bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figure S5 from Discovery of a Long Half-Life AURKA Inhibitor to Treat MYC-Amplified Solid Tumors as a Monotherapy and in Combination with Everolimus
Authors: Chang Chun-Ping , Yeh Teng-Kuang , Chen Chiung-Tong , Wang Wan-Ping , Chen Yen-Ting , Tsai Chia-Hua , Chen Yan-Fu , Ke Yi-Yu , Wang Jing-Ya , Chen Ching-Ping , Hsieh Tsung-Chih , Wu Mine-Hsine , Huang Chen-Lung , Chen Ya-Ping , Zhuang Hong , Chi Ya-Hui
Published: June 2024

Supplementary Figure S5. DBPR728 is efficacious in multiple c-MYC overexpressing preclinical tumor models. (A) Growth curve of NCI-H446 xenografts in NU/NU mice dosed with vehicle (10 ml/kg, 5W) or alisertib (50 mg/kg, 5W) for two weeks. The vehicle control is the same as the one in Fig. 3D. Amp, amplified. (B) Summary of preclinical tumor models used for DBPR728 and alisertib treatment. (C) Comparison of treatment efficacy between DBPR728 and alisertib in D341 (medulloblastoma, c-MYC amplified), SNU-398 (HCC, c-MYC overexpression) and PSN-1 (pancreatic cancer, c-MYC amplified) preclinical mouse models. OE, overexpression. (A, C) Errors are mean ± SEM.
Supplementary Figure 1 from Patient-Derived Tumor Xenograft Study with CDK4/6 Inhibitor Plus AKT Inhibitor for the Management of Metastatic Castration-Resistant Prostate Cancer
Authors: Kase Adam M. , Gleba Justyna , Miller James L. , Miller Erin , Petit Joachim , Barrett Michael T. , Zhou Yumei , Parent Ephraim E. , Cai Hancheng , Knight Joshua A. , Orme Jacob , Reynolds Jordan , Durham William F. , Metz Thomas M. , Meurice Nathalie , Edenfield Brandy , Alasonyalilar Demirer Aylin , Bilgili Ahmet , Hickman Peyton G. , Pawlush Matthew L. , Marlow Laura , Wickland Daniel P. , Tan Winston , Copland John A.
Published: June 2024

Supplementary Figure 1
Supplementary Figure S3 from Discovery of a Long Half-Life AURKA Inhibitor to Treat MYC-Amplified Solid Tumors as a Monotherapy and in Combination with Everolimus
Authors: Chang Chun-Ping , Yeh Teng-Kuang , Chen Chiung-Tong , Wang Wan-Ping , Chen Yen-Ting , Tsai Chia-Hua , Chen Yan-Fu , Ke Yi-Yu , Wang Jing-Ya , Chen Ching-Ping , Hsieh Tsung-Chih , Wu Mine-Hsine , Huang Chen-Lung , Chen Ya-Ping , Zhuang Hong , Chi Ya-Hui
Published: June 2024

Supplementary Figure S3. Discovery, in vivo tumor suppression efficacy and toxicity profile of DBPR728. (A) N-acyl derivatization of 6K465 leads to DBPR728 and its regioisomer 6. (B) Individual tumor growth curve of NCI-H446 xenografts as presented in Fig. 3C. (C) Individual tumor growth curve of NCI-H446 xenografts as presented in Fig. 3E. (D-F) Body weight change of the mice during the experimental course as presented in Fig. 3, C-E. Errors are mean ± SEM. (G) Blood cell count in mice treated with DBPR728 at 100 mpk QD for 14 days. Blood samples were collected at day 15. *, P < 0.05 (t-test, two-tailed). (H) Sera biochemistry profiles for liver and kidney functions in mice treated with DBPR728 at 300 or 600 mpk QW for 3 doses. Sera were harvest 7 days after the last dose. (I) Sera biochemistry profiles in mice treated with DBPR728 at 100 mpk QD for 14 days. Sera were collected at day 15. (G-I) Errors are mean ± SD. Abbreviations in (H-I), GOT, aspartate aminotransferase; GPT, alanine aminotransferase; ALP, alkaline phosphatase; ALB, albumin; BUN, blood urea nitrogen; CRE, creatinine.
Figure S8 from A Novel Dual ATM/DNA-PK Inhibitor, XRD-0394, Potently Radiosensitizes and Potentiates PARP and Topoisomerase I Inhibitors
Authors: Gilmer Tona M. , Lai Chun-Hsiang , Guo Kexiao , Deland Katherine , Ashcraft Kathleen A. , Stewart Amy E. , Wang Yaode , Fu Jianmin , Wood Kris C. , Kirsch David G. , Kastan Michael B.
Published: June 2024

Plots of CTG assays
Figure S5 from A Novel Dual ATM/DNA-PK Inhibitor, XRD-0394, Potently Radiosensitizes and Potentiates PARP and Topoisomerase I Inhibitors
Authors: Gilmer Tona M. , Lai Chun-Hsiang , Guo Kexiao , Deland Katherine , Ashcraft Kathleen A. , Stewart Amy E. , Wang Yaode , Fu Jianmin , Wood Kris C. , Kirsch David G. , Kastan Michael B.
Published: June 2024

Plasma concentrations
Figure S4 from A Novel Dual ATM/DNA-PK Inhibitor, XRD-0394, Potently Radiosensitizes and Potentiates PARP and Topoisomerase I Inhibitors
Authors: Gilmer Tona M. , Lai Chun-Hsiang , Guo Kexiao , Deland Katherine , Ashcraft Kathleen A. , Stewart Amy E. , Wang Yaode , Fu Jianmin , Wood Kris C. , Kirsch David G. , Kastan Michael B.
Published: June 2024

XRD-0394 radiosensitization compared with ATRi
Figure S3 from A Novel Dual ATM/DNA-PK Inhibitor, XRD-0394, Potently Radiosensitizes and Potentiates PARP and Topoisomerase I Inhibitors
Authors: Gilmer Tona M. , Lai Chun-Hsiang , Guo Kexiao , Deland Katherine , Ashcraft Kathleen A. , Stewart Amy E. , Wang Yaode , Fu Jianmin , Wood Kris C. , Kirsch David G. , Kastan Michael B.
Published: June 2024

clonogenic survival colonies
Supplemental Table S4 from Mitochondrial and Cytosolic One-Carbon Metabolism Is a Targetable Metabolic Vulnerability in Cisplatin-Resistant Ovarian Cancer
Authors: Wallace-Povirk Adrianne , O'Connor Carrie , Dekhne Aamod S. , Bao Xun , Nayeen Md. Junayed , Schneider Mathew , Katinas Jade M. , Wong-Roushar Jennifer , Kim Seongho , Polin Lisa , Li Jing , Back Jessica B. , Dann Charles E. , Gangjee Aleem , Hou Zhanjun , Matherly Larry H.
Published: June 2024

This table shows IC50 values for antiproliferative activities toward EOC versus normal ovary cell lines by 5-substituted pyrrolo[3,2-d]pyrimidine inhibitors.
Supplemental Figure S6 from Mitochondrial and Cytosolic One-Carbon Metabolism Is a Targetable Metabolic Vulnerability in Cisplatin-Resistant Ovarian Cancer
Authors: Wallace-Povirk Adrianne , O'Connor Carrie , Dekhne Aamod S. , Bao Xun , Nayeen Md. Junayed , Schneider Mathew , Katinas Jade M. , Wong-Roushar Jennifer , Kim Seongho , Polin Lisa , Li Jing , Back Jessica B. , Dann Charles E. , Gangjee Aleem , Hou Zhanjun , Matherly Larry H.
Published: June 2024

This figure shows purine nucleotides in SKOV3 EOC cells treated with pyrrolo[3,2-d]pyrimidine antifolates.
Supplemental Figure S3 from Mitochondrial and Cytosolic One-Carbon Metabolism Is a Targetable Metabolic Vulnerability in Cisplatin-Resistant Ovarian Cancer
Authors: Wallace-Povirk Adrianne , O'Connor Carrie , Dekhne Aamod S. , Bao Xun , Nayeen Md. Junayed , Schneider Mathew , Katinas Jade M. , Wong-Roushar Jennifer , Kim Seongho , Polin Lisa , Li Jing , Back Jessica B. , Dann Charles E. , Gangjee Aleem , Hou Zhanjun , Matherly Larry H.
Published: June 2024

This figure shows FRα, PCFT and RFC expression in EOC cell line models and EOC patient cDNAs.
Supplemental Figure S1 from Mitochondrial and Cytosolic One-Carbon Metabolism Is a Targetable Metabolic Vulnerability in Cisplatin-Resistant Ovarian Cancer
Authors: Wallace-Povirk Adrianne , O'Connor Carrie , Dekhne Aamod S. , Bao Xun , Nayeen Md. Junayed , Schneider Mathew , Katinas Jade M. , Wong-Roushar Jennifer , Kim Seongho , Polin Lisa , Li Jing , Back Jessica B. , Dann Charles E. , Gangjee Aleem , Hou Zhanjun , Matherly Larry H.
Published: June 2024

This figure shows immunohistochemical staining of tumor microarray
(TMA) for SHMT2 protein.
Figure S6 from 89Zr-ImmunoPET for the Specific Detection of EMP2-Positive Tumors
Authors: Chan Ann M. , Olafsen Tove , Tsui Jessica , Salazar Felix B. , Aguirre Brian , Zettlitz Kirstin A. , Condro Michael , Wu Anna M. , Braun Jonathan , Gordon Lynn K. , Ashki Negin , Whitelegge Julian , Xu Shili , Ikotun Oluwatayo , Lee Jason Thanh , Wadehra Madhuri
Published: June 2024

S6. Pharmacokinetics and in vivo tumor expression. A. Tumor growth of syngeneic 4T1FLuc, CT26, and Panc02 tumors over the imaging period. B. Correlation of the average EMP2 histological score and mean %ID/cc in 4T1FLuc, CT26 and Panc02 tumors. C. Representative staining of EMP2 in 4T1FLuc, CT26 and Panc02 tumors. Magnification: 100m. D. Pharmacokinetics of the anti-EMP2 mAb as measured by western blot detection of the anti-Fc portion of the mAb. Mice were injected with 200 g or 20 g of the anti-EMP2 mAb. Cmax was defined by quantitation at t=2 hrs with the PK estimated at 140 hrs.
Figure S5 from 89Zr-ImmunoPET for the Specific Detection of EMP2-Positive Tumors
Authors: Chan Ann M. , Olafsen Tove , Tsui Jessica , Salazar Felix B. , Aguirre Brian , Zettlitz Kirstin A. , Condro Michael , Wu Anna M. , Braun Jonathan , Gordon Lynn K. , Ashki Negin , Whitelegge Julian , Xu Shili , Ikotun Oluwatayo , Lee Jason Thanh , Wadehra Madhuri
Published: June 2024

S5. Binding characteristics. Analysis of the various anti-EMP2−DFO conjugates using flow cytometry binding on U87MG/EMP2FLuc. N=3, with the EC50 determined using nonlinear regression. B. 10:1 DFO:mAb ratio retains specific binding to EMP2 high (4T1FLuc, CT26) murine cell lines compared to low cells (Panc02). N=3, with a representative experiment shown.
Figure S4 from 89Zr-ImmunoPET for the Specific Detection of EMP2-Positive Tumors
Authors: Chan Ann M. , Olafsen Tove , Tsui Jessica , Salazar Felix B. , Aguirre Brian , Zettlitz Kirstin A. , Condro Michael , Wu Anna M. , Braun Jonathan , Gordon Lynn K. , Ashki Negin , Whitelegge Julian , Xu Shili , Ikotun Oluwatayo , Lee Jason Thanh , Wadehra Madhuri
Published: June 2024

S4. DFO-conjugated anti-EMP2 mAb characteristics. A. Analysis of the various anti-EMP2−DFO conjugates using polyacrylamide gel electrophoresis (PAGE) showing changes in the migration of the intact antibody. B. Analysis of the various anti-EMP2−DFO conjugates to the EMP2 peptide or a non-specific peptide by ELISA. C. Predicted number of chelators per mAb based on MALDI-TOF analysis. Changes in the molecular weight of the native antibody (~150kD) are attributed to modification with the various molar equivalents of DFO.
Figure S3 from 89Zr-ImmunoPET for the Specific Detection of EMP2-Positive Tumors
Authors: Chan Ann M. , Olafsen Tove , Tsui Jessica , Salazar Felix B. , Aguirre Brian , Zettlitz Kirstin A. , Condro Michael , Wu Anna M. , Braun Jonathan , Gordon Lynn K. , Ashki Negin , Whitelegge Julian , Xu Shili , Ikotun Oluwatayo , Lee Jason Thanh , Wadehra Madhuri
Published: June 2024

S3. EMP2 expression in cancer cell lines. A. Based on public repositories, upregulation of EMP2 occurs in breast, brain, and ovarian cancers, while downregulation is predicted in hematopoietic cancers. B, C. Flow cytometry studies using a panel of human (B) and murine (C) cancer cell lines to validate differential EMP2 expression.
Figure S2 from 89Zr-ImmunoPET for the Specific Detection of EMP2-Positive Tumors
Authors: Chan Ann M. , Olafsen Tove , Tsui Jessica , Salazar Felix B. , Aguirre Brian , Zettlitz Kirstin A. , Condro Michael , Wu Anna M. , Braun Jonathan , Gordon Lynn K. , Ashki Negin , Whitelegge Julian , Xu Shili , Ikotun Oluwatayo , Lee Jason Thanh , Wadehra Madhuri
Published: June 2024

S2. EMP2 expression in the mouse. Expression of EMP2 was determined by immunohistochemical staining in C57B/6 WT or EMP2 knockout mice with representative images shown from select tissue. Magnification: 400X.
Figure S3 from Proton FLASH Radiotherapy Ameliorates Radiation-induced Salivary Gland Dysfunction and Oral Mucositis and Increases Survival in a Mouse Model of Head and Neck Cancer
Authors: Chowdhury Priyanka , Velalopoulou Anastasia , Verginadis Ioannis I. , Morcos George , Loo Phoebe E. , Kim Michele M. , Motlagh Seyyedeh Azar Oliaei , Shoniyozov Khayrullo , Diffenderfer Eric S. , Ocampo Emilio A. , Putt Mary , Assenmacher Charles-Antoine , Radaelli Enrico , Lu Jiawei , Qin Ling , Liu Hengxi , Leli Nektaria Maria , Girdhani Swati , Denef Nicolas , Vander Stappen Francois , Cengel Keith A. , Busch Theresa M. , Metz James M. , Dong Lei , Lin Alexander , Koumenis Constantinos
Published: June 2024

Estimation of saliva flow in male C57BL/6 mice following irradiation with a single dose of 16 Gy of proton irradiation.
Figure S2 from Proton FLASH Radiotherapy Ameliorates Radiation-induced Salivary Gland Dysfunction and Oral Mucositis and Increases Survival in a Mouse Model of Head and Neck Cancer
Authors: Chowdhury Priyanka , Velalopoulou Anastasia , Verginadis Ioannis I. , Morcos George , Loo Phoebe E. , Kim Michele M. , Motlagh Seyyedeh Azar Oliaei , Shoniyozov Khayrullo , Diffenderfer Eric S. , Ocampo Emilio A. , Putt Mary , Assenmacher Charles-Antoine , Radaelli Enrico , Lu Jiawei , Qin Ling , Liu Hengxi , Leli Nektaria Maria , Girdhani Swati , Denef Nicolas , Vander Stappen Francois , Cengel Keith A. , Busch Theresa M. , Metz James M. , Dong Lei , Lin Alexander , Koumenis Constantinos
Published: June 2024

The percent difference in body weight of mice after irradiation with a hypofractionated regime of 8 Gy x 3.
Supplementary Table 1 from Thio-2 Inhibits Key Signaling Pathways Required for the Development and Progression of Castration-resistant Prostate Cancer
Authors: Neeb Antje , Figueiredo Ines , Bogdan Denisa , Cato Laura , Stober Jutta , Jiménez-Vacas Juan M. , Gourain Victor , Lee Irene I. , Seeger Rebecca , Muhle-Goll Claudia , Gurel Bora , Welti Jonathan , Nava Rodrigues Daniel , Rekowski Jan , Qiu Xintao , Jiang Yija , Di Micco Patrizio , Mateos Borja , Bielskutė Stasė , Riisnaes Ruth , Ferreira Ana , Miranda Susana , Crespo Mateus , Buroni Lorenzo , Ning Jian , Carreira Suzanne , Bräse Stefan , Jung Nicole , Gräßle Simone , Swain Amanda , Salvatella Xavier , Plymate Stephen R. , Al-Lazikani Bissan , Long Henry W. , Yuan Wei , Brown Myles , Cato Andrew C.B. , de Bono Johann S. , Sharp Adam
Published: June 2024

List of the 44 3D structures of HSC70 (HSPA8) in complex with the BAG domain of BAG-1 used in comparative structural analyses.
Supplementary Materials and Methods from Thio-2 Inhibits Key Signaling Pathways Required for the Development and Progression of Castration-resistant Prostate Cancer
Authors: Neeb Antje , Figueiredo Ines , Bogdan Denisa , Cato Laura , Stober Jutta , Jiménez-Vacas Juan M. , Gourain Victor , Lee Irene I. , Seeger Rebecca , Muhle-Goll Claudia , Gurel Bora , Welti Jonathan , Nava Rodrigues Daniel , Rekowski Jan , Qiu Xintao , Jiang Yija , Di Micco Patrizio , Mateos Borja , Bielskutė Stasė , Riisnaes Ruth , Ferreira Ana , Miranda Susana , Crespo Mateus , Buroni Lorenzo , Ning Jian , Carreira Suzanne , Bräse Stefan , Jung Nicole , Gräßle Simone , Swain Amanda , Salvatella Xavier , Plymate Stephen R. , Al-Lazikani Bissan , Long Henry W. , Yuan Wei , Brown Myles , Cato Andrew C.B. , de Bono Johann S. , Sharp Adam
Published: June 2024

Description of Materials and Methods not contained within the main Materials and Methods section
Supplementary Figure 9 from Thio-2 Inhibits Key Signaling Pathways Required for the Development and Progression of Castration-resistant Prostate Cancer
Authors: Neeb Antje , Figueiredo Ines , Bogdan Denisa , Cato Laura , Stober Jutta , Jiménez-Vacas Juan M. , Gourain Victor , Lee Irene I. , Seeger Rebecca , Muhle-Goll Claudia , Gurel Bora , Welti Jonathan , Nava Rodrigues Daniel , Rekowski Jan , Qiu Xintao , Jiang Yija , Di Micco Patrizio , Mateos Borja , Bielskutė Stasė , Riisnaes Ruth , Ferreira Ana , Miranda Susana , Crespo Mateus , Buroni Lorenzo , Ning Jian , Carreira Suzanne , Bräse Stefan , Jung Nicole , Gräßle Simone , Swain Amanda , Salvatella Xavier , Plymate Stephen R. , Al-Lazikani Bissan , Long Henry W. , Yuan Wei , Brown Myles , Cato Andrew C.B. , de Bono Johann S. , Sharp Adam
Published: June 2024

Thio-2 downregulates C-MYC expression through a BAG-1 independent mechanism.
Supplementary Figure 6 from Thio-2 Inhibits Key Signaling Pathways Required for the Development and Progression of Castration-resistant Prostate Cancer
Authors: Neeb Antje , Figueiredo Ines , Bogdan Denisa , Cato Laura , Stober Jutta , Jiménez-Vacas Juan M. , Gourain Victor , Lee Irene I. , Seeger Rebecca , Muhle-Goll Claudia , Gurel Bora , Welti Jonathan , Nava Rodrigues Daniel , Rekowski Jan , Qiu Xintao , Jiang Yija , Di Micco Patrizio , Mateos Borja , Bielskutė Stasė , Riisnaes Ruth , Ferreira Ana , Miranda Susana , Crespo Mateus , Buroni Lorenzo , Ning Jian , Carreira Suzanne , Bräse Stefan , Jung Nicole , Gräßle Simone , Swain Amanda , Salvatella Xavier , Plymate Stephen R. , Al-Lazikani Bissan , Long Henry W. , Yuan Wei , Brown Myles , Cato Andrew C.B. , de Bono Johann S. , Sharp Adam
Published: June 2024

In-vivo treatment of patient derived model of lethal prostate cancer demonstrates Thio-2 to be well tolerated with associated impact on AR signaling and growth.
Supplementary Figure S6 from Structural Basis for Multivalent MUC16 Recognition and Robust Anti-Pancreatic Cancer Activity of Humanized Antibody AR9.6
Authors: Aguilar Eric N. , Sagar Satish , Murray Brandy R. , Rajesh Christabelle , Lei Eric K. , Michaud Sarah A. , Goodlett David R. , Caffrey Thomas C. , Grandgenett Paul M. , Swanson Benjamin , Brooks Teresa M. , Black Adrian R. , van Faassen Henk , Hussack Greg , Henry Kevin A. , Hollingsworth Michael A. , Brooks Cory L. , Radhakrishnan Prakash
Published: June 2024

Fig. S6. huAR9.6 reduces tumor burden in models of PDAC. (A) Schematic of subcutaneous PDAC model using T3M4 cells implanted in athymic nude mice (n=5). On day 9 post implantation, mice were randomized to two treatment groups: vehicle (PBS) and huAR9.6 (500 µg/25 g bodyweight, i.p. every 72 h) for 4 doses. At the experimental endpoint (day 19), mice were euthanized. (B) Hematoxylin and eosin (H&E) staining, Ki67 staining and CD31 staining of formalin-fixed paraffin embedded (FFPE) subcutaneous tumor tissues (n=5) treated with vehicle and huAR9.6. Scale bar 100 µm. (C) Schematic of orthotopic PDAC model using T3M4 cells implanted in athymic nude mice. On day 18 post implantation, mice were randomized to three treatment groups (n=7 per group): vehicle (PBS), isotype control huIgG and huAR9.6 (500 µg/25 g bodyweight, i.p.) for 4 doses. At the experimental endpoint (day 28), mice were euthanized. (D) Differences in tumor size from the three treatment groups. (E) Schematic of PDAC patient-derived organoid (PDO) development and treatment (n=3) with huAR9.6 (40 µg/mL for 24 h) and isotype control huIgG and subjected to further studies with cell proliferation and signaling. (F) Immunofluorescent staining for MUC16 with huAR9.6 on primary human PDAC tissue and matched PDO. Scale bar 50 µm.
Supplementary Figure S4 from Structural Basis for Multivalent MUC16 Recognition and Robust Anti-Pancreatic Cancer Activity of Humanized Antibody AR9.6
Authors: Aguilar Eric N. , Sagar Satish , Murray Brandy R. , Rajesh Christabelle , Lei Eric K. , Michaud Sarah A. , Goodlett David R. , Caffrey Thomas C. , Grandgenett Paul M. , Swanson Benjamin , Brooks Teresa M. , Black Adrian R. , van Faassen Henk , Hussack Greg , Henry Kevin A. , Hollingsworth Michael A. , Brooks Cory L. , Radhakrishnan Prakash
Published: June 2024

Fig. S4. huAR9.6 effects on PDAC cells and PDXs. Representative wound healing assay of vehicle (PBS), isotype control huIgG (40 µg/mL) and huAR9.6 (40 µg/mL) treated (A) T3M4 and (B) Capan-1 cells. (C) Schematic of patient-derived xenograft (PDX) derived cells obtained from primary human PDAC and liver metastasis. (D) Flow cytometric assessment of apoptosis using the Annexin-V/PI assay in T3M4 and Capan-1 cells treated with vehicle (PBS), isotype control huIgG (40 µg/mL) and huAR9.6 (40 µg/mL). Mean ± SD (n=3), p < 0.05 was considered as statistically significant using one-way ANOVA with Tukey’s multiple comparisons.
Supplementary Data from Evaluation of the Role of AXL in Fusion-positive Pediatric Rhabdomyosarcoma Identifies the Small-molecule Inhibitor Bemcentinib (BGB324) as Potent Chemosensitizer
Authors: Danielli Sara G. , Wurth Jakob , Morice Sarah , Kisele Samanta , Surdez Didier , Delattre Olivier , Bode Peter K. , Wachtel Marco , Schäfer Beat W.
Published: June 2024

Supplementary Figures and Tables
Supplementary Figure S2 from Structural Basis for Multivalent MUC16 Recognition and Robust Anti-Pancreatic Cancer Activity of Humanized Antibody AR9.6
Authors: Aguilar Eric N. , Sagar Satish , Murray Brandy R. , Rajesh Christabelle , Lei Eric K. , Michaud Sarah A. , Goodlett David R. , Caffrey Thomas C. , Grandgenett Paul M. , Swanson Benjamin , Brooks Teresa M. , Black Adrian R. , van Faassen Henk , Hussack Greg , Henry Kevin A. , Hollingsworth Michael A. , Brooks Cory L. , Radhakrishnan Prakash
Published: June 2024

Fig. S2. Representative deuterium uptake plots of SEA5 regions with significantly reduced deuteration owing to interaction with mAR9.6 and huAR9.6
Figure S4 from Evaluation of the Role of AXL in Fusion-positive Pediatric Rhabdomyosarcoma Identifies the Small-molecule Inhibitor Bemcentinib (BGB324) as Potent Chemosensitizer
Authors: Danielli Sara G. , Wurth Jakob , Morice Sarah , Kisele Samanta , Surdez Didier , Delattre Olivier , Bode Peter K. , Wachtel Marco , Schäfer Beat W.
Published: June 2024

Combination of chemotherapy and AXL inhibitors.
Supplementary Figure S10 from Structural Basis for Multivalent MUC16 Recognition and Robust Anti-Pancreatic Cancer Activity of Humanized Antibody AR9.6
Authors: Aguilar Eric N. , Sagar Satish , Murray Brandy R. , Rajesh Christabelle , Lei Eric K. , Michaud Sarah A. , Goodlett David R. , Caffrey Thomas C. , Grandgenett Paul M. , Swanson Benjamin , Brooks Teresa M. , Black Adrian R. , van Faassen Henk , Hussack Greg , Henry Kevin A. , Hollingsworth Michael A. , Brooks Cory L. , Radhakrishnan Prakash
Published: June 2024

Fig. S10. Conservation of AR9.6 epitope in homologous SEA domains. The epitope deduced from the X-ray structure of AR9.6 in complex with SEA5 (yellow ribbon diagram) occurs in 3 regions of the protein (shown in orange). (A) Alignment of SEA5 with homologous MUC16 SEA domains reveals that the epitope is well conserved among SEA domains 3-13, (B) less well conserved in SEA domains 1-2 (C), and the least conserved in SEA domains 13,14,16. (D) No significant epitope conservation occurs in SEA domain 15.
Figure S2 from Evaluation of the Role of AXL in Fusion-positive Pediatric Rhabdomyosarcoma Identifies the Small-molecule Inhibitor Bemcentinib (BGB324) as Potent Chemosensitizer
Authors: Danielli Sara G. , Wurth Jakob , Morice Sarah , Kisele Samanta , Surdez Didier , Delattre Olivier , Bode Peter K. , Wachtel Marco , Schäfer Beat W.
Published: June 2024

AXL genetic removal and pathway activation.
Figure S1 from Evaluation of the Role of AXL in Fusion-positive Pediatric Rhabdomyosarcoma Identifies the Small-molecule Inhibitor Bemcentinib (BGB324) as Potent Chemosensitizer
Authors: Danielli Sara G. , Wurth Jakob , Morice Sarah , Kisele Samanta , Surdez Didier , Delattre Olivier , Bode Peter K. , Wachtel Marco , Schäfer Beat W.
Published: June 2024

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

Supplementary tables S1-S9
Supplementary Figure 6 from ATPase Copper Transporting Beta (ATP7B) Is a Novel Target for Improving the Therapeutic Efficacy of Docetaxel by Disulfiram/Copper in Human Prostate Cancer
Authors: Song Liankun , Nguyen Vyvyan , Xie Jun , Jia Shang , Chang Christopher J. , Uchio Edward , Zi Xiaolin
Published: June 2024

Western blotting analysis of COMMED1, Skp2, p21, and α-Clusterin
protein expression in vehicle control and DSF/CuCl2 treated 22Rv1-DR xenograft tumors.
Supplementary Figure 4 from ATPase Copper Transporting Beta (ATP7B) Is a Novel Target for Improving the Therapeutic Efficacy of Docetaxel by Disulfiram/Copper in Human Prostate Cancer
Authors: Song Liankun , Nguyen Vyvyan , Xie Jun , Jia Shang , Chang Christopher J. , Uchio Edward , Zi Xiaolin
Published: June 2024

Knock-down of COMMD1 expression by siRNAs attenuates the effects of DSF/Cu++ reducing Skp2 protein levels in DU145-DR cells
Supplementary Figure 1 from ATPase Copper Transporting Beta (ATP7B) Is a Novel Target for Improving the Therapeutic Efficacy of Docetaxel by Disulfiram/Copper in Human Prostate Cancer
Authors: Song Liankun , Nguyen Vyvyan , Xie Jun , Jia Shang , Chang Christopher J. , Uchio Edward , Zi Xiaolin
Published: June 2024

ATP7B protein expression in prostate epithelial cells and prostate cancer cell lines
Data from Mitochondrial and Cytosolic One-Carbon Metabolism Is a Targetable Metabolic Vulnerability in Cisplatin-Resistant Ovarian Cancer
Authors: Wallace-Povirk Adrianne , O'Connor Carrie , Dekhne Aamod S. , Bao Xun , Nayeen Md. Junayed , Schneider Mathew , Katinas Jade M. , Wong-Roushar Jennifer , Kim Seongho , Polin Lisa , Li Jing , Back Jessica B. , Dann Charles E. , Gangjee Aleem , Hou Zhanjun , Matherly Larry H.
Published: June 2024

Abstract
One-carbon (C1) metabolism is compartmentalized between the cytosol and mitochondria with the mitochondrial C1 pathway as the major source of glycine and C1 units for cellular biosynthesis. Expression of mitochondrial C1 genes including SLC25A32, serine hydroxymethyl transferase (SHMT) 2, 5,10-methylene tetrahydrofolate dehydrogenase 2, and 5,10-methylene tetrahydrofolate dehydrogenase 1-like was significantly elevated in primary epithelial ovarian cancer (EOC) specimens compared with normal ovaries. 5-Substituted pyrrolo[3,2-d]pyrimidine antifolates (AGF347, AGF359, AGF362) inhibited proliferation of cisplatin-sensitive (A2780, CaOV3, IGROV1) and cisplatin-resistant (A2780-E80, SKOV3) EOC cells. In SKOV3 and A2780-E80 cells, colony formation was inhibited. AGF347 induced apoptosis in SKOV3 cells. In IGROV1 cells, AGF347 was transported by folate receptor (FR) α. AGF347 was also transported into IGROV1 and SKOV3 cells by the proton-coupled folate transporter (SLC46A1) and the reduced folate carrier (SLC19A1). AGF347 accumulated to high levels in the cytosol and mitochondria of SKOV3 cells. By targeted metabolomics with [2,3,3–2H]L-serine, AGF347, AGF359, and AGF362 inhibited SHMT2 in the mitochondria. In the cytosol, SHMT1 and de novo purine biosynthesis (i.e., glycinamide ribonucleotide formyltransferase, 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase) were targeted; AGF359 also inhibited thymidylate synthase. Antifolate treatments of SKOV3 cells depleted cellular glycine, mitochondrial NADH and glutathione, and showed synergistic in vitro inhibition toward SKOV3 and A2780-E80 cells when combined with cisplatin. In vivo studies with subcutaneous SKOV3 EOC xenografts in SCID mice confirmed significant antitumor efficacy of AGF347. Collectively, our studies demonstrate a unique metabolic vulnerability in EOC involving mitochondrial and cytosolic C1 metabolism, which offers a promising new platform for therapy.
Data from Structural Basis for Multivalent MUC16 Recognition and Robust Anti-Pancreatic Cancer Activity of Humanized Antibody AR9.6
Authors: Aguilar Eric N. , Sagar Satish , Murray Brandy R. , Rajesh Christabelle , Lei Eric K. , Michaud Sarah A. , Goodlett David R. , Caffrey Thomas C. , Grandgenett Paul M. , Swanson Benjamin , Brooks Teresa M. , Black Adrian R. , van Faassen Henk , Hussack Greg , Henry Kevin A. , Hollingsworth Michael A. , Brooks Cory L. , Radhakrishnan Prakash
Published: June 2024

Abstract
Mucin-16 (MUC16) is a target for antibody-mediated immunotherapy in pancreatic ductal adenocarcinoma (PDAC) among other malignancies. The MUC16-specific monoclonal antibody AR9.6 has shown promise for PDAC immunotherapy and imaging. Here, we report the structural and biological characterization of the humanized AR9.6 antibody (huAR9.6). The structure of huAR9.6 was determined in complex with a MUC16 SEA (Sea urchin sperm, Enterokinase, Agrin) domain. Binding of huAR9.6 to recombinant, shed, and cell-surface MUC16 was characterized, and anti-PDAC activity was evaluated in vitro and in vivo. HuAR9.6 bound a discontinuous, SEA domain epitope with an overall affinity of 88 nmol/L. Binding affinity depended on the specific SEA domain(s) present, and glycosylation modestly enhanced affinity driven by favorable entropy and enthalpy and via distinct transition state thermodynamic pathways. Treatment with huAR9.6 reduced the in vitro growth, migration, invasion, and clonogenicity of MUC16-positive PDAC cells and patient-derived organoids (PDO). HuAR9.6 blocked MUC16-mediated ErbB and AKT activation in PDAC cells, PDOs, and patient-derived xenografts and induced antibody-dependent cellular cytotoxicity and complement-dependent cytotoxicity. More importantly, huAR9.6 treatment caused substantial PDAC regression in subcutaneous and orthotopic tumor models. The mechanism of action of huAR9.6 may depend on dense avid binding to homologous SEA domains on MUC16. The results of this study validate the translational therapeutic potential of huAR9.6 against MUC16-positive PDACs.
Data from Evaluation of the Role of AXL in Fusion-positive Pediatric Rhabdomyosarcoma Identifies the Small-molecule Inhibitor Bemcentinib (BGB324) as Potent Chemosensitizer
Authors: Danielli Sara G. , Wurth Jakob , Morice Sarah , Kisele Samanta , Surdez Didier , Delattre Olivier , Bode Peter K. , Wachtel Marco , Schäfer Beat W.
Published: June 2024

Abstract
Rhabdomyosarcoma (RMS) is a highly aggressive pediatric cancer with features of skeletal muscle differentiation. More than 80% of the high-risk patients ultimately fail to respond to chemotherapy treatment, leading to limited therapeutic options and dismal prognostic rates. The lack of response and subsequent tumor recurrence is driven in part by stem cell–like cells, the tumor subpopulation that is enriched after treatment, and characterized by expression of the AXL receptor tyrosine kinase (AXL). AXL mediates survival, migration, and therapy resistance in several cancer types; however, its function in RMS remains unclear. In this study, we investigated the role of AXL in RMS tumorigenesis, migration, and chemotherapy response, and whether targeting of AXL with small-molecule inhibitors could potentiate the efficacy of chemotherapy. We show that AXL is expressed in a heterogeneous manner in patient-derived xenografts (PDX), primary cultures and cell line models of RMS, consistent with its stem cell–state selectivity. By generating a CRISPR/Cas9 AXL knock-out and overexpressing models, we show that AXL contributes to the migratory phenotype of RMS, but not to chemotherapy resistance. Instead, pharmacologic blockade with the AXL inhibitors bemcentinib (BGB324), cabozantinib and NPS-1034 rapidly killed RMS cells in an AXL-independent manner and augmented the efficacy of the chemotherapeutics vincristine and cyclophosphamide. In vivo administration of the combination of bemcentinib and vincristine exerted strong antitumoral activity in a rapidly progressing PDX mouse model, significantly reducing tumor burden compared with single-agent treatment. Collectively, our data identify bemcentinib as a promising drug to improve chemotherapy efficacy in patients with RMS.
Supplementary Table 2 from FATP5 Is Indispensable for the Growth of Intrahepatic Cholangiocarcinoma
Authors: Shihadih Diyala , Wang Xue , Zushin Peter-James H. , Khodakivskyi Pavlo , Park Hyo Min , Tso Emily , Shiblak Jena , Misic Angela , Louie Sharon M. , Ward Catherine , Hellerstein Marc , Nomura Daniel K. , Goun Elena , Urigo Francesco , Calvisi Diego F. , Chen Xin , Stahl Andreas
Published: June 2024

Clinicopathological features of ICC patients
Supplementary Table S2 from Systematic Characterization of p53-Regulated Long Noncoding RNAs across Human Cancers Reveals Remarkable Heterogeneity among Different Tumor Types
Authors: Regunath Kausik , Fomin Vitalay , Liu Zhaoqi , Wang Pingzhang , Hoque Mainul , Tian Bin , Rabadan Raul , Prives Carol
Published: June 2024

Supplementary Table S2 shows p53LTCC lncRNAs (activated and repressed) associated with patient survival in colon cancers.
Supplementary Figure S5 from Systematic Characterization of p53-Regulated Long Noncoding RNAs across Human Cancers Reveals Remarkable Heterogeneity among Different Tumor Types
Authors: Regunath Kausik , Fomin Vitalay , Liu Zhaoqi , Wang Pingzhang , Hoque Mainul , Tian Bin , Rabadan Raul , Prives Carol
Published: June 2024

Supplementary Figure S5 shows Kaplan Meier curves from TCGA cancer datasets
Supplementary Figure S3 from Systematic Characterization of p53-Regulated Long Noncoding RNAs across Human Cancers Reveals Remarkable Heterogeneity among Different Tumor Types
Authors: Regunath Kausik , Fomin Vitalay , Liu Zhaoqi , Wang Pingzhang , Hoque Mainul , Tian Bin , Rabadan Raul , Prives Carol
Published: June 2024

Supplementary Figure S3 shows heatmap of p53LTCC expression in breast, colon and prostate cancers
Supplementary Figure S2 from Systematic Characterization of p53-Regulated Long Noncoding RNAs across Human Cancers Reveals Remarkable Heterogeneity among Different Tumor Types
Authors: Regunath Kausik , Fomin Vitalay , Liu Zhaoqi , Wang Pingzhang , Hoque Mainul , Tian Bin , Rabadan Raul , Prives Carol
Published: June 2024

Supplementary Figure S2 shows Venn diagram of overlap of lncRNAs and p21 locus
List of Supplementary Tables from Systematic Characterization of p53-Regulated Long Noncoding RNAs across Human Cancers Reveals Remarkable Heterogeneity among Different Tumor Types
Authors: Regunath Kausik , Fomin Vitalay , Liu Zhaoqi , Wang Pingzhang , Hoque Mainul , Tian Bin , Rabadan Raul , Prives Carol
Published: June 2024

List of Supplementary Tables with description of each table in the manuscript
Supplementary Figure S4 from Serotonin Receptor HTR2B Facilitates Colorectal Cancer Metastasis via CREB1–ZEB1 Axis–Mediated Epithelial–Mesenchymal Transition
Authors: Li Tao , Wei Lei , Zhang Xin , Fu Bin , Zhou Yunjiang , Yang Mengdi , Cao Mengran , Chen Yaxin , Tan Yingying , Shi Yongwei , Wu Leyin , Xuan Chenyuan , Du Qianming , Hu Rong
Published: June 2024

This file contains Supplementary Figure S4 and its legend.
Supplementary Figure S3 from Serotonin Receptor HTR2B Facilitates Colorectal Cancer Metastasis via CREB1–ZEB1 Axis–Mediated Epithelial–Mesenchymal Transition
Authors: Li Tao , Wei Lei , Zhang Xin , Fu Bin , Zhou Yunjiang , Yang Mengdi , Cao Mengran , Chen Yaxin , Tan Yingying , Shi Yongwei , Wu Leyin , Xuan Chenyuan , Du Qianming , Hu Rong
Published: June 2024

This file contains Supplementary Figure S3 and its legend.
Supplementary Figure S20 from Serotonin Receptor HTR2B Facilitates Colorectal Cancer Metastasis via CREB1–ZEB1 Axis–Mediated Epithelial–Mesenchymal Transition
Authors: Li Tao , Wei Lei , Zhang Xin , Fu Bin , Zhou Yunjiang , Yang Mengdi , Cao Mengran , Chen Yaxin , Tan Yingying , Shi Yongwei , Wu Leyin , Xuan Chenyuan , Du Qianming , Hu Rong
Published: June 2024

This file contains Supplementary Figure S20 and its legend.
Supplementary Figure S2 from Serotonin Receptor HTR2B Facilitates Colorectal Cancer Metastasis via CREB1–ZEB1 Axis–Mediated Epithelial–Mesenchymal Transition
Authors: Li Tao , Wei Lei , Zhang Xin , Fu Bin , Zhou Yunjiang , Yang Mengdi , Cao Mengran , Chen Yaxin , Tan Yingying , Shi Yongwei , Wu Leyin , Xuan Chenyuan , Du Qianming , Hu Rong
Published: June 2024

This file contains Supplementary Figure S2 and its legend.
Supplementary Figure S19 from Serotonin Receptor HTR2B Facilitates Colorectal Cancer Metastasis via CREB1–ZEB1 Axis–Mediated Epithelial–Mesenchymal Transition
Authors: Li Tao , Wei Lei , Zhang Xin , Fu Bin , Zhou Yunjiang , Yang Mengdi , Cao Mengran , Chen Yaxin , Tan Yingying , Shi Yongwei , Wu Leyin , Xuan Chenyuan , Du Qianming , Hu Rong
Published: June 2024

This file contains Supplementary Figure S19 and its legend.
Supplementary Figure S15 from Serotonin Receptor HTR2B Facilitates Colorectal Cancer Metastasis via CREB1–ZEB1 Axis–Mediated Epithelial–Mesenchymal Transition
Authors: Li Tao , Wei Lei , Zhang Xin , Fu Bin , Zhou Yunjiang , Yang Mengdi , Cao Mengran , Chen Yaxin , Tan Yingying , Shi Yongwei , Wu Leyin , Xuan Chenyuan , Du Qianming , Hu Rong
Published: June 2024

This file contains Supplementary Figure S15 and its legend.
Supplementary Figure S1 from Serotonin Receptor HTR2B Facilitates Colorectal Cancer Metastasis via CREB1–ZEB1 Axis–Mediated Epithelial–Mesenchymal Transition
Authors: Li Tao , Wei Lei , Zhang Xin , Fu Bin , Zhou Yunjiang , Yang Mengdi , Cao Mengran , Chen Yaxin , Tan Yingying , Shi Yongwei , Wu Leyin , Xuan Chenyuan , Du Qianming , Hu Rong
Published: June 2024

This file contains Supplementary Figure S1 and its legend.
Supplementary Figure S5 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis
Authors: Meuser Elena , Chang Kyle , Walters Angharad , Hurley Joanna J. , West Hannah D. , Perry Iain , Mort Matthew , Reyes-Uribe Laura , Truscott Rebekah , Jones Nicholas , Lawrence Rachel , Jenkins Gareth , Giles Peter , Dolwani Sunil , Al-Sarireh Bilal , Hawkes Neil , Short Emma , Williams Geraint T. , Taggart Melissa W. , Luetchford Kim , Lynch Patrick M. , Terlouw Diantha , Nielsen Maartje , Walton Sarah-Jane , Latchford Andrew , Clark Susan K. , Sampson Julian R. , Vilar Eduardo , Thomas Laura E.
Published: June 2024

Gene Ontology of DEGs between duodenal adenomas with and without PIGA somatic mutation. Enriched terms are plotted for Biological process(BP), A. Cellular Component (CC), B. and Molecular Function(MF), C. Terms are coloured by Log2-Padj value for term enrichment and sized by semantic similarity of GO term. DEGs for the most enriched terms; Apical plasma membrane (GO0016324), Salt transmembrane transporter activity (GO1901702), Organic anion transport (GO0015711), lipid transport (GO0006869) and the PPAR signalling pathway (KEGG03320) are plotted, D. Genes are coloured by Log2FC and sized by Log10 Padj. The central role of CD36 is highlighted.
Supplementary Figure S2 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis
Authors: Meuser Elena , Chang Kyle , Walters Angharad , Hurley Joanna J. , West Hannah D. , Perry Iain , Mort Matthew , Reyes-Uribe Laura , Truscott Rebekah , Jones Nicholas , Lawrence Rachel , Jenkins Gareth , Giles Peter , Dolwani Sunil , Al-Sarireh Bilal , Hawkes Neil , Short Emma , Williams Geraint T. , Taggart Melissa W. , Luetchford Kim , Lynch Patrick M. , Terlouw Diantha , Nielsen Maartje , Walton Sarah-Jane , Latchford Andrew , Clark Susan K. , Sampson Julian R. , Vilar Eduardo , Thomas Laura E.
Published: June 2024

Somatic mutation rates in FAP and MAP-associated duodenal adenomas. A. Total, non-silent and silent mutation rate for all FAP and MAP adenomas. For FAP-associated duodenal adenomas, the average total mutation rate was 3.3 mutations per Mb (0.33-10.65 mutations/Mb), whilst for MAP adenomas, it was 4.9 mutations per Mb (0.94-15.1 mutations/Mb). The average non-silent mutational rate for FAP duodenal adenomas was 1.96 non-silent mutations/Mb (0.23-7.69 mutations/Mb), whilst for MAP adenomas it was 2.95 non-silent mutations/Mb (0.43-8.44 mutations/Mb). B. Differences in total, non-silent and silent mutational rates between the two diseases. There were no significant differences in total, non-silent and silent mutational rates between the two diseases. n.s. P>0.05; * P ≤0.05; ** P≤0.01; *** P ≤0.001.
Supplementary Figure S1 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis
Authors: Meuser Elena , Chang Kyle , Walters Angharad , Hurley Joanna J. , West Hannah D. , Perry Iain , Mort Matthew , Reyes-Uribe Laura , Truscott Rebekah , Jones Nicholas , Lawrence Rachel , Jenkins Gareth , Giles Peter , Dolwani Sunil , Al-Sarireh Bilal , Hawkes Neil , Short Emma , Williams Geraint T. , Taggart Melissa W. , Luetchford Kim , Lynch Patrick M. , Terlouw Diantha , Nielsen Maartje , Walton Sarah-Jane , Latchford Andrew , Clark Susan K. , Sampson Julian R. , Vilar Eduardo , Thomas Laura E.
Published: June 2024

Whole transcriptome sequencing quality control and read distribution for data sets from Cardiff and MD Anderson. A. Sequencing quality assessment, batch aggregates are shown. B. Read distribution across the genome per batch demonstrating that over 80% of reads mapped to known exons. CDS=Coding sequence; MDA=MD Anderson Cancer Center data; TES=Transcription end site; TSS=Transcription start site; UTR=Untranslated region.
Figure 3 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis
Authors: Meuser Elena , Chang Kyle , Walters Angharad , Hurley Joanna J. , West Hannah D. , Perry Iain , Mort Matthew , Reyes-Uribe Laura , Truscott Rebekah , Jones Nicholas , Lawrence Rachel , Jenkins Gareth , Giles Peter , Dolwani Sunil , Al-Sarireh Bilal , Hawkes Neil , Short Emma , Williams Geraint T. , Taggart Melissa W. , Luetchford Kim , Lynch Patrick M. , Terlouw Diantha , Nielsen Maartje , Walton Sarah-Jane , Latchford Andrew , Clark Susan K. , Sampson Julian R. , Vilar Eduardo , Thomas Laura E.
Published: June 2024

Volcano plot of DEGs of FAP and MAP patients with and without PIGA mutation. Genes have been filtered to remove those with a mean expression ≤10 read counts. Red dots indicate DEGs with Padj ≤ 0.01 at ≥±1.5 LFC. Purple dots indicate genes with a Padj ≤ 0.01 but ≤±1.5 LFC. Nonsignificant genes are greyed out. Highly DEGs are highlighted, including CD36, TREH, and LPD8. HLA-DRA1 has been transformed (diamond) from −10.3 LFC to fit on the plot.
Figure 2 from PIGA Mutations and Glycosylphosphatidylinositol Anchor Dysregulation in Polyposis-Associated Duodenal Tumorigenesis
Authors: Meuser Elena , Chang Kyle , Walters Angharad , Hurley Joanna J. , West Hannah D. , Perry Iain , Mort Matthew , Reyes-Uribe Laura , Truscott Rebekah , Jones Nicholas , Lawrence Rachel , Jenkins Gareth , Giles Peter , Dolwani Sunil , Al-Sarireh Bilal , Hawkes Neil , Short Emma , Williams Geraint T. , Taggart Melissa W. , Luetchford Kim , Lynch Patrick M. , Terlouw Diantha , Nielsen Maartje , Walton Sarah-Jane , Latchford Andrew , Clark Susan K. , Sampson Julian R. , Vilar Eduardo , Thomas Laura E.
Published: June 2024

Flow cytometry analysis of FLAER positive cells in 11 FAP duodenal organoids with and without somatic PIGA variants. Fluorescence from FLAER is detected using the FITC-A channel (emission:475–650 nm). A, Abundance of FLAER positive cells detected in organoid lines with and without PIGA somatic mutations demonstrating lack of FLAER positive cells in PIGA mutant lines, indicating loss of GPI-anchors (Supplementary Table S2). B, Representative histogram of FITC-A/FLAER (selecting for FLAER positive cells), light grey = wild-type adenoma, dark grey = PIGA mutant adenoma. Repeats are denoted with a black triangle, circle, and square.
Supplementary Table 7 from Surgical Tumor Resection Deregulates Hallmarks of Cancer in Resected Tissue and the Surrounding Microenvironment
Authors: Chaubal Rohan , Gardi Nilesh , Joshi Shalaka , Pantvaidya Gouri , Kadam Rasika , Vanmali Vaibhav , Hawaldar Rohini , Talker Elizabeth , Chitra Jaya , Gera Poonam , Bhatia Dimple , Kalkar Prajakta , Gurav Mamta , Shetty Omshree , Desai Sangeeta , Krishnan Neeraja M. , Nair Nita , Parmar Vani , Dutt Amit , Panda Binay , Gupta Sudeep , Badwe Rajendra
Published: June 2024

Supplementary Table 7 shows Genes de-regulated between various time-points during surgery in HNSCC Microarray data.
Supplementary Table 6 from Surgical Tumor Resection Deregulates Hallmarks of Cancer in Resected Tissue and the Surrounding Microenvironment
Authors: Chaubal Rohan , Gardi Nilesh , Joshi Shalaka , Pantvaidya Gouri , Kadam Rasika , Vanmali Vaibhav , Hawaldar Rohini , Talker Elizabeth , Chitra Jaya , Gera Poonam , Bhatia Dimple , Kalkar Prajakta , Gurav Mamta , Shetty Omshree , Desai Sangeeta , Krishnan Neeraja M. , Nair Nita , Parmar Vani , Dutt Amit , Panda Binay , Gupta Sudeep , Badwe Rajendra
Published: June 2024

Supplementary Table 6 shows the Clinical characteristics of CA HNSCC patients. All staging was done using AJCC 7th edition of the Oral cavity cancer staging systems.
Supplementary Table 4 from Surgical Tumor Resection Deregulates Hallmarks of Cancer in Resected Tissue and the Surrounding Microenvironment
Authors: Chaubal Rohan , Gardi Nilesh , Joshi Shalaka , Pantvaidya Gouri , Kadam Rasika , Vanmali Vaibhav , Hawaldar Rohini , Talker Elizabeth , Chitra Jaya , Gera Poonam , Bhatia Dimple , Kalkar Prajakta , Gurav Mamta , Shetty Omshree , Desai Sangeeta , Krishnan Neeraja M. , Nair Nita , Parmar Vani , Dutt Amit , Panda Binay , Gupta Sudeep , Badwe Rajendra
Published: June 2024

Supplementary Table 4 shows Genes deregulated in replicate analysis for breast cancer patients with their log-fold change values.
Supplementary Table 2 from Surgical Tumor Resection Deregulates Hallmarks of Cancer in Resected Tissue and the Surrounding Microenvironment
Authors: Chaubal Rohan , Gardi Nilesh , Joshi Shalaka , Pantvaidya Gouri , Kadam Rasika , Vanmali Vaibhav , Hawaldar Rohini , Talker Elizabeth , Chitra Jaya , Gera Poonam , Bhatia Dimple , Kalkar Prajakta , Gurav Mamta , Shetty Omshree , Desai Sangeeta , Krishnan Neeraja M. , Nair Nita , Parmar Vani , Dutt Amit , Panda Binay , Gupta Sudeep , Badwe Rajendra
Published: June 2024

Supplementary Table 2 shows the 4854 unique genes found to be de-regulated in any one comparison across all comparisons for AvB, BvC and AvC in for breast cancer individual patient specific RNA-Seq analysis.
Supplementary Table 10 from Surgical Tumor Resection Deregulates Hallmarks of Cancer in Resected Tissue and the Surrounding Microenvironment
Authors: Chaubal Rohan , Gardi Nilesh , Joshi Shalaka , Pantvaidya Gouri , Kadam Rasika , Vanmali Vaibhav , Hawaldar Rohini , Talker Elizabeth , Chitra Jaya , Gera Poonam , Bhatia Dimple , Kalkar Prajakta , Gurav Mamta , Shetty Omshree , Desai Sangeeta , Krishnan Neeraja M. , Nair Nita , Parmar Vani , Dutt Amit , Panda Binay , Gupta Sudeep , Badwe Rajendra
Published: June 2024

Supplementary Table 10 shows Genes de-regulated between normal at start of surgery and tumour tissues at differing points of surgery in HNSCC Microarray data.
Supplementary Table 1 from Surgical Tumor Resection Deregulates Hallmarks of Cancer in Resected Tissue and the Surrounding Microenvironment
Authors: Chaubal Rohan , Gardi Nilesh , Joshi Shalaka , Pantvaidya Gouri , Kadam Rasika , Vanmali Vaibhav , Hawaldar Rohini , Talker Elizabeth , Chitra Jaya , Gera Poonam , Bhatia Dimple , Kalkar Prajakta , Gurav Mamta , Shetty Omshree , Desai Sangeeta , Krishnan Neeraja M. , Nair Nita , Parmar Vani , Dutt Amit , Panda Binay , Gupta Sudeep , Badwe Rajendra
Published: June 2024

Supplementary Table 1 shows the Breast cancer patient assay distribution and clinical info
Supplementary Figure 4 from Surgical Tumor Resection Deregulates Hallmarks of Cancer in Resected Tissue and the Surrounding Microenvironment
Authors: Chaubal Rohan , Gardi Nilesh , Joshi Shalaka , Pantvaidya Gouri , Kadam Rasika , Vanmali Vaibhav , Hawaldar Rohini , Talker Elizabeth , Chitra Jaya , Gera Poonam , Bhatia Dimple , Kalkar Prajakta , Gurav Mamta , Shetty Omshree , Desai Sangeeta , Krishnan Neeraja M. , Nair Nita , Parmar Vani , Dutt Amit , Panda Binay , Gupta Sudeep , Badwe Rajendra
Published: June 2024

Supplementary Figure 4 shows the ClueGO Gene Ontology analysis for 85 genes de-regulated in both patient-specific analysis and replicate analysis for breast cancer RNA-Seq data.
Supplementary Figure 2 from Surgical Tumor Resection Deregulates Hallmarks of Cancer in Resected Tissue and the Surrounding Microenvironment
Authors: Chaubal Rohan , Gardi Nilesh , Joshi Shalaka , Pantvaidya Gouri , Kadam Rasika , Vanmali Vaibhav , Hawaldar Rohini , Talker Elizabeth , Chitra Jaya , Gera Poonam , Bhatia Dimple , Kalkar Prajakta , Gurav Mamta , Shetty Omshree , Desai Sangeeta , Krishnan Neeraja M. , Nair Nita , Parmar Vani , Dutt Amit , Panda Binay , Gupta Sudeep , Badwe Rajendra
Published: June 2024

Supplementary Figure 2 shows unsupervised clustering of Breast Cancer patients based on genome-wide expression counts.
Supplementary Figure 1 from Surgical Tumor Resection Deregulates Hallmarks of Cancer in Resected Tissue and the Surrounding Microenvironment
Authors: Chaubal Rohan , Gardi Nilesh , Joshi Shalaka , Pantvaidya Gouri , Kadam Rasika , Vanmali Vaibhav , Hawaldar Rohini , Talker Elizabeth , Chitra Jaya , Gera Poonam , Bhatia Dimple , Kalkar Prajakta , Gurav Mamta , Shetty Omshree , Desai Sangeeta , Krishnan Neeraja M. , Nair Nita , Parmar Vani , Dutt Amit , Panda Binay , Gupta Sudeep , Badwe Rajendra
Published: June 2024

Supplementary Figure 1 shows the effect of various transformation methods on RNA-Seq data from breast cancer patients.