bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figure S23 from Transcriptional Phenocopies of Deleterious KEAP1 Mutations Correlate with Survival Outcomes in Lung Cancer Treated with Immunotherapy
Authors: Scalera Stefano , Ricciuti Biagio , Marinelli Daniele , Mazzotta Marco , Cipriani Laura , Bon Giulia , Schiavoni Giulia , Terrenato Irene , Di Federico Alessandro , Alessi Joao V. , Fanciulli Maurizio , Ciuffreda Ludovica , De Nicola Francesca , Goeman Frauke , Caravagna Giulio , Santini Daniele , De Maria Ruggero , Cappuzzo Federico , Ciliberto Gennaro , Jamal-Hanjani Mariam , Awad Mark M. , McGranahan Nicholas , Maugeri-Saccà Marcello
Published: October 2024

Supplementary Figure 23. KEAPness and the 29 tumor microenvironment (TIME)-related signatures in the TRACERx421 cohort
Supplementary Figure S10 from Transcriptional Phenocopies of Deleterious KEAP1 Mutations Correlate with Survival Outcomes in Lung Cancer Treated with Immunotherapy
Authors: Scalera Stefano , Ricciuti Biagio , Marinelli Daniele , Mazzotta Marco , Cipriani Laura , Bon Giulia , Schiavoni Giulia , Terrenato Irene , Di Federico Alessandro , Alessi Joao V. , Fanciulli Maurizio , Ciuffreda Ludovica , De Nicola Francesca , Goeman Frauke , Caravagna Giulio , Santini Daniele , De Maria Ruggero , Cappuzzo Federico , Ciliberto Gennaro , Jamal-Hanjani Mariam , Awad Mark M. , McGranahan Nicholas , Maugeri-Saccà Marcello
Published: October 2024

Supplementary Figure 10. Multivariable Cox regression models in the SU2C and OAK/POPLAR cohorts
Supplemental Methods 1 from Genomic Profiling to Contextualize the Results of Intervention for Smoldering Multiple Myeloma
Authors: Kazandjian Dickran , Diamond Benjamin , Papadimitriou Marios , Hill Elizabeth , Sklavenitis-Pistofidis Romanos , Ziccheddu Bachisio , Blaney Patrick , Chojnacka Monika , Durante Michael , Maclachlan Kylee , Young Ryan , Usmani Saad , Davies Faith , Getz Gad , Ghobrial Irene , Korde Neha , Morgan Gareth , Maura Francesco , Landgren Ola
Published: October 2024

Supplemental Methods
Supplemental Figure S7 from Genomic Profiling to Contextualize the Results of Intervention for Smoldering Multiple Myeloma
Authors: Kazandjian Dickran , Diamond Benjamin , Papadimitriou Marios , Hill Elizabeth , Sklavenitis-Pistofidis Romanos , Ziccheddu Bachisio , Blaney Patrick , Chojnacka Monika , Durante Michael , Maclachlan Kylee , Young Ryan , Usmani Saad , Davies Faith , Getz Gad , Ghobrial Irene , Korde Neha , Morgan Gareth , Maura Francesco , Landgren Ola
Published: October 2024

Supplemental Figure S7. Circos Plots for KRd/R Patients.
Supplementary Figure S6 from Targeting the Dendritic Cell-Secreted Immunoregulatory Cytokine CCL22 Alleviates Radioresistance
Authors: Bugno Jason , Wang Liangliang , Yu Xianbin , Cao Xuezhi , Wang Jiaai , Huang Xiaona , Yang Kaiting , Piffko Andras , Chen Katherine , Luo Stephen Y. , Naccasha Emile , Hou Yuzhu , Fu Sherry , He Chuan , Fu Yang-xin , Liang Hua L. , Weichselbaum Ralph R.
Published: October 2024

Supplementary Figure S6. Treg tumor infiltration after local RT in MC38 tumors and splenic cDC isolation strategy.
Supplementary Table S2 from Spatial Transcriptome Mapping of the Desmoplastic Growth Pattern of Colorectal Liver Metastases by In Situ Sequencing Reveals a Biologically Relevant Zonation of the Desmoplastic Rim
Authors: Andersson Axel , Escriva Conde Maria , Surova Olga , Vermeulen Peter , Wählby Carolina , Nilsson Mats , Nyström Hanna
Published: October 2024

Supplementary Table S2. L-probe sequence for each gene in the in situ sequencing panel.
Supplementary Figure S7 from Spatial Transcriptome Mapping of the Desmoplastic Growth Pattern of Colorectal Liver Metastases by In Situ Sequencing Reveals a Biologically Relevant Zonation of the Desmoplastic Rim
Authors: Andersson Axel , Escriva Conde Maria , Surova Olga , Vermeulen Peter , Wählby Carolina , Nilsson Mats , Nyström Hanna
Published: October 2024

Supplementary Figure S7. Immunohistochemistry of DHGP CLM for COL IV,SPP1, POSTN, and NGFR. COL IV (A, brown), SPP1 (B, brown), POSTN (C, brown) and NGFR (D, brown). Counterstain (blue). T = tumor, L = Liver. Scale bar (red) corresponds to 50 μm.
Supplementary Figure S5 from Spatial Transcriptome Mapping of the Desmoplastic Growth Pattern of Colorectal Liver Metastases by In Situ Sequencing Reveals a Biologically Relevant Zonation of the Desmoplastic Rim
Authors: Andersson Axel , Escriva Conde Maria , Surova Olga , Vermeulen Peter , Wählby Carolina , Nilsson Mats , Nyström Hanna
Published: October 2024

Supplementary Figure S5. Differentially expressed genes (DEG) for each cluster. Color scale represents the log fold change obtained by comparing the average number of reads per bin within a particular cluster against the average number of reads per bin among the other clusters. Genes with a log fold change above 1,5 are defined as differentially expressed.
Supplementary Figure S1 from Early Detection of Malignant and Premalignant Peripheral Nerve Tumors Using Cell-Free DNA Fragmentomics
Authors: Sundby R. Taylor , Szymanski Jeffrey J. , Pan Alexander C. , Jones Paul A. , Mahmood Sana Z. , Reid Olivia H. , Srihari Divya , Armstrong Amy E. , Chamberlain Stacey , Burgic Sanita , Weekley Kara , Murray Béga , Patel Sneh , Qaium Faridi , Lucas Andrea N. , Fagan Margaret , Dufek Anne , Meyer Christian F. , Collins Natalie B. , Pratilas Christine A. , Dombi Eva , Gross Andrea M. , Kim AeRang , Chrisinger John S.A. , Dehner Carina A. , Widemann Brigitte C. , Hirbe Angela C. , Chaudhuri Aadel A. , Shern Jack F.
Published: October 2024

Supplemental Figure 1. Attributes of atypical neurofibroma samples. Histologic characteristics and, when available, TSO500 clinical sequencing results for paired tissue corresponding with AN cell-free DNA.
Supplemental Figure 1 from Abiraterone, Olaparib, or Abiraterone + Olaparib in First-Line Metastatic Castration-Resistant Prostate Cancer with DNA Repair Defects (BRCAAway)
Authors: Hussain Maha , Kocherginsky Masha , Agarwal Neeraj , Adra Nabil , Zhang Jingsong , Paller Channing J. , Picus Joel , Reichert Zachery R. , Szmulewitz Russell Z. , Tagawa Scott T. , Kuzel Timothy M. , Bazzi Latifa A. , Daignault-Newton Stephanie , Whang Young E. , Dreicer Robert , Stephenson Ryan D. , Rettig Matthew B. , Shevrin Daniel , Gerke Travis , Chinnaiyan Arul M. , Antonarakis Emmanuel S.
Published: October 2024

Supplemental Figure 1. PFS for primary arms.
Supplementary Table S1 from Pharmacologic Inhibition of EIF4A Blocks NRF2 Synthesis to Prevent Osteosarcoma Metastasis
Authors: Lizardo Michael M. , Hughes Christopher , Huang Yue Z. , Shyp Taras , Delaidelli Alberto , Zhang Hai-Feng , Shaool Sol Snir , Renner Annalena F. , Burwag Farez , Sayles Leanne C. , Lee Alex G. , Sweet-Cordero Alejandro , Sorensen Poul H.
Published: October 2024

Supplemental Table 1. Limited small-molecule inhibitor screen of mRNA translation factors on MG63.3 OS cells.
Supplementary Table S2 from Tyrosine Protein Kinase SYK-Related Gene Signature in Baseline Immune Cells Associated with Adjuvant Immunotherapy–Induced Immune-Related Adverse Events in Melanoma
Authors: Monson Kelsey R. , Ferguson Robert , Handzlik Joanna E. , Xiong Jiahan , Dagayev Sasha , Morales Leah , Chat Vylyny , Bunis Anabelle , Sreenivasaiah Chaitra , Dolfi Sonia , Tenney Daniel J. , Shao Yongzhao , Osman Iman , Weber Jeffrey S. , Kirchhoff Tomas
Published: October 2024

Supplementary Table S2. Complete list of differentially expressed genes identified in the study.
Supplementary Figure S2 from Tyrosine Protein Kinase SYK-Related Gene Signature in Baseline Immune Cells Associated with Adjuvant Immunotherapy–Induced Immune-Related Adverse Events in Melanoma
Authors: Monson Kelsey R. , Ferguson Robert , Handzlik Joanna E. , Xiong Jiahan , Dagayev Sasha , Morales Leah , Chat Vylyny , Bunis Anabelle , Sreenivasaiah Chaitra , Dolfi Sonia , Tenney Daniel J. , Shao Yongzhao , Osman Iman , Weber Jeffrey S. , Kirchhoff Tomas
Published: October 2024

Supplementary Figure S2. Top 10 Gene Ontology (GO) results for top DEGs (p < 0.05) comparing low/no irAEs to high irAEs.
Supplementary Table 4 from Colorectal Cancer Recurrence Prediction Using a Tissue-Free Epigenomic Minimal Residual Disease Assay
Authors: Nakamura Yoshiaki , Tsukada Yuichiro , Matsuhashi Nobuhisa , Murano Tatsuro , Shiozawa Manabu , Takahashi Yusuke , Oki Eiji , Goto Masahiro , Kagawa Yoshinori , Kanazawa Akiyoshi , Ohta Takashi , Ouchi Akira , Bando Hideaki , Uchigata Hiroshi , Notake Chiemi , Ikematsu Hiroaki , Yoshino Takayuki
Published: October 2024

Supplementary Table 4. Risk of recurrence based on ctDNA detection 28 days post-surgery for patients with stage II or higher CRC. Tables to accompany Figures 4B-D.
Supplementary Figure S1 from The Innate Immune Landscape of dMMR/MSI Cancers Predicts the Outcome of Nivolumab Treatment: Results from the Drug Rediscovery Protocol
Authors: Zeverijn Laurien J. , Geurts Birgit S. , Battaglia Thomas W. , van Berge Henegouwen Jade M. , de Wit Gijs F. , Hoes Louisa R. , van der Wijngaart Hanneke , van der Noort Vincent , Roepman Paul , de Leng Wendy W.J. , Jansen Anne M.L. , Chalabi Myriam , van Herpen Carla M.L. , Devriese Lot A. , Erdkamp Frans L.G. , Labots Mariette , de Jonge Maja J.A. , Kerver Emile D. , Bins Adriaan D. , Leek Lindsay V.M. , Notohardjo Jessica C.L. , van den Eertwegh Alfonsus J.M. , Wessels Lodewyk F.A. , Verheul Henk M.W. , Gelderblom Hans , van de Haar Joris , Voest Emile E.
Published: October 2024

Supplementary Figure S1. Accrual flowchart including reasons for ineligibility.
Supplementary Table S1 from FDA Approval Summary: Asciminib for Ph+ CML in Chronic Phase Treated with Two or More Tyrosine Kinase Inhibitors and for the T315I Mutation
Authors: Pamuk Gulsum E. , Chow Edwin C.Y. , Ionan Alexei C. , Chen Haiyan , Lee Shwu-Luan , Hsu Vicky , Grimstein Manuela , Zheng Nan , Sun Jielin , Charlab Rosane , Gehrke Brenda J. , Vallejo Jonathon , Ehrlich Lori A. , de Claro R. Angelo , Theoret Marc R.
Published: October 2024

Specific dose modification strategies for concomitant use of asciminib with other drug products
Supplementary Table S2 from Clinical Value of Liquid Biopsy in Patients with FGFR2 Fusion–Positive Cholangiocarcinoma During Targeted Therapy
Authors: González-Medina Alberto , Vila-Casadesús Maria , Gomez-Rey Marina , Fabregat-Franco Carles , Sierra Alexandre , Tian Tian V. , Castet Florian , Castillo Gloria , Matito Judit , Martinez Paola , Miquel Josep M. , Nuciforo Paolo , Pérez-López Raquel , Macarulla Teresa , Vivancos Ana
Published: October 2024

Supplementary Table S2. VAFs detected by the iCCA panel using commercial references (0.5% SeraSeq and 1% SeraSeq) at different coverage depths.
Supplementary Table S1 from Clinical Value of Liquid Biopsy in Patients with FGFR2 Fusion–Positive Cholangiocarcinoma During Targeted Therapy
Authors: González-Medina Alberto , Vila-Casadesús Maria , Gomez-Rey Marina , Fabregat-Franco Carles , Sierra Alexandre , Tian Tian V. , Castet Florian , Castillo Gloria , Matito Judit , Martinez Paola , Miquel Josep M. , Nuciforo Paolo , Pérez-López Raquel , Macarulla Teresa , Vivancos Ana
Published: October 2024

Supplementary Table S1. Covered regions for each capture-hybrid panel.
Supplementary Figure S5 from Clinical Value of Liquid Biopsy in Patients with FGFR2 Fusion–Positive Cholangiocarcinoma During Targeted Therapy
Authors: González-Medina Alberto , Vila-Casadesús Maria , Gomez-Rey Marina , Fabregat-Franco Carles , Sierra Alexandre , Tian Tian V. , Castet Florian , Castillo Gloria , Matito Judit , Martinez Paola , Miquel Josep M. , Nuciforo Paolo , Pérez-López Raquel , Macarulla Teresa , Vivancos Ana
Published: October 2024

Supplementary Figure S5. Coverage profiles for intron 17 and exon 18 of FGFR2 (patients 1–9).
Supplementary Figure S2 from Clinical Value of Liquid Biopsy in Patients with FGFR2 Fusion–Positive Cholangiocarcinoma During Targeted Therapy
Authors: González-Medina Alberto , Vila-Casadesús Maria , Gomez-Rey Marina , Fabregat-Franco Carles , Sierra Alexandre , Tian Tian V. , Castet Florian , Castillo Gloria , Matito Judit , Martinez Paola , Miquel Josep M. , Nuciforo Paolo , Pérez-López Raquel , Macarulla Teresa , Vivancos Ana
Published: October 2024

Supplementary Figure S2. Scheme of VHIO iCCA panel.
Table 3 from Elacestrant in ER+, HER2− Metastatic Breast Cancer with ESR1-Mutated Tumors: Subgroup Analyses from the Phase III EMERALD Trial by Prior Duration of Endocrine Therapy plus CDK4/6 Inhibitor and in Clinical Subgroups
Authors: Bardia Aditya , Cortés Javier , Bidard François-Clément , Neven Patrick , Garcia-Sáenz José , Aftimos Phillipe , O’Shaughnessy Joyce , Lu Janice , Tonini Giulia , Scartoni Simona , Paoli Alessandro , Binaschi Monica , Wasserman Tomer , Kaklamani Virginia
Published: October 2024

Most common AEs (≥10% in either arm) in the overall population (16).
Data from Targeting the Dendritic Cell-Secreted Immunoregulatory Cytokine CCL22 Alleviates Radioresistance
Authors: Bugno Jason , Wang Liangliang , Yu Xianbin , Cao Xuezhi , Wang Jiaai , Huang Xiaona , Yang Kaiting , Piffko Andras , Chen Katherine , Luo Stephen Y. , Naccasha Emile , Hou Yuzhu , Fu Sherry , He Chuan , Fu Yang-xin , Liang Hua L. , Weichselbaum Ralph R.
Published: October 2024

AbstractPurpose:
Radiation-mediated immune suppression limits efficacy and is a barrier in cancer therapy. Radiation induces negative regulators of tumor immunity including regulatory T cells (Treg). Mechanisms underlying Treg infiltration after radiotherapy (RT) are poorly defined. Given that conventional dendritic cells (cDC) maintain Treg, we sought to identify and target cDC signaling to block Treg infiltration after radiation.
Experimental Design:
Transcriptomics and high dimensional flow cytometry revealed changes in murine tumor cDC that not only mediate Treg infiltration after RT but also associate with worse survival in human cancer datasets. Antibodies perturbing a cDC-CCL22-Treg axis were tested in syngeneic murine tumors. A prototype interferon–anti-epidermal growth factor receptor fusion protein (αEGFR-IFNα) was examined to block Treg infiltration and promote a CD8+ T cell response after RT.
Results:
Radiation expands a population of mature cDC1 enriched in immunoregulatory markers that mediates Treg infiltration via the Treg-recruiting chemokine CCL22. Blocking CCL22 or Treg depletion both enhanced RT efficacy. αEGFR-IFNα blocked cDC1 CCL22 production while simultaneously inducing an antitumor CD8+ T cell response to enhance RT efficacy in multiple EGFR-expressing murine tumor models, including following systemic administration.
Conclusions:
We identify a previously unappreciated cDC mechanism mediating Treg tumor infiltration after RT. Our findings suggest blocking the cDC1-CCL22-Treg axis augments RT efficacy. αEGFR-IFNα added to RT provided robust antitumor responses better than systemic free interferon administration and may overcome clinical limitations to interferon therapy. Our findings highlight the complex behavior of cDC after RT and provide novel therapeutic strategies for overcoming RT-driven immunosuppression to improve RT efficacy.

See related commentary by Kalinski et al., p. 4260
Data from Cervical Cancer Evades the Host Immune System through the Inhibition of Type I Interferon and CXCL9 by LIF
Authors: Bonfill-Teixidor Ester , Neva-Alejo Almudena , Arias Alexandra , Cuartas Isabel , Iurlaro Raffaella , Planas-Rigol Ester , Solé Laura , Pecharromán Irene , Cabrera Silvia , García Ángel , Garcia-Illescas David , Espinosa Lluís , Gil-Moreno Antonio , Oaknin Ana , Seoane Joan
Published: October 2024

AbstractPurpose:
Cervical cancer is a viral-associated tumor caused by the infection with the human papilloma virus. Cervical cancer is an immunogenic cancer that expresses viral antigens. Despite being immunogenic, cervical cancer does not fully respond to immune checkpoint inhibitors (ICI). LIF is a crucial cytokine in embryo implantation, involved in maternal tolerance that acts as an immunomodulatory factor in cancer. LIF is expressed in cervical cancer and high levels of LIF is associated with poor prognosis in cervical cancer.
Experimental Design:
We evaluated the impact of LIF on the immune response to ICI using primary plasmocytoid dendritic cells (pDC) and macrophage cultures, syngeneic animals and patient-derived models that recapitulate the human tumor microenvironment.
Results:
We found that the viral proteins E6 and E7 induce the expression of LIF via the NFκB pathway. The secreted LIF can then repress type I interferon expressed in pDCs and CXCL9 expressed in tumor-associated macrophages. Blockade of LIF promotes the induction of type I interferon and CXCL9 inducing the tumor infiltration of CD8 T cells. This results in the sensitization of the tumor to ICI. Importantly, we observed that patients with cervical cancer expressing high levels of LIF tend to be resistant to ICI.
Conclusions:
Our data show that the HPV virus induces the expression of LIF to provide a selective advantage to the tumor cell by generating local immunosuppression via the repression of type I interferon and CXCL9. Combinatory treatment with blocking antibodies against LIF and ICI could be effective against cervical cancer expressing high levels of LIF.
Data from First-Line Anlotinib Treatment for Soft-Tissue Sarcoma in Chemotherapy-Ineligible Patients: An Open-Label, Single-Arm, Phase 2 Clinical Trial
Authors: Li Tao , Dong Ying , Wei Yongzhong , Wang Shoufeng , Liu Yunxia , Chen Jia , Xiong Wenhua , Lin Nong , Huang Xin , Liu Meng , Yan Xiaobo , Ye Zhaoming , Li Binghao
Published: October 2024

AbstractPurpose:
Standard treatment for patients with unresectable locally advanced or metastatic soft-tissue sarcoma (LA/M STS) is chemotherapy based on anthracyclines, but patient tolerance of chemotherapy is limited. The present trial (NCT03792542) investigated the use of anlotinib as first-line treatment for patients with advanced STS, in particular liposarcoma.
Patients and Methods:
Eligible patients were previously untreated, pathologically confirmed, unresectable LA/M STS cases. Anlotinib was given orally at a dose of 12 mg once daily from days 1 to 14 every 3 weeks until disease progression or intolerable adverse events (AE) occurred. The primary endpoint was progression-free survival (PFS), and the secondary endpoints were overall survival (OS), objective response rate, and disease control rate (DCR). The safety profile was also evaluated.
Results:
Forty patients were enrolled from April 2019 to June 2022 and are included in the intention-to-treat analysis. The median PFS was 6.83 months [95% confidence interval (CI), 4.17–8.71] and the median OS 27.40 months (95% CI, 16.43–not evaluable); 1 patient reached partial response and 26 attained stable disease, with a DCR of 67.5% (27/40). Median PFS and OS times for liposarcoma patients were 8.71 and 16.23 months, respectively. Ten (25.0%) patients had treatment-related AEs ≥ grade 3, with in particular a higher incidence of hypertension (15.0%) and proteinuria (7.5%).
Conclusions:
The findings suggest a potential benefit in using front-line anlotinib to treat patients with STS, who are not eligible for cytotoxic chemotherapy. Of note, the clinical outcomes for the liposarcoma subgroup of patients were encouraging.

See related commentary by Napolitano et al., p. 4257
Data from Abiraterone, Olaparib, or Abiraterone + Olaparib in First-Line Metastatic Castration-Resistant Prostate Cancer with DNA Repair Defects (BRCAAway)
Authors: Hussain Maha , Kocherginsky Masha , Agarwal Neeraj , Adra Nabil , Zhang Jingsong , Paller Channing J. , Picus Joel , Reichert Zachery R. , Szmulewitz Russell Z. , Tagawa Scott T. , Kuzel Timothy M. , Bazzi Latifa A. , Daignault-Newton Stephanie , Whang Young E. , Dreicer Robert , Stephenson Ryan D. , Rettig Matthew B. , Shevrin Daniel , Gerke Travis , Chinnaiyan Arul M. , Antonarakis Emmanuel S.
Published: October 2024

AbstractPurpose:
Deleterious germline/somatic homologous recombination repair mutations (HRRm) are present in ∼25% of patients with metastatic castration-resistant prostate cancer (mCRPC). Preclinically, poly(ADP-ribose) polymerase (PARP) inhibition demonstrated synergism with androgen receptor pathway (ARP)–targeted therapy. This trial evaluated the efficacy of ARP inhibitor versus PARP inhibitor versus their combination as first-line therapy in patients with mCRPC with HRRms.
Patients and Methods:
BRCAAway is a biomarker preselected, randomized, phase 2 trial. Patients with BRCA1/2 and/or ATM alterations were randomized 1:1:1 to Arm1: abiraterone (1,000 mg)/prednisone (5 mg BID) (Abi/pred), Arm2: olaparib (300 mg BID) (Ola), or Arm3: abiraterone/prednisone + olaparib (Abi/pred + Ola). Single-agent arms could cross over at progression. Exploratory Arm4 patients with other HRRms received olaparib alone. The primary endpoint was progression-free survival (PFS), and secondary endpoints were objective response, PSA response, and safety.
Results:
Sixty-one of 165 eligible patients had BRCA1/2 or ATM mutations: median age: 67 (IQR, 62–73) years. Mutations: BRCA1 n = 3, BRCA2 n = 46, ATM n = 11, and multiple n = 1; 33 germline and 28 somatic mutations. Median PFS [95% confidence interval (CI)]: Abi/pred, 8.6 months (m; 2.9, 17), Ola, 14 m (8.4, 20), and Abi/pred + Ola, 39 m [22, not reached (NR)]. There were no G4/5 adverse events; 8/19 patients on Abi/pred treatment crossed over to Ola, and 8/21 vice versa. Median PFS (95% CI) from crossover: Ola-after-Abi/pred, 8.3 m (5.5, 15) and Abi/pred-after-Ola, 7.2 m (2.8, NR). Median PFS (95% CI) from randomization: Ola-after-Abi/pred, 16 m (7.8, 25) and Abi/pred-after-Ola, 16 m (11, NR). Seventeen of 165 patients with other HRRms received olaparib: median PFS (95% CI): 5.5 m (2, 11).
Conclusions:
In patients with mCRPC with BRCA1/2 or ATM HRRm, Abi/pred + Ola was well tolerated and demonstrated longer PFS versus either agent alone or sequentially.
Data from The Innate Immune Landscape of dMMR/MSI Cancers Predicts the Outcome of Nivolumab Treatment: Results from the Drug Rediscovery Protocol
Authors: Zeverijn Laurien J. , Geurts Birgit S. , Battaglia Thomas W. , van Berge Henegouwen Jade M. , de Wit Gijs F. , Hoes Louisa R. , van der Wijngaart Hanneke , van der Noort Vincent , Roepman Paul , de Leng Wendy W.J. , Jansen Anne M.L. , Chalabi Myriam , van Herpen Carla M.L. , Devriese Lot A. , Erdkamp Frans L.G. , Labots Mariette , de Jonge Maja J.A. , Kerver Emile D. , Bins Adriaan D. , Leek Lindsay V.M. , Notohardjo Jessica C.L. , van den Eertwegh Alfonsus J.M. , Wessels Lodewyk F.A. , Verheul Henk M.W. , Gelderblom Hans , van de Haar Joris , Voest Emile E.
Published: October 2024

AbstractPurpose:
The treatment efficacy of nivolumab was evaluated in patients with advanced, treatment-refractory solid mismatch repair deficiency/microsatellite-instable (dMMR/MSI) tumors, and in-depth biomarker analyses were performed to inform precision immunotherapy approaches.
Patients and Methods:
Patients with dMMR/MSI tumors who exhausted standard-of-care treatment options were enrolled in the Drug Rediscovery Protocol, a pan-cancer clinical trial that treats patients with cancer based on their tumor molecular profile with off-label anticancer drugs (NCT02925234). Patients received nivolumab (four cycles of 240 mg every 2 weeks, thereafter 480 mg every 4 weeks). The primary endpoint was clinical benefit (CB: objective response or stable disease ≥16 weeks). Whole-genome sequencing and RNA sequencing were performed on pretreatment tumor biopsies.
Results:
A total of 130 evaluable patients were enrolled with 16 different cancer types. CB was observed in 62% [95% confidence interval (CI), 53–70], with an objective response in 45% (95% CI, 36–54). After a median follow-up of 14.5 months (95% CI, 13–19), the median progression-free survival was 18 months (95% CI, 9–not reached), and the median overall survival was not reached. Whereas CB was not, or only weakly, associated with markers of adaptive immune cell infiltration, CB was strongly associated with expression of a broad set of innate immune receptors/ligands. This clearly contrasted findings in melanoma, in which markers of adaptive immunity dominated the biomarker landscape.
Conclusions:
Nivolumab proved highly effective in advanced dMMR/MSI tumors. Expression of key innate immune receptors/ligands was the main predictor of a good treatment outcome, contrasting findings in melanoma and strengthening the rationale for tumor type–specific biomarkers for guiding immunotherapy.
Supplementary Figure S4 from Anti-Claudin-2 Antibody–Drug Conjugates for the Treatment of Colorectal Cancer Liver Metastasis
Authors: Tabariès Sébastien , Robert Alma , Marcil Anne , Ling Binbing , Acchione Mauro , Lippens Julie , Pagé Martine , Fortin Annie , Meury Luc , Coutu Mathieu , Annis Matthew G. , Girondel Charlotte , Navarre Julie , Jaramillo Maria , Moraitis Anna N. , Siegel Peter M.
Published: October 2024

Supplementary Figure S4
Supplementary Figure S3 from Anti-Claudin-2 Antibody–Drug Conjugates for the Treatment of Colorectal Cancer Liver Metastasis
Authors: Tabariès Sébastien , Robert Alma , Marcil Anne , Ling Binbing , Acchione Mauro , Lippens Julie , Pagé Martine , Fortin Annie , Meury Luc , Coutu Mathieu , Annis Matthew G. , Girondel Charlotte , Navarre Julie , Jaramillo Maria , Moraitis Anna N. , Siegel Peter M.
Published: October 2024

Supplementary Figure S3
Figure S11 from Characterization of AB598, a CD39 Enzymatic Inhibitory Antibody for the Treatment of Solid Tumors
Authors: Anderson Amy E. , Parashar Kaustubh , Jin Ke , Clor Julie , Stagnaro Carlo E. , Vani Urvi , Singh Jaskirat , Chen Ada , Guan Yihong , Talukdar Priyanka , Sathishkumar Pavithra , Juat Damie J. , Singh Hema , Kushwaha Ritu , Zhao Xiaoning , Kaplan Angelo , Seitz Lisa , Walters Matthew J. , Fernandez-Salas Ester , Walker Nigel P.C. , Bowman Christine E.
Published: October 2024

Figure S11
Figure S10 from Characterization of AB598, a CD39 Enzymatic Inhibitory Antibody for the Treatment of Solid Tumors
Authors: Anderson Amy E. , Parashar Kaustubh , Jin Ke , Clor Julie , Stagnaro Carlo E. , Vani Urvi , Singh Jaskirat , Chen Ada , Guan Yihong , Talukdar Priyanka , Sathishkumar Pavithra , Juat Damie J. , Singh Hema , Kushwaha Ritu , Zhao Xiaoning , Kaplan Angelo , Seitz Lisa , Walters Matthew J. , Fernandez-Salas Ester , Walker Nigel P.C. , Bowman Christine E.
Published: October 2024

Figure S10
Table S6 from PKMYT1 Is a Marker of Treatment Response and a Therapeutic Target for CDK4/6 Inhibitor-Resistance in ER+ Breast Cancer
Authors: Chen Anran , Kim Beom-Jun , Mitra Aparna , Vollert Craig T. , Lei Jonathan T. , Fandino Diana , Anurag Meenakshi , Holt Matthew V. , Gou Xuxu , Pilcher Jacob B. , Goetz Matthew P. , Northfelt Donald W. , Hilsenbeck Susan G. , Marshall C. Gary , Hyer Marc L. , Papp Robert , Yin Shou-Yun , De Angelis Carmine , Schiff Rachel , Fuqua Suzanne A.W. , Ma Cynthia X. , Foulds Charles E. , Ellis Matthew J.
Published: October 2024

Converted Free Plasma Level of RP-6306 in treated BCM-7441 PDX mice
Table S5 from PKMYT1 Is a Marker of Treatment Response and a Therapeutic Target for CDK4/6 Inhibitor-Resistance in ER+ Breast Cancer
Authors: Chen Anran , Kim Beom-Jun , Mitra Aparna , Vollert Craig T. , Lei Jonathan T. , Fandino Diana , Anurag Meenakshi , Holt Matthew V. , Gou Xuxu , Pilcher Jacob B. , Goetz Matthew P. , Northfelt Donald W. , Hilsenbeck Susan G. , Marshall C. Gary , Hyer Marc L. , Papp Robert , Yin Shou-Yun , De Angelis Carmine , Schiff Rachel , Fuqua Suzanne A.W. , Ma Cynthia X. , Foulds Charles E. , Ellis Matthew J.
Published: October 2024

Statistical analyses of data in Figures 6B, 6C, and S3.
Table S3 from PKMYT1 Is a Marker of Treatment Response and a Therapeutic Target for CDK4/6 Inhibitor-Resistance in ER+ Breast Cancer
Authors: Chen Anran , Kim Beom-Jun , Mitra Aparna , Vollert Craig T. , Lei Jonathan T. , Fandino Diana , Anurag Meenakshi , Holt Matthew V. , Gou Xuxu , Pilcher Jacob B. , Goetz Matthew P. , Northfelt Donald W. , Hilsenbeck Susan G. , Marshall C. Gary , Hyer Marc L. , Papp Robert , Yin Shou-Yun , De Angelis Carmine , Schiff Rachel , Fuqua Suzanne A.W. , Ma Cynthia X. , Foulds Charles E. , Ellis Matthew J.
Published: October 2024

Hallmark pathways enriched in ER+ PDX tumors
Table S2 from PKMYT1 Is a Marker of Treatment Response and a Therapeutic Target for CDK4/6 Inhibitor-Resistance in ER+ Breast Cancer
Authors: Chen Anran , Kim Beom-Jun , Mitra Aparna , Vollert Craig T. , Lei Jonathan T. , Fandino Diana , Anurag Meenakshi , Holt Matthew V. , Gou Xuxu , Pilcher Jacob B. , Goetz Matthew P. , Northfelt Donald W. , Hilsenbeck Susan G. , Marshall C. Gary , Hyer Marc L. , Papp Robert , Yin Shou-Yun , De Angelis Carmine , Schiff Rachel , Fuqua Suzanne A.W. , Ma Cynthia X. , Foulds Charles E. , Ellis Matthew J.
Published: October 2024

Analysis of E2-regulated genes located on chromosome 16 near ERα ChIP peaks in MCF7 cells from The Signaling Pathways Project
Figures S1 through S19 from PKMYT1 Is a Marker of Treatment Response and a Therapeutic Target for CDK4/6 Inhibitor-Resistance in ER+ Breast Cancer
Authors: Chen Anran , Kim Beom-Jun , Mitra Aparna , Vollert Craig T. , Lei Jonathan T. , Fandino Diana , Anurag Meenakshi , Holt Matthew V. , Gou Xuxu , Pilcher Jacob B. , Goetz Matthew P. , Northfelt Donald W. , Hilsenbeck Susan G. , Marshall C. Gary , Hyer Marc L. , Papp Robert , Yin Shou-Yun , De Angelis Carmine , Schiff Rachel , Fuqua Suzanne A.W. , Ma Cynthia X. , Foulds Charles E. , Ellis Matthew J.
Published: October 2024

This file contains 19 Supplementary Figures.
Figure S1 from FZ-AD005, a Novel DLL3-Targeted Antibody–Drug Conjugate with Topoisomerase I Inhibitor, Shows Potent Antitumor Activity in Preclinical Models
Authors: Guo Qingsong , Gao Bei , Song Ruiwen , Li Weinan , Zhu Shulei , Xie Qian , Lou Sensen , Wang Lei , Shen Jiafei , Zhao Teng , Zhang Yifan , Wu Jinsong , Lu Wei , Yang Tong
Published: October 2024

Supplementary Fig.S1
Figure S12 from PKMYT1 Is a Marker of Treatment Response and a Therapeutic Target for CDK4/6 Inhibitor-Resistance in ER+ Breast Cancer
Authors: Chen Anran , Kim Beom-Jun , Mitra Aparna , Vollert Craig T. , Lei Jonathan T. , Fandino Diana , Anurag Meenakshi , Holt Matthew V. , Gou Xuxu , Pilcher Jacob B. , Goetz Matthew P. , Northfelt Donald W. , Hilsenbeck Susan G. , Marshall C. Gary , Hyer Marc L. , Papp Robert , Yin Shou-Yun , De Angelis Carmine , Schiff Rachel , Fuqua Suzanne A.W. , Ma Cynthia X. , Foulds Charles E. , Ellis Matthew J.
Published: October 2024

Synergy and viability analysis of AZD1775 and gemcitabine combination in T47D parental and Palbo-R cells
Figure S11 from PKMYT1 Is a Marker of Treatment Response and a Therapeutic Target for CDK4/6 Inhibitor-Resistance in ER+ Breast Cancer
Authors: Chen Anran , Kim Beom-Jun , Mitra Aparna , Vollert Craig T. , Lei Jonathan T. , Fandino Diana , Anurag Meenakshi , Holt Matthew V. , Gou Xuxu , Pilcher Jacob B. , Goetz Matthew P. , Northfelt Donald W. , Hilsenbeck Susan G. , Marshall C. Gary , Hyer Marc L. , Papp Robert , Yin Shou-Yun , De Angelis Carmine , Schiff Rachel , Fuqua Suzanne A.W. , Ma Cynthia X. , Foulds Charles E. , Ellis Matthew J.
Published: October 2024

RP-6306 treatment did not restore the sensitivity of T47D Palbo-R cells to palbociclib
Figure S10 from PKMYT1 Is a Marker of Treatment Response and a Therapeutic Target for CDK4/6 Inhibitor-Resistance in ER+ Breast Cancer
Authors: Chen Anran , Kim Beom-Jun , Mitra Aparna , Vollert Craig T. , Lei Jonathan T. , Fandino Diana , Anurag Meenakshi , Holt Matthew V. , Gou Xuxu , Pilcher Jacob B. , Goetz Matthew P. , Northfelt Donald W. , Hilsenbeck Susan G. , Marshall C. Gary , Hyer Marc L. , Papp Robert , Yin Shou-Yun , De Angelis Carmine , Schiff Rachel , Fuqua Suzanne A.W. , Ma Cynthia X. , Foulds Charles E. , Ellis Matthew J.
Published: October 2024

PKMYT1 mRNA significantly correlates with Ki67 mRNA in Luminal A and B breast cancer samples from the METABRIC cohort
Supplementary Table S4 from Blocking M2-Like Macrophage Polarization Using Decoy Oligodeoxynucleotide-Based Gene Therapy Prevents Immune Evasion for Pancreatic Cancer Treatment
Authors: Chen Chang-Jung , Wang Hao-Chen , Hou Ya-Chin , Wu Yi-Ying , Shieh Chi-Chang , Shan Yan-Shen
Published: October 2024

Supplementary Table S4. Clinical parameters of pancreatic cancer patients in TMAs
Supplementary Table S1 from Blocking M2-Like Macrophage Polarization Using Decoy Oligodeoxynucleotide-Based Gene Therapy Prevents Immune Evasion for Pancreatic Cancer Treatment
Authors: Chen Chang-Jung , Wang Hao-Chen , Hou Ya-Chin , Wu Yi-Ying , Shieh Chi-Chang , Shan Yan-Shen
Published: October 2024

Supplementary Table S1. List of antibodies used in this study
Supplementary Figure S9 from Blocking M2-Like Macrophage Polarization Using Decoy Oligodeoxynucleotide-Based Gene Therapy Prevents Immune Evasion for Pancreatic Cancer Treatment
Authors: Chen Chang-Jung , Wang Hao-Chen , Hou Ya-Chin , Wu Yi-Ying , Shieh Chi-Chang , Shan Yan-Shen
Published: October 2024

Supplementary Figure S9. Knocking down STAT6 or HDAC2 in U937 cells prevents pancreatic cancer cells co-culture-induced CYBB downregulation. A, B, and C, RT-qPCR analysis for M1/M2 markers and CYBB in shSTAT6 or shHDAC2 U937 cells co-cultured with PANC-1 cells for 72h. The bar graphs depict relative mRNA expression. ***, p < 0.001, significant differences between groups. Data represent the mean of 3 independent experiments. D, shSTAT6 or shHDAC2 U937 cells were co-cultured with PANC-1 cells for 72h. Cell lysates were subjected to Western blotting for indicated proteins. GAPDH was used as a loading control. The bar graph depicts the ratio of CYBB/GAPDH. **, p < 0.01; ***, p < 0.001, compared with the group without co-culture. Data represent the mean of 3 independent experiments.
Supplementary Figure S3 from Discovery of Monovalent Direct Degraders of BRD4 that Act via the Recruitment of DCAF11
Authors: Parker Gregory S. , Toth Julia I. , Fish Sarah , Blanco Gabrielle , Kampert Taylor , Li Xiaoming , Yang Linette , Stumpf Craig R. , Steadman Kenneth , Jamborcic Aleksandar , Chien Stephen , Daniele Elizabeth , Dearie Alejandro , Leriche Geoffray , Bailey Simon , Thompson Peggy A.
Published: October 2024

Supplementary Figure S3 shows megakaryocyte colony formation data
Supplementary Data from Discovery of Monovalent Direct Degraders of BRD4 that Act via the Recruitment of DCAF11
Authors: Parker Gregory S. , Toth Julia I. , Fish Sarah , Blanco Gabrielle , Kampert Taylor , Li Xiaoming , Yang Linette , Stumpf Craig R. , Steadman Kenneth , Jamborcic Aleksandar , Chien Stephen , Daniele Elizabeth , Dearie Alejandro , Leriche Geoffray , Bailey Simon , Thompson Peggy A.
Published: October 2024

Supplementary file containing Figures S1-3 and Tables S1-4
Supplementary Materials and Methods from The SOS1 Inhibitor MRTX0902 Blocks KRAS Activation and Demonstrates Antitumor Activity in Cancers Dependent on KRAS Nucleotide Loading
Authors: Sudhakar Niranjan , Yan Larry , Qiryaqos Fadia , Engstrom Lars D. , Laguer Jade , Calinisan Andrew , Hebbert Allan , Waters Laura , Moya Krystal , Bowcut Vickie , Vegar Laura , Ketcham John M. , Ivetac Anthony , Smith Christopher R. , Lawson J. David , Rahbaek Lisa , Clarine Jeffrey , Nguyen Natalie , Saechao Barbara , Parker Cody , Elliott Adam J. , Vanderpool Darin , He Leo , Hover Laura D. , Fernandez-Banet Julio , Coma Silvia , Pachter Jonathan A. , Hallin Jill , Marx Matthew A. , Briere David M. , Christensen James G. , Olson Peter , Haling Jacob , Khare Shilpi
Published: October 2024

Supplementary Materials and Methods section includes detailed protocols for the following: Experimental Preparation of MRTX0902 and Avutometinib, SOS1 Biochemical Binding Assay, SOS1 and SOS2 Functional Assays, KRAS-SOS1 Protein-Protiein Interaction (PPI) HTRF Assay, In-Cell Western Assay, 3D Ultra-Low Attachment (ULA) Viability Assay, Immunoblotting and Densitometry Analysis, DUSP6 Quantification from Naive and Tumor-Bearing Mouse Blood, Bioanalysis and Pharmacokinetic Analysis, Synergy Analysis, CRISPR/Cas9 Screening and Data Analysis Methodology, RNAseq Pre-Processing, RNAseq Data Analysis, and Whole Genome Sequencing.
Supplementary Figure S3 from The SOS1 Inhibitor MRTX0902 Blocks KRAS Activation and Demonstrates Antitumor Activity in Cancers Dependent on KRAS Nucleotide Loading
Authors: Sudhakar Niranjan , Yan Larry , Qiryaqos Fadia , Engstrom Lars D. , Laguer Jade , Calinisan Andrew , Hebbert Allan , Waters Laura , Moya Krystal , Bowcut Vickie , Vegar Laura , Ketcham John M. , Ivetac Anthony , Smith Christopher R. , Lawson J. David , Rahbaek Lisa , Clarine Jeffrey , Nguyen Natalie , Saechao Barbara , Parker Cody , Elliott Adam J. , Vanderpool Darin , He Leo , Hover Laura D. , Fernandez-Banet Julio , Coma Silvia , Pachter Jonathan A. , Hallin Jill , Marx Matthew A. , Briere David M. , Christensen James G. , Olson Peter , Haling Jacob , Khare Shilpi
Published: October 2024

Supplementary Figure S3 details the antitumor effects and gene set enrichment analysis data associated with coadministration of MRTX0902 and adagrasib in KRAS G12C-mutant human tumor xenograft models.
Supplementary Table S1 from Cancer History and Social Support Impact Colorectal Cancer Screening Utilization by Race/Ethnicity
Authors: Tsai Meng-Han , Lee Minjee , Coughlin Steven S. , Eberth Jan M. , Rogers Charles R.
Published: October 2024

Supplementary Table S1 showed the characteristics of excluding and including participants
Figure S5 from NK Receptor Signaling Lowers TCR Activation Threshold, Enhancing Selective Recognition of Cancer Cells by TAA-Specific CTLs
Authors: Dong Bowen , Obermajer Nataša , Tsuji Takemasa , Matsuzaki Junko , Bonura Cindy M. , Sander Cindy , Withers Henry , Long Mark D. , Chavel Colin , Olejniczak Scott H. , Minderman Hans , Kirkwood John M. , Edwards Robert P. , Storkus Walter J. , Romero Pedro , Kalinski Pawel
Published: October 2024

Human peripheral blood CD8+ T cells require NKR-mediated co-stimulation for optimal effector response to weak TCR stimulation.
Figure S6 from Atypical B Cells Promote Cancer Progression and Poor Response to Bacillus Calmette-Guérin in Non–Muscle Invasive Bladder Cancer
Authors: Yolmo Priyanka , Rahimi Sadaf , Chenard Stephen , Conseil Gwenaëlle , Jenkins Danielle , Sachdeva Kartik , Emon Isaac , Hamilton Jake , Xu Minqi , Rangachari Manu , Michaud Eva , Mansure Jose J. , Kassouf Wassim , Berman David M. , Siemens David R. , Koti Madhuri
Published: October 2024

Splenic ABC expansion is enhanced by a combination of BBN exposure and BCG treatment.
Figure S1 from Atypical B Cells Promote Cancer Progression and Poor Response to Bacillus Calmette-Guérin in Non–Muscle Invasive Bladder Cancer
Authors: Yolmo Priyanka , Rahimi Sadaf , Chenard Stephen , Conseil Gwenaëlle , Jenkins Danielle , Sachdeva Kartik , Emon Isaac , Hamilton Jake , Xu Minqi , Rangachari Manu , Michaud Eva , Mansure Jose J. , Kassouf Wassim , Berman David M. , Siemens David R. , Koti Madhuri
Published: October 2024

Gating strategy for identifying atypical B cells (ABCs) and myeloid cell population.
Supplemental Table S6 from Machine Learning–Directed Conversion of Glioblastoma Cells to Dendritic Cell–Like Antigen-Presenting Cells as Cancer Immunotherapy
Authors: Liu Tianyi , Jin Dan , Le Son B. , Chen Dongjiang , Sebastian Mathew , Riva Alberto , Liu Ruixuan , Tran David D.
Published: October 2024

All 2882 nSCORE validation configurations and all Datasets Used (Supporting the Materials and Methods Section)
Figure S5 from RNA-encoded Interleukin 2 with Extended Bioavailability Amplifies RNA Vaccine–Induced Antitumor T-cell Immunity
Authors: Peters Daniel , Kranz Lena M. , Eisel David , Diken Mustafa , Kreiter Sebastian , Türeci Özlem , Sahin Ugur , Vormehr Mathias
Published: October 2024

Gating strategy for antigen-specific CD8+ T cells and Tregs in the blood.
Supplemental Table S16 from Machine Learning–Directed Conversion of Glioblastoma Cells to Dendritic Cell–Like Antigen-Presenting Cells as Cancer Immunotherapy
Authors: Liu Tianyi , Jin Dan , Le Son B. , Chen Dongjiang , Sebastian Mathew , Riva Alberto , Liu Ruixuan , Tran David D.
Published: October 2024

Epitope prediction using NetMHC 4.0 of the 4 vector cassettes to express CFDs in the murine GBM → iDC-APC conversion (Supporting Main Figure 1)
Supplemental Table S11 from Machine Learning–Directed Conversion of Glioblastoma Cells to Dendritic Cell–Like Antigen-Presenting Cells as Cancer Immunotherapy
Authors: Liu Tianyi , Jin Dan , Le Son B. , Chen Dongjiang , Sebastian Mathew , Riva Alberto , Liu Ruixuan , Tran David D.
Published: October 2024

Bulk RNA-seq characteristics of the 3 LN GBM cell lines and human monocyte-derived DC for the human GBM ➝ iDC-APC conversion (Supporting Main Figure 7)
Supplemental Figure S6 from Machine Learning–Directed Conversion of Glioblastoma Cells to Dendritic Cell–Like Antigen-Presenting Cells as Cancer Immunotherapy
Authors: Liu Tianyi , Jin Dan , Le Son B. , Chen Dongjiang , Sebastian Mathew , Riva Alberto , Liu Ruixuan , Tran David D.
Published: October 2024

Expression of cDC1 markers in iDC-APCs (Supporting Main Figure 1D)
Supplemental Figure S16 from Machine Learning–Directed Conversion of Glioblastoma Cells to Dendritic Cell–Like Antigen-Presenting Cells as Cancer Immunotherapy
Authors: Liu Tianyi , Jin Dan , Le Son B. , Chen Dongjiang , Sebastian Mathew , Riva Alberto , Liu Ruixuan , Tran David D.
Published: October 2024

The human equivalences of dP-mF3 (both hP-hF3 or dhP-hF3) did not consistently produce human iDC-APCs. (Supporting Main Figure 7)
Supplemental Figure S12 from Machine Learning–Directed Conversion of Glioblastoma Cells to Dendritic Cell–Like Antigen-Presenting Cells as Cancer Immunotherapy
Authors: Liu Tianyi , Jin Dan , Le Son B. , Chen Dongjiang , Sebastian Mathew , Riva Alberto , Liu Ruixuan , Tran David D.
Published: October 2024

Phagocytic capacity of reprogrammed KR158 and GL261 GBM cells (Supporting Main Figure 3A)
Supplementary Table 2 from Intermittent MEK Inhibition with GITR Costimulation Rescues T-cell Function for Increased Efficacy with CTLA-4 Blockade in Solid Tumor Models
Authors: Dong Lauren , Choi Hyejin , Budhu Sadna , Schulze Isabell , Verma Svena , Mangarin Levi M. , Estrada Nevarro Valeria , Mehanna Nezar , Khan Jonathan F. , Venkatesh Divya , Thach Daniel , Rosen Neal , Wolchok Jedd D. , Merghoub Taha
Published: October 2024

Supplementary Table 2. Gene list associated with each cluster.
Supplementary Table 1 from Intermittent MEK Inhibition with GITR Costimulation Rescues T-cell Function for Increased Efficacy with CTLA-4 Blockade in Solid Tumor Models
Authors: Dong Lauren , Choi Hyejin , Budhu Sadna , Schulze Isabell , Verma Svena , Mangarin Levi M. , Estrada Nevarro Valeria , Mehanna Nezar , Khan Jonathan F. , Venkatesh Divya , Thach Daniel , Rosen Neal , Wolchok Jedd D. , Merghoub Taha
Published: October 2024

Supplementary Table 1. Flow cytometry antibody details:
Figure S3 from Hypoxia-Induced Long Noncoding RNA HIF1A-AS2 Regulates Stability of MHC Class I Protein in Head and Neck Cancer
Authors: Liao Tsai-Tsen , Chen Yu-Hsien , Li Zih-Yu , Hsiao An-Ching , Huang Ya-Li , Hao Ruo-Xin , Tai Shyh-Kuan , Chu Pen-Yuan , Shih Jing-Wen , Kung Hsing-Jien , Yang Muh-Hwa
Published: October 2024

HIF1A-AS2 does not influence the characteristics of HNSCC cells.
Figure S2 from Hypoxia-Induced Long Noncoding RNA HIF1A-AS2 Regulates Stability of MHC Class I Protein in Head and Neck Cancer
Authors: Liao Tsai-Tsen , Chen Yu-Hsien , Li Zih-Yu , Hsiao An-Ching , Huang Ya-Li , Hao Ruo-Xin , Tai Shyh-Kuan , Chu Pen-Yuan , Shih Jing-Wen , Kung Hsing-Jien , Yang Muh-Hwa
Published: October 2024

The experimental replicates of ChIP assays.
Supplementary Figure 11 from Intermittent MEK Inhibition with GITR Costimulation Rescues T-cell Function for Increased Efficacy with CTLA-4 Blockade in Solid Tumor Models
Authors: Dong Lauren , Choi Hyejin , Budhu Sadna , Schulze Isabell , Verma Svena , Mangarin Levi M. , Estrada Nevarro Valeria , Mehanna Nezar , Khan Jonathan F. , Venkatesh Divya , Thach Daniel , Rosen Neal , Wolchok Jedd D. , Merghoub Taha
Published: October 2024

Supplemental Figure 11. The triple combination increases activation of CD8+ T cells and CD4+ Teffs while Tregs remain unaffected in LLC TDLN. (A) Schema of LLC tumor bearing mice treated with vehicle, CKI27, isotypes, GITR, and/or CTLA-4. All timepoints were harvested on day 21 (7 days post treatment). (B) Image of TDLNs from LLC tumor bearing mice. (C) Gating strategy for all in vivo flow experiments. (D) Absolute number of immune cell populations in the TDLN; n=4-5. (E) Phenotypes of T cells from the TDLN; n=9-10. Data are shown as mean±SEM. One-way ANOVA test with Bonferroni’s correction for multiple comparisons was used in all panels. Significance levels are indicated by asterisks (*p ≤ 0.05; **p ≤ 0.01; ***p ≤ 0.001; ****p ≤ 0.0001).
Supplemental Figure 1 from Augmenting CAR T-cell Functions with LIGHT
Authors: Cai Winson , Tanaka Kento , Mi Xiaoli , Rajasekhar Vinagolu K. , Khan Jonathan F. , Yoo Sarah , de Stanchina Elisa , Rahman Jahan , Mathew Serena , Abrahimi Parwiz , Souness Sydney , Purdon Terence J. , McDowell James R. , Meyerberg Jeremy , Fujino Takeshi , Healey John H. , Abdel-Wahab Omar , Scheinberg David A. , Brentjens Renier J. , Daniyan Anthony F.
Published: October 2024

(A) Transgene expression of the CAR constructs after retroviral transduction of human T cells by flow cytometry. CD19 CAR T cells were used as irrelevant CAR T cell control. (B-D) Healthy human donor-derived mesothelin-targeted CAR T cells were cocultured with tumor cells expressing GFP and firefly luciferase at different effector to tumor ratios. Bioluminescence was measured 72 hours later and plotted as a percentage of the signal detected with tumor cells alone (max bioluminescence signal). Associated expression of mesothelin with the corresponding mesothelin-positive cell lines are shown. JMN (left), SW620 (middle), and MDA-MB-231 (right). Plots represent 3 independent experiments. Data errors were analyzed with mean ± SEM. (E) HVEM expression in PDAC cell lines (CAPAN2, AsPC1, BxPC3, Panc1) (F) Flow cytometric analysis of overexpression constructs derived from Panc1 wildtype. Panc1 Mesothelin overexpression, Panc1 LTβR overexpression, and Panc1 Mesothelin and LTβR Overexpression
Supplementary Table 1 from The E3 Ubiquitin Ligase FBXO38 Maintains the Antitumor Function of Natural Killer Cells by Sustaining IL15R Signaling
Authors: Shi Yongjing , Zheng Xiaodong , Peng Hui , Xu Chenqi , Sun Rui , Tian Zhigang , Sun Haoyu , Wang Xianwei
Published: October 2024

Supplemental Table 1. Antibodies used for flow cytometry in this study
Supplementary Figure S2 from MR1 Gene and Protein Expression Are Enhanced by Inhibition of the Extracellular Signal-Regulated Kinase ERK
Authors: Constantin Daniel , Nosi Vladimir , Kehrer Natalie , Vacchini Alessandro , Chancellor Andrew , Contassot Emmanuel , Beshirova Aisha , Prota Gennaro , Navarini Alexander , Mori Lucia , De Libero Gennaro
Published: October 2024

Supplementary Figure S2