bluuebunny/crossref_metadata_2025 huggingface dataset:
Data from Amplified EPOR/JAK2 Genes Define a Unique Subtype of Acute Erythroid Leukemia
Authors: Takeda June , Yoshida Kenichi , Nakagawa Masahiro M. , Nannya Yasuhito , Yoda Akinori , Saiki Ryunosuke , Ochi Yotaro , Zhao Lanying , Okuda Rurika , Qi Xingxing , Mori Takuto , Kon Ayana , Chiba Kenichi , Tanaka Hiroko , Shiraishi Yuichi , Kuo Ming-Chung , Kerr Cassandra M. , Nagata Yasunobu , Morishita Daisuke , Hiramoto Nobuhiro , Hangaishi Akira , Nakazawa Hideyuki , Ishiyama Ken , Miyano Satoru , Chiba Shigeru , Miyazaki Yasushi , Kitano Toshiyuki , Usuki Kensuke , Sezaki Nobuo , Tsurumi Hisashi , Miyawaki Shuichi , Maciejewski Jaroslaw P. , Ishikawa Takayuki , Ohyashiki Kazuma , Ganser Arnold , Heuser Michael , Thol Felicitas , Shih Lee-Yung , Takaori-Kondo Akifumi , Makishima Hideki , Ogawa Seishi
Published: April 2023

Abstract
Acute erythroid leukemia (AEL) is a unique subtype of acute myeloid leukemia characterized by prominent erythroid proliferation whose molecular basis is poorly understood. To elucidate the underlying mechanism of erythroid proliferation, we analyzed 121 AEL using whole-genome, whole-exome, and/or targeted-capture sequencing, together with transcriptome analysis of 21 AEL samples. Combining publicly available sequencing data, we found a high frequency of gains and amplifications involving EPOR/JAK2 in TP53-mutated cases, particularly those having >80% erythroblasts designated as pure erythroid leukemia (10/13). These cases were frequently accompanied by gains and amplifications of ERG/ETS2 and associated with a very poor prognosis, even compared with other TP53-mutated AEL. In addition to activation of the STAT5 pathway, a common feature across all AEL cases, these AEL cases exhibited enhanced cell proliferation and heme metabolism and often showed high sensitivity to ruxolitinib in vitro and in xenograft models, highlighting a potential role of JAK2 inhibition in therapeutics of AEL.
Significance:
This study reveals the major role of gains, amplifications, and mutations of EPOR and JAK2 in the pathogenesis of pure erythroleukemia. Their frequent response to ruxolitinib in patient-derived xenograft and cell culture models highlights a possible therapeutic role of JAK2 inhibition for erythroleukemia with EPOR/JAK2-involving lesions.

This article is highlighted in the In This Issue feature, p. 369
Data from Pharmacogenomic Profiling of Pediatric Acute Myeloid Leukemia to Identify Therapeutic Vulnerabilities and Inform Functional Precision Medicine
Authors: Wang Han , Chan Kathy Yuen Yee , Cheng Chi Keung , Ng Margaret H.L. , Lee Po Yi , Cheng Frankie Wai Tsoi , Lam Grace Kee See , Chow Tin Wai , Ha Shau Yin , Chiang Alan K.S. , Leung Wing Hang , Leung Anskar Y.H. , Wang Chi Chiu , Zhang Tao , Zhang Xiao-Bing , So Chi Chiu , Yuen Yuet Ping , Sun Qiwei , Zhang Chi , Xu Yaqun , Cheung John Tak Kit , Ng Wing Hei , Tang Patrick Ming-Kuen , Kang Wei , To Ka-Fai , Lee Wayne Yuk Wai , Wong Raymond S.M. , Poon Ellen Ngar Yun , Zhao Qi , Huang Junbin , Chen Chun , Yuen Patrick Man Pan , Li Chi-kong , Leung Alex Wing Kwan , Leung Kam Tong
Published: April 2023

Abstract
Despite the expanding portfolio of targeted therapies for adults with acute myeloid leukemia (AML), direct implementation in children is challenging due to inherent differences in underlying genetics. Here we established the pharmacologic profile of pediatric AML by screening myeloblast sensitivity to approved and investigational agents, revealing candidates of immediate clinical relevance. Drug responses ex vivo correlated with patient characteristics, exhibited age-specific alterations, and concorded with activities in xenograft models. Integration with genomic data uncovered new gene–drug associations, suggesting actionable therapeutic vulnerabilities. Transcriptome profiling further identified gene-expression signatures associated with on- and off-target drug responses. We also demonstrated the feasibility of drug screening–guided treatment for children with high-risk AML, with two evaluable cases achieving remission. Collectively, this study offers a high-dimensional gene–drug clinical data set that could be leveraged to research the unique biology of pediatric AML and sets the stage for realizing functional precision medicine for the clinical management of the disease.
Significance:
We conducted integrated drug and genomic profiling of patient biopsies to build the functional genomic landscape of pediatric AML. Age-specific differences in drug response and new gene–drug interactions were identified. The feasibility of functional precision medicine–guided management of children with high-risk AML was successfully demonstrated in two evaluable clinical cases.

This article is highlighted in the In This Issue feature, p. 476
Data from PU.1-Dependent Enhancer Inhibition Separates Tet2-Deficient Hematopoiesis from Malignant Transformation
Authors: Aivalioti Maria M. , Bartholdy Boris A. , Pradhan Kith , Bhagat Tushar D. , Zintiridou Aliona , Jeong Jong Jin , Thiruthuvanathan Victor J. , Pujato Mario , Paranjpe Aditi , Zhang Chi , Levine Ross L. , Viny Aaron D. , Wickrema Amittha , Verma Amit , Will Britta
Published: April 2023

Abstract
Cytosine hypermethylation in and around DNA-binding sites of master transcription factors, including PU.1, occurs in aging hematopoietic stem cells following acquired loss-of-function mutations of DNA methyl-cytosine dioxygenase ten–eleven translocation-2 (TET2), albeit functional relevance has been unclear. We show that Tet2-deficient mouse hematopoietic stem and progenitor cells undergo malignant transformation upon compromised gene regulation through heterozygous deletion of an upstream regulatory region (UREΔ/WT) of the PU.1 gene. Although compatible with multilineage blood formation at young age, Tet2-deficient PU.1 UREΔ/WT mice develop highly penetrant, transplantable acute myeloid leukemia (AML) during aging. Leukemic stem and progenitor cells show hypermethylation at putative PU.1-binding sites, fail to activate myeloid enhancers, and are hallmarked by a signature of genes with impaired expression shared with human AML. Our study demonstrates that Tet2 and PU.1 jointly suppress leukemogenesis and uncovers a methylation-sensitive PU.1-dependent gene network as a unifying molecular vulnerability associated with AML.
Significance:
We identify moderately impaired PU.1 mRNA expression as a biological modality predisposing Tet2-deficient hematopoietic stem and progenitor cells to malignant transformation. Our study furthermore uncovers a methylation-sensitive PU.1 gene network as a common feature of myeloid leukemia potentially allowing for the identification of patients at risk for malignant transformation.

See related commentary by Schleicher and Pietras, p. 378.

This article is highlighted in the In This Issue feature, p. 369
Data from Progenitor Hierarchy of Chronic Myelomonocytic Leukemia Identifies Inflammatory Monocytic-Biased Trajectory Linked to Worse Outcomes
Authors: Ferrall-Fairbanks Meghan C. , Dhawan Abhishek , Johnson Brian , Newman Hannah , Volpe Virginia , Letson Christopher , Ball Markus , Hunter Anthony M. , Balasis Maria E. , Kruer Traci , Ben-Crentsil Nana Adjoa , Kroeger Jodi L. , Balderas Robert , Komrokji Rami S. , Sallman David A. , Zhang Jing , Bejar Rafael , Altrock Philipp M. , Padron Eric
Published: April 2023

Abstract
Myeloblast expansion is a hallmark of disease progression and comprises CD34+ hematopoietic stem and progenitor cells (HSPC). How this compartment evolves during disease progression in chronic myeloid neoplasms is unknown. Using single-cell RNA sequencing and high-parameter flow cytometry, we show that chronic myelomonocytic leukemia (CMML) CD34+ HSPC can be classified into three differentiation trajectories: monocytic, megakaryocyte-erythroid progenitor (MEP), and normal-like. Hallmarks of monocytic-biased trajectory were enrichment of CD120b+ inflammatory granulocyte–macrophage progenitor (GMP)-like cells, activated cytokine receptor signaling, phenotypic hematopoietic stem cell (HSC) depletion, and adverse outcomes. Cytokine receptor diversity was generally an adverse feature and elevated in CD120b+ GMPs. Hypomethylating agents decreased monocytic-biased cells in CMML patients. Given the enrichment of RAS pathway mutations in monocytic-biased cells, NRAS-competitive transplants and LPS-treated xenograft models recapitulated monocytic-biased CMML, suggesting that hematopoietic stress precipitates the monocytic-biased state. Deconvolution of HSPC compartments in other myeloid neoplasms and identifying therapeutic strategies to mitigate the monocytic-biased differentiation trajectory should be explored.
Significance:
Our findings establish that multiple differentiation states underlie CMML disease progression. These states are negatively augmented by inflammation and positively affected by hypomethylating agents. Furthermore, we identify HSC depletion and expansion of GMP-like cells with increased cytokine receptor diversity as a feature of myeloblast expansion in inflammatory chronic myeloid neoplasms.

This article is highlighted in the In This Issue feature, p. 476
Data from A Therapeutically Targetable NOTCH1–SIRT1–KAT7 Axis in T-cell Leukemia
Authors: Lancho Olga , Singh Amartya , da Silva-Diz Victoria , Aleksandrova Maya , Khatun Jesminara , Tottone Luca , Nunes Patricia Renck , Luo Shirley , Zhao Caifeng , Zheng Haiyan , Chiles Eric , Zuo Zhenyu , Rocha Pedro P. , Su Xiaoyang , Khiabanian Hossein , Herranz Daniel
Published: April 2023

Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is a NOTCH1-driven disease in need of novel therapies. Here, we identify a NOTCH1–SIRT1–KAT7 link as a therapeutic vulnerability in T-ALL, in which the histone deacetylase SIRT1 is overexpressed downstream of a NOTCH1-bound enhancer. SIRT1 loss impaired leukemia generation, whereas SIRT1 overexpression accelerated leukemia and conferred resistance to NOTCH1 inhibition in a deacetylase-dependent manner. Moreover, pharmacologic or genetic inhibition of SIRT1 resulted in significant antileukemic effects. Global acetyl proteomics upon SIRT1 loss uncovered hyperacetylation of KAT7 and BRD1, subunits of a histone acetyltransferase complex targeting H4K12. Metabolic and gene-expression profiling revealed metabolic changes together with a transcriptional signature resembling KAT7 deletion. Consistently, SIRT1 loss resulted in reduced H4K12ac, and overexpression of a nonacetylatable KAT7-mutant partly rescued SIRT1 loss-induced proliferation defects. Overall, our results uncover therapeutic targets in T-ALL and reveal a circular feedback mechanism balancing deacetylase/acetyltransferase activation with potentially broad relevance in cancer.
Significance:
We identify a T-ALL axis whereby NOTCH1 activates SIRT1 through an enhancer region, and SIRT1 deacetylates and activates KAT7. Targeting SIRT1 shows antileukemic effects, partly mediated by KAT7 inactivation. Our results reveal T-ALL therapeutic targets and uncover a rheostat mechanism between deacetylase/acetyltransferase activities with potentially broader cancer relevance.

This article is highlighted in the In This Issue feature, p. 1
Data from Impaired SARS-CoV-2 Variant Neutralization and CD8+ T-cell Responses Following 3 Doses of mRNA Vaccines in Myeloma: Correlation with Breakthrough Infections
Authors: Azeem Maryam I. , Nooka Ajay K. , Shanmugasundaram Uma , Cheedarla Narayanaiah , Potdar Sayalee , Manalo Renee Julia , Moreno Alberto , Switchenko Jeffrey M. , Cheedarla Suneethamma , Doxie Deon Bryant , Radzievski Roman , Ellis Madison Leigh , Manning Kelly E. , Wali Bushra , Valanparambil Rajesh M. , Maples Kathryn T. , Baymon Essence , Kaufman Jonathan L. , Hofmeister Craig C. , Joseph Nisha S. , Lonial Sagar , Roback John D. , Sette Alessandro , Ahmed Rafi , Suthar Mehul S. , Neish Andrew S. , Dhodapkar Madhav V. , Dhodapkar Kavita M.
Published: April 2023

Abstract
Patients with multiple myeloma (MM) mount suboptimal neutralizing antibodies (nAb) following 2 doses of SARS-CoV-2 mRNA vaccines. Currently, circulating SARS-CoV-2 variants of concern (VOC) carry the risk of breakthrough infections. We evaluated immune recognition of current VOC including BA.1, BA.2, and BA.5 in 331 racially representative patients with MM following 2 or 3 doses of mRNA vaccines. The third dose increased nAbs against WA1 in 82%, but against BA variants in only 33% to 44% of patients. Vaccine-induced nAbs correlated with receptor-binding domain (RBD)–specific class-switched memory B cells. Vaccine-induced spike-specific T cells were detected in patients without seroconversion and cross-recognized variant-specific peptides but were predominantly CD4+ T cells. Detailed clinical/immunophenotypic analysis identified features correlating with nAb/B/T-cell responses. Patients who developed breakthrough infections following 3 vaccine doses had lower live-virus nAbs, including against VOC. Patients with MM remain susceptible to SARS-CoV-2 variants following 3 vaccine doses and should be prioritized for emerging approaches to elicit variant-nAb and CD8+ T cells.
Significance:
Three doses of SARS-CoV-2 mRNA vaccines fail to yield detectable VOC nAbs in nearly 60% and spike-specific CD8+ T cells in >80% of myeloma patients. Patients who develop breakthrough infections following vaccination have low levels of live-virus nAb.

This article is highlighted in the In This Issue feature, p. 101
Supplementary Data S6 from Multiple germline events contribute to cancer development in patients with Li-Fraumeni syndrome
Authors: Subasri Vallijah , Light Nicholas , Kanwar Nisha , Brzezinski Jack , Luo Ping , Hansford Jordan R , Cairney Elizabeth , Portwine Carol , Elser Christine , Finlay Jonathan L. , Nichols Kim E. , Alon Noa , Brunga Ledia , Anson Jo , Kohlmann Wendy , de Andrade Kelvin C. , Khincha Payal P. , Savage Sharon A. , Schiffman Joshua D , Weksberg Rosanna , Pugh Trevor J. , Villani Anita , Shlien Adam , Goldenberg Anna , Malkin David
Published: April 2023

cisCSCE
Supplementary Data S2 from Multiple germline events contribute to cancer development in patients with Li-Fraumeni syndrome
Authors: Subasri Vallijah , Light Nicholas , Kanwar Nisha , Brzezinski Jack , Luo Ping , Hansford Jordan R , Cairney Elizabeth , Portwine Carol , Elser Christine , Finlay Jonathan L. , Nichols Kim E. , Alon Noa , Brunga Ledia , Anson Jo , Kohlmann Wendy , de Andrade Kelvin C. , Khincha Payal P. , Savage Sharon A. , Schiffman Joshua D , Weksberg Rosanna , Pugh Trevor J. , Villani Anita , Shlien Adam , Goldenberg Anna , Malkin David
Published: April 2023

Tier 1-3 Gene Lists
Supplementary Figures 1-4, Tables 1-2 from Inhibitor of the Nuclear Transport Protein XPO1 Enhances the Anticancer Efficacy of KRAS G12C Inhibitors in Preclinical Models of KRAS G12C–Mutant Cancers
Authors: Khan Husain Yar , Nagasaka Misako , Li Yiwei , Aboukameel Amro , Uddin Md. Hafiz , Sexton Rachel , Bannoura Sahar , Mzannar Yousef , Al-Hallak Mohammed Najeeb , Kim Steve , Beydoun Rafic , Landesman Yosef , Mamdani Hirva , Uprety Dipesh , Philip Philip A. , Mohammad Ramzi M. , Shields Anthony F. , Azmi Asfar S.
Published: April 2023

Supplementary Figure 1. XPO1-KRAS synthetic lethal interaction identified using the Slorth database. Supplementary Figure 2. KRAS WT, KRAS G12D and KRAS G12V MEF cell lines were refractory to growth inhibition by selinexor or MRTX1257 or their combinations. Supplementary Figure 3. KRAS G12D mutant PDAC cell line Panc-1 was refractory to growth inhibition by KRAS G12C inhibitor AMG510. Supplementary Figure 4. Body weights of mice xenografted with MiaPaCa2 tumors were measured during the treatment period. Supplementary Table 1. Sequences of primers used. Supplementary Table 2. Combination Index (CI) values at various dose combinations of the drugs tested on different KRAS G12C mutant cell lines.
Supplementary Data from MYC Inhibition Halts Metastatic Breast Cancer Progression by Blocking Growth, Invasion, and Seeding
Authors: Massó-Vallés Daniel , Beaulieu Marie-Eve , Jauset Toni , Giuntini Fabio , Zacarías-Fluck Mariano F. , Foradada Laia , Martínez-Martín Sandra , Serrano Erika , Martín-Fernández Génesis , Casacuberta-Serra Sílvia , Castillo Cano Virginia , Kaur Jastrinjan , López-Estévez Sergio , Morcillo Miguel Ángel , Alzrigat Mohammad , Mahmoud Loay , Luque-García Antonio , Escorihuela Marta , Guzman Marta , Arribas Joaquín , Serra Violeta , Larsson Lars-Gunnar , Whitfield Jonathan R. , Soucek Laura
Published: April 2023

Supplementary Figures 1-6 and Supplementary Tables 1-2
Supplement 6 from The Vaginal Microbiome is Associated with Endometrial Cancer Grade and Histology
Authors: Hakimjavadi Hesamedin , George Sophia H. , Taub Michael , Dodds Leah V. , Sanchez-Covarrubias Alex P. , Huang Marilyn , Pearson J. Matt , Slomovitz Brian M. , Kobetz Erin N. , Gharaibeh Raad , Sowamber Ramlogan , Pinto Andre , Chamala Srikar , Schlumbrecht Matthew P.
Published: April 2023

Heatmap of protein functions
Supplement 3 from The Vaginal Microbiome is Associated with Endometrial Cancer Grade and Histology
Authors: Hakimjavadi Hesamedin , George Sophia H. , Taub Michael , Dodds Leah V. , Sanchez-Covarrubias Alex P. , Huang Marilyn , Pearson J. Matt , Slomovitz Brian M. , Kobetz Erin N. , Gharaibeh Raad , Sowamber Ramlogan , Pinto Andre , Chamala Srikar , Schlumbrecht Matthew P.
Published: April 2023

Individual Specimen Reads
Figure S8 from Inhibiting ERK5 Overcomes Breast Cancer Resistance to Anti-HER2 Therapy By Targeting the G1–S Cell-Cycle Transition
Authors: Zhang Jingwei , Pearson Adam J. , Sabherwal Nitin , Telfer Brian A. , Ali Nisha , Kan Karmern , Xu Qiuping , Zhang Wei , Chen Fuhui , Li Shiyang , Wang Jinhua , Gray Nathanael S. , Risa-Ebrí Blanca , Finegan Katherine G. , Cross Michael J. , Giurisato Emanuele , Whitmarsh Alan J. , Tournier Cathy
Published: April 2023

AX-15836 and BIX-02189 reproduce the inhibitory effect of JWG-045 on the level of phospho-RB and MDA-MB-361 cell density.
Figure S6 from Inhibiting ERK5 Overcomes Breast Cancer Resistance to Anti-HER2 Therapy By Targeting the G1–S Cell-Cycle Transition
Authors: Zhang Jingwei , Pearson Adam J. , Sabherwal Nitin , Telfer Brian A. , Ali Nisha , Kan Karmern , Xu Qiuping , Zhang Wei , Chen Fuhui , Li Shiyang , Wang Jinhua , Gray Nathanael S. , Risa-Ebrí Blanca , Finegan Katherine G. , Cross Michael J. , Giurisato Emanuele , Whitmarsh Alan J. , Tournier Cathy
Published: April 2023

The effect of lapatinib and JWG-045 as single treatments was compared to that achieved in combination therapy on the cell cycle profile of sensitive and resistant breast cancer cell lines.
Figure S3 from Inhibiting ERK5 Overcomes Breast Cancer Resistance to Anti-HER2 Therapy By Targeting the G1–S Cell-Cycle Transition
Authors: Zhang Jingwei , Pearson Adam J. , Sabherwal Nitin , Telfer Brian A. , Ali Nisha , Kan Karmern , Xu Qiuping , Zhang Wei , Chen Fuhui , Li Shiyang , Wang Jinhua , Gray Nathanael S. , Risa-Ebrí Blanca , Finegan Katherine G. , Cross Michael J. , Giurisato Emanuele , Whitmarsh Alan J. , Tournier Cathy
Published: April 2023

Lapatinib treatment inhibits tyrosine phosphorylation of HER1/2/3 in both sensitive and resistant breast cancer cells.
Figure S10 from Inhibiting ERK5 Overcomes Breast Cancer Resistance to Anti-HER2 Therapy By Targeting the G1–S Cell-Cycle Transition
Authors: Zhang Jingwei , Pearson Adam J. , Sabherwal Nitin , Telfer Brian A. , Ali Nisha , Kan Karmern , Xu Qiuping , Zhang Wei , Chen Fuhui , Li Shiyang , Wang Jinhua , Gray Nathanael S. , Risa-Ebrí Blanca , Finegan Katherine G. , Cross Michael J. , Giurisato Emanuele , Whitmarsh Alan J. , Tournier Cathy
Published: April 2023

Inhibition of ERK5 by AX-15836 or MEK5 by BIX-02189 enhance HER2+ breast cancer cell sensitivity to trastuzumab through decreasing RB phosphorylation.
Supplemental Table 4 from Race-associated Molecular Changes in Gynecologic Malignancies
Authors: Asare Amma , Yao Hui , Lara Olivia D. , Wang Ying , Zhang Lin , Sood Anil K.
Published: April 2023

Differentially expressed microRNAs in Pan-Gyn cohort EA vs AA
Table S3 from Targeting the Ezrin Adaptor Protein Sensitizes Metastatic Breast Cancer Cells to Chemotherapy and Reduces Neoadjuvant Therapy–induced Metastasis
Authors: Hoskin Victoria , Ghaffari Abdi , Laight Brian J. , SenGupta Sandip , Madarnas Yolanda , Nicol Christopher J.B. , Elliott Bruce E. , Varma Sonal , Greer Peter A.
Published: April 2023

Drug synergy analysis of DOX or DTX in combination with NSC
Table S2 from Targeting the Ezrin Adaptor Protein Sensitizes Metastatic Breast Cancer Cells to Chemotherapy and Reduces Neoadjuvant Therapy–induced Metastasis
Authors: Hoskin Victoria , Ghaffari Abdi , Laight Brian J. , SenGupta Sandip , Madarnas Yolanda , Nicol Christopher J.B. , Elliott Bruce E. , Varma Sonal , Greer Peter A.
Published: April 2023

Summary of IC50 values
Figure S6 from Targeting the Ezrin Adaptor Protein Sensitizes Metastatic Breast Cancer Cells to Chemotherapy and Reduces Neoadjuvant Therapy–induced Metastasis
Authors: Hoskin Victoria , Ghaffari Abdi , Laight Brian J. , SenGupta Sandip , Madarnas Yolanda , Nicol Christopher J.B. , Elliott Bruce E. , Varma Sonal , Greer Peter A.
Published: April 2023

Ezrin protein expression after DOX and DTX drug challenge
Figure S5 from Targeting the Ezrin Adaptor Protein Sensitizes Metastatic Breast Cancer Cells to Chemotherapy and Reduces Neoadjuvant Therapy–induced Metastasis
Authors: Hoskin Victoria , Ghaffari Abdi , Laight Brian J. , SenGupta Sandip , Madarnas Yolanda , Nicol Christopher J.B. , Elliott Bruce E. , Varma Sonal , Greer Peter A.
Published: April 2023

Anti-ezrin treatment does not alter levels of circulating tumor cells in vivo
Supplementary Data S1 from Depletion of Mannose Receptor–Positive Tumor-associated Macrophages via a Peptide-targeted Star-shaped Polyglutamate Inhibits Breast Cancer Progression in Mice
Authors: Lepland Anni , Malfanti Alessio , Haljasorg Uku , Asciutto Eliana K. , Pickholz Monica , Bringas Mauro , Đorđević Snežana , Salumäe Liis , Peterson Pärt , Teesalu Tambet , Vicent María J. , Scodeller Pablo
Published: April 2023

One .docx word file containing the following information:

Scheme S1. Synthetic approach for St-PGA-OG-mUNO.

Scheme S2. Synthetic approach for OximUNO.

Video S1. Fifty ns MD trajectory of St-PGA in solution.

Table S1. St-PGA-OG-mUNO and St-PGA-OG dye loading, mUNO loading, size and charge.

Table S2. OximUNO and St-PGA-DOX drug loading, mUNO loading, size and charge.

Table S3. Hepatic and renal toxicity analysed following one dose of OximUNO.

Fig. S1. Representative characterisation of St-PGA-OG and St-PGA-OG-mUNO.

Fig. S2. The angle used to characterise the rotation of mUNO around PGA.

Fig. S3. St-PGA-OG-mUNO shows low hepatic accumulation in the orthotopic TNBC.

Fig. S4. Immunostaining showing CD206 expression in the liver compared to the saturated signal of CD206 in the orthotopic 4T1 tumour.

Fig. S5. Immunostaining of endogenous IgG indicates leaky tumour vasculature in the orthotopic 4T1 tumours.

Fig. S6. Distribution of St-PGA-OG-mUNO in the lung, spleen, sentinel lymph node (SLN) and kidney.

Fig. S7. St-PGA-OG-mUNO shows low hepatic accumulation in the experimental metastasis of TNBC.

Fig. S8. St-PGA-OG-mUNO shows higher receptor colocalisation than FAM-mUNO.

Fig. S9. St-PGA-OG-mUNO shows high homing to M2 TAMs in the orthotopic TNBC but higher hepatic accumulation with a higher dose.

Fig. S10. Representative characterisation of St-PGA-DOX and OximUNO.

Fig. S11. LC-MS method development for the determination of DOX in drug release studies and stability studies of OximUNO in i.p. fluid and dPBS.

Fig. S12. OximUNO shows no signs of hepatic or renal toxicity.

Fig. S13. H&E on healthy Balb/c mouse lung.

Fig. S14. Localisation of St-PGA-OG/St-PGA-OG-mUNO and tumour vessels.

Fig. S15. H&E staining of hearts from the treatment of orthotopic TNBC.

Fig. S16. A repetition of OximUNO treatment on the orthotopic TNBC monitoring tumour growth and survival.

Fig. S17. Flow cytometry plots for M2 and M1 macrophages.

Fig. S18. Flow cytometry gating for cytotoxic T lymphocytes (CTLs).

Fig. S19. Flow cytometry gating for T regulatory cells (Tregs).

Fig. S20. Flow cytometry analysis showing total cells.

Fig. S21. Treatment with OximUNO does not affect splenic macrophages.
Supplementary Figures 1-3 from Conduit CAR: Redirecting CAR T-Cell Specificity with A Universal and Adaptable Bispecific Antibody Platform
Authors: Borrok M. Jack , Li Yonghai , Harvilla Paul B. , Vellalore Maruthachalam Bharathikumar , Tamot Ninkka , Prokopowitz Christine , Chen Jun , Venkataramani Sathya , Grewal Iqbal S. , Ganesan Rajkumar , Singh Sanjaya
Published: April 2023

Supplementary Figure 1. Bispecific GLPB30 x anti-PSMA constructs run on an SDS page gel under non-reduced and reduced conditions. Supplementary Figure 2. Cytokine profiles of anti-CD19 CAR-T supernatants. Supplementary Figure 3. 96-hour CAR-T and BsAb cytotoxicity analysis.
Table S4 from A Phenogenetic Axis that Modulates Clinical Manifestation and Predicts Treatment Outcome in Primary Myeloid Neoplasms
Authors: Shen Qiujin , Feng Yahui , Gong Xiaowen , Jia Yujiao , Gao Qingyan , Jiao Xiaokang , Qi Saibing , Liu Xueou , Wei Hui , Huang Bingqing , Zhao Ningning , Song Xiaoqiang , Ma Yueshen , Liang Shihao , Zhang Donglei , Qin Li , Wang Ying , Qu Shiqiang , Zou Yao , Chen Yumei , Guo Ye , Yi Shuhua , An Gang , Jiao Zengtao , Zhang Song , Li Linfeng , Yan Jun , Wang Huijun , Song Zhen , Mi Yingchang , Qiu Lugui , Zhu Xiaofan , Wang Jianxiang , Xiao Zhijian , Chen Junren
Published: April 2023

Table S4. Experimental validation of next-generation sequencing variant calls by Sanger sequencing.
Table S2 from A Phenogenetic Axis that Modulates Clinical Manifestation and Predicts Treatment Outcome in Primary Myeloid Neoplasms
Authors: Shen Qiujin , Feng Yahui , Gong Xiaowen , Jia Yujiao , Gao Qingyan , Jiao Xiaokang , Qi Saibing , Liu Xueou , Wei Hui , Huang Bingqing , Zhao Ningning , Song Xiaoqiang , Ma Yueshen , Liang Shihao , Zhang Donglei , Qin Li , Wang Ying , Qu Shiqiang , Zou Yao , Chen Yumei , Guo Ye , Yi Shuhua , An Gang , Jiao Zengtao , Zhang Song , Li Linfeng , Yan Jun , Wang Huijun , Song Zhen , Mi Yingchang , Qiu Lugui , Zhu Xiaofan , Wang Jianxiang , Xiao Zhijian , Chen Junren
Published: April 2023

Table S2. Clinicopathologic characteristics of the 462 lymphoid neoplasm patients in THAMP.
Table S1 from A Phenogenetic Axis that Modulates Clinical Manifestation and Predicts Treatment Outcome in Primary Myeloid Neoplasms
Authors: Shen Qiujin , Feng Yahui , Gong Xiaowen , Jia Yujiao , Gao Qingyan , Jiao Xiaokang , Qi Saibing , Liu Xueou , Wei Hui , Huang Bingqing , Zhao Ningning , Song Xiaoqiang , Ma Yueshen , Liang Shihao , Zhang Donglei , Qin Li , Wang Ying , Qu Shiqiang , Zou Yao , Chen Yumei , Guo Ye , Yi Shuhua , An Gang , Jiao Zengtao , Zhang Song , Li Linfeng , Yan Jun , Wang Huijun , Song Zhen , Mi Yingchang , Qiu Lugui , Zhu Xiaofan , Wang Jianxiang , Xiao Zhijian , Chen Junren
Published: April 2023

Table S1. Clinicopathologic characteristics of the 730 myeloid neoplasm patients in THAMP.
Supplemental Table S1 from BRCA1-Associated RING Domain-1 (BARD1) Loss and GBP1 Expression Enhance Sensitivity to DNA Damage in Ewing Sarcoma
Authors: Maurer Lisa M. , Daley Jessica D. , Mukherjee Elina , Venier Rosemarie E. , Julian Claire M. , Bailey Nathanael G. , Jacobs Michelle F. , Kumar-Sinha Chandan , Raphael Haley , Periyapatna Nivitha , Weiss Kurt , Janeway Katherine A. , Mody Rajen , Lucas Peter C. , McAllister-Lucas Linda M. , Bailey Kelly M.
Published: April 2023

Benign germline BARD1 variants.
Fig S8 from World Trade Center Dust Exposure Promotes Cancer in PTEN-deficient Mouse Prostates
Authors: Wang Lin , Xu Yitian , Zhang Licheng , Kang Kyeongah , Kobryn Andriy , Portman Kensey , Gordon Ronald E , Pan Ping-Ying , Taioli Emanuela , Aaronson Stuart A , Chen Shu-Hsia , Mulholland David J
Published: April 2023

Fig. S8. Pseudo images showing the spatial distribution between representative clusters in WTC and non-WTC human prostate cancer cohorts.
Table S3 from Proteome Analysis of Pancreatic Tumors Implicates Extracellular Matrix in Patient Outcome
Authors: Silwal-Pandit Laxmi , Stålberg Stina M. , Johansson Henrik J. , Mermelekas Georgios , Lothe Inger Marie B. , Skrede Martina L. , Dalsgaard Astrid Marie , Nebdal Daniel J. H. , Helland Åslaug , Lingjærde Ole Christian , Labori Knut Jørgen , Skålhegg Bjørn S. , Lehtiö Janne , Kure Elin H.
Published: April 2023

Top 25% most variable proteins used in WGCNA
Table S12 from Proteome Analysis of Pancreatic Tumors Implicates Extracellular Matrix in Patient Outcome
Authors: Silwal-Pandit Laxmi , Stålberg Stina M. , Johansson Henrik J. , Mermelekas Georgios , Lothe Inger Marie B. , Skrede Martina L. , Dalsgaard Astrid Marie , Nebdal Daniel J. H. , Helland Åslaug , Lingjærde Ole Christian , Labori Knut Jørgen , Skålhegg Bjørn S. , Lehtiö Janne , Kure Elin H.
Published: April 2023

Univariate cox regression analysis (left) including clinical, pathological, and molecular variables. Multivariate cox regression analysis (right) including the variables with significant or trending association with patient survival in the univariate analysis.
Supplementary Data from Brain Neural Progenitors are New Predictive Biomarkers for Breast Cancer Hormonotherapy
Authors: Basseville Agnes , Cordier Chiara , Ben Azzouz Fadoua , Gouraud Wilfried , Lasla Hamza , Panloup Fabien , Campone Mario , Jézéquel Pascal
Published: April 2023

Supplementary Table S1: R package references

Supplementary Table S2: Merged Affymetrix cohort patient characteristics

Supplementary Table S3: Validation cohort patient characteristics

Supplementary Table S4: Algorithm parameter optimization

Supplementary Figure S1: Patient selection and algorithm pipeline configuration

Supplementary Figure S2: Generation of NervSign24

Supplementary Figure S3: ML-generated gene lists for the first signature and second signature generations

Supplementary Figure S4: Supplementary information related to Figure 2

Supplementary Figure S5: Supplementary information related to Figure 3

Supplementary Figure S6: Univariate Cox analyses in cohorts of patients with early or late recurrence

Supplementary Figure S7: Supplementary information related to Figure 4

Supplementary Figure S8: Multivariable and univariate Cox analyses in merged Affymetrix, METABRIC and Saal cohorts

Supplementary Figure S9: Correlation between nervous system mechanisms and NervSign97

Supplementary Figure S10: Kaplan-Meier analysis of previously published biomarkers
Supplementary File 1 (proteomics) from NetrinG1+ Cancer-Associated Fibroblasts Generate Unique Extracellular Vesicles that Support the Survival of Pancreatic Cancer Cells Under Nutritional Stress
Authors: Raghavan Kristopher S. , Francescone Ralph , Franco-Barraza Janusz , Gardiner Jaye C. , Vendramini-Costa Débora B. , Luong Tiffany , Pourmandi Narges , Andren Anthony , Kurimchak Alison , Ogier Charline , Campbell Paul M. , Duncan James S. , Lyssiotis Costas A. , Languino Lucia R. , Cukierman Edna
Published: April 2023

Spreadsheet including the proteomic analyses corresponding to the experiments indicated by the naming of the assorted tabs. Specific analysis parameters for each experiment are provided within the respective main figure legends.
Supplementary Tables 1-5 from Dietary Nonstarch Polysaccharide Intake and Risk of Colorectal Cancer: Findings from the Singapore Chinese Health Study
Authors: Yu Yi-Chuan , Paragomi Pedram , Jin Aizhen , Wang Renwei , Schoen Robert E. , Koh Woon-Puay , Yuan Jian-Min , Luu Hung N.
Published: April 2023

Supplementary Table 1. Distributions of baseline characteristics among study participants by levels of dietary fibers and non-starch polysaccharide intake, the Singapore Chinese Health Study, 1993-2015. Supplementary Table 2. Association between soluble, insoluble non-starch polysaccharide intake with the risk of colorectal cancer in the Singapore Chinese Health Study, 1993-2015. Supplementary Table 3. Risk of colorectal cancer in relation to dietary fiber intake levels, the Singapore Chinese Health Study, 1993-2015. Supplementary Table 4. Association between dietary fibers intake and dietary non-starch polysaccharide with the risk of colorectal cancer in the Singapore Chinese Health Study, 1993-2015, excluding cases and person-years within the first 2 years of observation. Supplementary Table 5. Food Composition Table of dietary fiber, soluble non-starch polysaccharide, and insoluble non-starch polysaccharide: The Singapore Chinese Health Study.
Figure S2 from A Phase I Study of Pelabresib (CPI-0610), a Small-Molecule Inhibitor of BET Proteins, in Patients with Relapsed or Refractory Lymphoma
Authors: Blum Kristie A. , Supko Jeffrey G. , Maris Michael B. , Flinn Ian W. , Goy Andre , Younes Anas , Bobba Suresh , Senderowicz Adrian M. , Efuni Sergey , Rippley Ronda , Colak Gozde , Trojer Patrick , Abramson Jeremy S.
Published: April 2023

Representative image of complete response after treatment with pelabresib.
Table S1 from Bintrafusp Alfa, an Anti-PD-L1:TGFβ Trap Fusion Protein, in Patients with ctDNA-positive, Liver-limited Metastatic Colorectal Cancer
Authors: Morris Van K. , Overman Michael J. , Lam Michael , Parseghian Christine M. , Johnson Benny , Dasari Arvind , Raghav Kanwal , Kee Bryan K. , Huey Ryan , Wolff Robert A. , Shen John Paul , Li June , Zorrilla Isabel , Tzeng Ching-Wei D. , Tran Cao Hop S. , Chun Yun Shin , Newhook Timothy E. , Vauthey Nicolas , Duose Dzifa , Luthra Raja , Haymaker Cara , Kopetz Scott
Published: April 2023

Supplemental Table S1
Supplementary qPCR Data qPCR1 from Loss of Vascular Endothelial Glutaminase Inhibits Tumor Growth and Metastasis, and Increases Sensitivity to Chemotherapy
Authors: Ngwa Verra M. , Edwards Deanna N. , Hwang Yoonha , Karno Breelyn , Wang Xiaoyong , Yan Chi , Richmond Ann , Brantley-Sieders Dana M. , Chen Jin
Published: April 2023

Excel file showing qPCR Data.
Supplementary Figure 10 from Remodeling of the Tumor Microenvironment Through PAK4 Inhibition Sensitizes Tumors to Immune Checkpoint Blockade
Authors: Abril-Rodriguez Gabriel , Torrejon Davis Y. , Karin Daniel , Campbell Katie M. , Medina Egmidio , Saco Justin D. , Galvez Mildred , Champhekar Ameya S. , Perez-Garcilazo Ivan , Baselga-Carretero Ignacio , Singh Jas , Comin-Anduix Begoña , Puig-Saus Cristina , Ribas Antoni
Published: April 2023

Supplementary Figure 10: PAK4 kinase inhibition modulates WNT signalling in vivo.
Supplementary Fig. S7 from Loss of Vascular Endothelial Glutaminase Inhibits Tumor Growth and Metastasis, and Increases Sensitivity to Chemotherapy
Authors: Ngwa Verra M. , Edwards Deanna N. , Hwang Yoonha , Karno Breelyn , Wang Xiaoyong , Yan Chi , Richmond Ann , Brantley-Sieders Dana M. , Chen Jin
Published: April 2023

This figure shows tumor growth curves of B16F10 and LLC-GFP-Luc tumors grown subcutaneously in GLSECKO versus WT mice
Supplementary Fig. S3 from Loss of Vascular Endothelial Glutaminase Inhibits Tumor Growth and Metastasis, and Increases Sensitivity to Chemotherapy
Authors: Ngwa Verra M. , Edwards Deanna N. , Hwang Yoonha , Karno Breelyn , Wang Xiaoyong , Yan Chi , Richmond Ann , Brantley-Sieders Dana M. , Chen Jin
Published: April 2023

This figure shows flow cytometry data from GLSECKO compared to WT from E0771 and MMTV-PyMT tumor models
Supplementary Table 1 from Protein Kinase C Alpha is a Central Node for Tumorigenic Transcriptional Networks in Human Prostate Cancer
Authors: Cooke Mariana , Zhang Xuyao , Zhang Suli , Eruslanov Evgeniy , Lal Priti , Daniel Reba E. , Feldman Michael D. , Abba Martin C. , Kazanietz Marcelo G.
Published: April 2023

Differentially expressed genes in PKCalpha silenced PC3 cells.
Supplementary Figure 5 from Protein Kinase C Alpha is a Central Node for Tumorigenic Transcriptional Networks in Human Prostate Cancer
Authors: Cooke Mariana , Zhang Xuyao , Zhang Suli , Eruslanov Evgeniy , Lal Priti , Daniel Reba E. , Feldman Michael D. , Abba Martin C. , Kazanietz Marcelo G.
Published: April 2023

Relationship between PRKCA and AR expression in prostate cancer. Correlation graphs for individual datasets as well as a meta-analysis are shown.
Supplementary Figure S5 from ZL-1211 Exhibits Robust Antitumor Activity by Enhancing ADCC and Activating NK Cell–mediated Inflammation in CLDN18.2-High and -Low Expressing Gastric Cancer Models
Authors: Konno Hiroyasu , Lin Tracey , Wu Renyi , Dai Xinchuan , Li Shou , Wang Grace , Chen Min , Li Wenying , Wang Lina , Sun Bee-Chun , Luo Zhen , Huang Tom , Chen Yuping , Zhang John , Ye Qiuping , Bellovin David , Wan Bing , Kang Lishan , Szeto Christopher , Hsu Karl , Kabbarah Omar
Published: April 2023

Supplementary Figure 5 shows IHC for gastric PDX models with anti-CLDN18.2, human IgG, or NKp46 antibody.
Supplementary Figure S6 from Mitochondrial Matrix Protease ClpP Agonists Inhibit Cancer Stem Cell Function in Breast Cancer Cells by Disrupting Mitochondrial Homeostasis
Authors: Greer Yoshimi Endo , Hernandez Lidia , Fennell Emily M.J. , Kundu Manjari , Voeller Donna , Chari Raj , Gilbert Samuel F. , Gilbert Thomas S.K. , Ratnayake Shashikala , Tang Binwu , Hafner Markus , Chen Qingrong , Meerzaman Daoud , Iwanowicz Edwin , Annunziata Christina M. , Graves Lee M. , Lipkowitz Stanley
Published: April 2023

The effects of ClpP agonists and other mitochondria-targeting drugs on mevalonate pathway, YAP/TAZ pathway
Supplementary Figure S10 from Mitochondrial Matrix Protease ClpP Agonists Inhibit Cancer Stem Cell Function in Breast Cancer Cells by Disrupting Mitochondrial Homeostasis
Authors: Greer Yoshimi Endo , Hernandez Lidia , Fennell Emily M.J. , Kundu Manjari , Voeller Donna , Chari Raj , Gilbert Samuel F. , Gilbert Thomas S.K. , Ratnayake Shashikala , Tang Binwu , Hafner Markus , Chen Qingrong , Meerzaman Daoud , Iwanowicz Edwin , Annunziata Christina M. , Graves Lee M. , Lipkowitz Stanley
Published: April 2023

The effect of ClpP agonist on glutamine-proline axis and proline biosynthesis
Supplemental Figure SF2: IHC staining on original patient tissue from which ACRJ-PC28 was derived. from Expanding the Prostate Cancer Cell Line Repertoire with ACRJ-PC28, an AR-negative Neuroendocrine Cell Line Derived From an African-Caribbean Patient
Authors: Valentine Henkel , Aiken William , Morrison Belinda , Zhao Ziran , Fowle Holly , Wasserman Jason S. , Thompson Elon , Chin Warren , Young Mark , Clarke Shannique , Gibbs Denise , Harrison Sharon , McLaughlin Wayne , Kwok Tim , Jin Fang , Campbell Kerry S. , Horvath Anelia , Thompson Rory , Lee Norman H. , Zhou Yan , Graña Xavier , Ragin Camille , Badal Simone
Published: April 2023

Tissue sample was obtained from a transrectal needle biopsy of the prostate gland of a patient with PSA
Supplemental Figure SF1: STR profiling for ACRJ-PC28 cells. from Expanding the Prostate Cancer Cell Line Repertoire with ACRJ-PC28, an AR-negative Neuroendocrine Cell Line Derived From an African-Caribbean Patient
Authors: Valentine Henkel , Aiken William , Morrison Belinda , Zhao Ziran , Fowle Holly , Wasserman Jason S. , Thompson Elon , Chin Warren , Young Mark , Clarke Shannique , Gibbs Denise , Harrison Sharon , McLaughlin Wayne , Kwok Tim , Jin Fang , Campbell Kerry S. , Horvath Anelia , Thompson Rory , Lee Norman H. , Zhou Yan , Graña Xavier , Ragin Camille , Badal Simone
Published: April 2023

STR profile of ACRJ-PC28 generated by IDEXX using PC indicates the novelty of the cell line (A) as the cell line senctic profile was compared to the profiles of other cell lines in the DSMZ STR database and did not match anv other reported profiles here: (B) that the cclls were purely of humar origin and (C) the absence of mycoplasma intection
Supplementary Table S4 from SLFN11 Negatively Regulates Noncanonical NFκB Signaling to Promote Glioblastoma Progression
Authors: Fischietti Mariafausta , Eckerdt Frank , Perez Ricardo E. , Guillen Magaña Jamie N. , Mazewski Candice , Ho Sang , Gonzalez Christopher , Streich Lukas D. , Beauchamp Elspeth M. , Heimberger Amy B. , Baran Aneta H. , Yue Feng , James C. David , Platanias Leonidas C.
Published: April 2023

Supplementary Table S4 lists proteins that were found to bind SLFN11 after irradiation.
Supplementary Table S2 from SLFN11 Negatively Regulates Noncanonical NFκB Signaling to Promote Glioblastoma Progression
Authors: Fischietti Mariafausta , Eckerdt Frank , Perez Ricardo E. , Guillen Magaña Jamie N. , Mazewski Candice , Ho Sang , Gonzalez Christopher , Streich Lukas D. , Beauchamp Elspeth M. , Heimberger Amy B. , Baran Aneta H. , Yue Feng , James C. David , Platanias Leonidas C.
Published: April 2023

Supplementary Table S2 lists putative SLFN11 binding partners detected after untreated and/or irradiated cells.
Supplementary Figure 1 from A Phase II Study Investigating Cabozantinib in Patients with Refractory Metastatic Colorectal Cancer (AGICC 17CRC01)
Authors: Scott Aaron J. , Basu Mallick Atrayee , Dotan Efrat , Cohen Steven J. , Gold Philip J. , Hochster Howard S. , Subramaniam Somasundaram , Barzi Afsaneh , Watts George S. , Blatchford Patrick J. , Messersmith Wells A.
Published: April 2023

KM curves for PIK3CA mutant subjects.
Supplementary Figure S4 from Real-world Studies Link NSAID Use to Improved Overall Lung Cancer Survival
Authors: Roszik Jason , Lee J. Jack , Wu Yi-Hung , Liu Xi , Kawakami Masanori , Kurie Jonathan M. , Belouali Anas , Boca Simina M. , Gupta Samir , Beckman Robert A. , Madhavan Subha , Dmitrovsky Ethan
Published: April 2023

Supplemental Figure 4. Landmark analysis of the MedStar-Georgetown University Hospital Database (Georgetown cohort).
Supplementary Table S2 from Smoking-associated Downregulation of FILIP1L Enhances Lung Adenocarcinoma Progression Through Mucin Production, Inflammation, and Fibrosis
Authors: Kwon Mijung , Rubio Genesaret , Wang Haitao , Riedlinger Gregory , Adem Asha , Zhong Hua , Slegowski Daniel , Post-Zwicker Louisa , Chidananda Anshruta , Schrump David S. , Pine Sharon R. , Libutti Steven K.
Published: April 2023

Supplementary Table S2
Supplementary Table S1 from Smoking-associated Downregulation of FILIP1L Enhances Lung Adenocarcinoma Progression Through Mucin Production, Inflammation, and Fibrosis
Authors: Kwon Mijung , Rubio Genesaret , Wang Haitao , Riedlinger Gregory , Adem Asha , Zhong Hua , Slegowski Daniel , Post-Zwicker Louisa , Chidananda Anshruta , Schrump David S. , Pine Sharon R. , Libutti Steven K.
Published: April 2023

Supplementary Table S1
Supplementary Primers and shRNA Information from DDR2 Coordinates EMT and Metabolic Reprogramming as a Shared Effector of FOXQ1 and SNAI1
Authors: Mitchell Allison V. , Wu Jason , Meng Fanyan , Dong Lun , Block C. James , Song Won-min , Zhang Bin , Li Jing , Wu Guojun
Published: April 2023

Information of PCR primers for all gene tested and information for shRNA sequences for targeting several genes.
Supplementary Figures 1-8, Table 1 from DDR2 Coordinates EMT and Metabolic Reprogramming as a Shared Effector of FOXQ1 and SNAI1
Authors: Mitchell Allison V. , Wu Jason , Meng Fanyan , Dong Lun , Block C. James , Song Won-min , Zhang Bin , Li Jing , Wu Guojun
Published: April 2023

Supplementary Figure 1. Gene ontology molecular function and PANTHER pathway enrichment analysis for genes uniquely dyregulated in HMLE/FOXQ1 and HMLE/SNAI1 cells. Supplementary Figure 2. Gene set enrichment analysis (GSEA) based on 2201 genes commonly dyregulated in HMLE/FOXQ1 and HMLE/SNAL1 cells. Supplementary Figure 3. DDR2 expression in breast cancer. Supplementary Figure 4. DDR2 has minimal effect on EMT. Supplementary Figure 5. The effect of DDR2 on cell proliferation, EMT, cell migration, and invasion in HMLE/LacZ control cells. Supplementary Figure 6. The effect of DDR2 on stemness properties in EMT cell models. Supplementary Figure 7. The effect of DDR2 knockdown on cellular metabolism. Supplementary Figure 8. Model-specific metabolites changes in HMLE/FOXQ1 cells (EMT) and BT549 cells (TNBC) within the TCA. Supplementary Table 1. Twenty-three metabolites commonly dysregulated by DDR2 knockdown in HMLE/FOXQ1 and BT549 cells.
Supplementary Table ST4 from Tumor Cell Extrinsic Synaptogyrin 3 Expression as a Diagnostic and Prognostic Biomarker in Head and Neck Cancer
Authors: Murphy Ryan M. , Tasoulas Jason , Porrello Alessandro , Carper Miranda B. , Tsai Yi-Hsuan , Coffey Alisha R. , Kumar Sunil , Zeng Peter YF. , Schrank Travis P. , Midkiff Bentley R. , Cohen Stephanie , Salazar Ashley H. , Hayward Michele C. , Hayes D. Neil , Olshan Andrew , Gupta Gaorav P. , Nichols Anthony C. , Yarbrough Wendell G. , Pecot Chad V. , Amelio Antonio L.
Published: April 2023

Differentially expressed genes from the TCGA Cervical Squamous Cell Carcinoma (CESC).
Figure S4 from Tumor Cell Extrinsic Synaptogyrin 3 Expression as a Diagnostic and Prognostic Biomarker in Head and Neck Cancer
Authors: Murphy Ryan M. , Tasoulas Jason , Porrello Alessandro , Carper Miranda B. , Tsai Yi-Hsuan , Coffey Alisha R. , Kumar Sunil , Zeng Peter YF. , Schrank Travis P. , Midkiff Bentley R. , Cohen Stephanie , Salazar Ashley H. , Hayward Michele C. , Hayes D. Neil , Olshan Andrew , Gupta Gaorav P. , Nichols Anthony C. , Yarbrough Wendell G. , Pecot Chad V. , Amelio Antonio L.
Published: April 2023

Association of SYNGR3 expression patient survival.
Figure S9 from Pharmacologic Inhibition of SHP2 Blocks Both PI3K and MEK Signaling in Low-epiregulin HNSCC via GAB1
Authors: Kurupi Richard , Floros Konstantinos V. , Jacob Sheeba , Chawla Ayesha T. , Cai Jinyang , Hu Bin , Puchalapalli Madhavi , Coon Colin M. , Khatri Rishabh , Crowther Giovanna Stein , Egan Regina K. , Murchie Ellen , Greninger Patricia , Dalton Krista M. , Ghotra Maninderjit S. , Boikos Sosipatros A. , Koblinski Jennifer E. , Harada Hisashi , Sun Yue , Morgan Iain M. , Basu Devraj , Dozmorov Mikhail G. , Benes Cyril H. , Faber Anthony C.
Published: April 2023

Biological importance of Gab1 in HNSCC cells
Figure S8 from Pharmacologic Inhibition of SHP2 Blocks Both PI3K and MEK Signaling in Low-epiregulin HNSCC via GAB1
Authors: Kurupi Richard , Floros Konstantinos V. , Jacob Sheeba , Chawla Ayesha T. , Cai Jinyang , Hu Bin , Puchalapalli Madhavi , Coon Colin M. , Khatri Rishabh , Crowther Giovanna Stein , Egan Regina K. , Murchie Ellen , Greninger Patricia , Dalton Krista M. , Ghotra Maninderjit S. , Boikos Sosipatros A. , Koblinski Jennifer E. , Harada Hisashi , Sun Yue , Morgan Iain M. , Basu Devraj , Dozmorov Mikhail G. , Benes Cyril H. , Faber Anthony C.
Published: April 2023

Neuregulin-1 does not rescue PI3K and MEK signaling in HNSCC treated with SHP2 inhibitor
Figure S5 from Pharmacologic Inhibition of SHP2 Blocks Both PI3K and MEK Signaling in Low-epiregulin HNSCC via GAB1
Authors: Kurupi Richard , Floros Konstantinos V. , Jacob Sheeba , Chawla Ayesha T. , Cai Jinyang , Hu Bin , Puchalapalli Madhavi , Coon Colin M. , Khatri Rishabh , Crowther Giovanna Stein , Egan Regina K. , Murchie Ellen , Greninger Patricia , Dalton Krista M. , Ghotra Maninderjit S. , Boikos Sosipatros A. , Koblinski Jennifer E. , Harada Hisashi , Sun Yue , Morgan Iain M. , Basu Devraj , Dozmorov Mikhail G. , Benes Cyril H. , Faber Anthony C.
Published: April 2023

Western blot analysis of ErbB members
Figure S2 from Pharmacologic Inhibition of SHP2 Blocks Both PI3K and MEK Signaling in Low-epiregulin HNSCC via GAB1
Authors: Kurupi Richard , Floros Konstantinos V. , Jacob Sheeba , Chawla Ayesha T. , Cai Jinyang , Hu Bin , Puchalapalli Madhavi , Coon Colin M. , Khatri Rishabh , Crowther Giovanna Stein , Egan Regina K. , Murchie Ellen , Greninger Patricia , Dalton Krista M. , Ghotra Maninderjit S. , Boikos Sosipatros A. , Koblinski Jennifer E. , Harada Hisashi , Sun Yue , Morgan Iain M. , Basu Devraj , Dozmorov Mikhail G. , Benes Cyril H. , Faber Anthony C.
Published: April 2023

HNSCC tumor cell lines are effective to SHP099 through dual PI3K and MEK inhibition
Table S1 from Pathway-based Approach Reveals Differential Sensitivity to E2F1 Inhibition in Glioblastoma
Authors: Alvarado Alvaro G. , Tessema Kaleab , Muthukrishnan Sree Deepthi , Sober Mackenzie , Kawaguchi Riki , Laks Dan R. , Bhaduri Aparna , Swarup Vivek , Nathanson David A. , Geschwind Daniel H. , Goldman Steven A. , Kornblum Harley I.
Published: April 2023

Gene Lists for each PC and direction from TCGA and GS datasets