bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Table S2 from Understanding and Overcoming Resistance to Selective FGFR Inhibitors across FGFR2-Driven Malignancies
Authors: Facchinetti Francesco , Loriot Yohann , Brayé Floriane , Vasseur Damien , Bahleda Rastislav , Bigot Ludovic , Barbé Rémy , Nobre Catline , Combarel David , Michiels Stefan , Italiano Antoine , Smolenschi Cristina , Tselikas Lambros , Scoazec Jean-Yves , Ponce-Aix Santiago , Besse Benjamin , André Fabrice , Olaussen Ken A. , Hollebecque Antoine , Friboulet Luc
Published: November 2024

Specific FGFR2 drivers of the 27 patients suffering from intrahepatic cholangiocarcinoma.
Supplementary Table S1 from Understanding and Overcoming Resistance to Selective FGFR Inhibitors across FGFR2-Driven Malignancies
Authors: Facchinetti Francesco , Loriot Yohann , Brayé Floriane , Vasseur Damien , Bahleda Rastislav , Bigot Ludovic , Barbé Rémy , Nobre Catline , Combarel David , Michiels Stefan , Italiano Antoine , Smolenschi Cristina , Tselikas Lambros , Scoazec Jean-Yves , Ponce-Aix Santiago , Besse Benjamin , André Fabrice , Olaussen Ken A. , Hollebecque Antoine , Friboulet Luc
Published: November 2024

Baseline characteristics of patients included in the study and treatment with selective FGFR inhibitors.
Supplementary Figure S4 from Understanding and Overcoming Resistance to Selective FGFR Inhibitors across FGFR2-Driven Malignancies
Authors: Facchinetti Francesco , Loriot Yohann , Brayé Floriane , Vasseur Damien , Bahleda Rastislav , Bigot Ludovic , Barbé Rémy , Nobre Catline , Combarel David , Michiels Stefan , Italiano Antoine , Smolenschi Cristina , Tselikas Lambros , Scoazec Jean-Yves , Ponce-Aix Santiago , Besse Benjamin , André Fabrice , Olaussen Ken A. , Hollebecque Antoine , Friboulet Luc
Published: November 2024

Clinico-radiological and molecular evolution of patients MR822 (A, FGFR2-rearranged intrahepatic cholangiocarcinoma) and MR1154 (B, FGFR2-rearranged pancreatic ductal adenocarcinoma).
Supplementary Figure S1 from Understanding and Overcoming Resistance to Selective FGFR Inhibitors across FGFR2-Driven Malignancies
Authors: Facchinetti Francesco , Loriot Yohann , Brayé Floriane , Vasseur Damien , Bahleda Rastislav , Bigot Ludovic , Barbé Rémy , Nobre Catline , Combarel David , Michiels Stefan , Italiano Antoine , Smolenschi Cristina , Tselikas Lambros , Scoazec Jean-Yves , Ponce-Aix Santiago , Besse Benjamin , André Fabrice , Olaussen Ken A. , Hollebecque Antoine , Friboulet Luc
Published: November 2024

Clinico-radiological and molecular evolution of patient ST1056, suffering from a FGFR2-rearranged lung adenocarcinoma.
Supplementary Figure S3 from The Immune-Related 27-Gene Signature DetermaIO Predicts Response to Neoadjuvant Atezolizumab plus Chemotherapy in Triple-Negative Breast Cancer
Authors: Dugo Matteo , Huang Chiun-Sheng , Egle Daniel , Bermejo Begoña , Zamagni Claudio , Seitz Robert S. , Nielsen Tyler J. , Thill Marc , Antón-Torres Antonio , Russo Stefania , Ciruelos Eva Maria , Schweitzer Brock L. , Ross Douglas T. , Galbardi Barbara , Greil Richard , Semiglazov Vladimir , Gyorffy Balázs , Colleoni Marco , Kelly Catherine M. , Mariani Gabriella , Del Mastro Lucia , Blasi Olivia , Callari Maurizio , Pusztai Lajos , Valagussa Pinuccia , Viale Giuseppe , Gianni Luca , Bianchini Giampaolo
Published: November 2024

Supplementary Figure 3. Continuous baseline RT-qPCR DetermaIO score. Distribution of continuous IO score by treatment arm and pCR status. P-values by logistic regression.
Supplementary Figure S1 from The Immune-Related 27-Gene Signature DetermaIO Predicts Response to Neoadjuvant Atezolizumab plus Chemotherapy in Triple-Negative Breast Cancer
Authors: Dugo Matteo , Huang Chiun-Sheng , Egle Daniel , Bermejo Begoña , Zamagni Claudio , Seitz Robert S. , Nielsen Tyler J. , Thill Marc , Antón-Torres Antonio , Russo Stefania , Ciruelos Eva Maria , Schweitzer Brock L. , Ross Douglas T. , Galbardi Barbara , Greil Richard , Semiglazov Vladimir , Gyorffy Balázs , Colleoni Marco , Kelly Catherine M. , Mariani Gabriella , Del Mastro Lucia , Blasi Olivia , Callari Maurizio , Pusztai Lajos , Valagussa Pinuccia , Viale Giuseppe , Gianni Luca , Bianchini Giampaolo
Published: November 2024

Supplementary Figure 1. Quality control of NeoTRIP RNA-Seq data. Boxplots showing the distribution of read depth of targeted coding regions by arm and response status. Dots represent the read depth of single samples. The horizontal grey dashed line represents the cut-off of 40 million paired-end reads.
Supplementary Data 1 from Incorporating Supramaximal Resection into Survival Stratification of IDH-wildtype Glioblastoma: A Refined Multi-institutional Recursive Partitioning Analysis
Authors: Park Yae Won , Choi Kyu Sung , Foltyn-Dumitru Martha , Brugnara Gianluca , Banan Rouzbeh , Kim Sooyon , Han Kyunghwa , Park Ji Eun , Kessler Tobias , Bendszus Martin , Krieg Sandro , Wick Wolfgang , Sahm Felix , Choi Seung Hong , Kim Ho Sung , Chang Jong Hee , Kim Se Hoon , Wongsawaeng Doonyaporn , Pollock Jeffrey Michael , Lee Seung-Koo , Barajas Ramon Francisco , Vollmuth Philipp , Ahn Sung Soo
Published: November 2024

Supplementary Data
Supplementary Table S2 from Multiomics Profiling Distinguishes Sebaceous Carcinoma from Benign Sebaceous Neoplasms and Provides Insight into the Genetic Evolution of Sebaceous Carcinogenesis
Authors: Starrett Gabriel J. , Baikie Brittany C. , Stoff Benjamin K. , Grossniklaus Hans E. , Van Buren Inga , Berry Elizabeth G. , Novoa Roberto A. , Rieger Kerri E. , Sarin Kavita Y. , Lynch Charles F. , Royer Michael C. , Piaskowski Mary L. , Brownell Isaac , Chu Emily Y. , Godse Rama , Chen Suephy C. , Yu Kelly J. , Goldstein Alisa M. , Engels Eric A. , Sargen Michael R.
Published: November 2024

Sequencing metrics.
Supplementary Table S1 from Multiomics Profiling Distinguishes Sebaceous Carcinoma from Benign Sebaceous Neoplasms and Provides Insight into the Genetic Evolution of Sebaceous Carcinogenesis
Authors: Starrett Gabriel J. , Baikie Brittany C. , Stoff Benjamin K. , Grossniklaus Hans E. , Van Buren Inga , Berry Elizabeth G. , Novoa Roberto A. , Rieger Kerri E. , Sarin Kavita Y. , Lynch Charles F. , Royer Michael C. , Piaskowski Mary L. , Brownell Isaac , Chu Emily Y. , Godse Rama , Chen Suephy C. , Yu Kelly J. , Goldstein Alisa M. , Engels Eric A. , Sargen Michael R.
Published: November 2024

Summary of non-malignant control tissues used for transcriptome comparisons.
Supplementary Figure S7 from Multiomics Profiling Distinguishes Sebaceous Carcinoma from Benign Sebaceous Neoplasms and Provides Insight into the Genetic Evolution of Sebaceous Carcinogenesis
Authors: Starrett Gabriel J. , Baikie Brittany C. , Stoff Benjamin K. , Grossniklaus Hans E. , Van Buren Inga , Berry Elizabeth G. , Novoa Roberto A. , Rieger Kerri E. , Sarin Kavita Y. , Lynch Charles F. , Royer Michael C. , Piaskowski Mary L. , Brownell Isaac , Chu Emily Y. , Godse Rama , Chen Suephy C. , Yu Kelly J. , Goldstein Alisa M. , Engels Eric A. , Sargen Michael R.
Published: November 2024

Correlation between tumor purity as determined by pathology and PURPLE versus single base substitution signature abundance (counts) and relative fraction within a sample. A blue line with a light grey confidence interval represents the general linear model for the data points.
Supplementary Figure S5 from Multiomics Profiling Distinguishes Sebaceous Carcinoma from Benign Sebaceous Neoplasms and Provides Insight into the Genetic Evolution of Sebaceous Carcinogenesis
Authors: Starrett Gabriel J. , Baikie Brittany C. , Stoff Benjamin K. , Grossniklaus Hans E. , Van Buren Inga , Berry Elizabeth G. , Novoa Roberto A. , Rieger Kerri E. , Sarin Kavita Y. , Lynch Charles F. , Royer Michael C. , Piaskowski Mary L. , Brownell Isaac , Chu Emily Y. , Godse Rama , Chen Suephy C. , Yu Kelly J. , Goldstein Alisa M. , Engels Eric A. , Sargen Michael R.
Published: November 2024

Heatmaps of selected significantly altered pathways. A. Sirtuin signaling. B. Rho signaling C. TP53 signaling.
Supplementary Figure S4 from Multiomics Profiling Distinguishes Sebaceous Carcinoma from Benign Sebaceous Neoplasms and Provides Insight into the Genetic Evolution of Sebaceous Carcinogenesis
Authors: Starrett Gabriel J. , Baikie Brittany C. , Stoff Benjamin K. , Grossniklaus Hans E. , Van Buren Inga , Berry Elizabeth G. , Novoa Roberto A. , Rieger Kerri E. , Sarin Kavita Y. , Lynch Charles F. , Royer Michael C. , Piaskowski Mary L. , Brownell Isaac , Chu Emily Y. , Godse Rama , Chen Suephy C. , Yu Kelly J. , Goldstein Alisa M. , Engels Eric A. , Sargen Michael R.
Published: November 2024

Raw output of pathway prediction between adenomas and carcinomas from Ingenuity Pathway Analysis.
Supplementary Figure S3 from Multiomics Profiling Distinguishes Sebaceous Carcinoma from Benign Sebaceous Neoplasms and Provides Insight into the Genetic Evolution of Sebaceous Carcinogenesis
Authors: Starrett Gabriel J. , Baikie Brittany C. , Stoff Benjamin K. , Grossniklaus Hans E. , Van Buren Inga , Berry Elizabeth G. , Novoa Roberto A. , Rieger Kerri E. , Sarin Kavita Y. , Lynch Charles F. , Royer Michael C. , Piaskowski Mary L. , Brownell Isaac , Chu Emily Y. , Godse Rama , Chen Suephy C. , Yu Kelly J. , Goldstein Alisa M. , Engels Eric A. , Sargen Michael R.
Published: November 2024

A. Violin plot of xCell immune, stroma, and microenviroment scores for extraocular sebaceous adenomas and carcinomas. B. Boxplot of CIBERSORTx significantly different cell populations between extraocular adenomas and carcinomas. C. Boxplot of CIBERSORTx significantly different cell populations between extraocular carcinomas of immunosuppressed and immunocompetent patients.
Supplementary Table S3 from A Phase II Study of Atezolizumab, Pertuzumab, and High-Dose Trastuzumab for Central Nervous System Metastases in Patients with HER2-Positive Breast Cancer
Authors: Giordano Antonio , Kumthekar Priya U. , Jin Qingchun , Binboga Kurt Busem , Ren Siyang , Li Tianyu , Leone Jose Pablo , Mittendorf Elizabeth A. , Pereslete Alyssa M. , Sharp Laura , Davis Raechel , DiLullo Molly , Tayob Nabihah , Mayer Erica L. , Winer Eric P. , Tolaney Sara M. , Lin Nancy U.
Published: November 2024

Supplementary Table S3. Baseline patient and disease characteristics continued from Table 1.
Supplementary Table S1 from A Phase II Study of Atezolizumab, Pertuzumab, and High-Dose Trastuzumab for Central Nervous System Metastases in Patients with HER2-Positive Breast Cancer
Authors: Giordano Antonio , Kumthekar Priya U. , Jin Qingchun , Binboga Kurt Busem , Ren Siyang , Li Tianyu , Leone Jose Pablo , Mittendorf Elizabeth A. , Pereslete Alyssa M. , Sharp Laura , Davis Raechel , DiLullo Molly , Tayob Nabihah , Mayer Erica L. , Winer Eric P. , Tolaney Sara M. , Lin Nancy U.
Published: November 2024

Supplementary Table S1. Data on the representativeness of the study population.
Supplementary Figure S4 from Genomic Profiling and Immune Phenotyping of Neuroendocrine Bladder Cancer
Authors: Zang Jingyu , Shahatiaili Akezhouli , Cai Mei-Chun , Jin Di , Shen Peiye , Qian Lei , Zhang Lu , Zhang Tianxiang , Wu Yuchen , Yang Fan , Wu Zheng , Hou Yanli , Bai Yongrui , Xia Jun , Cheng Liang , Zhang Ruiyun , Zhuang Guanglei , Chen Haige
Published: November 2024

Kataegis events in NEBC.
Data from Clinical and Genomic Features of Classical and Basal Transcriptional Subtypes in Pancreatic Cancer
Authors: Singh Harshabad , Xiu Joanne , Kapner Kevin S. , Yuan Chen , Narayan Raja R. , Oberley Matthew , Farrell Alex , Surana Rishi , Huffman Brandon M. , Perez Kimberly , Cleary James M. , Jordan Alexander C. , Dias Costa Andressa , Williams Hannah L. , Raghavan Srivatsan , Weinberg Benjamin , Pishvaian Michael J. , Shroff Rachna T. , Goel Sanjay , Dougan Stephanie K. , Nowak Jonathan A. , Spetzler David , Sledge George , Wolpin Brian M. , Aguirre Andrew J.
Published: November 2024

AbstractPurpose:
Transcriptional profiling of pancreatic cancers has defined two main transcriptional subtypes: classical and basal. Initial data suggest shorter survival for patients with basal tumors and differing treatment sensitivity to FOLFIRINOX and gemcitabine plus nab-paclitaxel by transcriptional subtype.
Experimental Design:
We examined 8,743 patients with RNA sequencing from pancreatic cancers performed at Caris Life Sciences. Classical and basal subtypes were identified using purity independent subtyping algorithm on RNA sequencing, and two cohorts were analyzed: (i) the biomarker cohort included patients with complete molecular profiling data (n = 7,250) and (ii) the outcome cohort included patients with metastatic disease with available survival outcomes (n = 5,335). A total of 3,842 patients were shared between the two cohorts. Kaplan–Meier curves and Cox proportional hazards regression were used to assess patient survival.
Results:
In the biomarker cohort, 3,063 tumors (42.2%) were strongly classical (SC) and 2,015 tumors (27.8%) were strongly basal (SB). SC and SB tumors showed strong associations with histologic phenotypes and biopsy sites. SB tumors had higher rates of KRAS, TP53, and ARID1A mutations, lower rates of SMAD4 mutation, and transcriptional evidence of epithelial-mesenchymal transition. Sixty of 77 cases (78%) maintained their transcriptional subtype between temporally and/or spatially disparate lesions. In the outcome cohort, the SB subtype was associated with shorter overall survival time, regardless of whether they received FOLFIRINOX or gemcitabine plus nab-paclitaxel as first-line chemotherapy. The mutant KRAS allele type was prognostic of outcomes; however, this impact was restricted to SC tumors, whereas all mutant KRAS alleles had similarly poor outcomes in SB tumors.
Conclusions:
The SB subtype is a strong independent predictor of worse outcomes, regardless of the up-front chemotherapy regimen used. Clinical trials should further investigate pancreatic cancer transcriptional subtypes as a prognostic and predictive biomarker.
Data from Exploiting WEE1 Kinase Activity as FUS::DDIT3-Dependent Therapeutic Vulnerability in Myxoid Liposarcoma
Authors: Heinst Lorena , Lee Kwang Seok , Berthold Ruth , Isfort Ilka , Wosnig Svenja , Kuntze Anna , Hafner Susanne , Altvater Bianca , Rossig Claudia , Åman Pierre , Wardelmann Eva , Scholl Claudia , Hartmann Wolfgang , Fröhling Stefan , Trautmann Marcel
Published: November 2024

AbstractPurpose:
The pathognomonic FUS::DDIT3 fusion protein drives myxoid liposarcoma (MLS) tumorigenesis via aberrant transcriptional activation of oncogenic signaling. As FUS::DDIT3 has so far not been pharmacologically tractable to selectively target MLS cells, this study investigated the functional role of the cell cycle regulator WEE1 as novel FUS::DDIT3-dependent therapeutic vulnerability in MLS.
Experimental Design:
Immunohistochemical evaluation of the cell cycle regulator WEE1 was performed in a large cohort of MLS specimens. FUS::DDIT3 dependency and biological function of the G1/S cell cycle checkpoint were analyzed in a mesenchymal stem cell model and liposarcoma cell lines in vitro. WEE1 activity was modulated by RNAi-mediated knockdown and the small molecule inhibitor MK-1775 (adavosertib). An established MLS cell line–based chicken chorioallantoic membrane model was employed for in vivo confirmation.
Results:
We demonstrate that enhanced WEE1 pathway activity represents a hallmark of FUS::DDIT3-expressing cell lines as well as MLS tissue specimens and that WEE1 is required for MLS cellular survival in vitro and in vivo. Pharmacologic inhibition of WEE1 activity results in DNA damage accumulation and cell cycle progression forcing cells to undergo apoptotic cell death. In addition, our results uncover FUS::DDIT3-dependent WEE1 expression as an oncogenic survival mechanism to tolerate high proliferation and resulting replication stress in MLS. Fusion protein–driven G1/S cell cycle checkpoint deregulation via overactive Cyclin E/CDK2 complexes thereby contributes to enhanced WEE1 inhibitor sensitivity in MLS.
Conclusions:
Our preclinical study identifies WEE1-mediated replication stress tolerance as molecular vulnerability in FUS::DDIT3-driven MLS tumorigenesis that could represent a novel target for therapeutic intervention.
Data from A Histopathologic Correlation Study Evaluating Glymphatic Function in Brain Tumors by Multiparametric MRI
Authors: Gao Min , Liu Zhengliang , Zang Hongjing , Wu Xiong , Yan Yizhong , Lin Hai , Yuan Jianmin , Liu Tianming , Zhou Yu , Liu Jun
Published: November 2024

AbstractPurpose:
This study aimed to elucidate the impact of brain tumors on cerebral edema and glymphatic drainage by leveraging advanced MRI techniques to explore the relationships among tumor characteristics, glymphatic function, and aquaporin-4 (AQP4) expression levels.
Experimental Design:
In a prospective cohort from March 2022 to April 2023, patients with glioblastoma, brain metastases, and aggressive meningiomas, alongside age- and sex-matched healthy controls, underwent 3.0T MRI, including diffusion tensor imaging analysis along the perivascular space (DTI-ALPS) index and multiparametric MRI for quantitative brain mapping. Tumor and peritumor tissues were analyzed for AQP4 expression levels via immunofluorescence. Correlations among MRI parameters, glymphatic function (DTI-ALPS index), and AQP4 expression levels were statistically assessed.
Results:
Among 84 patients (mean age: 55 ± 12 years; 38 males) and 59 controls (mean age: 54 ± 8 years; 23 males), patients with brain tumor exhibited significantly reduced glymphatic function (DTI-ALPS index: 2.315 vs. 2.879; P = 0.001) and increased cerebrospinal fluid volume (201.376 cm³ vs. 115.957 cm³; P = 0.001). A negative correlation was observed between tumor volume and the DTI-ALPS index (r: −0.715, P < 0.001), whereas AQP4 expression levels correlated positively with peritumoral brain edema volume (r: 0.989, P < 0.001) and negatively with proton density in peritumoral brain edema areas (ρ: −0.506, P < 0.001).
Conclusions:
Our findings highlight the interplay among tumor-induced compression, glymphatic dysfunction, and altered fluid dynamics, demonstrating the utility of DTI-ALPS and multiparametric MRI in understanding the pathophysiology of tumor-related cerebral edema. These insights provide a radiological foundation for further neuro-oncological investigations into the glymphatic system.

See related commentary by Surov and Borggrefe, p. 4813
Data from Multiomics Profiling Distinguishes Sebaceous Carcinoma from Benign Sebaceous Neoplasms and Provides Insight into the Genetic Evolution of Sebaceous Carcinogenesis
Authors: Starrett Gabriel J. , Baikie Brittany C. , Stoff Benjamin K. , Grossniklaus Hans E. , Van Buren Inga , Berry Elizabeth G. , Novoa Roberto A. , Rieger Kerri E. , Sarin Kavita Y. , Lynch Charles F. , Royer Michael C. , Piaskowski Mary L. , Brownell Isaac , Chu Emily Y. , Godse Rama , Chen Suephy C. , Yu Kelly J. , Goldstein Alisa M. , Engels Eric A. , Sargen Michael R.
Published: November 2024

AbstractPurpose:
Sebaceous carcinoma is the third most common nonkeratinocyte skin cancer in the United States with 1,000 cases per year. The clinicopathologic features of sebaceous carcinoma and benign sebaceous neoplasms (adenomas, sebaceomas) can overlap, highlighting the need for molecular biomarkers to improve classification. This study describes the genomic and transcriptomic landscape of sebaceous neoplasms in order to understand tumor etiology and biomarkers relevant for diagnosis and treatment.
Experimental Design:
We performed whole-genome sequencing (WGS) and whole-transcriptome sequencing (WTS) of sebaceous neoplasms from six academic and two federal healthcare facilities in the United States diagnosed between January 1, 1999, and December 31, 2021.
Results:
We evaluated 98 sebaceous neoplasms: 64 tumors (32 adenomas, 2 sebaceomas, 5 atypical sebaceous neoplasms, 25 carcinomas) had sufficient material for WGS, 96 tumors (42 adenomas, 11 sebaceomas, 8 atypical sebaceous neoplasms, 35 carcinomas) had sufficient material for WTS, and 62 tumors (31 adenomas, 2 sebaceomas, 5 atypical sebaceous neoplasms, 24 carcinomas) had sufficient material for combined WGS and WTS. Overall, we found decreased cholesterol biosynthesis and increased TP53 mutations, copy number gains (chromosome 6, 8q, and/or 18), and tumor mutation burden-high (>10 mutations/MB) in carcinomas compared to adenomas. Although diminished compared to adenomas, most carcinomas still had higher cholesterol biosynthesis than nonmalignant skin. Multiomics profiling also supported a precancerous model of tumor evolution with sebaceomas and atypical sebaceous neoplasms being likely intermediate lesions.
Conclusions:
The study findings highlight key diagnostic biomarkers for sebaceous carcinoma and suggest that immunotherapy and modulation of cholesterol biosynthesis could be effective treatment strategies.
Data from Genomic Profiling and Immune Phenotyping of Neuroendocrine Bladder Cancer
Authors: Zang Jingyu , Shahatiaili Akezhouli , Cai Mei-Chun , Jin Di , Shen Peiye , Qian Lei , Zhang Lu , Zhang Tianxiang , Wu Yuchen , Yang Fan , Wu Zheng , Hou Yanli , Bai Yongrui , Xia Jun , Cheng Liang , Zhang Ruiyun , Zhuang Guanglei , Chen Haige
Published: November 2024

AbstractPurpose:
Neuroendocrine bladder cancer (NEBC) poses a formidable clinical challenge and attracts keen interests to explore immunotherapy as a viable treatment option. However, a comprehensive immunogenomic landscape has yet to be thoroughly investigated.
Experimental Design:
Leveraging a long-term cohort of natural NEBC cases, we employed a multimodal approach integrating genomic (n = 19), transcriptomic (n = 3), single-cell RNA sequencing (n = 1), and IHC analyses (n = 34) to meticulously characterize the immunogenicity and immunotypes of primary NEBC tumors. Information on clinical, pathologic, medical imaging, and treatment aspects was retrospectively retrieved and analyzed.
Results:
Our study unveiled that despite a considerable mutational burden, NEBC was typically immunologically inactive, as manifested by the “immune-excluded” or “immune-desert” microenvironment. Interestingly, a subset of mixed NEBC with concurrent urothelial bladder cancer histology displayed an “immune-infiltrated” phenotype with prognostic relevance. When compared with urothelial bladder cancer, NEBC lesions were distinguished by a denser cellular composition and augmented peritumoral extracellular matrix, which might collectively impede lymphatic infiltration. As a result, single-agent immune checkpoint inhibitors demonstrated limited efficacy against NEBC, whereas pharmacologic immunostimulation with combination chemotherapy conferred a more favorable response.
Conclusions:
These new insights derived from genomic profiling and immune phenotyping pave the way for rational immunotherapeutic interventions in patients with NEBC, with the potential to ultimately reduce mortality from this otherwise fatal disease.
Supplementary Figure 7 from METTL14-Mediated Bim mRNA m6A Modification Augments Osimertinib Sensitivity in EGFR-Mutant NSCLC Cells
Authors: Fan Siwen , Lv Xinwu , Zhang Chuantao , Zeng Bingbing , Liang Yanqing , Chen Danyang , Xu Zumin , Li Pan , Wu Shanshan , Liu Hao , Luo Kai , Liu Zongcai , Yi Yanmei
Published: November 2024

S7. The effect of METTL3 on m6A-modified Bim mRNA.
Supplementary Figure 4 from METTL14-Mediated Bim mRNA m6A Modification Augments Osimertinib Sensitivity in EGFR-Mutant NSCLC Cells
Authors: Fan Siwen , Lv Xinwu , Zhang Chuantao , Zeng Bingbing , Liang Yanqing , Chen Danyang , Xu Zumin , Li Pan , Wu Shanshan , Liu Hao , Luo Kai , Liu Zongcai , Yi Yanmei
Published: November 2024

S4. METTL14 promotes osimertinib-induced cell apoptosis in NSCLC cells.
Supplementary Figure 2 from METTL14-Mediated Bim mRNA m6A Modification Augments Osimertinib Sensitivity in EGFR-Mutant NSCLC Cells
Authors: Fan Siwen , Lv Xinwu , Zhang Chuantao , Zeng Bingbing , Liang Yanqing , Chen Danyang , Xu Zumin , Li Pan , Wu Shanshan , Liu Hao , Luo Kai , Liu Zongcai , Yi Yanmei
Published: November 2024

S2. The effect of METTL14 knockdown on cell proliferation of H1975 and PC9 cells.
Supplementary Table 5 from NAP1L1 Promotes Endometrial Cancer Progression via EP300-Mediated DDX5 Promoter Acetylation
Authors: Zhu Xiangfei , Li Yishan , Shao Zhiying , Lu Xiaoyuan , Chen Youguo
Published: November 2024

Clinic pathological variables of the patients included in this study.
Supplementary Table 4 from NAP1L1 Promotes Endometrial Cancer Progression via EP300-Mediated DDX5 Promoter Acetylation
Authors: Zhu Xiangfei , Li Yishan , Shao Zhiying , Lu Xiaoyuan , Chen Youguo
Published: November 2024

Antibodies
Supplementary Table 2 from NAP1L1 Promotes Endometrial Cancer Progression via EP300-Mediated DDX5 Promoter Acetylation
Authors: Zhu Xiangfei , Li Yishan , Shao Zhiying , Lu Xiaoyuan , Chen Youguo
Published: November 2024

Primer sequences of plasmids
Table S7 from lncRNA-WAL Promotes Triple-Negative Breast Cancer Aggression by Inducing β-Catenin Nuclear Translocation
Authors: Huang Hongyan , Jin Haiyun , Lei Rong , He Zhanghai , He Shishi , Chen Jiewen , Saw Phei E. , Qiu Zhu , Ren Guosheng , Nie Yan
Published: November 2024

Reagent or resource for this project.
Table S3 from lncRNA-WAL Promotes Triple-Negative Breast Cancer Aggression by Inducing β-Catenin Nuclear Translocation
Authors: Huang Hongyan , Jin Haiyun , Lei Rong , He Zhanghai , He Shishi , Chen Jiewen , Saw Phei E. , Qiu Zhu , Ren Guosheng , Nie Yan
Published: November 2024

Results of TNBC tissue microarray.
Table S2 from lncRNA-WAL Promotes Triple-Negative Breast Cancer Aggression by Inducing β-Catenin Nuclear Translocation
Authors: Huang Hongyan , Jin Haiyun , Lei Rong , He Zhanghai , He Shishi , Chen Jiewen , Saw Phei E. , Qiu Zhu , Ren Guosheng , Nie Yan
Published: November 2024

Primer sequences for RACE analyses.
Figure S6 from lncRNA-WAL Promotes Triple-Negative Breast Cancer Aggression by Inducing β-Catenin Nuclear Translocation
Authors: Huang Hongyan , Jin Haiyun , Lei Rong , He Zhanghai , He Shishi , Chen Jiewen , Saw Phei E. , Qiu Zhu , Ren Guosheng , Nie Yan
Published: November 2024

lnc-WAL promotes MDA-MB-231 cell growth and metastasis in vivo.
Supplementary Table S1 and S2 from hnRNPAB Promotes Pancreatic Ductal Adenocarcinoma Extravasation and Liver Metastasis by Stabilizing MYC mRNA
Authors: Lei Ke , Sun Mingyue , Chen Xianghan , Wang Jia , Liu Xiaolan , Ning Ying , Ping Shuai , Gong Ruining , Zhang Yu , Qing Gong , Zhao Chenyang , Ren He
Published: November 2024

Primers used for PCR amplification and Summary of clinicopathologic characteristics
Supplementary Methods from hnRNPAB Promotes Pancreatic Ductal Adenocarcinoma Extravasation and Liver Metastasis by Stabilizing MYC mRNA
Authors: Lei Ke , Sun Mingyue , Chen Xianghan , Wang Jia , Liu Xiaolan , Ning Ying , Ping Shuai , Gong Ruining , Zhang Yu , Qing Gong , Zhao Chenyang , Ren He
Published: November 2024

catRAPID ATtRACT and JASPAR analysis
Data from NAP1L1 Promotes Endometrial Cancer Progression via EP300-Mediated DDX5 Promoter Acetylation
Authors: Zhu Xiangfei , Li Yishan , Shao Zhiying , Lu Xiaoyuan , Chen Youguo
Published: November 2024

Abstract
Endometrial cancer is one of the predominant tumors of the female reproductive system. In this current study, we investigated the functions and related mechanisms of nucleosome assembly protein 1 like 1 (NAP1L1)/ DEAD-box helicase 5 (DDX5) in endometrial cancer. This retrospective study analyzed the medical records of patients with endometrial cancer, collected tissue samples for NAP1L1 and DDX5 staining, and conducted survival analysis using the Kaplan–Meier method. To evaluate the impact of NAP1L1 and/or DDX5 on cellular processes in endometrial cancer cells, several techniques were employed. These included Cell Counting Kit-8 assay, wound healing assay, Transwell assay, as well as overexpression or knockdown of target gene expression. Additionally, chromatin immunoprecipitation, dual luciferase reporter gene, and coimmunoprecipitation (Co-IP) assay were utilized to confirm the interaction between NAP1L1, E1A-binding protein p300 (EP300), and DDX5. Furthermore, qRT-PCR, Western blot, and Co-IP assay were performed to analyze the modulation of NAP1L1/DDX5 in Wnt/β-catenin. NAP1L1 and DDX5 expression were upregulated in endometrial cancer tissues, and correlated with poor prognosis. NAP1L1/DDX5 promoted endometrial cancer cell proliferation, migration, and invasion. NAP1L1 promotes acetylation and transcription by recruiting EP300 to the DDX5 promoter. DDX5 could activate Wnt/β-catenin signal by binding to β-catenin. In animal models, knockdown of NAP1L1 inhibits endometrial cancer tumor growth and lung metastasis. To sum up, our study demonstrated that NAP1L1 promoted the malignant phenotypes of endometrial cancer cells via recruiting EP300 to promote DDX5 acetylation, thus activating the Wnt/β-catenin signaling pathway.

Implications: Our research findings indicate that targeting the NAP1L1/EP300/DX5 axis might be a new potential treatment option for endometrial cancer.
Data from lncRNA-WAL Promotes Triple-Negative Breast Cancer Aggression by Inducing β-Catenin Nuclear Translocation
Authors: Huang Hongyan , Jin Haiyun , Lei Rong , He Zhanghai , He Shishi , Chen Jiewen , Saw Phei E. , Qiu Zhu , Ren Guosheng , Nie Yan
Published: November 2024

Abstract
Because of its insensitivity to existing radiotherapy, namely, chemotherapy and targeted treatments, triple-negative breast cancer (TNBC) remains a great challenge to overcome. Increasing evidence has indicated abnormal Wnt/β-catenin pathway activation in TNBC but not luminal or HER2+ breast cancer, and lncRNAs play a key role in a variety of cancers. Through lncRNA microarray profiling between activated and inactivated Wnt/β-catenin pathway of TNBC tissues, lnc-WAL (Wnt/β-catenin-associated lncRNA; WAL) was selected as the top upregulated lncRNA in Wnt/β-catenin pathway activation compared with the inactivation group. RNA immunoprecipitation sequencing was used to compare the β-catenin and IgG groups, in which lnc-WAL could interact with β-catenin. Clinically, increased lnc-WAL in TNBC tumor tissue was associated with shorter survival. lnc-WAL promoted epithelial–mesenchymal transition, the proliferation, migration, and invasion of breast cancer stem cells and TNBC cells. Mechanistically, lnc-WAL inhibited β-catenin protein degradation via AXIN-mediated phosphorylation at serine 45. Subsequently, β-catenin accumulated in the nucleus and activated the target genes. Importantly, Wnt/β-catenin pathway activation stimulated the transcription of lnc-WAL. These results pointed to a master regulatory role of lnc-WAL/AXIN/β-catenin in the malignant progression of TNBC. Our findings provide important clinical translational evidence that lnc-WAL may be a potential therapeutic target against TNBC.

Implications: The positive feedback between lnc-WAL and the Wnt/β-catenin pathway promotes TNBC progression, and lnc-WAL could be a potential prognostic marker for patients with TNBC.
Supplementary Table S6 from Single-Cell View of Tumor Microenvironment Gradients in Pleural Mesothelioma
Authors: Giotti Bruno , Dolasia Komal , Zhao William , Cai Peiwen , Sweeney Robert , Merritt Elliot , Kiner Evgeny , Kim Grace S. , Bhagwat Atharva , Nguyen Thinh , Hegde Samarth , Fitzgerald Bailey G. , Shroff Sanjana , Dawson Travis , Garcia-Barros Monica , Abdul-Ghafar Jamshid , Chen Rachel , Gnjatic Sacha , Soto Alan , Brody Rachel , Kim-Schulze Seunghee , Chen Zhihong , Beaumont Kristin G. , Merad Miriam , Flores Raja M. , Sebra Robert P. , Horowitz Amir , Marron Thomas U. , Tocheva Anna , Wolf Andrea , Tsankov Alexander M.
Published: November 2024

SCENIC-predicted regulon targets of ETS1 and MEF2C in PM endothelial cells
Supplementary Table S4 from Single-Cell View of Tumor Microenvironment Gradients in Pleural Mesothelioma
Authors: Giotti Bruno , Dolasia Komal , Zhao William , Cai Peiwen , Sweeney Robert , Merritt Elliot , Kiner Evgeny , Kim Grace S. , Bhagwat Atharva , Nguyen Thinh , Hegde Samarth , Fitzgerald Bailey G. , Shroff Sanjana , Dawson Travis , Garcia-Barros Monica , Abdul-Ghafar Jamshid , Chen Rachel , Gnjatic Sacha , Soto Alan , Brody Rachel , Kim-Schulze Seunghee , Chen Zhihong , Beaumont Kristin G. , Merad Miriam , Flores Raja M. , Sebra Robert P. , Horowitz Amir , Marron Thomas U. , Tocheva Anna , Wolf Andrea , Tsankov Alexander M.
Published: November 2024

De novo markers discovered for each detailed cell type annotation in the peripheral blood samples
Supplementary Table S3 from Single-Cell View of Tumor Microenvironment Gradients in Pleural Mesothelioma
Authors: Giotti Bruno , Dolasia Komal , Zhao William , Cai Peiwen , Sweeney Robert , Merritt Elliot , Kiner Evgeny , Kim Grace S. , Bhagwat Atharva , Nguyen Thinh , Hegde Samarth , Fitzgerald Bailey G. , Shroff Sanjana , Dawson Travis , Garcia-Barros Monica , Abdul-Ghafar Jamshid , Chen Rachel , Gnjatic Sacha , Soto Alan , Brody Rachel , Kim-Schulze Seunghee , Chen Zhihong , Beaumont Kristin G. , Merad Miriam , Flores Raja M. , Sebra Robert P. , Horowitz Amir , Marron Thomas U. , Tocheva Anna , Wolf Andrea , Tsankov Alexander M.
Published: November 2024

De novo markers discovered for each major cell type annotation in the peripheral blood samples
Supplementary Figure S6 from Single-Cell View of Tumor Microenvironment Gradients in Pleural Mesothelioma
Authors: Giotti Bruno , Dolasia Komal , Zhao William , Cai Peiwen , Sweeney Robert , Merritt Elliot , Kiner Evgeny , Kim Grace S. , Bhagwat Atharva , Nguyen Thinh , Hegde Samarth , Fitzgerald Bailey G. , Shroff Sanjana , Dawson Travis , Garcia-Barros Monica , Abdul-Ghafar Jamshid , Chen Rachel , Gnjatic Sacha , Soto Alan , Brody Rachel , Kim-Schulze Seunghee , Chen Zhihong , Beaumont Kristin G. , Merad Miriam , Flores Raja M. , Sebra Robert P. , Horowitz Amir , Marron Thomas U. , Tocheva Anna , Wolf Andrea , Tsankov Alexander M.
Published: November 2024

NK cell IC blockade targeting NKG2A as a novel therapeutic strategy in PM
Supplementary Figure S4 from Single-Cell View of Tumor Microenvironment Gradients in Pleural Mesothelioma
Authors: Giotti Bruno , Dolasia Komal , Zhao William , Cai Peiwen , Sweeney Robert , Merritt Elliot , Kiner Evgeny , Kim Grace S. , Bhagwat Atharva , Nguyen Thinh , Hegde Samarth , Fitzgerald Bailey G. , Shroff Sanjana , Dawson Travis , Garcia-Barros Monica , Abdul-Ghafar Jamshid , Chen Rachel , Gnjatic Sacha , Soto Alan , Brody Rachel , Kim-Schulze Seunghee , Chen Zhihong , Beaumont Kristin G. , Merad Miriam , Flores Raja M. , Sebra Robert P. , Horowitz Amir , Marron Thomas U. , Tocheva Anna , Wolf Andrea , Tsankov Alexander M.
Published: November 2024

Macrophages in scS-high PM express CXCL9/10/11 and likely contribute to T-cell infiltration
Supplementary Figure S1 from Single-Cell View of Tumor Microenvironment Gradients in Pleural Mesothelioma
Authors: Giotti Bruno , Dolasia Komal , Zhao William , Cai Peiwen , Sweeney Robert , Merritt Elliot , Kiner Evgeny , Kim Grace S. , Bhagwat Atharva , Nguyen Thinh , Hegde Samarth , Fitzgerald Bailey G. , Shroff Sanjana , Dawson Travis , Garcia-Barros Monica , Abdul-Ghafar Jamshid , Chen Rachel , Gnjatic Sacha , Soto Alan , Brody Rachel , Kim-Schulze Seunghee , Chen Zhihong , Beaumont Kristin G. , Merad Miriam , Flores Raja M. , Sebra Robert P. , Horowitz Amir , Marron Thomas U. , Tocheva Anna , Wolf Andrea , Tsankov Alexander M.
Published: November 2024

Single-cell catalogue of PM tumor and PBMC samples
Supplementary Video S3 from The N6-methyladenosine Epitranscriptomic Landscape of Lung Adenocarcinoma
Authors: Wang Shiyan , Zeng Yong , Zhu Lin , Zhang Min , Zhou Lei , Yang Weixiong , Luo Weishan , Wang Lina , Liu Yanming , Zhu Helen , Xu Xin , Su Peiran , Zhang Xinyue , Ahmed Musaddeque , Chen Wei , Chen Moliang , Chen Sujun , Slobodyanyuk Mykhaylo , Xie Zhongpeng , Guan Jiansheng , Zhang Wen , Khan Aafaque Ahmad , Sakashita Shingo , Liu Ni , Pham Nhu-An , Boutros Paul C. , Ke Zunfu , Moran Michael F. , Cai Zongwei , Cheng Chao , Yu Jun , Tsao Ming S. , He Housheng H.
Published: November 2024

Live cell imaging of control H358 cells in wound healing assay.
Supplementary Video S1 from The N6-methyladenosine Epitranscriptomic Landscape of Lung Adenocarcinoma
Authors: Wang Shiyan , Zeng Yong , Zhu Lin , Zhang Min , Zhou Lei , Yang Weixiong , Luo Weishan , Wang Lina , Liu Yanming , Zhu Helen , Xu Xin , Su Peiran , Zhang Xinyue , Ahmed Musaddeque , Chen Wei , Chen Moliang , Chen Sujun , Slobodyanyuk Mykhaylo , Xie Zhongpeng , Guan Jiansheng , Zhang Wen , Khan Aafaque Ahmad , Sakashita Shingo , Liu Ni , Pham Nhu-An , Boutros Paul C. , Ke Zunfu , Moran Michael F. , Cai Zongwei , Cheng Chao , Yu Jun , Tsao Ming S. , He Housheng H.
Published: November 2024

Live cell imaging of control A549 cells in wound healing assay.
Supplementary Table S7 from The N6-methyladenosine Epitranscriptomic Landscape of Lung Adenocarcinoma
Authors: Wang Shiyan , Zeng Yong , Zhu Lin , Zhang Min , Zhou Lei , Yang Weixiong , Luo Weishan , Wang Lina , Liu Yanming , Zhu Helen , Xu Xin , Su Peiran , Zhang Xinyue , Ahmed Musaddeque , Chen Wei , Chen Moliang , Chen Sujun , Slobodyanyuk Mykhaylo , Xie Zhongpeng , Guan Jiansheng , Zhang Wen , Khan Aafaque Ahmad , Sakashita Shingo , Liu Ni , Pham Nhu-An , Boutros Paul C. , Ke Zunfu , Moran Michael F. , Cai Zongwei , Cheng Chao , Yu Jun , Tsao Ming S. , He Housheng H.
Published: November 2024

RNA-seq analysis of EML4-overexpressing, EML4-knockdown and control NSCLC cell samples.
Supplementary Table S6 from The N6-methyladenosine Epitranscriptomic Landscape of Lung Adenocarcinoma
Authors: Wang Shiyan , Zeng Yong , Zhu Lin , Zhang Min , Zhou Lei , Yang Weixiong , Luo Weishan , Wang Lina , Liu Yanming , Zhu Helen , Xu Xin , Su Peiran , Zhang Xinyue , Ahmed Musaddeque , Chen Wei , Chen Moliang , Chen Sujun , Slobodyanyuk Mykhaylo , Xie Zhongpeng , Guan Jiansheng , Zhang Wen , Khan Aafaque Ahmad , Sakashita Shingo , Liu Ni , Pham Nhu-An , Boutros Paul C. , Ke Zunfu , Moran Michael F. , Cai Zongwei , Cheng Chao , Yu Jun , Tsao Ming S. , He Housheng H.
Published: November 2024

Sample information and analysis in the internal cohort.
Supplementary Table S3 from The N6-methyladenosine Epitranscriptomic Landscape of Lung Adenocarcinoma
Authors: Wang Shiyan , Zeng Yong , Zhu Lin , Zhang Min , Zhou Lei , Yang Weixiong , Luo Weishan , Wang Lina , Liu Yanming , Zhu Helen , Xu Xin , Su Peiran , Zhang Xinyue , Ahmed Musaddeque , Chen Wei , Chen Moliang , Chen Sujun , Slobodyanyuk Mykhaylo , Xie Zhongpeng , Guan Jiansheng , Zhang Wen , Khan Aafaque Ahmad , Sakashita Shingo , Liu Ni , Pham Nhu-An , Boutros Paul C. , Ke Zunfu , Moran Michael F. , Cai Zongwei , Cheng Chao , Yu Jun , Tsao Ming S. , He Housheng H.
Published: November 2024

m6A, mRNA and protein level-based clustering.
Supplementary Table S2 from The N6-methyladenosine Epitranscriptomic Landscape of Lung Adenocarcinoma
Authors: Wang Shiyan , Zeng Yong , Zhu Lin , Zhang Min , Zhou Lei , Yang Weixiong , Luo Weishan , Wang Lina , Liu Yanming , Zhu Helen , Xu Xin , Su Peiran , Zhang Xinyue , Ahmed Musaddeque , Chen Wei , Chen Moliang , Chen Sujun , Slobodyanyuk Mykhaylo , Xie Zhongpeng , Guan Jiansheng , Zhang Wen , Khan Aafaque Ahmad , Sakashita Shingo , Liu Ni , Pham Nhu-An , Boutros Paul C. , Ke Zunfu , Moran Michael F. , Cai Zongwei , Cheng Chao , Yu Jun , Tsao Ming S. , He Housheng H.
Published: November 2024

Gene enrichment of G1-3 groups.
Supplementary Figure S9 from The N6-methyladenosine Epitranscriptomic Landscape of Lung Adenocarcinoma
Authors: Wang Shiyan , Zeng Yong , Zhu Lin , Zhang Min , Zhou Lei , Yang Weixiong , Luo Weishan , Wang Lina , Liu Yanming , Zhu Helen , Xu Xin , Su Peiran , Zhang Xinyue , Ahmed Musaddeque , Chen Wei , Chen Moliang , Chen Sujun , Slobodyanyuk Mykhaylo , Xie Zhongpeng , Guan Jiansheng , Zhang Wen , Khan Aafaque Ahmad , Sakashita Shingo , Liu Ni , Pham Nhu-An , Boutros Paul C. , Ke Zunfu , Moran Michael F. , Cai Zongwei , Cheng Chao , Yu Jun , Tsao Ming S. , He Housheng H.
Published: November 2024

The effects of ARPC1A depletion in LUAD.
Supplementary Figure S7 from The N6-methyladenosine Epitranscriptomic Landscape of Lung Adenocarcinoma
Authors: Wang Shiyan , Zeng Yong , Zhu Lin , Zhang Min , Zhou Lei , Yang Weixiong , Luo Weishan , Wang Lina , Liu Yanming , Zhu Helen , Xu Xin , Su Peiran , Zhang Xinyue , Ahmed Musaddeque , Chen Wei , Chen Moliang , Chen Sujun , Slobodyanyuk Mykhaylo , Xie Zhongpeng , Guan Jiansheng , Zhang Wen , Khan Aafaque Ahmad , Sakashita Shingo , Liu Ni , Pham Nhu-An , Boutros Paul C. , Ke Zunfu , Moran Michael F. , Cai Zongwei , Cheng Chao , Yu Jun , Tsao Ming S. , He Housheng H.
Published: November 2024

The function of EML4 m6A.
Supplementary Figure S4 from The N6-methyladenosine Epitranscriptomic Landscape of Lung Adenocarcinoma
Authors: Wang Shiyan , Zeng Yong , Zhu Lin , Zhang Min , Zhou Lei , Yang Weixiong , Luo Weishan , Wang Lina , Liu Yanming , Zhu Helen , Xu Xin , Su Peiran , Zhang Xinyue , Ahmed Musaddeque , Chen Wei , Chen Moliang , Chen Sujun , Slobodyanyuk Mykhaylo , Xie Zhongpeng , Guan Jiansheng , Zhang Wen , Khan Aafaque Ahmad , Sakashita Shingo , Liu Ni , Pham Nhu-An , Boutros Paul C. , Ke Zunfu , Moran Michael F. , Cai Zongwei , Cheng Chao , Yu Jun , Tsao Ming S. , He Housheng H.
Published: November 2024

Association of m6A with clinical features and patient survival.
Supplementary Figure S1 from The N6-methyladenosine Epitranscriptomic Landscape of Lung Adenocarcinoma
Authors: Wang Shiyan , Zeng Yong , Zhu Lin , Zhang Min , Zhou Lei , Yang Weixiong , Luo Weishan , Wang Lina , Liu Yanming , Zhu Helen , Xu Xin , Su Peiran , Zhang Xinyue , Ahmed Musaddeque , Chen Wei , Chen Moliang , Chen Sujun , Slobodyanyuk Mykhaylo , Xie Zhongpeng , Guan Jiansheng , Zhang Wen , Khan Aafaque Ahmad , Sakashita Shingo , Liu Ni , Pham Nhu-An , Boutros Paul C. , Ke Zunfu , Moran Michael F. , Cai Zongwei , Cheng Chao , Yu Jun , Tsao Ming S. , He Housheng H.
Published: November 2024

Characteristics of m6A peaks and methodological comparison for m6A level calculation.
Supplementary Table 2 from The SCRUM-MONSTAR Cancer-Omics Ecosystem: Striving for a Quantum Leap in Precision Medicine
Authors: Hashimoto Tadayoshi , Nakamura Yoshiaki , Fujisawa Takao , Imai Mitsuho , Shibuki Taro , Iida Naoko , Ozaki Hiroshi , Nonomura Norio , Morizane Chigusa , Iwata Hiroji , Okano Susumu , Yamagami Wataru , Yamazaki Naoya , Kadowaki Shigenori , Taniguchi Hiroya , Ueno Makoto , Boku Shogen , Oki Eiji , Komatsu Yoshito , Yuki Satoshi , Makiyama Akitaka , Otsuka Tomoyuki , Hara Hiroki , Okano Naohiro , Nishina Tomohiro , Sakamoto Yasutoshi , Miki Izumi , Kobayashi Shin , Yuda Junichiro , Kageyama Shun-Ichiro , Nagamine Michiko , Sakashita Shingo , Sakamoto Naoya , Yamashita Riu , Koga Yoshikatsu , Bando Hideaki , Ishii Genichiro , Kuwata Takeshi , Park Woong-Yang , Ohtsu Atsushi , Yoshino Takayuki
Published: November 2024

List of regulatory approvals for companion diagnostic therapeutics in SCRUM-Japan MONSTAR-SCREEN project
Supplementary Figure 4 from The SCRUM-MONSTAR Cancer-Omics Ecosystem: Striving for a Quantum Leap in Precision Medicine
Authors: Hashimoto Tadayoshi , Nakamura Yoshiaki , Fujisawa Takao , Imai Mitsuho , Shibuki Taro , Iida Naoko , Ozaki Hiroshi , Nonomura Norio , Morizane Chigusa , Iwata Hiroji , Okano Susumu , Yamagami Wataru , Yamazaki Naoya , Kadowaki Shigenori , Taniguchi Hiroya , Ueno Makoto , Boku Shogen , Oki Eiji , Komatsu Yoshito , Yuki Satoshi , Makiyama Akitaka , Otsuka Tomoyuki , Hara Hiroki , Okano Naohiro , Nishina Tomohiro , Sakamoto Yasutoshi , Miki Izumi , Kobayashi Shin , Yuda Junichiro , Kageyama Shun-Ichiro , Nagamine Michiko , Sakashita Shingo , Sakamoto Naoya , Yamashita Riu , Koga Yoshikatsu , Bando Hideaki , Ishii Genichiro , Kuwata Takeshi , Park Woong-Yang , Ohtsu Atsushi , Yoshino Takayuki
Published: November 2024

Concept of no-placebo initiative
Supplementary Figure 6 from Rational Protein Engineering to Enhance MHC-Independent T-cell Receptors
Authors: Chang Ju-Fang , Landmann Jack H. , Chang Tien-Ching , Selli Mehmet Emrah , Tenzin Yangdon , Warrington John M. , Ritchey Julie , Hsu Yu-Sung , Slade Michael , Gupta Deepesh Kumar , DiPersio John F. , Holehouse Alex S. , Singh Nathan
Published: November 2024

Supplementary Figure 6 | a-b, Cytotoxicity of a, miTCR1 and b, miTCR2 variants against Nalm6. c-d, Long-term flow cytometry-based cytotoxicity of lead c, miTCR1 and d, miTCR2 variants. e, Quantification of cytokines in supernatants 24h after co-culture of engineered T cells with Nalm6. f, Expression of TCRC chains in αCD22 miTCR1, CD22 miTCR2 and CD19 miTCR1 engineered Jurkat cells. g, Induction of reporter NFAT-GFP upon exposure to CD19+CD22+ Nalm6 in Jurkat cells. Screening studies in a-b performed using two independent donors; c-d, representative data from three independent donors; e, data from one donor. ****P < 0.0001 by two-way ANOVA (c-d).
Supplementary Figure 3 from Rational Protein Engineering to Enhance MHC-Independent T-cell Receptors
Authors: Chang Ju-Fang , Landmann Jack H. , Chang Tien-Ching , Selli Mehmet Emrah , Tenzin Yangdon , Warrington John M. , Ritchey Julie , Hsu Yu-Sung , Slade Michael , Gupta Deepesh Kumar , DiPersio John F. , Holehouse Alex S. , Singh Nathan
Published: November 2024

Supplementary Figure 3 | a, Predicted structures of miTCR1 and miTCR2 α and β chains overlaid on resolved structures of TCR α and β chains. b, Overlay of five highest-ranking predictions for miTCR1 and miTCR2 variable-constant chain interface. c, Resolved native TCR α chain V-C interface structure and predicted V-C interface structures of miTCR2 WT and modified α chains. d, Resolved native TCR β chain V-C interface structure and predicted V-C interface structures of miTCR1 WT, miTCR2 WT and modified β chains.
Table 1 from Clinical Validation of a Cell-Free DNA Fragmentome Assay for Augmentation of Lung Cancer Early Detection
Authors: Mazzone Peter J. , Bach Peter B. , Carey Jacob , Schonewolf Caitlin A. , Bognar Katalin , Ahluwalia Manmeet S. , Cruz-Correa Marcia , Gierada David , Kotagiri Sonali , Lloyd Kathryn , Maldonado Fabien , Ortendahl Jesse D. , Sequist Lecia V. , Silvestri Gerard A. , Tanner Nichole , Thompson Jeffrey C. , Vachani Anil , Wong Kwok-Kin , Zaidi Ali H. , Catallini Joseph , Gershman Ariel , Lumbard Keith , Millberg Laurel K. , Nawrocki Jeff , Portwood Carter , Rangnekar Aakanksha , Sheridan Carolina Campos , Trivedi Niti , Wu Tony , Zong Yuhua , Cotton Lindsey , Ryan Allison , Cisar Christopher , Leal Alessandro , Dracopoli Nicholas , Scharpf Robert B. , Velculescu Victor E. , Pike Luke R. G.
Published: November 2024

Participant demographics and clinical characteristics.
Supplementary Methods from Clinical Validation of a Cell-Free DNA Fragmentome Assay for Augmentation of Lung Cancer Early Detection
Authors: Mazzone Peter J. , Bach Peter B. , Carey Jacob , Schonewolf Caitlin A. , Bognar Katalin , Ahluwalia Manmeet S. , Cruz-Correa Marcia , Gierada David , Kotagiri Sonali , Lloyd Kathryn , Maldonado Fabien , Ortendahl Jesse D. , Sequist Lecia V. , Silvestri Gerard A. , Tanner Nichole , Thompson Jeffrey C. , Vachani Anil , Wong Kwok-Kin , Zaidi Ali H. , Catallini Joseph , Gershman Ariel , Lumbard Keith , Millberg Laurel K. , Nawrocki Jeff , Portwood Carter , Rangnekar Aakanksha , Sheridan Carolina Campos , Trivedi Niti , Wu Tony , Zong Yuhua , Cotton Lindsey , Ryan Allison , Cisar Christopher , Leal Alessandro , Dracopoli Nicholas , Scharpf Robert B. , Velculescu Victor E. , Pike Luke R. G.
Published: November 2024

Additional detailed methods
Supp Figs (Fig S1-4) and Tables (Tables S1-4) from Clinical Validation of a Cell-Free DNA Fragmentome Assay for Augmentation of Lung Cancer Early Detection
Authors: Mazzone Peter J. , Bach Peter B. , Carey Jacob , Schonewolf Caitlin A. , Bognar Katalin , Ahluwalia Manmeet S. , Cruz-Correa Marcia , Gierada David , Kotagiri Sonali , Lloyd Kathryn , Maldonado Fabien , Ortendahl Jesse D. , Sequist Lecia V. , Silvestri Gerard A. , Tanner Nichole , Thompson Jeffrey C. , Vachani Anil , Wong Kwok-Kin , Zaidi Ali H. , Catallini Joseph , Gershman Ariel , Lumbard Keith , Millberg Laurel K. , Nawrocki Jeff , Portwood Carter , Rangnekar Aakanksha , Sheridan Carolina Campos , Trivedi Niti , Wu Tony , Zong Yuhua , Cotton Lindsey , Ryan Allison , Cisar Christopher , Leal Alessandro , Dracopoli Nicholas , Scharpf Robert B. , Velculescu Victor E. , Pike Luke R. G.
Published: November 2024

Cross-validated test; DELFI score distribution; Annual transitions.