bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Table 3 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

Antibodies used for western blot analyses.
Supplementary Figure 7 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

Thio-2 reduces genome-wide androgen receptor binding in LNCaP prostate cancer cells.
Supplementary Figure 2 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

BAG-1 knockout female mice are fertile and viable with reduced gestation.
Supplementary Figure 11 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

Treatment with Thio-2 inhibits transactivation of the unstimulated and stimulated androgen receptor and the constitutively active androgen receptor splice variant-7.
Supplementary Figure 10 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

Thio-2, may bind the N-terminus of the androgen receptor through a similar binding mode to EPI-001.
Supplementary Table 1 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

Growth inhibitory effects of DSF and DSF/CuCl2 on parental and docetaxel-resistant prostate cancer cell lines
Supplementary Figure 5 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

H & E staining of 22Rv1-DR xenograft tumor tissues from mice treated with Vehicle control, docetaxel alone, DSF/CuCl2, and docetaxel plus DSF/CuCl2.
Data 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

Abstract
Metastatic castration-resistant prostate cancer (mCRPC) is an aggressive malignancy with poor outcomes. To investigate novel therapeutic strategies, we characterized three new metastatic prostate cancer patient derived-tumor xenograft (PDTX) models and developed 3D spheroids from each to investigate molecular targeted therapy combinations including CDK4/6 inhibitors (CDK4/6i) with AKT inhibitors (ATKi).

Metastatic prostate cancer tissue was collected and three PDTX models were established and characterized using whole-exome sequencing. PDTX 3D spheroids were developed from these three PDTXs to show resistance patterns and test novel molecular-targeted therapies. CDK4/6i's were combined with AKTi's to assess synergistic antitumor response to prove our hypothesis that blockade of AKT overcomes drug resistance to CDK4/6i. This combination was evaluated in PDTX three-dimensional (3D) spheroids and in vivo experiments with responses measured by tumor volumes, PSA, and Ga-68 PSMA-11 PET-CT imaging.

We demonstrated CDK4/6i's with AKTi's possess synergistic antitumor activity in three mCRPC PDTX models. These models have multiple unique pathogenic and deleterious genomic alterations with resistance to single-agent CDK4/6i's. Despite this, combination therapy with AKTi's was able to overcome resistance mechanisms. The IHC and Western blot analysis confirmed on target effects, whereas tumor volume, serum PSA ELISA, and radionuclide imaging demonstrated response to therapy with statistically significant SUV differences seen with Ga-68 PSMA-11 PET-CT.

These preclinical data demonstrating antitumor synergy by overcoming single-agent CDK 4/6i as well as AKTi drug resistance provide the rational for a clinical trial combining a CDK4/6i with an AKTi in patients with mCRPC whose tumor expresses wild-type retinoblastoma 1.
Data 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

Abstract
Head and neck cancer radiotherapy often damages salivary glands and oral mucosa, severely negatively impacting patients’ quality of life. The ability of FLASH proton radiotherapy (F-PRT) to decrease normal tissue toxicity while maintaining tumor control compared with standard proton radiotherapy (S-PRT) has been previously demonstrated for several tissues. However, its potential in ameliorating radiation-induced salivary gland dysfunction and oral mucositis and controlling orthotopic head and neck tumor growth has not been reported.

The head and neck area of C57BL/6 mice was irradiated with a single dose of radiotherapy (ranging from 14–18 Gy) or a fractionated dose of 8 Gy × 3 of F-PRT (128 Gy/second) or S-PRT (0.95 Gy/second). Following irradiation, the mice were studied for radiation-induced xerostomia by measuring their salivary flow. Oral mucositis was analyzed by histopathologic examination. To determine the ability of F-PRT to control orthotopic head and neck tumors, tongue tumors were generated in the mice and then irradiated with either F-PRT or S-PRT.

Mice treated with either a single dose or fractionated dose of F-PRT showed significantly improved survival than those irradiated with S-PRT. F-PRT–treated mice showed improvement in their salivary flow. S-PRT–irradiated mice demonstrated increased fibrosis in their tongue epithelium. F-PRT significantly increased the overall survival of the mice with orthotopic tumors compared with the S-PRT–treated mice.

The demonstration that F-PRT decreases radiation-induced normal tissue toxicity without compromising tumor control, suggests that this modality could be useful for the clinical management of patients with head and neck cancer.
Data 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

Abstract
Therapies that abrogate persistent androgen receptor (AR) signaling in castration-resistant prostate cancer (CRPC) remain an unmet clinical need. The N-terminal domain of the AR that drives transcriptional activity in CRPC remains a challenging therapeutic target. Herein we demonstrate that BCL-2–associated athanogene-1 (BAG-1) mRNA is highly expressed and associates with signaling pathways, including AR signaling, that are implicated in the development and progression of CRPC. In addition, interrogation of geometric and physiochemical properties of the BAG domain of BAG-1 isoforms identifies it to be a tractable but challenging drug target. Furthermore, through BAG-1 isoform mouse knockout studies, we confirm that BAG-1 isoforms regulate hormone physiology and that therapies targeting the BAG domain will be associated with limited “on-target” toxicity. Importantly, the postulated inhibitor of BAG-1 isoforms, Thio-2, suppressed AR signaling and other important pathways implicated in the development and progression of CRPC to reduce the growth of treatment-resistant prostate cancer cell lines and patient-derived models. However, the mechanism by which Thio-2 elicits the observed phenotype needs further elucidation as the genomic abrogation of BAG-1 isoforms was unable to recapitulate the Thio-2–mediated phenotype. Overall, these data support the interrogation of related compounds with improved drug-like properties as a novel therapeutic approach in CRPC, and further highlight the clinical potential of treatments that block persistent AR signaling which are currently undergoing clinical evaluation in CRPC.
Pretargeted Radioimmunotherapy with the Novel Anti-oxMIF/HSG Bispecific Antibody ON105 Results in Significant Tumor Regression in Murine Models of Cancer
Authors: Puchol Tarazona Alejandro A. , Schinagl Alexander , Mirkina Irina , Rossmueller Gregor , Kerschbaumer Randolf J. , Bachmann Friedmund , Thiele Michael
Published: June 2024

Radioimmunotherapy (RIT) uses monoclonal antibodies to deliver radionuclides to cancer cells or the tumor microenvironment and has shown promise in treating localized and diffuse tumors. Although RIT agents have gained FDA/EMA approval for certain hematologic malignancies, effectiveness of RIT in treating solid tumors remains limited. In this study, we present PreTarg-it, a novel approach for pretargeted RIT, providing optimized delivery of payloads in a two-step regimen. The effectiveness of PreTarg-it is demonstrated by a powerful combination of ON105, a novel bispecific antibody against both oxidized macrophage migration inhibitory factor (oxMIF) and the histamine-succinyl-glycyl (HSG) hapten, as the first component and the radioactively labeled DOTA-di-HSG peptide as the second component in murine models of cancer. Mice bearing either subcutaneous mouse colorectal CT26 or human pancreatic CFPAC-1 tumors received an i.v. injection of ON105. After ON105 had accumulated in the tumor and cleared from circulation to approximately 1% to 3% of its peak concentration, 177Lu-DOTA-di-HSG peptide was administered. A single PreTarg-it treatment cycle resulted in tumor regression when mice bearing CT26 tumors were given the highest treatment dose with a pretargeting delay of 3 days. Administered with a 5-day interval, the highest dose arrested tumor growth in both CT26 syngrafts and CFPAC-1 xenografts. In all cases, the highest treatment dose resulted in 100% survival at the study endpoint, whereas the control cohorts showed 0% and 60% survival in the CT26 and CFPAC-1 models, respectively. Therefore, PreTarg-it holds potential as a novel and potent therapy for patients with hard-to-treat solid tumors, such as pancreatic cancer, as well as those with late-stage malignancies.
Supplementary Table S8 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 S8 shows publicly available ChIP-seq datasets pertaining to p53
Supplementary Table S6 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 S6 shows p53LTCC LncRNAs differentially expressed in three cancers (comparing samples with wild-type vs mutant p53)
Supplementary Table S1 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 S1 shows p53LTCC lncRNAs (activated and repressed) associated with patient survival in breast cancers.
Supplementary Figure Legends 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

Legends for all Supplementary Figures in the manuscript
Supplementary Figure S8 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 S8 and its legend.
Supplementary Figure S10 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 S10 and its legend.
Supplementary Table S5 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

A VCF file containing putatively pathogenic variants found in 1142 intestinal cancer associated genes in 21 of the duodenal adenomas studied here (see supplementary table 1 for sample details). Full genomic datasets for these samples are available through EGA under accession: EGAD00001009332.
Supplementary Table 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

A VCF file containing putatively pathogenic variants found in 1142 intestinal cancer associated genes in 27 of the duodenal adenomas studied here (see supplementary table 1 for sample details). Full genomic datasets for these samples are available through EGA under accession: EGAD00001009332.
Table S1 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 sequences of the shRNA and siRNA oligonucleotides are listed.
Figure S1 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 overexpression induces the proliferation and migration of cutaneous melanoma cells.
Supplementary Table 9 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 9 shows the Genes significantly de-regulated at three timepoints of surgery in breast cancer NanoString nCounter targeted assays.
Supplementary Figure 5 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 Figure shows Venn diagram representation & heatmap for time-series microarray-based gene expression comparison between tumor-adjacent normal tissue at the start of surgery & tumor tissue obtained at various timepoints in head & neck cancer patients.
Data 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

Abstract
The pathogenesis of duodenal tumors in the inherited tumor syndromes familial adenomatous polyposis (FAP) and MUTYH-associated polyposis (MAP) is poorly understood. This study aimed to identify genes that are significantly mutated in these tumors and to explore the effects of these mutations. Whole exome and whole transcriptome sequencing identified recurrent somatic coding variants of phosphatidylinositol N-acetylglucosaminyltransferase subunit A (PIGA) in 19/70 (27%) FAP and MAP duodenal adenomas, and further confirmed the established driver roles for APC and KRAS. PIGA catalyzes the first step in glycosylphosphatidylinositol (GPI) anchor biosynthesis. Flow cytometry of PIGA-mutant adenoma-derived and CRISPR-edited duodenal organoids confirmed loss of GPI anchors in duodenal epithelial cells and transcriptional profiling of duodenal adenomas revealed transcriptional signatures associated with loss of PIGA.
Implications:
PIGA somatic mutation in duodenal tumors from patients with FAP and MAP and loss of membrane GPI-anchors may present new opportunities for understanding and intervention in duodenal tumorigenesis.
Table S5 from Circulating miRNA Signature Predicts Cancer Incidence in Lynch Syndrome—A Pilot Study
Authors: Sievänen Tero , Jokela Tiina , Hyvärinen Matti , Korhonen Tia-Marje , Pylvänäinen Kirsi , Mecklin Jukka-Pekka , Karvanen Juha , Sillanpää Elina , Seppälä Toni T. , Laakkonen Eija K.
Published: June 2024

Table S5: 5-fold cross-validation of c-miR risk sum score models.
Table S14 from Circulating miRNA Signature Predicts Cancer Incidence in Lynch Syndrome—A Pilot Study
Authors: Sievänen Tero , Jokela Tiina , Hyvärinen Matti , Korhonen Tia-Marje , Pylvänäinen Kirsi , Mecklin Jukka-Pekka , Karvanen Juha , Sillanpää Elina , Seppälä Toni T. , Laakkonen Eija K.
Published: June 2024

Table S14: Pearson correlations of c-miR risk sum score and physical activity, BMI, dietary fiber consumption, NSAID usage and age in the complete-case analysis. Lifestyle data was collected in 2017 or 2020 with a questionnaire. Blood sample was taken at regular colonoscopy visit between 2018 and 2020. The average time-period between lifestyle data collection and blood sample was 2.0 (0.3-3.9) years.
Table S13 from Circulating miRNA Signature Predicts Cancer Incidence in Lynch Syndrome—A Pilot Study
Authors: Sievänen Tero , Jokela Tiina , Hyvärinen Matti , Korhonen Tia-Marje , Pylvänäinen Kirsi , Mecklin Jukka-Pekka , Karvanen Juha , Sillanpää Elina , Seppälä Toni T. , Laakkonen Eija K.
Published: June 2024

Table S13: The significantly enriched Reactome pathways. FDR = False discovery rate.
Figure S2 from Circulating miRNA Signature Predicts Cancer Incidence in Lynch Syndrome—A Pilot Study
Authors: Sievänen Tero , Jokela Tiina , Hyvärinen Matti , Korhonen Tia-Marje , Pylvänäinen Kirsi , Mecklin Jukka-Pekka , Karvanen Juha , Sillanpää Elina , Seppälä Toni T. , Laakkonen Eija K.
Published: June 2024

Figure S2: STRING database complete gene node map. Edges represent gene-gene associations. Thickness of edges indicates association confidence (www.string-db.org).
Figure S1 from Circulating miRNA Signature Predicts Cancer Incidence in Lynch Syndrome—A Pilot Study
Authors: Sievänen Tero , Jokela Tiina , Hyvärinen Matti , Korhonen Tia-Marje , Pylvänäinen Kirsi , Mecklin Jukka-Pekka , Karvanen Juha , Sillanpää Elina , Seppälä Toni T. , Laakkonen Eija K.
Published: June 2024

Figure S1: Schoenfeld residuals of the c-miR risk prediction models. A, Unadjusted c-miR risk sum score prediction model. B, Sex and MMR-variant adjusted c-miR risk sum score prediction model.
Supplementary Table S5 from Efficacy and Safety of Adagrasib plus Cetuximab in Patients with KRASG12C-Mutated Metastatic Colorectal Cancer
Authors: Yaeger Rona , Uboha Nataliya V. , Pelster Meredith S. , Bekaii-Saab Tanios S. , Barve Minal , Saltzman Joel , Sabari Joshua K. , Peguero Julio A. , Paulson Andrew Scott , Jänne Pasi A. , Cruz-Correa Marcia , Anderes Kenna , Velastegui Karen , Yan Xiaohong , Der-Torossian Hirak , Klempner Samuel J. , Kopetz Scott E.
Published: June 2024

Table S5. Summary of TRAEs with adagrasib monotherapy in previously treated patients with KRASG12C-mutated unresectable or metastatic CRC.
Supplementary Table S7 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 S7 showes final processing and refinement statistics used for RMC-6236 Crystallography data collection and refinement.
Supplementary Table S4 from Efficacy and Safety of Adagrasib plus Cetuximab in Patients with KRASG12C-Mutated Metastatic Colorectal Cancer
Authors: Yaeger Rona , Uboha Nataliya V. , Pelster Meredith S. , Bekaii-Saab Tanios S. , Barve Minal , Saltzman Joel , Sabari Joshua K. , Peguero Julio A. , Paulson Andrew Scott , Jänne Pasi A. , Cruz-Correa Marcia , Anderes Kenna , Velastegui Karen , Yan Xiaohong , Der-Torossian Hirak , Klempner Samuel J. , Kopetz Scott E.
Published: June 2024

Table S4. Overall efficacy summary with adagrasib monotherapy in previously treated patients with KRASG12C-mutated unresectable or metastatic CRCa.
Supplementary Table S3 from Efficacy and Safety of Adagrasib plus Cetuximab in Patients with KRASG12C-Mutated Metastatic Colorectal Cancer
Authors: Yaeger Rona , Uboha Nataliya V. , Pelster Meredith S. , Bekaii-Saab Tanios S. , Barve Minal , Saltzman Joel , Sabari Joshua K. , Peguero Julio A. , Paulson Andrew Scott , Jänne Pasi A. , Cruz-Correa Marcia , Anderes Kenna , Velastegui Karen , Yan Xiaohong , Der-Torossian Hirak , Klempner Samuel J. , Kopetz Scott E.
Published: June 2024

Table S3. Efficacy summary per BICR with adagrasib plus cetuximab in previously treated patients with KRASG12C-mutated unresectable or metastatic CRC, overall, and in phase 1 and phase 2 cohorts.
Supplementary Figure S2 from Efficacy and Safety of Adagrasib plus Cetuximab in Patients with KRASG12C-Mutated Metastatic Colorectal Cancer
Authors: Yaeger Rona , Uboha Nataliya V. , Pelster Meredith S. , Bekaii-Saab Tanios S. , Barve Minal , Saltzman Joel , Sabari Joshua K. , Peguero Julio A. , Paulson Andrew Scott , Jänne Pasi A. , Cruz-Correa Marcia , Anderes Kenna , Velastegui Karen , Yan Xiaohong , Der-Torossian Hirak , Klempner Samuel J. , Kopetz Scott E.
Published: June 2024

Supplementary Figure S2: Efficacy outcomes with adagrasib monotherapy in previously treated patients with KRASG12C-mutated unresecable or metastatic CRC.
Supplementary Table S2 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 S2 shows cell panel screening data with a panel of 78 cancer cell lines harboring mutant and wild-type RAS selected for screening at Crown Bioscience.
Figure S5 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. S5. Subsets of NK cells in lung of control and DHA-treated mice with B16F10 melanoma tumour growth.
Figure S2 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. S2. The effects of DHA supplementation for eight weeks on T, B and NK cells without B16F10 injection. WT mice were fed with control or DHA-enriched diets for eight weeks.
Figure S7 from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy
Authors: Martin Michael V. , Aguilar-Rosas Salvador , Franke Katka , Pieterse Mark , Langelaar Jamie van , Schreurs Renée , Bijlsma Maarten F. , Besselink Marc G. , Koster Jan , Timens Wim , Khasraw Mustafa , Ashley David M. , Keir Stephen T. , Ottensmeier Christian H. , King Emma V. , Verheij Joanne , Waasdorp Cynthia , Valk Peter J.M. , Engels Sem A.G. , Oostenbach Ellen , van Dinter Jip T. , Hofman Damon A. , Mok Juk Yee , van Esch Wim J.E. , Wilmink Hanneke , Monkhorst Kim , Verheul Henk M.W. , Poel Dennis , Hiltermann T. Jeroen N. , Kempen Léon C.L.T. van , Groen Harry J.M. , Aerts Joachim G.J.V. , Heesch Sebastiaan van , Löwenberg Bob , Plasterk Ronald , Kloosterman Wigard P.
Published: June 2024

Figure S7: Protein mass spectrometry results for A375 NOPs.
Supplementary Table S2 from An IRF2-Expressing Oncolytic Virus Changes the Susceptibility of Tumor Cells to Antitumor T Cells and Promotes Tumor Clearance
Authors: Shao Lulu , Srivastava Rashmi , Delgoffe Greg M. , Thorne Stephen H. , Sarkar Saumendra N.
Published: June 2024

Supplementary Table S2
Supplementary Table S1 from An IRF2-Expressing Oncolytic Virus Changes the Susceptibility of Tumor Cells to Antitumor T Cells and Promotes Tumor Clearance
Authors: Shao Lulu , Srivastava Rashmi , Delgoffe Greg M. , Thorne Stephen H. , Sarkar Saumendra N.
Published: June 2024

Supplementary Table S1
Supplementary Figure S4 from An IRF2-Expressing Oncolytic Virus Changes the Susceptibility of Tumor Cells to Antitumor T Cells and Promotes Tumor Clearance
Authors: Shao Lulu , Srivastava Rashmi , Delgoffe Greg M. , Thorne Stephen H. , Sarkar Saumendra N.
Published: June 2024

Supplementary Figure S4 with legend
Supplementary Figure S2 from An IRF2-Expressing Oncolytic Virus Changes the Susceptibility of Tumor Cells to Antitumor T Cells and Promotes Tumor Clearance
Authors: Shao Lulu , Srivastava Rashmi , Delgoffe Greg M. , Thorne Stephen H. , Sarkar Saumendra N.
Published: June 2024

Supplementary Figure S2 with legend
Figure S13 from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy
Authors: Martin Michael V. , Aguilar-Rosas Salvador , Franke Katka , Pieterse Mark , Langelaar Jamie van , Schreurs Renée , Bijlsma Maarten F. , Besselink Marc G. , Koster Jan , Timens Wim , Khasraw Mustafa , Ashley David M. , Keir Stephen T. , Ottensmeier Christian H. , King Emma V. , Verheij Joanne , Waasdorp Cynthia , Valk Peter J.M. , Engels Sem A.G. , Oostenbach Ellen , van Dinter Jip T. , Hofman Damon A. , Mok Juk Yee , van Esch Wim J.E. , Wilmink Hanneke , Monkhorst Kim , Verheul Henk M.W. , Poel Dennis , Hiltermann T. Jeroen N. , Kempen Léon C.L.T. van , Groen Harry J.M. , Aerts Joachim G.J.V. , Heesch Sebastiaan van , Löwenberg Bob , Plasterk Ronald , Kloosterman Wigard P.
Published: June 2024

Figure S13: In silico determined immunogenic properties of NOPs.
Supplementary Figure S1 from An IRF2-Expressing Oncolytic Virus Changes the Susceptibility of Tumor Cells to Antitumor T Cells and Promotes Tumor Clearance
Authors: Shao Lulu , Srivastava Rashmi , Delgoffe Greg M. , Thorne Stephen H. , Sarkar Saumendra N.
Published: June 2024

Supplementary Figure S1 with legend
Supplementary Data File 3 from An IRF2-Expressing Oncolytic Virus Changes the Susceptibility of Tumor Cells to Antitumor T Cells and Promotes Tumor Clearance
Authors: Shao Lulu , Srivastava Rashmi , Delgoffe Greg M. , Thorne Stephen H. , Sarkar Saumendra N.
Published: June 2024

MDSC gating strategy
Supplemental Figure 2 from Unleashing Natural IL18 Activity Using an Anti-IL18BP Blocker Induces Potent Immune Stimulation and Antitumor Effects
Authors: Menachem Assaf , Alteber Zoya , Cojocaru Gady , Fridman Kfir Tal , Blat Dan , Leiderman Olga , Galperin Moran , Sever Lital , Cohen Nadav , Cohen Keren , Granit Roy Z. , Vols Sandra , Frenkel Masha , Soffer Liron , Meyer Karin , Menachem Keren , Galon Tilleman Hadas , Morein Dina , Borukhov Itamar , Toporik Amir , Perpinial Shahor Michal , Tatirovsky Evgeny , Mizrachi Aviram , Levy-Barda Adva , Sadot Eran , Strenov Yulia , Eitan Ram , Jakobson-Setton Ariella , Yanichkin Natalia , Ferre Pierre , Ophir Eran
Published: June 2024

Supplemental Figure S2. COM503 releases IL-18 activity in biochemical and functional assays.
Supplementary Figure S3 from Preclinical Evaluation of Off-The-Shelf PD-L1+ Human Natural Killer Cells Secreting IL15 to Treat Non–Small Cell Lung Cancer
Authors: Lu Ting , Ma Rui , Mansour Anthony G. , Bustillos Christian , Li Zhiyao , Li Zhenlong , Ma Shoubao , Teng Kun-Yu , Chen Hanyu , Zhang Jianying , Villalona-Calero Miguel A. , Caligiuri Michael A. , Yu Jianhua
Published: June 2024

Supplementary Figure S3
Supplementary Figure S2 from Preclinical Evaluation of Off-The-Shelf PD-L1+ Human Natural Killer Cells Secreting IL15 to Treat Non–Small Cell Lung Cancer
Authors: Lu Ting , Ma Rui , Mansour Anthony G. , Bustillos Christian , Li Zhiyao , Li Zhenlong , Ma Shoubao , Teng Kun-Yu , Chen Hanyu , Zhang Jianying , Villalona-Calero Miguel A. , Caligiuri Michael A. , Yu Jianhua
Published: June 2024

Supplementary Figure S2
Supplementary Figure 8 from Intratumoral TREX1 Induction Promotes Immune Evasion by Limiting Type I IFN
Authors: Toufektchan Eléonore , Dananberg Alexandra , Striepen Josefine , Hickling James H. , Shim Abraham , Chen Yanyang , Nichols Ashley , Duran Paez Mercedes A. , Mohr Lisa , Bakhoum Samuel F. , Maciejowski John
Published: June 2024

Individual growth curves of tumors treated with anti-PD-1 and isotype controls.
Supplementary Figure 7 from Intratumoral TREX1 Induction Promotes Immune Evasion by Limiting Type I IFN
Authors: Toufektchan Eléonore , Dananberg Alexandra , Striepen Josefine , Hickling James H. , Shim Abraham , Chen Yanyang , Nichols Ashley , Duran Paez Mercedes A. , Mohr Lisa , Bakhoum Samuel F. , Maciejowski John
Published: June 2024

Individual growth curves of tumors transplanted in Rag1 KO and NU/J hosts.
Supplementary Figure 5 from Intratumoral TREX1 Induction Promotes Immune Evasion by Limiting Type I IFN
Authors: Toufektchan Eléonore , Dananberg Alexandra , Striepen Josefine , Hickling James H. , Shim Abraham , Chen Yanyang , Nichols Ashley , Duran Paez Mercedes A. , Mohr Lisa , Bakhoum Samuel F. , Maciejowski John
Published: June 2024

TREX1 promotes tumor growth, but not in vitro cell proliferation.
Supplementary Figure 2 from Intratumoral TREX1 Induction Promotes Immune Evasion by Limiting Type I IFN
Authors: Toufektchan Eléonore , Dananberg Alexandra , Striepen Josefine , Hickling James H. , Shim Abraham , Chen Yanyang , Nichols Ashley , Duran Paez Mercedes A. , Mohr Lisa , Bakhoum Samuel F. , Maciejowski John
Published: June 2024

cGAS-STING-dependent TREX1 upregulation.
Supplementary Figure 1 from Intratumoral TREX1 Induction Promotes Immune Evasion by Limiting Type I IFN
Authors: Toufektchan Eléonore , Dananberg Alexandra , Striepen Josefine , Hickling James H. , Shim Abraham , Chen Yanyang , Nichols Ashley , Duran Paez Mercedes A. , Mohr Lisa , Bakhoum Samuel F. , Maciejowski John
Published: June 2024

Generation of KO cell lines and extracellular cGAMP measurements.
Supplementary File 3 from Randomized Phase II Study Evaluating the Addition of Pembrolizumab to Radium-223 in Metastatic Castration-resistant Prostate Cancer
Authors: Choudhury Atish D. , Kwak Lucia , Cheung Alexander , Allaire Kathryn M. , Marquez Jaqueline , Yang David D. , Tripathi Abhishek , Kilar Jacqueline M. , Flynn Meredith , Maynard Brianna , Reichel Rebecca , Pace Amanda F. , Chen Brandon K. , Van Allen Eliezer M. , Kilbridge Kerry , Wei Xiao X. , McGregor Bradley A. , Pomerantz Mark M. , Bhatt Rupal S. , Sweeney Christopher J. , Bubley Glenn J. , Jacene Heather A. , Taplin Mary-Ellen , Huang Franklin W. , Harshman Lauren C. , Fong Lawrence
Published: June 2024

Supplementary File 3
Supplemental Table 2 from Randomized Phase II Study Evaluating the Addition of Pembrolizumab to Radium-223 in Metastatic Castration-resistant Prostate Cancer
Authors: Choudhury Atish D. , Kwak Lucia , Cheung Alexander , Allaire Kathryn M. , Marquez Jaqueline , Yang David D. , Tripathi Abhishek , Kilar Jacqueline M. , Flynn Meredith , Maynard Brianna , Reichel Rebecca , Pace Amanda F. , Chen Brandon K. , Van Allen Eliezer M. , Kilbridge Kerry , Wei Xiao X. , McGregor Bradley A. , Pomerantz Mark M. , Bhatt Rupal S. , Sweeney Christopher J. , Bubley Glenn J. , Jacene Heather A. , Taplin Mary-Ellen , Huang Franklin W. , Harshman Lauren C. , Fong Lawrence
Published: June 2024

Maximum grade adverse events, regardless of attribution. AEs are summarized as n (%) for each maximum grade.
Supplemental Table 1 from Randomized Phase II Study Evaluating the Addition of Pembrolizumab to Radium-223 in Metastatic Castration-resistant Prostate Cancer
Authors: Choudhury Atish D. , Kwak Lucia , Cheung Alexander , Allaire Kathryn M. , Marquez Jaqueline , Yang David D. , Tripathi Abhishek , Kilar Jacqueline M. , Flynn Meredith , Maynard Brianna , Reichel Rebecca , Pace Amanda F. , Chen Brandon K. , Van Allen Eliezer M. , Kilbridge Kerry , Wei Xiao X. , McGregor Bradley A. , Pomerantz Mark M. , Bhatt Rupal S. , Sweeney Christopher J. , Bubley Glenn J. , Jacene Heather A. , Taplin Mary-Ellen , Huang Franklin W. , Harshman Lauren C. , Fong Lawrence
Published: June 2024

Summary of biopsy yield
Supplemental Figure 7 from Randomized Phase II Study Evaluating the Addition of Pembrolizumab to Radium-223 in Metastatic Castration-resistant Prostate Cancer
Authors: Choudhury Atish D. , Kwak Lucia , Cheung Alexander , Allaire Kathryn M. , Marquez Jaqueline , Yang David D. , Tripathi Abhishek , Kilar Jacqueline M. , Flynn Meredith , Maynard Brianna , Reichel Rebecca , Pace Amanda F. , Chen Brandon K. , Van Allen Eliezer M. , Kilbridge Kerry , Wei Xiao X. , McGregor Bradley A. , Pomerantz Mark M. , Bhatt Rupal S. , Sweeney Christopher J. , Bubley Glenn J. , Jacene Heather A. , Taplin Mary-Ellen , Huang Franklin W. , Harshman Lauren C. , Fong Lawrence
Published: June 2024

Immunofluorescence staining of PD-L1+ CD68 myeloid cells in the bone biopsies. A. RNAscope staining of DAPI (cyan), CD68 (orange), PD-L1 (magenta), Tim3 (green), TIGIT (white) and overlay of bone marrow metastasis. CD68+ cells that co-express PD-L1 are indicated with arrow. Tim3+ cells are indicated with pointer. Scale bar, 20 μm. B. Scatterplot of PDL1+ CD68+ cell frequencies of tissue imaging data and PDL1+ CD14+ CD3-CD19- myeloid cell frequencies of CyTOF data from blood samples taken at the same timepoint (baseline, n=10 patients). R2 value is based on Pearson correlation. C. Scatterplot of TIM3+ CD68- cell frequencies on tissue imaging and TIM3+ CD3+ T cell frequencies of CyTOF data from blood samples taken at the same timepoint (baseline, n=10 patients). R2 value is based on Pearson correlation.
Supplemental Figure 4 from Randomized Phase II Study Evaluating the Addition of Pembrolizumab to Radium-223 in Metastatic Castration-resistant Prostate Cancer
Authors: Choudhury Atish D. , Kwak Lucia , Cheung Alexander , Allaire Kathryn M. , Marquez Jaqueline , Yang David D. , Tripathi Abhishek , Kilar Jacqueline M. , Flynn Meredith , Maynard Brianna , Reichel Rebecca , Pace Amanda F. , Chen Brandon K. , Van Allen Eliezer M. , Kilbridge Kerry , Wei Xiao X. , McGregor Bradley A. , Pomerantz Mark M. , Bhatt Rupal S. , Sweeney Christopher J. , Bubley Glenn J. , Jacene Heather A. , Taplin Mary-Ellen , Huang Franklin W. , Harshman Lauren C. , Fong Lawrence
Published: June 2024

Changes in A. CD4+FoxP3- effector cells and B. ratio of CD8+ to CD4+/FoxP3+ (Treg) cells from baseline to 8 weeks on treatment
Supplementary Methods from Engineering CD3/CD137 Dual Specificity into a DLL3-Targeted T-Cell Engager Enhances T-Cell Infiltration and Efficacy against Small-Cell Lung Cancer
Authors: Mikami Hirofumi , Feng Shu , Matsuda Yutaka , Ishii Shinya , Naoi Sotaro , Azuma Yumiko , Nagano Hiroaki , Asanuma Kentaro , Kayukawa Yoko , Tsunenari Toshiaki , Kamikawaji Shogo , Iwabuchi Ryutaro , Shinozuka Junko , Yamazaki Masaki , Kuroi Haruka , Ho Samantha Shu Wen , Gan Siok Wan , Chichili Priyanka , Pang Chai Ling , Yeo Chiew Ying , Shimizu Shun , Hironiwa Naoka , Kinoshita Yasuko , Shimizu Yuichiro , Sakamoto Akihisa , Muraoka Masaru , Takahashi Noriyuki , Kawa Tatsuya , Shiraiwa Hirotake , Mimoto Futa , Kashima Kenji , Kamata-Sakurai Mika , Ishikawa Shumpei , Aburatani Hiroyuki , Kitazawa Takehisa , Igawa Tomoyuki
Published: June 2024

Supplementary Methods
Figure S8 from Engineering CD3/CD137 Dual Specificity into a DLL3-Targeted T-Cell Engager Enhances T-Cell Infiltration and Efficacy against Small-Cell Lung Cancer
Authors: Mikami Hirofumi , Feng Shu , Matsuda Yutaka , Ishii Shinya , Naoi Sotaro , Azuma Yumiko , Nagano Hiroaki , Asanuma Kentaro , Kayukawa Yoko , Tsunenari Toshiaki , Kamikawaji Shogo , Iwabuchi Ryutaro , Shinozuka Junko , Yamazaki Masaki , Kuroi Haruka , Ho Samantha Shu Wen , Gan Siok Wan , Chichili Priyanka , Pang Chai Ling , Yeo Chiew Ying , Shimizu Shun , Hironiwa Naoka , Kinoshita Yasuko , Shimizu Yuichiro , Sakamoto Akihisa , Muraoka Masaru , Takahashi Noriyuki , Kawa Tatsuya , Shiraiwa Hirotake , Mimoto Futa , Kashima Kenji , Kamata-Sakurai Mika , Ishikawa Shumpei , Aburatani Hiroyuki , Kitazawa Takehisa , Igawa Tomoyuki
Published: June 2024

Supplementary Figure S8. DLL3 trispecific induced activation of tumor-infiltrating T cells.
Data from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy
Authors: Martin Michael V. , Aguilar-Rosas Salvador , Franke Katka , Pieterse Mark , Langelaar Jamie van , Schreurs Renée , Bijlsma Maarten F. , Besselink Marc G. , Koster Jan , Timens Wim , Khasraw Mustafa , Ashley David M. , Keir Stephen T. , Ottensmeier Christian H. , King Emma V. , Verheij Joanne , Waasdorp Cynthia , Valk Peter J.M. , Engels Sem A.G. , Oostenbach Ellen , van Dinter Jip T. , Hofman Damon A. , Mok Juk Yee , van Esch Wim J.E. , Wilmink Hanneke , Monkhorst Kim , Verheul Henk M.W. , Poel Dennis , Hiltermann T. Jeroen N. , Kempen Léon C.L.T. van , Groen Harry J.M. , Aerts Joachim G.J.V. , Heesch Sebastiaan van , Löwenberg Bob , Plasterk Ronald , Kloosterman Wigard P.
Published: June 2024

Abstract
Identification of immunogenic cancer neoantigens as targets for therapy is challenging. Here, we integrate the whole-genome and long-read transcript sequencing of cancers to identify the collection of neo-open reading frame peptides (NOP) expressed in tumors. We termed this collection of NOPs the tumor framome. NOPs represent tumor-specific peptides that are different from wild-type proteins and may be strongly immunogenic. We describe a class of hidden NOPs that derive from structural genomic variants involving an upstream protein coding gene driving expression and translation of noncoding regions of the genome downstream of a rearrangement breakpoint, i.e., where no gene annotation or evidence for transcription exists. The entire collection of NOPs represents a vast number of possible neoantigens particularly in tumors with many structural genomic variants and a low number of missense mutations. We show that NOPs are immunogenic and epitopes derived from NOPs can bind to MHC class I molecules. Finally, we provide evidence for the presence of memory T cells specific for hidden NOPs in peripheral blood from a patient with lung cancer. This work highlights NOPs as a major source of possible neoantigens for personalized cancer immunotherapy and provides a rationale for analyzing the complete cancer genome and transcriptome as a basis for the detection of NOPs.
Supplementary figure 4 from B7-H3–Targeting Chimeric Antigen Receptors Epstein-Barr Virus–specific T Cells Provides a Tumor Agnostic Off-The-Shelf Therapy Against B7-H3–positive Solid Tumors
Authors: Yeo Siok Ping , Kua Lindsay , Tan Jin Wei , Lim Joanna Kristyn , Wong Fiona HS , Santos May Delos , Poh Chek Meng , Goh Angeline XH , Koh Xin Yu , Zhou Xiaohua , Rajarethinam Ravisankar , Chen Qingfeng , Her Zhisheng , Horak Ivan D. , Low Lionel , Tan Kar Wai
Published: June 2024

Supplementary figure 4