. The therapeutic efficacy of the anti-EMP2 mAb was initially evaluated in high- and low-expressing tumors, and the mAb reduced tumor load for the high EMP2-expressing 4T1 and HEC-1-A tumors. To create an imaging agent, the anti-EMP2 mAb was conjugated to p-SCN-Bn-deferoxamine (DFO) and radiolabeled with 89Zr. Tumor targeting and tissue biodistribution were evaluated in syngeneic tumor models (4T1, CT26, and Panc02) and human tumor xenograft models (Ramos, HEC-1-A, and U87MG/EMP2). PET imaging revealed radioactive accumulation in EMP2-positive tumors within 24 hours after injection, and the signal was retained for 5 days. High specific uptake was observed in tumors with high EMP2 expression (4T1, CT26, HEC-1-A, and U87MG/EMP2), with less accumulation in tumors with low EMP2 expression (Panc02 and Ramos). Biodistribution at 5 days after injection revealed that the tumor uptake ranged from 2 to approximately 16%ID/cc. The results show that anti-EMP2 mAbs exhibit EMP2-dependent tumor uptake with low off-target accumulation in preclinical cancer models. The development of improved anti-EMP2 Ab fragments may be useful to track EMP2-positive tumors for subsequent therapeutic interventions.
Supplementary Figure 2 from FATP5 Is Indispensable for the Growth of Intrahepatic Cholangiocarcinoma
Authors: Shihadih Diyala , Wang Xue , Zushin Peter-James H. , Khodakivskyi Pavlo , Park Hyo Min , Tso Emily , Shiblak Jena , Misic Angela , Louie Sharon M. , Ward Catherine , Hellerstein Marc , Nomura Daniel K. , Goun Elena , Urigo Francesco , Calvisi Diego F. , Chen Xin , Stahl Andreas
Published: June 2024

Gene expression levels of Fatp5, and Fasn were measured using qPCR in AAV-shSCR and AAV-shFatp5 ICC tumors.
Supplementary Figure 1 from FATP5 Is Indispensable for the Growth of Intrahepatic Cholangiocarcinoma
Authors: Shihadih Diyala , Wang Xue , Zushin Peter-James H. , Khodakivskyi Pavlo , Park Hyo Min , Tso Emily , Shiblak Jena , Misic Angela , Louie Sharon M. , Ward Catherine , Hellerstein Marc , Nomura Daniel K. , Goun Elena , Urigo Francesco , Calvisi Diego F. , Chen Xin , Stahl Andreas
Published: June 2024

Gene expression levels of FATP5 were measured using qPCR in 5
normal livers (NL), 33 ICC, and related surrounding livers (SL).
Supplementary Table S5 from Systematic Characterization of p53-Regulated Long Noncoding RNAs across Human Cancers Reveals Remarkable Heterogeneity among Different Tumor Types
Authors: Regunath Kausik , Fomin Vitalay , Liu Zhaoqi , Wang Pingzhang , Hoque Mainul , Tian Bin , Rabadan Raul , Prives Carol
Published: June 2024

Supplementary Table S5 shows p53LTCC lncRNAs (activated and repressed) associated with patient survival in pancreatic cancers.
Supplementary Table S3 from Systematic Characterization of p53-Regulated Long Noncoding RNAs across Human Cancers Reveals Remarkable Heterogeneity among Different Tumor Types
Authors: Regunath Kausik , Fomin Vitalay , Liu Zhaoqi , Wang Pingzhang , Hoque Mainul , Tian Bin , Rabadan Raul , Prives Carol
Published: June 2024

Supplementary Table S3 shows p53LTCC lncRNAs (activated and repressed) associated with patient survival in glioblastoma.
Supplementary Figure S4 from Systematic Characterization of p53-Regulated Long Noncoding RNAs across Human Cancers Reveals Remarkable Heterogeneity among Different Tumor Types
Authors: Regunath Kausik , Fomin Vitalay , Liu Zhaoqi , Wang Pingzhang , Hoque Mainul , Tian Bin , Rabadan Raul , Prives Carol
Published: June 2024

Supplementary Figure S4 shows heatmap of p53LTCC expression in breast cancer samples comparing tumors with wild-type p53 vs mutant p53
Supplementary Table S4 from Serotonin Receptor HTR2B Facilitates Colorectal Cancer Metastasis via CREB1–ZEB1 Axis–Mediated Epithelial–Mesenchymal Transition
Authors: Li Tao , Wei Lei , Zhang Xin , Fu Bin , Zhou Yunjiang , Yang Mengdi , Cao Mengran , Chen Yaxin , Tan Yingying , Shi Yongwei , Wu Leyin , Xuan Chenyuan , Du Qianming , Hu Rong
Published: June 2024

This file contains Supplementary Table S4.
Supplementary Table S1 from Serotonin Receptor HTR2B Facilitates Colorectal Cancer Metastasis via CREB1–ZEB1 Axis–Mediated Epithelial–Mesenchymal Transition
Authors: Li Tao , Wei Lei , Zhang Xin , Fu Bin , Zhou Yunjiang , Yang Mengdi , Cao Mengran , Chen Yaxin , Tan Yingying , Shi Yongwei , Wu Leyin , Xuan Chenyuan , Du Qianming , Hu Rong
Published: June 2024

This file contains Supplementary Table S1.
Supplementary Figure S9 from Serotonin Receptor HTR2B Facilitates Colorectal Cancer Metastasis via CREB1–ZEB1 Axis–Mediated Epithelial–Mesenchymal Transition
Authors: Li Tao , Wei Lei , Zhang Xin , Fu Bin , Zhou Yunjiang , Yang Mengdi , Cao Mengran , Chen Yaxin , Tan Yingying , Shi Yongwei , Wu Leyin , Xuan Chenyuan , Du Qianming , Hu Rong
Published: June 2024

This file contains Supplementary Figure S9 and its legend.
Supplementary Figure S7 from Serotonin Receptor HTR2B Facilitates Colorectal Cancer Metastasis via CREB1–ZEB1 Axis–Mediated Epithelial–Mesenchymal Transition
Authors: Li Tao , Wei Lei , Zhang Xin , Fu Bin , Zhou Yunjiang , Yang Mengdi , Cao Mengran , Chen Yaxin , Tan Yingying , Shi Yongwei , Wu Leyin , Xuan Chenyuan , Du Qianming , Hu Rong
Published: June 2024

This file contains Supplementary Figure S7 and its legend.
Supplementary Figure S6 from Serotonin Receptor HTR2B Facilitates Colorectal Cancer Metastasis via CREB1–ZEB1 Axis–Mediated Epithelial–Mesenchymal Transition
Authors: Li Tao , Wei Lei , Zhang Xin , Fu Bin , Zhou Yunjiang , Yang Mengdi , Cao Mengran , Chen Yaxin , Tan Yingying , Shi Yongwei , Wu Leyin , Xuan Chenyuan , Du Qianming , Hu Rong
Published: June 2024

This file contains Supplementary Figure S6 and its legend.
Supplementary Figure S5 from Serotonin Receptor HTR2B Facilitates Colorectal Cancer Metastasis via CREB1–ZEB1 Axis–Mediated Epithelial–Mesenchymal Transition
Authors: Li Tao , Wei Lei , Zhang Xin , Fu Bin , Zhou Yunjiang , Yang Mengdi , Cao Mengran , Chen Yaxin , Tan Yingying , Shi Yongwei , Wu Leyin , Xuan Chenyuan , Du Qianming , Hu Rong
Published: June 2024

This file contains Supplementary Figure S5 and its legend.
Supplementary Figure S18 from Serotonin Receptor HTR2B Facilitates Colorectal Cancer Metastasis via CREB1–ZEB1 Axis–Mediated Epithelial–Mesenchymal Transition
Authors: Li Tao , Wei Lei , Zhang Xin , Fu Bin , Zhou Yunjiang , Yang Mengdi , Cao Mengran , Chen Yaxin , Tan Yingying , Shi Yongwei , Wu Leyin , Xuan Chenyuan , Du Qianming , Hu Rong
Published: June 2024

This file contains Supplementary Figure S18 and its legend.
Supplementary Figure S14 from Serotonin Receptor HTR2B Facilitates Colorectal Cancer Metastasis via CREB1–ZEB1 Axis–Mediated Epithelial–Mesenchymal Transition
Authors: Li Tao , Wei Lei , Zhang Xin , Fu Bin , Zhou Yunjiang , Yang Mengdi , Cao Mengran , Chen Yaxin , Tan Yingying , Shi Yongwei , Wu Leyin , Xuan Chenyuan , Du Qianming , Hu Rong
Published: June 2024

This file contains Supplementary Figure S14 and its legend.
Table S2 from lncRNA JPX Promotes Tumor Progression by Interacting with and Destabilizing YTHDF2 in Cutaneous Melanoma
Authors: Luo Dan , Tang Hui , Tan Liuchang , Zhang Long , Wang Lei , Cheng Qionghui , Lei Xia , Wu Jinjin
Published: June 2024

The primer sequences used are listed.
Figure S3 from lncRNA JPX Promotes Tumor Progression by Interacting with and Destabilizing YTHDF2 in Cutaneous Melanoma
Authors: Luo Dan , Tang Hui , Tan Liuchang , Zhang Long , Wang Lei , Cheng Qionghui , Lei Xia , Wu Jinjin
Published: June 2024

JPX knockout reduces the proliferation and migration of cutaneous melanoma cells.
Figure S2 from lncRNA JPX Promotes Tumor Progression by Interacting with and Destabilizing YTHDF2 in Cutaneous Melanoma
Authors: Luo Dan , Tang Hui , Tan Liuchang , Zhang Long , Wang Lei , Cheng Qionghui , Lei Xia , Wu Jinjin
Published: June 2024

JPX could directly bind with YTHDF2 and USP10, respectively. YTHDF2 knockdown increased BMP2 and activated the AKT pathway in cutaneous melanoma.
Supplementary Table S1 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis
Authors: Meuser Elena , Chang Kyle , Walters Angharad , Hurley Joanna J. , West Hannah D. , Perry Iain , Mort Matthew , Reyes-Uribe Laura , Truscott Rebekah , Jones Nicholas , Lawrence Rachel , Jenkins Gareth , Giles Peter , Dolwani Sunil , Al-Sarireh Bilal , Hawkes Neil , Short Emma , Williams Geraint T. , Taggart Melissa W. , Luetchford Kim , Lynch Patrick M. , Terlouw Diantha , Nielsen Maartje , Walton Sarah-Jane , Latchford Andrew , Clark Susan K. , Sampson Julian R. , Vilar Eduardo , Thomas Laura E.
Published: June 2024

Overview of all intestinal samples used in this study. *Sequenced previously (Thomas et al, 2017) and reanalysed here. Somatic mutations in APC, KRAS and PIGA as identified by WES and WTS analysis of CU and MDACC duodenal adenomas. Samples where matched WTS data was available are indicated with * and those where the variant was present in both WES and WTS data are denoted with **. 1All protein changes refer to the respective canonical isoforms. 2CADD is a meta-estimator for the deleteriousness of SNVs and indels in the human genome. The score given here ranks a variant relative to all possible substitutions of the genome on a logarithmic scale, i.e. a variant with a score >10 is predicted to be amongst the 10% most deleterious mutations possible, a variant with a score >20 indicates the 1% most deleterious. The developers suggest a cut-off of 15 to identify potentially pathogenic variants (Kircher et al, 2014). C=Colectomy (exact surgical procedure unspecified); Can=Cancer; CRC=Colorectal cancer; DUO=Duodenum; H=Homozygous; IPAA=Ileoanal pouch anastomosis; IRA=Ileo-rectal anastomosis; IS=Ileostomy; PC=Proctocolectomy; NA=Not available,
CADD=Combined Annotation Dependent Depletion; DEL=Deletion; FS=Frameshift, INS=Insertion; SNV=Single nucleotide variant; VAF=Variant allele frequency. WES. Whole exome sequencing only. WES/WTS. Whole exome and whole transcriptome sequencing. WTS. Whole transcriptome sequencing only
Supplementary Figure S4 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis
Authors: Meuser Elena , Chang Kyle , Walters Angharad , Hurley Joanna J. , West Hannah D. , Perry Iain , Mort Matthew , Reyes-Uribe Laura , Truscott Rebekah , Jones Nicholas , Lawrence Rachel , Jenkins Gareth , Giles Peter , Dolwani Sunil , Al-Sarireh Bilal , Hawkes Neil , Short Emma , Williams Geraint T. , Taggart Melissa W. , Luetchford Kim , Lynch Patrick M. , Terlouw Diantha , Nielsen Maartje , Walton Sarah-Jane , Latchford Andrew , Clark Susan K. , Sampson Julian R. , Vilar Eduardo , Thomas Laura E.
Published: June 2024

RNASeq WTS pipeline validation by quantitative RT-PCR (qRT-PCR) and IHC A. Comparison of normalised RNA-Seq read counts (orange) to relative qRT-PCR expression levels (purple) for four top DEGs. Δ CT values are shown, with low values indicative of low mRNA abundances. High concordance between the two methods can be observed. qRT-PCR confirms increased levels of S100P and KRT7 and decreased levels of FCER2 and CA4 mRNA in duodenal adenomas in comparison to normal duodenal mucosa samples (purple bars). B. IHC results for S100 and CK7 expression in duodenal normal mucosa or duodenal adenoma tissue sections. Moderate and relatively strong positive staining for CK7 and S100, respectively, was also confirmed in duodenal adenomas compared to corresponding normal duodenal mucosa samples. Representative samples that had undergone RNA-Seq are shown. Scale bar: 50μm. COL=Colorectal samples; DUO=Duodenal samples
Supplementary Table 8 from Surgical Tumor Resection Deregulates Hallmarks of Cancer in Resected Tissue and the Surrounding Microenvironment
Authors: Chaubal Rohan , Gardi Nilesh , Joshi Shalaka , Pantvaidya Gouri , Kadam Rasika , Vanmali Vaibhav , Hawaldar Rohini , Talker Elizabeth , Chitra Jaya , Gera Poonam , Bhatia Dimple , Kalkar Prajakta , Gurav Mamta , Shetty Omshree , Desai Sangeeta , Krishnan Neeraja M. , Nair Nita , Parmar Vani , Dutt Amit , Panda Binay , Gupta Sudeep , Badwe Rajendra
Published: June 2024

Supplementary Table 8 shows the Genes included in qPCR validation.
Supplementary Table S4 from Translational and Therapeutic Evaluation of RAS-GTP Inhibition by RMC-6236 in RAS-Driven Cancers
Authors: Jiang Jingjing , Jiang Lingyan , Maldonato Benjamin J. , Wang Yingyun , Holderfield Matthew , Aronchik Ida , Winters Ian P. , Salman Zeena , Blaj Cristina , Menard Marie , Brodbeck Jens , Chen Zhe , Wei Xing , Rosen Michael J. , Gindin Yevgeniy , Lee Bianca J. , Evans James W. , Chang Stephanie , Wang Zhican , Seamon Kyle J. , Parsons Dylan , Cregg James , Marquez Abby , Tomlinson Aidan C.A. , Yano Jason K. , Knox John E. , Quintana Elsa , Aguirre Andrew J. , Arbour Kathryn C. , Reed Abby , Gustafson W. Clay , Gill Adrian L. , Koltun Elena S. , Wildes David , Smith Jacqueline A.M. , Wang Zhengping , Singh Mallika
Published: June 2024

Supplementary Table S4 shows % mean tumor volume change, % mean body weight change of RMC-6236 treatment group on mRECIST response calling date; and PPIA mRNA expression levels of each xenograft model in RMC-6236 mouse clinical trial.
Supplementary Method from Translational and Therapeutic Evaluation of RAS-GTP Inhibition by RMC-6236 in RAS-Driven Cancers
Authors: Jiang Jingjing , Jiang Lingyan , Maldonato Benjamin J. , Wang Yingyun , Holderfield Matthew , Aronchik Ida , Winters Ian P. , Salman Zeena , Blaj Cristina , Menard Marie , Brodbeck Jens , Chen Zhe , Wei Xing , Rosen Michael J. , Gindin Yevgeniy , Lee Bianca J. , Evans James W. , Chang Stephanie , Wang Zhican , Seamon Kyle J. , Parsons Dylan , Cregg James , Marquez Abby , Tomlinson Aidan C.A. , Yano Jason K. , Knox John E. , Quintana Elsa , Aguirre Andrew J. , Arbour Kathryn C. , Reed Abby , Gustafson W. Clay , Gill Adrian L. , Koltun Elena S. , Wildes David , Smith Jacqueline A.M. , Wang Zhengping , Singh Mallika
Published: June 2024

RMC-6236 synthetic route and detailed PK/PD/Efficacy Modeling method
Figure S7 from The ω-3 Polyunsaturated Fatty Acid Docosahexaenoic Acid Enhances NK-Cell Antitumor Effector Functions
Authors: Wu Shuting , Peng Hongyan , Li Songyang , Huang Lanlan , Wang Xiangyu , Li Yana , Liu Yongjie , Xiong Peiwen , Yang Qinglan , Tian Kunpeng , Wu Weiru , Pu Rongxi , Lu Xiulan , Xiao Zhenghui , Yang Jian , Zhong Zhaoyang , Gao Yuan , Deng Yafei , Deng Youcai
Published: June 2024

Figure. S7. NK cells were effectively depleted by injecting PK136 antibodies in various tissues. WT Mice were treated as described in Figure. 4E. Flow cytometric analysis and cumulative frequencies of NK cells in the indicated tissues were performed. n= 11 were pooled from 2-3 independent experiments. Each symbol represents one individual mouse. The error bars represent the interquartile range. Two-tailed Student’s t test.
Figure S4 from The ω-3 Polyunsaturated Fatty Acid Docosahexaenoic Acid Enhances NK-Cell Antitumor Effector Functions
Authors: Wu Shuting , Peng Hongyan , Li Songyang , Huang Lanlan , Wang Xiangyu , Li Yana , Liu Yongjie , Xiong Peiwen , Yang Qinglan , Tian Kunpeng , Wu Weiru , Pu Rongxi , Lu Xiulan , Xiao Zhenghui , Yang Jian , Zhong Zhaoyang , Gao Yuan , Deng Yafei , Deng Youcai
Published: June 2024

Figure. S4. The effect of continuous DHA supplementation on T, B and NK cells in mice challenged with B16F10 cell i.v. injection. WT mice were first fed with control or DHA-enriched diets for three weeks and then intravenously (i.v.) injected with B16F10 melanoma cells. On day 21 post injection, the following analyses were performed.