bluuebunny/crossref_metadata_2025 huggingface dataset:
Data from Associations between ambient air pollutants and clonal hematopoiesis of indeterminate potential (CHIP)
Authors: Leiser Claire L. , Whitsel Eric A. , Reiner Alexander , Rich Stephen S. , Rotter Jerome I. , Taylor Kent D. , Tracy Russel P. , Kooperberg Charles , Smith Albert Vernon , Mason JoAnn E. , Mychaleckyj Josyf C. , Bick Alexander G. , Szpiro Adam A. , Kaufman Joel D.
Published: September 2024

Abstract
Background
Clonal hematopoiesis of indeterminate potential (CHIP) is an age-related somatic mutation associated with incident hematologic cancer. Environmental stressors which, like air pollution, generate oxidative stress at the cellular level, may induce somatic mutations and some mutations may provide a selection advantage for persistence and expansion of specific clones.

Materials and Methods
We used data from the Multi-Ethnic Study of Atherosclerosis (MESA) N=4,379 and the Women’s Health Initiative (WHI) N=7,701 to estimate cross-sectional associations between annual average air pollution concentrations at participant address the year before blood draw using validated spatiotemporal models. We used covariate-adjusted logistic regression to estimate risk of CHIP per interquartile range increases in PM2.5 (4 ug/m3) and NO2 (10 ppb) as odds ratios (95% confidence intervals).

Results
Prevalence of CHIP at blood draw (variant allele fraction > 2%) was 4.4% and 8.7% in MESA and WHI, respectively. The most common CHIP driver mutation was in DNMT3A. Neither pollutant was associated with CHIP: ORMESA PM2.5=1.00 (0.68-1.45), ORMESA NO2=1.05 (0.69-1.61), ORWHI PM2.5=0.97 (0.86-1.09), ORWHI NO2=0.98 (0.88-1.10); or with DNMT3A-driven CHIP.

Conclusions
We did not find evidence that air pollution contributes to CHIP prevalence in two large observational cohorts.

Impact
This is the first study to estimate associations between air pollution and CHIP.
Data from Racial and ethnic variation in diagnostic mammography performance among women reporting a breast lump
Authors: Nyante Sarah J. , Abraham Linn , Aiello Bowles Erin J. , Lee Christoph I. , Kerlikowske Karla , Miglioretti Diana L. , Sprague Brian L. , Henderson Louise M.
Published: September 2024

Abstract
Background: We evaluated diagnostic mammography among women with a breast lump to determine whether performance varied across racial and ethnic groups.

Methods: This study included 51,014 diagnostic mammograms performed between 2005-2018 in the Breast Cancer Surveillance Consortium among Asian/Pacific Islander (12%), Black (7%), Hispanic/Latina (6%), and White (75%) women reporting a lump. Breast cancers occurring within one year were ascertained from cancer registry linkages. Multivariable regression was used to adjust performance statistic comparisons for breast cancer risk factors, mammogram modality, demographics, additional imaging, and imaging facility.

Results: Cancer detection rates were highest among Asian/Pacific Islander (per 1000 exams, 84.2 [95%CI 72.0-98.2]) and Black women (81.4 95%CI 69.4-95.2]) and lowest among Hispanic/Latina women (42.9 [95%CI 34.2-53.6]). Positive predictive values (PPV) were higher among Black (37.0% [95%CI 31.2%-43.3%]) and White (37.0% [95%CI 30.0%-44.6%]) women and lowest among Hispanic/Latina women (22.0% [95%CI 17.2%-27.7%]). False-positive results were most common among Asian/Pacific Islander women (per 1000 exams, 183.9 [95%CI 126.7-259.2]) and lowest among White women (112.4 [95%CI 86.1-145.5]). After adjustment, false-positive and cancer detection rates remained higher for Asian/Pacific Islander and Black women (vs. Hispanic/Latina and White). Adjusted PPV was highest among Asian/Pacific Islander women.

Conclusions: Among women with a lump, Asian/Pacific Islander and Black women were more likely to have cancer detected and more likely to receive a false-positive result compared with White and Hispanic/Latina women.

Impact: Strategies for optimizing diagnostic mammography among women with a lump may vary by racial/ethnic group, but additional factors that influence performance differences need to be identified.
Data from The Association of Kidney Function and Inflammatory Biomarkers with Epithelial Ovarian Cancer Risk
Authors: Hathaway Cassandra A. , Townsend Mary K. , Sklar Elliot M. , Thomas-Purcell Kamilah B. , Terry Kathryn L. , Trabert Britton , Tworoger Shelley S.
Published: September 2024

Abstract
Background: One of the mechanisms of ovarian tumorigenesis is through inflammation. Kidney dysfunction is associated with increased inflammation; thus we assessed its relationship with ovarian cancer risk.
Methods: In prospectively collected samples, we evaluated the association of kidney function markers and C reactive protein (CRP) with ovarian cancer risk in the UK Biobank. We used multivariable-adjusted Cox proportional hazards models to evaluate quartiles of serum and urine markers with ovarian cancer risk overall and by histology. We assessed effect modification by CRP (≤3.0, >3.0 mg/L).
Results: Among 232,908 women (1,110 ovarian cancer cases diagnosed from 2006-2020), we observed no association between estimated glomerular filtration rate and ovarian cancer risk (Q4 vs. Q1: Hazard Ratio: 1.00, 95% Confidence Intervals: 0.83,1.22). Potassium was associated with endometrioid (Q4 vs. Q1: 0.33 [0.11,0.98]) and clear cell (4.74 [1.39,16.16]) tumors. Poor kidney function was associated with a non-significant increase in ovarian cancer risk among women with CRP >3.0 mg/L (e.g., uric acid Q4 vs. Q1. 1.23 [0.81,1.86]), but not CRP ≤3.0 mg/L (0.83 [0.66,1.05]). Other associations did not vary across CRP categories.
Conclusions: Kidney function was not clearly associated with ovarian cancer risk. Larger studies are needed to evaluate possible histology specific associations. Given the suggestive trend for increased ovarian cancer risk in women with poor kidney function and high CRP, future work is needed, particularly in populations with a high prevalence of inflammatory conditions.
Impact: This study provided the first evaluation of markers of kidney function in relation to ovarian cancer risk.
Figure S3 from Preclinical Efficacy of the Antibody-Drug-Conjugate CLDN6-23-ADC for the Treatment of CLDN6 Positive Solid Tumors
Authors: McDermott Martina S.J. , O'Brien Neil A. , Hoffstrom Benjamin , Gong KeWei , Lu Ming , Zhang Jun , Luo Tong , Liang Min , Jia Weiping , Hong Jenny , Chau Kevin , Davenport Simon , Xie Bin , Press Michael F. , Panayiotou Richard , Handly-Santana Abram , Brugge Joan S. , Presta Leonard , Glaspy John , Slamon Dennis J.
Published: September 2024

Supplemental Figure S3. A, Efficacy of anti-CLDN6 mouse antibodies in CLDN6 positive OV90 ovarian cancer cell line xenografts. B, Efficacy in CLDN6 positive UMUC4 bladder cancer cell line xenografts. C, No efficacy in CLDN6 negative M202 melanoma cell line xenografts. All antibodies are dosed at 10 mg/kg QW IV in each study. Errors bars represent SEM of 8 replicate animals per group.
Figure S8 from Treatment of prostate cancer with CD46 targeted 225Ac alpha particle radioimmunotherapy
Authors: Bidkar Anil P. , Wang Sinan , Bobba Kondapa Naidu. , Chan Emily , Bidlingmaier Scott , Egusa Emily A. , Peter Robin , Ali Umama , Meher Niranjan , Wadhwa Anju , Dhrona Suchi , Dasari Chandrashekhar , Beckford-Vera Denis , Su Yang , Tang Ryan , Zhang Li , He Jiang , Wilson David M. , Aggarwal Rahul , VanBrocklin Henry F. , Seo Youngho , Chou Jonathan , Liu Bin , Flavell Robert R.
Published: September 2024

Figure S8: Acute toxicity study of the [225Ac]DOTA-YS5 in nude mice (n=5). A The body weights of mice injected with [225Ac]DOTA-YS5 showed no significant change in treatment groups over the 15 days study period. B&C: Liver and kidney function tests (B) and blood parameters (C) show no significant changes for saline vs. treated groups indicating the short-term safety of [225Ac]DOTA-YS5.
Figure S6 from Treatment of prostate cancer with CD46 targeted 225Ac alpha particle radioimmunotherapy
Authors: Bidkar Anil P. , Wang Sinan , Bobba Kondapa Naidu. , Chan Emily , Bidlingmaier Scott , Egusa Emily A. , Peter Robin , Ali Umama , Meher Niranjan , Wadhwa Anju , Dhrona Suchi , Dasari Chandrashekhar , Beckford-Vera Denis , Su Yang , Tang Ryan , Zhang Li , He Jiang , Wilson David M. , Aggarwal Rahul , VanBrocklin Henry F. , Seo Youngho , Chou Jonathan , Liu Bin , Flavell Robert R.
Published: September 2024

Figure S6: Number of H2AX-foci after the treatment of saline and [225Ac]DOTA-YS5 for 7 days and 14 days (n=3). t-test p value is indicated as * p<0.05.
Figure S6 from A Phase II Trial of Guadecitabine plus Atezolizumab in Metastatic Urothelial Carcinoma Progressing after Initial Immune Checkpoint Inhibitor Therapy
Authors: Jang H. Josh , Hostetter Galen , MacFarlane Alexander W. , Madaj Zachary , Ross Eric A. , Hinoue Toshinori , Kulchycki Justin R. , Burgos Ryan S. , Tafseer Mahvish , Alpaugh R. Katherine , Schwebel Candice L. , Kokate Rutika , Geynisman Daniel M. , Zibelman Matthew R. , Ghatalia Pooja , Nichols Peter W. , Chung Woonbok , Madzo Jozef , Hahn Noah M. , Quinn David I. , Issa Jean-Pierre J. , Topper Michael J. , Baylin Stephen B. , Shen Hui , Campbell Kerry S. , Jones Peter A. , Plimack Elizabeth R.
Published: September 2024

Supplementary Figure 6: Gene Set Enrichment Analysis reveals immune-related pathways discriminate PD and SD tumors.
Supplementary Figure S5 from A tumor suppressive-molecular axis EP300/circRERE/miR-6837-3p/MAVS activates type I interferon pathway and anti-tumor immunity to suppress colorectal cancer
Authors: Ding Nan , You A-Bin , Yang Hu , Hu Guo-sheng , Lai Chun-Ping , Liu Wen , Ye Feng
Published: September 2024

Figure S5: EP300 is lowly expressed in CRC tissues and positively correlated with RERE.
Supplementary Table S3 from Randomized Trial of Tepotinib Plus Gefitinib Versus Chemotherapy in EGFR-Mutant NSCLC with EGFR Inhibitor Resistance Due to MET Amplification: INSIGHT Final Analysis
Authors: Liam Chong Kin , Ahmad Azura Rozila , Hsia Te-Chun , Zhou Jianying , Kim Dong-Wan , Soo Ross Andrew. , Cheng Ying , Lu Shun , Shin Sang Won , Yang James Chi-Hsin , Zhang Yiping , Zhao Jun , Berghoff Karin , Bruns Rolf , Johne Andreas , Wu Yi-Long
Published: September 2024

Demographic data in the patient subgroup with MET overexpression
Supplementary Figure 1 from Co-clinical study of [fam-] trastuzumab deruxtecan (DS8201a) in patient-derived xenograft models of uterine carcinosarcoma and its association with clinical efficacy
Authors: Yagishita Shigehiro , Nishikawa Tadaaki , Yoshida Hiroshi , Shintani Daisuke , Sato Sho , Miwa Maiko , Suzuki Mikiko , Yasuda Masanori , Ogitani Yusuke , Jikoh Takahiro , Yonemori Kan , Hasegawa Kosei , Hamada Akinobu
Published: September 2024

Growth curve
Supplementary Table S5 from Osimertinib and selpercatinib efficacy, safety, and resistance in a multicenter, prospectively treated cohort of EGFR-mutant and RET fusion-positive lung cancers
Authors: Rotow Julia , Patel Jyoti D. , Hanley Matthew P. , Yu Helena , Awad Mark , Goldman Jonathan W. , Nechushtan Hovav , Scheffler Matthias , Kuo Chih-Hsi S. , Rajappa Senthil , Harada Guilherme , Clifford Sarah , Santucci Alison , Silva Laura , Tupper Rebecca , Oxnard Geoffrey R. , Kherani Jennifer , Drilon Alexander
Published: September 2024

Dose modification
Supplementary Table S3 from First-in-human study of the radioligand 68Ga-N188 targeting nectin-4 for PET/CT imaging of advanced urothelial carcinoma
Authors: Duan Xiaojiang , Xia Lei , Zhang Zhuochen , Ren Yanan , Pomper Martin G. , Rowe Steven P. , Li Xuesong , Li Nan , Zhang Ning , Zhu Hua , Yang Zhi , Sheng Xinan , Yang Xing
Published: September 2024

Quality control of 68Ga-N188 used in this study
Clinical trial protocol1 from Combination ATR (ceralasertib) and PARP (olaparib) Inhibitor (CAPRI) trial in acquired PARP-inhibitor-resistant homologous recombination deficient ovarian cancer
Authors: Wethington Stephanie L. , Shah Payal D. , Martin Lainie , Tanyi Janos L. , Latif Nawar , Morgan Mark , Torigian Drew A. , Rodriguez Diego , Smith Simon A. , Dean Emma , Domchek Susan M. , Drapkin Ronny , Shih Ie-Ming , Brown Eric J. , Hwang Wei-Ting , Armstrong Deborah K. , Gaillard Stephanie , Giuntoli Robert , Simpkins Fiona
Published: September 2024

Trial protocol
Supplementary Table 3 from Clinicopathologic, genomic, and immunophenotypic landscape of ATM mutations in non-small cell lung cancer
Authors: Ricciuti Biagio , Elkrief Arielle , Alessi Joao , Wang Xinan , Li Yvonne , Gupta Hersh , Muldoon Daniel M. , Bertram Arrien A. , Pecci Federica , Lamberti Giuseppe , Di Federico Alessandro , Barrichello Adriana , Vaz Victor R. , Gandhi Malini , Lee Elinton , Shapiro Geoffrey I. , Park Hyesun , Nishino Mizuki , Lindsay James , Felt Kristen D. , Sharma Bijaya , Cherniack Andrew D. , Rodig Scott , Gomez Daniel R. , Shaverdian Narek , Rakaee Mehrdad , Bandlamudi Chaitanya , Ladanyi Marc , Janne Pasi A. , Schoenfeld Adam J. , Sholl Lynette M. , Awad Mark M. , Cheng Michael L.
Published: September 2024

Supplementary Table 3. Baseline clinicopathologic features of patients with ATMMUT and ATMWT NSCLC at the Dana-Farber Cancer Institute and Memorial Sloan Kettering Cancer Center.
Supplementary Figure 5 from Clinicopathologic, genomic, and immunophenotypic landscape of ATM mutations in non-small cell lung cancer
Authors: Ricciuti Biagio , Elkrief Arielle , Alessi Joao , Wang Xinan , Li Yvonne , Gupta Hersh , Muldoon Daniel M. , Bertram Arrien A. , Pecci Federica , Lamberti Giuseppe , Di Federico Alessandro , Barrichello Adriana , Vaz Victor R. , Gandhi Malini , Lee Elinton , Shapiro Geoffrey I. , Park Hyesun , Nishino Mizuki , Lindsay James , Felt Kristen D. , Sharma Bijaya , Cherniack Andrew D. , Rodig Scott , Gomez Daniel R. , Shaverdian Narek , Rakaee Mehrdad , Bandlamudi Chaitanya , Ladanyi Marc , Janne Pasi A. , Schoenfeld Adam J. , Sholl Lynette M. , Awad Mark M. , Cheng Michael L.
Published: September 2024

Supplementary Figure 5. (A) Median distance of each missense mutation from the closest intron start. (B) Median distance of each missense mutation from the closest intron end. (C) Proportion of cases with ATM loss and ATM intact expression by IHC in NSCLC samples with ATM mutation and ATM loss-of-heterozygosity (LOH).
Supplementary Figure 26 from Clinicopathologic, genomic, and immunophenotypic landscape of ATM mutations in non-small cell lung cancer
Authors: Ricciuti Biagio , Elkrief Arielle , Alessi Joao , Wang Xinan , Li Yvonne , Gupta Hersh , Muldoon Daniel M. , Bertram Arrien A. , Pecci Federica , Lamberti Giuseppe , Di Federico Alessandro , Barrichello Adriana , Vaz Victor R. , Gandhi Malini , Lee Elinton , Shapiro Geoffrey I. , Park Hyesun , Nishino Mizuki , Lindsay James , Felt Kristen D. , Sharma Bijaya , Cherniack Andrew D. , Rodig Scott , Gomez Daniel R. , Shaverdian Narek , Rakaee Mehrdad , Bandlamudi Chaitanya , Ladanyi Marc , Janne Pasi A. , Schoenfeld Adam J. , Sholl Lynette M. , Awad Mark M. , Cheng Michael L.
Published: September 2024

Supplementary Figure 26. Proportion of (A) tumor, (B) non-tumor, and (C) total PD-L1+ cells according to ATM/TP53 co-mutation status.
Supplementary Figure 25 from Clinicopathologic, genomic, and immunophenotypic landscape of ATM mutations in non-small cell lung cancer
Authors: Ricciuti Biagio , Elkrief Arielle , Alessi Joao , Wang Xinan , Li Yvonne , Gupta Hersh , Muldoon Daniel M. , Bertram Arrien A. , Pecci Federica , Lamberti Giuseppe , Di Federico Alessandro , Barrichello Adriana , Vaz Victor R. , Gandhi Malini , Lee Elinton , Shapiro Geoffrey I. , Park Hyesun , Nishino Mizuki , Lindsay James , Felt Kristen D. , Sharma Bijaya , Cherniack Andrew D. , Rodig Scott , Gomez Daniel R. , Shaverdian Narek , Rakaee Mehrdad , Bandlamudi Chaitanya , Ladanyi Marc , Janne Pasi A. , Schoenfeld Adam J. , Sholl Lynette M. , Awad Mark M. , Cheng Michael L.
Published: September 2024

Supplementary Figure 25. (A) Intratumoral, (B) tumor-stroma interface, and (C) total CD8+ PD1+ T cells according to ATM/TP53 co-mutation status. (D) Intratumoral, (E) tumor-stroma interface, and (F) total FOXP3+ immune cells according to ATM/TP53 co-mutation status.
Supplementary Table S2 from Type 2 diabetes mellitus and efficacy outcomes from imune checkpoint blockade in patients with cancer
Authors: Cortellini Alessio , D'Alessio Antonio , Cleary Siobhan , Buti Sebastiano , Bersanelli Melissa , Bordi Paola , Tonini Giuseppe , Vincenzi Bruno , Tucci Marco , Russo Alessandro , Pantano Francesco , Russano Marco , Stucci Luigia Stefania , Sergi Maria Chiara , Falconi Martina , Zarzana Maria Antonietta. , Santini Daniele , Spagnolo Francesco , Tanda Enrica T. , Rastelli Francesca , Giorgi Francesca Chiara. , Pergolesi Federica , Giusti Raffaele , Filetti Marco , Lo Bianco Francesca , Marchetti Paolo , Botticelli Andrea , Gelibter Alain , Siringo Marco , Ferrari Marco , Marconcini Riccardo , Vitale Maria Giuseppa. , Nicolardi Linda , Chiari Rita , Ghidini Michele , Nigro Olga , Grossi Francesco , De Tursi Michele , Di Marino Pietro , Queirolo Paola , Bracarda Sergio , Macrini Serena , Inno Alessandro , Zoratto Federica , Veltri Enzo , Spoto Chiara , Vitale Maria Grazia. , Cannita Katia , Gennari Alessandra , Morganstein Daniel L. , Mallardo Domenico , Nibid Lorenzo , Sabarese Giovanna , Brunetti Leonardo , Perrone Giuseppe , Ascierto Paolo A. , Ficorella Corrado , Pinato David J.
Published: September 2024

Details of diabetes medications.
Supplementary Table S11 from Type 2 diabetes mellitus and efficacy outcomes from imune checkpoint blockade in patients with cancer
Authors: Cortellini Alessio , D'Alessio Antonio , Cleary Siobhan , Buti Sebastiano , Bersanelli Melissa , Bordi Paola , Tonini Giuseppe , Vincenzi Bruno , Tucci Marco , Russo Alessandro , Pantano Francesco , Russano Marco , Stucci Luigia Stefania , Sergi Maria Chiara , Falconi Martina , Zarzana Maria Antonietta. , Santini Daniele , Spagnolo Francesco , Tanda Enrica T. , Rastelli Francesca , Giorgi Francesca Chiara. , Pergolesi Federica , Giusti Raffaele , Filetti Marco , Lo Bianco Francesca , Marchetti Paolo , Botticelli Andrea , Gelibter Alain , Siringo Marco , Ferrari Marco , Marconcini Riccardo , Vitale Maria Giuseppa. , Nicolardi Linda , Chiari Rita , Ghidini Michele , Nigro Olga , Grossi Francesco , De Tursi Michele , Di Marino Pietro , Queirolo Paola , Bracarda Sergio , Macrini Serena , Inno Alessandro , Zoratto Federica , Veltri Enzo , Spoto Chiara , Vitale Maria Grazia. , Cannita Katia , Gennari Alessandra , Morganstein Daniel L. , Mallardo Domenico , Nibid Lorenzo , Sabarese Giovanna , Brunetti Leonardo , Perrone Giuseppe , Ascierto Paolo A. , Ficorella Corrado , Pinato David J.
Published: September 2024

Summary of baseline characteristics of patients included in the targeted transcriptome analysis.
Supplementary Table 1 from Metastatic Prostate Cancers with BRCA2 versus ATM Mutations Exhibit Divergent Molecular Features and Clinical Outcomes
Authors: Hwang Justin , Shi Xiaolei , Elliott Andrew , Arnoff Taylor E. , McGrath Julie , Xiu Joanne , Walker Phillip , Bergom Hannah E. , Day Abderrahman , Ahmed Shihab , Tape Sydney , Makovec Allison , Ali Atef , Shaker Rami M. , Toye Eamon , Passow Rachel , Lozada John R. , Wang Jinhua , Lou Emil , Mouw Kent W. , Carneiro Benedito A. , Heath Elisabeth I. , McKay Rana R. , Korn W. Michael , Nabhan Chadi , Ryan Charles J. , Antonarakis Emmanuel S.
Published: September 2024

Composition and rates of all detectable genomic features detectable through the Caris diagnostic platform.
Supplementary Material 1 from Uncoupling CD4+ TIL-mediated tumor killing from JAK-signaling in melanoma
Authors: Draghi Arianna , Presti Mario , Jensen Agnete W.P. , Chamberlain Christopher A. , Albieri Benedetta , Rasmussen Anne-Christine K. , Andersen Mads H. , Crowther Michael D. , Svane Inge Marie , Donia Marco
Published: September 2024

Supplementary Figures and Tables
Supplementary Fig. 5 from INTRAVENOUS N-ACETYLCYSTEINE TO PREVENT CISPLATIN-INDUCED HEARING LOSS IN CHILDREN: A NONRANDOMIZED CONTROLLED PHASE 1 TRIAL
Authors: Orgel Etan , Knight Kristin R. , Chi Yueh-Yun , Malvar Jemily , Rushing Teresa , Mena Victoria , Eisenberg Laurie S. , Rassekh Shahrad R. , Ross Colin JD. , Scott Erika N. , Neely Michael , Neuwelt Edward A. , Muldoon Leslie L. , Freyer David R.
Published: September 2024

Supplementary Fig. 5 Progression-free survival in NAC treated and observation patients
Table S3 from Resolving the pathogenesis of anaplastic Wilms tumors through spatial mapping of cancer cell evolution
Authors: Rastegar Bahar , Andersson Natalie , Petersson Alexandra , Karlsson Jenny , Chattopadhyay Subhayan , Valind Anders , Jansson Caroline , Durand Geoffroy , Romerius Patrik , Jirstrom Karin , Holmquist Mengelbier Linda , Gisselsson David
Published: September 2024

Supplementary Table 3. Table. Sample list with TP53 status. All 20 WT cases and their corresponding samples are listed. ‘Sample position’ refers to the individual sample and its position in a certain paraffin block (see Figure 1 for details.) IR= intermediate risk, BT= blastemal type, DA= diffuse anaplasia. Headings marked in grey show TP53 sequencing results; wt=wild type, mut=mutation, NA= not annotated (i.e. not sequenced), aa= amino acid, REF= reference nucleotide, ALT= alternative nucleotide, TP53 ref= number of wild type TP53 alleles, TP53 mut=number of TP53 mutated alleles. Genomic positions according to hg19. In all columns with grey headings (except column ‘TP53’), semicolons (;) denote when more than one unique TP53 mutation is present in the same tumor sample.
Fig S3 from Resolving the pathogenesis of anaplastic Wilms tumors through spatial mapping of cancer cell evolution
Authors: Rastegar Bahar , Andersson Natalie , Petersson Alexandra , Karlsson Jenny , Chattopadhyay Subhayan , Valind Anders , Jansson Caroline , Durand Geoffroy , Romerius Patrik , Jirstrom Karin , Holmquist Mengelbier Linda , Gisselsson David
Published: September 2024

Supplementary Figure 3. Relationship between anaplasia, copy number aberrations, regression and mitotic rate.
Fig S2 from Resolving the pathogenesis of anaplastic Wilms tumors through spatial mapping of cancer cell evolution
Authors: Rastegar Bahar , Andersson Natalie , Petersson Alexandra , Karlsson Jenny , Chattopadhyay Subhayan , Valind Anders , Jansson Caroline , Durand Geoffroy , Romerius Patrik , Jirstrom Karin , Holmquist Mengelbier Linda , Gisselsson David
Published: September 2024

Supplementary Figure 2. Complexity of phylogenetic tree, comparing WT DA to IR and BT WT.
Supplementary Figure S2 from Targeting Replication Stress and Chemotherapy Resistance with a Combination of Sacituzumab Govitecan and Berzosertib: A Phase I Clinical Trial
Authors: Abel Melissa L. , Takahashi Nobuyuki , Peer Cody , Redon Christophe E. , Nichols Samantha , Vilimas Rasa , Lee Min-Jung , Lee Sunmin , Shelat Meenakshi , Kattapuram Robbie , Sciuto Linda , Pinkiert Danielle , Graham Chante , Butcher Donna , Karim Baktiar , Sharma Ajit Kumar. , Malin Justin , Kumar Rajesh , Schultz Christopher W. , Goyal Shubhank , Del Rivero Jaydira , Krishnamurthy Manan , Upadhyay Deep , Schroeder Brett , Sissung Tristan , Tyagi Manoj , Kim Jung , Pommier Yves , Aladjem Mirit , Raffeld Mark , Figg William Douglas. , Trepel Jane , Xi Liqiang , Desai Parth , Thomas Anish
Published: September 2024

Pharmacokinetic assessment
Supplementary Table S4 from CD49d expression identifies a biologically distinct subtype of chronic lymphocytic leukemia with inferior progression-free survival on BTK inhibitor therapy.
Authors: Alsadhan Anfal , Chen Jonathan , Gaglione Erika M. , Underbayev Chingiz , Tuma Pamela L. , Tian Xin , Freeman Lita A. , Baskar Sivasubramanian , Nierman Pia , Soto Susan , Itsara Andy , Ahn Inhye E. , Sun Clare , Bibikova Elena , Hartmann Tanja Nicole. , Mhibik Maissa , Wiestner Adrian
Published: September 2024

Supplementary Table S4. Mutations status of patients with disease progression on BTKis
Supplementary Table S2 from Phase I study of SYNB1891, an engineered E coli Nissle strain expressing STING agonist, with and without atezolizumab in advanced malignancies
Authors: Luke Jason J. , Piha-Paul Sarina A. , Medina Theresa , Verschraegen Claire F. , Varterasian Mary , Brennan Aoife M. , Riese Richard J. , Sokolovska Anna , Strauss James F. , Hava David L. , Janku Filip
Published: September 2024

Supplemental Table 2. Tumor types and characteristics for Nanostring and immunofluorescence data analysis
Supplementary Figure S4 from Phase I study of SYNB1891, an engineered E coli Nissle strain expressing STING agonist, with and without atezolizumab in advanced malignancies
Authors: Luke Jason J. , Piha-Paul Sarina A. , Medina Theresa , Verschraegen Claire F. , Varterasian Mary , Brennan Aoife M. , Riese Richard J. , Sokolovska Anna , Strauss James F. , Hava David L. , Janku Filip
Published: September 2024

Supplemental Figure 4. SYNB1891 increases IFN-stimulated gene expression in mouse tumors.
Supplementary Figure S3 from Plasma 25-hydroxyvitamin D levels and survival in stage III colon cancer: Findings from CALGB/SWOG 80702 (Alliance)
Authors: Wang Qiao-Li , Ma Chao , Yuan Chen , Shi Qian , Wolpin Brian M. , Zhang Yin , Fuchs Charles S. , Meyer Jeffrey , Zemla Tyler , Cheng En , Kumthekar Priya , Guthrie Katherine A. , Couture Felix , Kuebler Philip , Kumar Pankaj , Tan Benjamin , Krishnamurthi Smitha , Goldberg Richard M. , Venook Alan , Blanke Charles , Shields Anthony F. , O'Reilly Eileen M. , Meyerhardt Jeffrey A. , Ng Kimmie
Published: September 2024

Figure S3. Multivariable hazard ratio and 95% confidence intervals for disease-free survival (A), overall survival (B), and time to recurrence (C), comparing plasma 25-hydroxyvitamin D ≥12 versus <12 ng/ml, across strata of potential effect modifiers
Supplementary Methods 1 from Alternating 17beta-estradiol and aromatase inhibitor therapies is efficacious in post-menopausal women with advanced endocrine-resistant ER+ breast cancer
Authors: Schwartz Gary N. , Kaufman Peter A. , Giridhar Karthik V. , Marotti Jonathan D. , Chamberlin Mary D. , Arrick Bradley A. , Makari-Judson Grace , Goetz Matthew P. , Soucy Shannon M. , Kolling Fred , Demidenko Eugene , Miller Todd W.
Published: September 2024

Suppl. methods
Supplementary Figure S2 from Genomic profiling of radiation-induced sarcomas reveals the immunological characteristics and its response to immune checkpoint blockade
Authors: Hong Dong-Chun , Yang Jing , Sun Cong , Liu Yuan-Tao , Shen Lu-Jun , Xu Bu-Shu , Que Yi , Xia Xiaojun , Zhang Xing
Published: September 2024

RNA-seq analysis between RIS and RIS groups and some subtypes.
(A) Venn plot showing differentially expressed genes (DEGs) of FS and OS subtype comparison between RIS and SARC groups.
(B) Volcano plot showing up-regulated and down-regulated genes in the RIFS group versus the RIOS group.
(C) GO pathway enrichment of mRNA-seq between the RIS group and SARC group, and between the RIFS and RIOS subtypes.
(D) Relative abundances of activated immune cells and immunosuppression-related cells in subtypes of RISs and primary sarcomas.
Supplementary Table S1 from Integrative single-cell and bulk transcriptomes analyses identify intrinsic HNSCC subtypes with distinct prognoses and therapeutic vulnerabilities
Authors: Dai Yibin , Wang Ziyu , Xia Yingcao , Li Jin , Wu Yaping , Wang Yanling , Jiang Hongbing , Cheng Jie
Published: September 2024

Detailed proportions of cells in 5 scRNA-seq datasets
Supplementary Fig. 4 from MEK inhibition sensitizes pancreatic cancer to STING agonism by tumor-cell intrinsic amplification of type I interferon signaling
Authors: Ghukasyan Razmik , Liang Keke , Chau Kevin , Li Luyi , Chan Charlotte , Abt Evan R. , Le Thuc , Park Joon Y. , Wu Nanping , Premji Alykhan , Damoiseaux Robert , Luu Tony , Labora Amanda , Rashid Khalid , Link Jason M. , Radu Caius G. , Donahue Timothy R.
Published: September 2024

Supplementary Fig. 4 Immunoblot analysis demonstrating the effect of ± 100 U/ml exogenous IFN on CFPAC-1 and SUIT2 parental cells compared to their respective IFNAR-deficient isogenic cell lines. (B) Immunoblot analysis of CFPAC-1 parental and IFNAR1-KO cells exposed to ± 1 µM diABZI ± 100 nM trametinib for 24 h (C)Immunoblot analysis of the effects of ± 100 U/ml exogenous IFN ± 1 µM diABZI for 24 h.
Figure S7 from Subsets of interferon signaling predict response to immune checkpoint blockade in melanoma patients
Authors: Horowitch Brooke , Lee Daniel Y. , Ding Min , Martinez-Morilla Sandra , Aung Thazin Nwe. , Ouerghi Feriel , Wang Xueting , Wei Wei , Damsky William , Sznol Mario , Kluger Harriet , Rimm David L. , Ishizuka Jeffrey
Published: September 2024

Supplemental Figure 7: pSTAT1Y701, CD3, and driver mutation status in tumors based on combined STAT1 and PD-L1 status.
Figure S4 from Subsets of interferon signaling predict response to immune checkpoint blockade in melanoma patients
Authors: Horowitch Brooke , Lee Daniel Y. , Ding Min , Martinez-Morilla Sandra , Aung Thazin Nwe. , Ouerghi Feriel , Wang Xueting , Wei Wei , Damsky William , Sznol Mario , Kluger Harriet , Rimm David L. , Ishizuka Jeffrey
Published: September 2024

Supplemental Figure 4: STAT1 in the nuclear compartment consistently predicts ICI response and survival but not nuclear pSTAT1Y701 or tumor/stromal PD-L1
Figure S2 from Subsets of interferon signaling predict response to immune checkpoint blockade in melanoma patients
Authors: Horowitch Brooke , Lee Daniel Y. , Ding Min , Martinez-Morilla Sandra , Aung Thazin Nwe. , Ouerghi Feriel , Wang Xueting , Wei Wei , Damsky William , Sznol Mario , Kluger Harriet , Rimm David L. , Ishizuka Jeffrey
Published: September 2024

Supplemental Figure 2: Receiver operator curve analyses to validate median AQUA score cutpoints
Supplementary Figure S5 from Targeting BET proteins downregulates miR-33a to promote synergy with PIM inhibitors in CMML
Authors: Letson Christopher T. , Balasis Maria E. , Newman Hannah , Binder Moritz , Vedder Alexis , Kinose Fumi , Ball Markus , Kruer Traci , Quintana Ariel , Lasho Terra L. , Finke Christy M. , Almada Luciana L. , Grants Jennifer M. , Zhang Guolin , Fernandez-Zapico Martin E. , Gaspar-Maia Alexandre , Lancet Jeffrey , Komrokji Rami , Haura Eric , Sallman David A. , Reuther Gary W. , Karsan Aly , Rix Uwe , Patnaik Mrinal M. , Padron Eric
Published: September 2024

Supplemental Figure 5 contains ChIP-seq tracks of all individual samples corresponding to Figure 5D.
Supplementary Figure S1 from Phase II study of docetaxel and trametinib in patients with KRAS mutation positive recurrent non-small cell lung cancer (NSCLC) (SWOG S1507, NCT-02642042)
Authors: Gadgeel Shirish M. , Miao Jieling , Riess Jonathan W. , Moon James , Mack Philip C. , Gerstner Gregory J. , Burns Timothy F. , Taj Asma , Akerley Wallace L. , Dragnev Konstantin H. , Laudi Noel , Redman Mary W. , Gray Jhanelle E. , Gandara David R. , Kelly Karen
Published: September 2024

Supplementary Figure 1. Progression-Free Survival and Overall Survival in patients with cancers with TP53 co-mutations, and STK11 co-mutations.
Figure S6 from BBT-176, a Novel Fourth-Generation Tyrosine Kinase Inhibitor for Osimertinib-Resistant Epidermal Growth Factor Receptor Mutations in Non-Small Cell Lung Cancer
Authors: Lim Sun Min , Fujino Toshio , Kim Chulwon , Lee Gwanghee , Lee Yong-Hee , Kim Dong-Wan , Ahn Jin Seok , Mitsudomi Tetsuya , Jin Taiguang , Lee Sang-Yoon
Published: September 2024

Supplementary Figure 6. Analysis of BBT-176 using in vivo models. A, Body weight changes in Ba/F3 EGFR 19Del/C797S, EGFR 19Del/T790M/C797S and patient-derived xenograft models. The patient-derived xenograft was derived from a patient with poorly-differentiated adenocarcinoma harboring an EGFR 19Del/T790M/C797S mutation. B, BBT-176 activity in a LU1235 EGFR 19Del patient-derived xenograft model. Abbreviations: PDX, patient-derived xenograft; PO, orally; QD, once daily.
Figure S3 from BBT-176, a Novel Fourth-Generation Tyrosine Kinase Inhibitor for Osimertinib-Resistant Epidermal Growth Factor Receptor Mutations in Non-Small Cell Lung Cancer
Authors: Lim Sun Min , Fujino Toshio , Kim Chulwon , Lee Gwanghee , Lee Yong-Hee , Kim Dong-Wan , Ahn Jin Seok , Mitsudomi Tetsuya , Jin Taiguang , Lee Sang-Yoon
Published: September 2024

Supplementary Figure 3. Activity of osimertinib in EGFR 19Del-derived BBT-176-resistant clones. Abbreviation: BR(1/2), BBT-176-resistant (clone 1/2).
Supplementary Figure S4 from A bi-functional PARP-HDAC inhibitor with activity in Ewing sarcoma
Authors: Ramos Louise , Truong Sarah , Zhai Beibei , Joshi Jay , Ghaidi Fariba , Lizardo Michael M. , Shyp Taras , Kung Sonia H.Y. , Rezakhanlou Alireza M. , Oo Htoo Zarni , Adomat Hans , Le Bihan Stephane , Collins Colin , Bacha Jeffrey , Brown Dennis , Langlands John , Shen Wang , Lallous Nada , Sorensen Poul H. , Daugaard Mads
Published: September 2024

Replicate data of DNA damage assays
Supplemental Figure 1 from Early changes in circulating cell free KRAS G12C predicts response to adagrasib in KRAS mutant non-small cell lung cancer patients
Authors: Paweletz Cloud P. , Heavey Grace A. , Kuang Yanan , Durlacher Emily , Kheoh Thian , Chao Richard C. , Spira Alexander I. , Leventakos Konstantinos , Johnson Melissa L. , Ou Sai-Hong Ignatius. , Riely Gregory J. , Anderes Kenna , Yang Wenjing , Christensen James G. , Janne Pasi A.
Published: September 2024

Supplemental Figure 1: Quantitative concordance between NGS and ddPCR KRASG12C results.
ctDNA, circulating tumor DNA; ddPCR, droplet digital polymerase chain reaction.
Supplementary Table S7 from Activin A-mediated polarization of cancer-associated fibroblasts and macrophages confers resistance to checkpoint immunotherapy in skin cancer
Authors: Pich-Bavastro Christine , Yerly Laura , Di Domizio Jeremy , Tissot-Renaud Stéphanie , Gilliet Michel , Kuonen François
Published: September 2024

Supplementary Table S7. Clinical response annotation of the scRNAseq dataset obtained from melanomas treated with ICI.
Supplementary Figure S3 from Genomic profiling of metastatic castration-resistant prostate cancer samples resistant to androgen-receptor pathway inhibitors
Authors: Menssouri Naoual , Poiraudeau Loic , Helissey Carole , Bigot Ludovic , Sabio Jonathan , Ibrahim Tony , Pobel Cedric , Nicotra Claudio , Ngo-Camus Maud , Lacroix Ludovic , Rouleau Etienne , Tselikas Lambros , CHAUCHEREAU Anne , Blanc-Durand Félix , Bernard-Tessier Alice , Patrikidou Anna , Naoun Natacha , Flippot Ronan , Colomba Emeline , Fuerea Alina , Albiges Laurence , Lavaud Pernelle , van de Wiel Paul , den Biezen-Timmermans Eveline , Wesseling-Rozendaal Yvonne , Ponce-Aix Santiago , Michiels Stefan , Massard Christophe , Gautheret Daniel , Barlesi Fabrice , Andre Fabrice , Besse Benjamin , Scoazec Jean-Yves , Friboulet Luc , Fizazi Karim , Loriot Yohann
Published: September 2024

Genomic landscape of the whole cohort
Supplementary Data S9 from Genomic profiling of metastatic castration-resistant prostate cancer samples resistant to androgen-receptor pathway inhibitors
Authors: Menssouri Naoual , Poiraudeau Loic , Helissey Carole , Bigot Ludovic , Sabio Jonathan , Ibrahim Tony , Pobel Cedric , Nicotra Claudio , Ngo-Camus Maud , Lacroix Ludovic , Rouleau Etienne , Tselikas Lambros , CHAUCHEREAU Anne , Blanc-Durand Félix , Bernard-Tessier Alice , Patrikidou Anna , Naoun Natacha , Flippot Ronan , Colomba Emeline , Fuerea Alina , Albiges Laurence , Lavaud Pernelle , van de Wiel Paul , den Biezen-Timmermans Eveline , Wesseling-Rozendaal Yvonne , Ponce-Aix Santiago , Michiels Stefan , Massard Christophe , Gautheret Daniel , Barlesi Fabrice , Andre Fabrice , Besse Benjamin , Scoazec Jean-Yves , Friboulet Luc , Fizazi Karim , Loriot Yohann
Published: September 2024

Supplementary Data 9 describes the results from OncoSIgnal analysis.
Supplementary Figure S7 from Dissecting the mechanisms underlying the Cytokine Release Syndrome (CRS) mediated by T Cell Bispecific Antibodies
Authors: Leclercq-Cohen Gabrielle , Steinhoff Nathalie , Albertí-Servera Llucia , Nassiri Sina , Danilin Sabrina , Piccione Emily , Yángüez Emilio , Hüsser Tamara , Herter Sylvia , Schmeing Stephan , Gerber Petra , Schwalie Petra , Sam Johannes , Briner Stefanie , Jenni Sylvia , Bianchi Roberta , Biehl Marlene , Cremasco Floriana , Apostolopoulou Katerina , Haegel Hélène , Klein Christian , Umana Pablo , Bacac Marina
Published: September 2024

Supplementary Figure S7. Overview of average expression and fraction positives per cell type, timepoint and treatment condition for cytokines that are differentially expressed in neutrophils, monocytes, pDC, cDC, B cells, CD4+ T cells, CD8+ T cells, MAIT cells and/or NK cells treatment vs. control any timepoint. The untreated condition corresponds to the pooled baseline samples and incubation control samples. Mean of n= 4 donors (baseline, and 20 hrs) and n=2 donors (2 hrs, 4 hrs and 6 hrs).
Figure S3 from De novo and histologically transformed small cell lung cancer is sensitive to lurbinectedin treatment through the modulation of EMT and NOTCH signaling pathways.
Authors: Chakraborty Subhamoy , Coleman Charles , Manoj Parvathy , Demircioglu Deniz , Shah Nisargbhai , de Stanchina Elisa , Rudin Charles M. , Hasson Dan , Sen Triparna
Published: September 2024

Figure S3: Lurbinectedin treatment induces regulators of
the DNA damage response pathway.
Supplementary Figure S19 from Trackable Intratumor Microdosing and Spatial Profiling Provide Early Insights into Activity of Investigational Agents in the Intact Tumor Microenvironment
Authors: Derry Jonathan M.J. , Burns Connor , Frazier Jason P. , Beirne Emily , Grenley Marc , DuFort Christopher C. , Killingbeck Emily , Leon Michael , Williams Claire , Gregory Mark , Houlton Jeffrey , Clayburgh Daniel , Swiecicki Paul , Huszar Dennis , Berger Allison , Klinghoffer Richard A.
Published: September 2024

Subasumstat initiates cell death and cytotoxic T cell activity
Supplementary Figure S14 from Trackable Intratumor Microdosing and Spatial Profiling Provide Early Insights into Activity of Investigational Agents in the Intact Tumor Microenvironment
Authors: Derry Jonathan M.J. , Burns Connor , Frazier Jason P. , Beirne Emily , Grenley Marc , DuFort Christopher C. , Killingbeck Emily , Leon Michael , Williams Claire , Gregory Mark , Houlton Jeffrey , Clayburgh Daniel , Swiecicki Paul , Huszar Dennis , Berger Allison , Klinghoffer Richard A.
Published: September 2024

Subasumstat induces changes in the TME associated with Interferon Signature expression
Table S6 from Combined CDK4/6 and ERK1/2 inhibition enhances anti-tumor activity in NF1-associated plexiform neurofibroma
Authors: Flint Alyssa C. , Mitchell Dana K. , Angus Steven P. , Smith Abbi E. , Bessler Waylan , Jiang Li , Mang Henry , Li Xiaohong , Lu Qingbo , Rodriguez Brooke , Sandusky George E. , Masters Andi R. , Zhang Chi , Dang Pengtao , Koenig Jenna , Johnson Gary L. , Shen Weihua , Liu Jiangang , Aggarwal Amit , Donoho Gregory P. , Willard Melinda D. , Bhagwat Shripad V. , Clapp D. Wade , Rhodes Steven D.
Published: September 2024

Dosing and schedule of abemaciclib and LY3214996
Table S5 from Combined CDK4/6 and ERK1/2 inhibition enhances anti-tumor activity in NF1-associated plexiform neurofibroma
Authors: Flint Alyssa C. , Mitchell Dana K. , Angus Steven P. , Smith Abbi E. , Bessler Waylan , Jiang Li , Mang Henry , Li Xiaohong , Lu Qingbo , Rodriguez Brooke , Sandusky George E. , Masters Andi R. , Zhang Chi , Dang Pengtao , Koenig Jenna , Johnson Gary L. , Shen Weihua , Liu Jiangang , Aggarwal Amit , Donoho Gregory P. , Willard Melinda D. , Bhagwat Shripad V. , Clapp D. Wade , Rhodes Steven D.
Published: September 2024

Statistics from DESeq2
Figure S1 from Combined CDK4/6 and ERK1/2 inhibition enhances anti-tumor activity in NF1-associated plexiform neurofibroma
Authors: Flint Alyssa C. , Mitchell Dana K. , Angus Steven P. , Smith Abbi E. , Bessler Waylan , Jiang Li , Mang Henry , Li Xiaohong , Lu Qingbo , Rodriguez Brooke , Sandusky George E. , Masters Andi R. , Zhang Chi , Dang Pengtao , Koenig Jenna , Johnson Gary L. , Shen Weihua , Liu Jiangang , Aggarwal Amit , Donoho Gregory P. , Willard Melinda D. , Bhagwat Shripad V. , Clapp D. Wade , Rhodes Steven D.
Published: September 2024

Hallmark KRAS Pathway Heatmap and Top DEGs
Supplementary Table S7 from Determinants of survival in HER2+ metastatic esophagogastric cancer
Authors: Maron Steven B. , Chatila Walid , Walch Henry , Chou Joanne F. , Ceglia Nicholas , Ptashkin Ryan , Do Richard Kinh Gian. , Paroder Viktoriya , Pandit-Taskar Neeta , Lewis Jason S. , Biachi De Castria TIago , Sabwa Shalom , Socolow Fiona , Feder Lara , Thomas Jasmine , Schulze Isabell , Kim Kwanghee , Elzein Arijh , Bojilova Viktoria , Zatzman Matthew , Bhanot Umesh , Nagy Rebecca J. , Lee Jeeyun , Simmons Marc , Segal Michal , Ku Geoffrey Y. , Ilson David H. , Capanu Marinela , Hechtman Jaclyn F. , Merghoub Taha , Shah Sohrab , Schultz Nikolaus , Solit David B. , Janjigian Yelena Y.
Published: September 2024

Univariable Cox Proportional Hazard for PFS in HER2-targeted retrospective cohort.
Supplementary Table S3 from Determinants of survival in HER2+ metastatic esophagogastric cancer
Authors: Maron Steven B. , Chatila Walid , Walch Henry , Chou Joanne F. , Ceglia Nicholas , Ptashkin Ryan , Do Richard Kinh Gian. , Paroder Viktoriya , Pandit-Taskar Neeta , Lewis Jason S. , Biachi De Castria TIago , Sabwa Shalom , Socolow Fiona , Feder Lara , Thomas Jasmine , Schulze Isabell , Kim Kwanghee , Elzein Arijh , Bojilova Viktoria , Zatzman Matthew , Bhanot Umesh , Nagy Rebecca J. , Lee Jeeyun , Simmons Marc , Segal Michal , Ku Geoffrey Y. , Ilson David H. , Capanu Marinela , Hechtman Jaclyn F. , Merghoub Taha , Shah Sohrab , Schultz Nikolaus , Solit David B. , Janjigian Yelena Y.
Published: September 2024

Correlation of 89Zr PET Uptake and HER2 Status
Supplementary Figure S3 from Determinants of survival in HER2+ metastatic esophagogastric cancer
Authors: Maron Steven B. , Chatila Walid , Walch Henry , Chou Joanne F. , Ceglia Nicholas , Ptashkin Ryan , Do Richard Kinh Gian. , Paroder Viktoriya , Pandit-Taskar Neeta , Lewis Jason S. , Biachi De Castria TIago , Sabwa Shalom , Socolow Fiona , Feder Lara , Thomas Jasmine , Schulze Isabell , Kim Kwanghee , Elzein Arijh , Bojilova Viktoria , Zatzman Matthew , Bhanot Umesh , Nagy Rebecca J. , Lee Jeeyun , Simmons Marc , Segal Michal , Ku Geoffrey Y. , Ilson David H. , Capanu Marinela , Hechtman Jaclyn F. , Merghoub Taha , Shah Sohrab , Schultz Nikolaus , Solit David B. , Janjigian Yelena Y.
Published: September 2024

Response to pembrolizumab and trastuzumab induction according to pre-treatment 89Zr-trastuzumab PET avidity.
Table S4 from A Novel HOXA10-Associated 5 Gene-Based Prognostic Signature for Stratification of Short-Term Survivors of Pancreatic Ductal Adenocarcinoma
Authors: Kisling Sophia G. , Atri Pranita , Shah Ashu , Cox Jesse L. , Sharma Sunandini , Smith Lynette M. , Ghersi Dario , Batra Surinder K.
Published: September 2024

PDAC cohort validated genes
Figure S3 from A Novel HOXA10-Associated 5 Gene-Based Prognostic Signature for Stratification of Short-Term Survivors of Pancreatic Ductal Adenocarcinoma
Authors: Kisling Sophia G. , Atri Pranita , Shah Ashu , Cox Jesse L. , Sharma Sunandini , Smith Lynette M. , Ghersi Dario , Batra Surinder K.
Published: September 2024

CIBERSORT analysis for HOXA10 and its driven signature
Supplementary Table S2 from Estrogen therapy induces receptor-dependent DNA damage enhanced by PARP inhibition in ER+ breast cancer
Authors: Traphagen Nicole A. , Schwartz Gary N. , Tau Steven , Roberts Alyssa M. , Jiang Amanda , Hosford Sarah R. , Marotti Jonathan D. , Goen Abigail E. , Romo Bianca A. , Johnson Anneka L. , Duffy Emily-Claire K. , Demidenko Eugene , Heverly Paul , Mosesson Yaron , Soucy Shannon M. , Kolling Fred , Miller Todd W.
Published: September 2024

Supplementary Table S2. Results of single-sample gene set enrichment analysis (ssGSEA) of transcriptomic profiles from HCC-1428 and HCC-1428/LTED cells.
Supplementary Figure S8 from Estrogen therapy induces receptor-dependent DNA damage enhanced by PARP inhibition in ER+ breast cancer
Authors: Traphagen Nicole A. , Schwartz Gary N. , Tau Steven , Roberts Alyssa M. , Jiang Amanda , Hosford Sarah R. , Marotti Jonathan D. , Goen Abigail E. , Romo Bianca A. , Johnson Anneka L. , Duffy Emily-Claire K. , Demidenko Eugene , Heverly Paul , Mosesson Yaron , Soucy Shannon M. , Kolling Fred , Miller Todd W.
Published: September 2024

Supplementary Figure S8- Individual tumor volumes from mice treated ± E2.
Supplementary Figure S5 from A Phase 1b trial of AVID200, a TGFβ 1/3 trap, in patients with myelofibrosis
Authors: Mascarenhas John , Migliaccio Anna Rita , Kosiorek Heidi , Bhave Rupali , Palmer Jeanne , Kuykendall Andrew , Mesa Ruben , Rampal Raajit K. , Gerds Aaron T. , Yacoub Abdulraheem , Pettit Kristen , Talpaz Moshe , Komrokji Rami , Kremyanskaya Marina , Gonzalez Agapito , Fabris Frank , Johnson Kathryn , Dougherty Mikaela , McGovern Erin , Arango Ossa Juan , Domenico Dylan , Farnoud Noushin , Weinberg Rona Singer. , Kong Amy , Najfeld Vesna , Vannucchi Alessandro Maria. , Arciprete Francesca , Zingariello Maria , Falchi Mario , Salama Mohamed E. , Mead-Harvey Carolyn , Dueck Amylou , Varricchio Lilian , Hoffman Ronald
Published: September 2024

The bone marrow from patients with MF contain more CD42pos cells than patients with ET or with hematopoietic malignancies without fibrosis (normal control).
Supplementary Figure S5 from Evaluation of somatic mutations in urine samples as a non-invasive method for the detection and molecular classification of endometrial cancer
Authors: Costas Laura , Onieva Irene , Pelegrina Beatriz , Marin Fátima , Carmona Alvaro , López-Querol Marta , Frias-Gomez Jon , Peremiquel-Trillas Paula , Martínez José Manuel , Dorca Eduard , Brunet Joan , Pineda Marta , Ponce Jordi , Matías-Guiu Xavier , de Sanjosé Silvia , Bosch Francesc Xavier , Alemany Laia , Paytubi Sonia
Published: September 2024

This graph illustrates the relationship between the number of interrogated genes and the sensitivity and specificity values.
Supplementary Figure S7 from Multiomic mapping of acquired chromosome 1 copy number and structural variants to identify therapeutic vulnerabilities in multiple myeloma.
Authors: Boyle Eileen M. , Blaney Patrick , Stoeckle James H. , Wang Yubao , Ghamlouch Hussein , Gagler Dylan , Braunstein Marc , Williams Louis , Tenenbaum Avital , Siegel Ariel , Chen Xiaoyi , Varma Gaurav , Avigan Jason , Li Alexander , Jinsi Monica , Kaminetzky David , Arbini Arnaldo , Montes Lydia , Corre Jill , Rustad Even H. , Landgren Ola , Maura Francesco , Walker Brian A. , Bauer Michael , Bruno Benedetto , Tsirigos Aristotelis , Davies Faith E. , Morgan Gareth J.
Published: September 2024

Hi-C interaction and TAD map of TI2 and G8 regions. A comparison of the chromatin conformation of the region which encompasses TI2 and G8 across the 3 HMCLs (U266, RPMI8226, and KMS11) and PC. We note that there are noticeable loss of TAD boundary within the G8 region between PC and U266 and RPMI8226 that may allow accessibility to distal super-enhancers and result in overexpression. A similar change is seen in KMS11 at the ELF3 locus.
Supplementary Figure S5 from Multiomic mapping of acquired chromosome 1 copy number and structural variants to identify therapeutic vulnerabilities in multiple myeloma.
Authors: Boyle Eileen M. , Blaney Patrick , Stoeckle James H. , Wang Yubao , Ghamlouch Hussein , Gagler Dylan , Braunstein Marc , Williams Louis , Tenenbaum Avital , Siegel Ariel , Chen Xiaoyi , Varma Gaurav , Avigan Jason , Li Alexander , Jinsi Monica , Kaminetzky David , Arbini Arnaldo , Montes Lydia , Corre Jill , Rustad Even H. , Landgren Ola , Maura Francesco , Walker Brian A. , Bauer Michael , Bruno Benedetto , Tsirigos Aristotelis , Davies Faith E. , Morgan Gareth J.
Published: September 2024

Hi-C interaction and TAD map of CT1, TI1, D7 regions. The chromatin confirmation of the region encompassing CT1, TI1, and D7 across the 3 HMCLs (U266, RPMI8226, and KMS11) and PC for comparison. The region shows significant variability in the TAD strucure at the TENT5C locus across all samples in comparision to PC which could explain its dysregulation