bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Table S6 from Botensilimab, an Fc-Enhanced Anti–CTLA-4 Antibody, Is Effective against Tumors Poorly Responsive to Conventional Immunotherapy
Authors: Chand Dhan , Savitsky David A. , Krishnan Shanmugarajan , Mednick Gabriel , Delepine Chloe , Garcia-Broncano Pilar , Soh Kah Teong , Wu Wei , Wilkens Margaret K. , Udartseva Olga , Vincent Sylvia , Joshi Bishnu , Keith Justin G. , Manrique Mariana , Marques Marilyn , Tanne Antoine , Levey Daniel L. , Han Haiyong , Ng Serina , Ridpath Jackson , Huber Olivia , Morin Benjamin , Galand Claire , Bourdelais Sean , Gombos Randi B. , Ward Rebecca , Qin Yu , Waight Jeremy D. , Costa Matthew R. , Sebastian-Yague Alvaro , Rudqvist Nils-Petter , Pupecka-Swider Malgorzata , Venkatraman Vignesh , Slee Andrew , Patel Jaymin M. , Grossman Joseph E. , Wilson Nicholas S. , Von Hoff Daniel D. , Stebbing Justin , Curiel Tyler J. , Buell Jennifer S. , O’Day Steven J. , Stein Robert B.
Published: December 2024

This dataset provides an overview of the baseline demographic characteristics of patients with advanced solid tumors who participated in the ongoing phase 1 trial of botensilimab. This demographic information is crucial for understanding the patient population studied and is valuable for interpreting the safety and efficacy outcomes of the study.
Table S4 from RNA Shielding of p65 Is Required to Potentiate Oncogenic Inflammation in TET2-Mutated Clonal Hematopoiesis
Authors: Ben-Crentsil Nana Adjoa , Mohammed Ismail Wazim , Balasis Maria E. , Newman Hannah , Quintana Ariel , Binder Moritz , Kruer Traci , Neupane Surendra , Ferrall-Fairbanks Meghan C. , Fernandez Jenna , Lasho Terra L. , Finke Christy M. , Ibrahim Mohammed L. , McGraw Kathy L. , Wysota Michael , Aldrich Amy L. , Ryder Christopher B. , Letson Christopher T. , Traina Joshua , McLemore Amy F. , Droin Nathalie , Shastri Aditi , Yun Seongseok , Solary Eric , Sallman David A. , Beg Amer A. , Ma Li , Gaspar-Maia Alexandre , Patnaik Mrinal M. , Padron Eric
Published: December 2024

Taqman assays for murine cytokine gene expression (related to Fig S6)
Table S3 from RNA Shielding of p65 Is Required to Potentiate Oncogenic Inflammation in TET2-Mutated Clonal Hematopoiesis
Authors: Ben-Crentsil Nana Adjoa , Mohammed Ismail Wazim , Balasis Maria E. , Newman Hannah , Quintana Ariel , Binder Moritz , Kruer Traci , Neupane Surendra , Ferrall-Fairbanks Meghan C. , Fernandez Jenna , Lasho Terra L. , Finke Christy M. , Ibrahim Mohammed L. , McGraw Kathy L. , Wysota Michael , Aldrich Amy L. , Ryder Christopher B. , Letson Christopher T. , Traina Joshua , McLemore Amy F. , Droin Nathalie , Shastri Aditi , Yun Seongseok , Solary Eric , Sallman David A. , Beg Amer A. , Ma Li , Gaspar-Maia Alexandre , Patnaik Mrinal M. , Padron Eric
Published: December 2024

qRT-PCR primer sequences (related to Fig 1, Fig S3, Fig S7)
Supplementary Table S10 from Botensilimab, an Fc-Enhanced Anti–CTLA-4 Antibody, Is Effective against Tumors Poorly Responsive to Conventional Immunotherapy
Authors: Chand Dhan , Savitsky David A. , Krishnan Shanmugarajan , Mednick Gabriel , Delepine Chloe , Garcia-Broncano Pilar , Soh Kah Teong , Wu Wei , Wilkens Margaret K. , Udartseva Olga , Vincent Sylvia , Joshi Bishnu , Keith Justin G. , Manrique Mariana , Marques Marilyn , Tanne Antoine , Levey Daniel L. , Han Haiyong , Ng Serina , Ridpath Jackson , Huber Olivia , Morin Benjamin , Galand Claire , Bourdelais Sean , Gombos Randi B. , Ward Rebecca , Qin Yu , Waight Jeremy D. , Costa Matthew R. , Sebastian-Yague Alvaro , Rudqvist Nils-Petter , Pupecka-Swider Malgorzata , Venkatraman Vignesh , Slee Andrew , Patel Jaymin M. , Grossman Joseph E. , Wilson Nicholas S. , Von Hoff Daniel D. , Stebbing Justin , Curiel Tyler J. , Buell Jennifer S. , O’Day Steven J. , Stein Robert B.
Published: December 2024

This key resource table provides a comprehensive list of all antibodies and proteins used in the study, thus allowing other researchers to accurately replicate or conduct similar studies using the same reagents.
Table S2 from RNA Shielding of p65 Is Required to Potentiate Oncogenic Inflammation in TET2-Mutated Clonal Hematopoiesis
Authors: Ben-Crentsil Nana Adjoa , Mohammed Ismail Wazim , Balasis Maria E. , Newman Hannah , Quintana Ariel , Binder Moritz , Kruer Traci , Neupane Surendra , Ferrall-Fairbanks Meghan C. , Fernandez Jenna , Lasho Terra L. , Finke Christy M. , Ibrahim Mohammed L. , McGraw Kathy L. , Wysota Michael , Aldrich Amy L. , Ryder Christopher B. , Letson Christopher T. , Traina Joshua , McLemore Amy F. , Droin Nathalie , Shastri Aditi , Yun Seongseok , Solary Eric , Sallman David A. , Beg Amer A. , Ma Li , Gaspar-Maia Alexandre , Patnaik Mrinal M. , Padron Eric
Published: December 2024

qRT-PCR primers for confirming MALAT1 knockout across transcript. (Related to Fig S7)
Supplementary Table S1 from Botensilimab, an Fc-Enhanced Anti–CTLA-4 Antibody, Is Effective against Tumors Poorly Responsive to Conventional Immunotherapy
Authors: Chand Dhan , Savitsky David A. , Krishnan Shanmugarajan , Mednick Gabriel , Delepine Chloe , Garcia-Broncano Pilar , Soh Kah Teong , Wu Wei , Wilkens Margaret K. , Udartseva Olga , Vincent Sylvia , Joshi Bishnu , Keith Justin G. , Manrique Mariana , Marques Marilyn , Tanne Antoine , Levey Daniel L. , Han Haiyong , Ng Serina , Ridpath Jackson , Huber Olivia , Morin Benjamin , Galand Claire , Bourdelais Sean , Gombos Randi B. , Ward Rebecca , Qin Yu , Waight Jeremy D. , Costa Matthew R. , Sebastian-Yague Alvaro , Rudqvist Nils-Petter , Pupecka-Swider Malgorzata , Venkatraman Vignesh , Slee Andrew , Patel Jaymin M. , Grossman Joseph E. , Wilson Nicholas S. , Von Hoff Daniel D. , Stebbing Justin , Curiel Tyler J. , Buell Jennifer S. , O’Day Steven J. , Stein Robert B.
Published: December 2024

This dataset contains the binding affinity measurements of the various mouse anti-CTLA-4 (αCTLA-4) antibodies to mouse Fc gamma receptors as determined by surface plasmon resonance. It also includes calculated activating to inhibitory (A/I) ratios for each antibody. This information is crucial for understanding the Fc-mediated effector functions of the αCTLA-4 antibodies used in the study, providing insight into their in vivo efficacy and mechanisms of action.
Figure S3 from RNA Shielding of p65 Is Required to Potentiate Oncogenic Inflammation in TET2-Mutated Clonal Hematopoiesis
Authors: Ben-Crentsil Nana Adjoa , Mohammed Ismail Wazim , Balasis Maria E. , Newman Hannah , Quintana Ariel , Binder Moritz , Kruer Traci , Neupane Surendra , Ferrall-Fairbanks Meghan C. , Fernandez Jenna , Lasho Terra L. , Finke Christy M. , Ibrahim Mohammed L. , McGraw Kathy L. , Wysota Michael , Aldrich Amy L. , Ryder Christopher B. , Letson Christopher T. , Traina Joshua , McLemore Amy F. , Droin Nathalie , Shastri Aditi , Yun Seongseok , Solary Eric , Sallman David A. , Beg Amer A. , Ma Li , Gaspar-Maia Alexandre , Patnaik Mrinal M. , Padron Eric
Published: December 2024

Contains data related to Figure 3 but which were not included in the main figure
Supplementary Figure S13 from Botensilimab, an Fc-Enhanced Anti–CTLA-4 Antibody, Is Effective against Tumors Poorly Responsive to Conventional Immunotherapy
Authors: Chand Dhan , Savitsky David A. , Krishnan Shanmugarajan , Mednick Gabriel , Delepine Chloe , Garcia-Broncano Pilar , Soh Kah Teong , Wu Wei , Wilkens Margaret K. , Udartseva Olga , Vincent Sylvia , Joshi Bishnu , Keith Justin G. , Manrique Mariana , Marques Marilyn , Tanne Antoine , Levey Daniel L. , Han Haiyong , Ng Serina , Ridpath Jackson , Huber Olivia , Morin Benjamin , Galand Claire , Bourdelais Sean , Gombos Randi B. , Ward Rebecca , Qin Yu , Waight Jeremy D. , Costa Matthew R. , Sebastian-Yague Alvaro , Rudqvist Nils-Petter , Pupecka-Swider Malgorzata , Venkatraman Vignesh , Slee Andrew , Patel Jaymin M. , Grossman Joseph E. , Wilson Nicholas S. , Von Hoff Daniel D. , Stebbing Justin , Curiel Tyler J. , Buell Jennifer S. , O’Day Steven J. , Stein Robert B.
Published: December 2024

This dataset presents additional evidence of botensilimab's immunological effects on peripheral T cell activation in patients with advanced solid cancers. It demonstrates dose-dependent increases in key T cell activation markers. These findings provide further insight into botensilimab's mechanism of action, offer potential biomarkers for treatment monitoring, and support its dose-response relationship. The data further help researchers and clinicians better understand botensilimab's immunomodulatory potential in cancer treatment.
Supplementary Table S5 from MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer
Authors: Klingbeil Olaf , Skopelitis Damianos , Tonelli Claudia , Yoshimoto Toyoki , Alpsoy Aktan , Panepinto Maria C. , Minicozzi Francesca , Merrill Joseph R. , Cafiero Amanda M. , Aggarwal Disha , Russo Suzanne , Ha Taehoon , Demerdash Osama E. , Wee Tse-Luen , Spector David L. , Lyons Scott K. , Tuveson David A. , Cifani Paolo , Vakoc Christopher R.
Published: December 2024

P value for synergy score paralog combinations. Table of P value corresponding to synergy scores calculated using GEMINI.
Supplementary Table S2 from MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer
Authors: Klingbeil Olaf , Skopelitis Damianos , Tonelli Claudia , Yoshimoto Toyoki , Alpsoy Aktan , Panepinto Maria C. , Minicozzi Francesca , Merrill Joseph R. , Cafiero Amanda M. , Aggarwal Disha , Russo Suzanne , Ha Taehoon , Demerdash Osama E. , Wee Tse-Luen , Spector David L. , Lyons Scott K. , Tuveson David A. , Cifani Paolo , Vakoc Christopher R.
Published: December 2024

Paralog CRISPR screening data 2. Table of calculated gene level log2(fold-changes) of Paralog
Figure S7 from A Targetable Secreted Neural Protein Drives Pancreatic Cancer Metastatic Colonization and HIF1α Nuclear Retention
Authors: Yamaguchi Norihiro , Wu Y. Gloria , Ravetch Ethan , Takahashi Mai , Khan Abdul G. , Hayashi Akimasa , Mei Wenbin , Hsu Dennis , Umeda Shigeaki , de Stanchina Elisa , Lorenz Ivo C. , Iacobuzio-Donahue Christine A. , Tavazoie Sohail F.
Published: December 2024

suppl. figure 7 showing therapeutic targeting of NPTX1 with monoclonal NPTX1 antibody
Supplementary Table S10B from MARK2/MARK3 Kinases Are Catalytic Codependencies of YAP/TAZ in Human Cancer
Authors: Klingbeil Olaf , Skopelitis Damianos , Tonelli Claudia , Yoshimoto Toyoki , Alpsoy Aktan , Panepinto Maria C. , Minicozzi Francesca , Merrill Joseph R. , Cafiero Amanda M. , Aggarwal Disha , Russo Suzanne , Ha Taehoon , Demerdash Osama E. , Wee Tse-Luen , Spector David L. , Lyons Scott K. , Tuveson David A. , Cifani Paolo , Vakoc Christopher R.
Published: December 2024

RNA-seq results. Combined tables for DESeq2 output of Ctrl, MARK2/3, YAP/TAZ double knockout in 20 cancer cell lines.
Figure S1 from A Targetable Secreted Neural Protein Drives Pancreatic Cancer Metastatic Colonization and HIF1α Nuclear Retention
Authors: Yamaguchi Norihiro , Wu Y. Gloria , Ravetch Ethan , Takahashi Mai , Khan Abdul G. , Hayashi Akimasa , Mei Wenbin , Hsu Dennis , Umeda Shigeaki , de Stanchina Elisa , Lorenz Ivo C. , Iacobuzio-Donahue Christine A. , Tavazoie Sohail F.
Published: December 2024

suppl. Figure 1 showing NPTX1 is highly expressed in both human and murine highly metastatic PDAC models.
Supplementary Figure S6 from Epigenetic and Oncogenic Inhibitors Cooperatively Drive Differentiation and Kill KRAS-Mutant Colorectal Cancers
Authors: Loi Patrick , Schade Amy E. , Rodriguez Carrie L. , Krishnan Anjana , Perurena Naiara , Nguyen Van T.M. , Xu Yilin , Watanabe Marina , Davis Rachel A. , Gardner Alycia , Pilla Natalie F. , Mattioli Kaia , Popow Olesja , Gunduz Nuray , Lannagan Tamsin R.M. , Fitzgerald Samantha , Sicinska Ewa T. , Lin Jia-Ren , Tan William , Brais Lauren K. , Haigis Kevin M. , Giannakis Marios , Ng Kimmie , Santagata Sandro , Helin Kristian , Sansom Owen J. , Cichowski Karen
Published: December 2024

Extended data related to Figure 6.
Supplementary Figure S4 from Epigenetic and Oncogenic Inhibitors Cooperatively Drive Differentiation and Kill KRAS-Mutant Colorectal Cancers
Authors: Loi Patrick , Schade Amy E. , Rodriguez Carrie L. , Krishnan Anjana , Perurena Naiara , Nguyen Van T.M. , Xu Yilin , Watanabe Marina , Davis Rachel A. , Gardner Alycia , Pilla Natalie F. , Mattioli Kaia , Popow Olesja , Gunduz Nuray , Lannagan Tamsin R.M. , Fitzgerald Samantha , Sicinska Ewa T. , Lin Jia-Ren , Tan William , Brais Lauren K. , Haigis Kevin M. , Giannakis Marios , Ng Kimmie , Santagata Sandro , Helin Kristian , Sansom Owen J. , Cichowski Karen
Published: December 2024

Related to Figure 4.
Supplementary Video S2 from TREM2-Expressing Multinucleated Giant Macrophages Are a Biomarker of Good Prognosis in Head and Neck Squamous Cell Carcinoma
Authors: Gessain Grégoire , Anzali Ahmed-Amine , Lerousseau Marvin , Mulder Kevin , Bied Mathilde , Auperin Anne , Stockholm Daniel , Signolle Nicolas , Sassi Farah , Marques Da Costa Maria Eugenia , Marchais Antonin , Sayadi Alexandre , Weidner Daniela , Uderhardt Stefan , Blampey Quentin , Nakkireddy Sumanth Reddy , Broutin Sophie , Dutertre Charles-Antoine , Busson Pierre , Walter Thomas , Marhic Alix , Moya-Plana Antoine , Guerlain Johanne , Breuskin Ingrid , Casiraghi Odile , Gorphe Philippe , Classe Marion , Scoazec Jean-Yves , Blériot Camille , Ginhoux Florent
Published: December 2024

Representative video of granulomas made of multiple MGC in oral cavity SCC from GR cohort
Supplementary Video S1 from TREM2-Expressing Multinucleated Giant Macrophages Are a Biomarker of Good Prognosis in Head and Neck Squamous Cell Carcinoma
Authors: Gessain Grégoire , Anzali Ahmed-Amine , Lerousseau Marvin , Mulder Kevin , Bied Mathilde , Auperin Anne , Stockholm Daniel , Signolle Nicolas , Sassi Farah , Marques Da Costa Maria Eugenia , Marchais Antonin , Sayadi Alexandre , Weidner Daniela , Uderhardt Stefan , Blampey Quentin , Nakkireddy Sumanth Reddy , Broutin Sophie , Dutertre Charles-Antoine , Busson Pierre , Walter Thomas , Marhic Alix , Moya-Plana Antoine , Guerlain Johanne , Breuskin Ingrid , Casiraghi Odile , Gorphe Philippe , Classe Marion , Scoazec Jean-Yves , Blériot Camille , Ginhoux Florent
Published: December 2024

Representative video of an isolated MGC in oral cavity SCC from GR cohort
Figure S4 from TREM2-Expressing Multinucleated Giant Macrophages Are a Biomarker of Good Prognosis in Head and Neck Squamous Cell Carcinoma
Authors: Gessain Grégoire , Anzali Ahmed-Amine , Lerousseau Marvin , Mulder Kevin , Bied Mathilde , Auperin Anne , Stockholm Daniel , Signolle Nicolas , Sassi Farah , Marques Da Costa Maria Eugenia , Marchais Antonin , Sayadi Alexandre , Weidner Daniela , Uderhardt Stefan , Blampey Quentin , Nakkireddy Sumanth Reddy , Broutin Sophie , Dutertre Charles-Antoine , Busson Pierre , Walter Thomas , Marhic Alix , Moya-Plana Antoine , Guerlain Johanne , Breuskin Ingrid , Casiraghi Odile , Gorphe Philippe , Classe Marion , Scoazec Jean-Yves , Blériot Camille , Ginhoux Florent
Published: December 2024

Performances of the deep-learning cell detection model in TCGA cohorts (oral cavity, uterine cervix and larynx SCC) and GR cohorts (oral cavity SCC)
Figure S3 from TREM2-Expressing Multinucleated Giant Macrophages Are a Biomarker of Good Prognosis in Head and Neck Squamous Cell Carcinoma
Authors: Gessain Grégoire , Anzali Ahmed-Amine , Lerousseau Marvin , Mulder Kevin , Bied Mathilde , Auperin Anne , Stockholm Daniel , Signolle Nicolas , Sassi Farah , Marques Da Costa Maria Eugenia , Marchais Antonin , Sayadi Alexandre , Weidner Daniela , Uderhardt Stefan , Blampey Quentin , Nakkireddy Sumanth Reddy , Broutin Sophie , Dutertre Charles-Antoine , Busson Pierre , Walter Thomas , Marhic Alix , Moya-Plana Antoine , Guerlain Johanne , Breuskin Ingrid , Casiraghi Odile , Gorphe Philippe , Classe Marion , Scoazec Jean-Yves , Blériot Camille , Ginhoux Florent
Published: December 2024

Pathological response to induction chemotherapy
Supplementary Figure 6 from TCR-Engineered T Cells Directed against Ropporin-1 Constitute a Safe and Effective Treatment for Triple-Negative Breast Cancer
Authors: Kortleve Dian , Hammerl Dora , van Brakel Mandy , Wijers Rebecca , Roelofs Daphne , Kroese Kim , Timmermans Mieke M. , Liao Chen-Yi , Huang Shaozhuo , Trapman-Jansen Anita , Foekens Renée , Michaux Justine , de Beijer Monique T.A. , Buschow Sonja I. , Demmers Jeroen A.A. , Kok Marleen , Danen Erik H.J. , Bassani-Sternberg Michal , Martens John W.M. , Abbott Rachel J.M. , Debets Reno
Published: December 2024

FLY-1A TCR T-cells recognize patient-derived melanoma cells.
Figure S1 from Identification and Characterization of Chemotherapy-Resistant High-Risk Neuroblastoma Persister Cells
Authors: Grossmann Liron D. , Chen Chia-Hui , Uzun Yasin , Thadi Anusha , Wolpaw Adam J. , Louault Kevin , Goldstein Yael , Surrey Lea F. , Martinez Daniel , Calafatti Matteo , Gerelus Mark , Gao Peng , Lee Lobin , Patel Khushbu , Kaufman Rebecca S. , Shani Guy , Farrel Alvin , Moshitch-Moshkovitz Sharon , Grimaldi Paris , Shapiro Matthew , Kendsersky Nathan M. , Lindsay Jarrett M. , Casey Colleen E. , Krytska Kateryna , Scolaro Laura , Tsang Matthew , Groff David , Matkar Smita , Kalna Josh R. , Mycek Emily , McDevitt Jayne , Runbeck Erin , Patel Tasleema , Bernt Kathrin M. , Asgharzadeh Shahab , DeClerck Yves A. , Mossé Yael P. , Tan Kai , Maris John M.
Published: December 2024

Supplementary Figure S1 shows cell type markers and inferred copy number of tumors as well as characterization of malignant, Schwann cells, tumor associated macrophages and cancer associated fibroblasts at time of definitive surgery
Data from RNA Shielding of p65 Is Required to Potentiate Oncogenic Inflammation in TET2-Mutated Clonal Hematopoiesis
Authors: Ben-Crentsil Nana Adjoa , Mohammed Ismail Wazim , Balasis Maria E. , Newman Hannah , Quintana Ariel , Binder Moritz , Kruer Traci , Neupane Surendra , Ferrall-Fairbanks Meghan C. , Fernandez Jenna , Lasho Terra L. , Finke Christy M. , Ibrahim Mohammed L. , McGraw Kathy L. , Wysota Michael , Aldrich Amy L. , Ryder Christopher B. , Letson Christopher T. , Traina Joshua , McLemore Amy F. , Droin Nathalie , Shastri Aditi , Yun Seongseok , Solary Eric , Sallman David A. , Beg Amer A. , Ma Li , Gaspar-Maia Alexandre , Patnaik Mrinal M. , Padron Eric
Published: December 2024

Abstract
TET2 mutations (mTET2) are common genetic events in myeloid malignancies and clonal hematopoiesis. These mutations arise in the founding clone and are implicated in many clinical sequelae associated with oncogenic feedforward inflammatory circuits. However, the direct downstream effector of mTET2 responsible for the potentiation of these inflammatory circuits is unknown. To address this, we performed scRNA-seq and scATAC-seq in patients with COVID-19 with and without TET2-mutated clonal hematopoiesis reasoning that inflammation from COVID-19 may highlight critical downstream transcriptional targets of mTET2. Using this approach, we identified metastasis-associated lung adenoma transcript 1 (MALAT1), a therapeutically tractable lncRNA, as a central downstream effector of mTET2 that is both necessary and sufficient to induce the oncogenic proinflammatory features of mTET2 in vivo. We also elucidate the mechanism by which mTET2 upregulate MALAT1 and describe an interaction between MALAT1 and p65, which leads to RNA “shielding” from protein phosphatase 2A dephosphorylation, thus preventing resolution of inflammatory signaling.
Significance:
This work identifies MALAT1 as a requisite downstream effector of oncogenic feedforward inflammatory circuits necessary for the development of TET2-mutated CH and fulminant myeloid malignancy. We elucidate a novel mechanism by which MALAT1 “shields” p65 from dephosphorylation to potentiate this circuit and nominate MALAT1 inhibition as a future therapeutic strategy.
Paralog Co-Targeting Identifies Selective Genetic Redundancies across Cancer Types
Authors: Gauthier-Coles Gregory , Sheltzer Jason M.
Published: December 2024

In this issue, Klingbeil and colleagues deploy a paralog co-targeting strategy to reveal microtubule affinity–regulating kinases 2 and 3 as redundant negative regulators of the Hippo pathway and potentially actionable targets in YAP/TAZ-addicted tumors.

See related article by Klingbeil et.al., p. 2471
Targeting RNA and Protein Turnover in Aneuploid Cancers
Authors: Bakhoum Samuel F.
Published: December 2024

Aneuploidy, an imbalance in chromosome number, is a hallmark of human cancers with chromosomal instability, and it remains a major therapeutic challenge. In this issue, Ippolito and colleagues identify RNA and protein turnover as targetable therapeutic vulnerabilities in aneuploid cancers.

See related article by Ippolito et al., p. 2532
Characterization of Persister Cells Provides Insights into Mechanisms of Therapy Resistance in Neuroblastoma
Authors: Wolf Amber B. , Reynolds C. Patrick , Barbieri Eveline
Published: December 2024

The study by Grossmann and colleagues uses single-nucleus RNA sequencing in a cohort of matched high-risk neuroblastoma primary tumor samples, obtained from the same patient at diagnosis and definitive surgery, to identify persister cells that survive induction chemotherapy. These persister cells utilize mechanisms of chemoresistance that are both tumor-intrinsic and tumor-extrinsic, are highly dependent on the original genetic profile of the tumor, and represent novel, patient-specific targets to precisely inhibit chemoresistance and disease recurrence.

See related article by Grossmann et.al., p. 2387
Precision Oncology: 2024 in Review
Authors: Repetto Matteo , Fernandez Nicole , Drilon Alexander , Chakravarty Debyani
Published: December 2024

This article discusses the specific advances made in precision oncology in 2024. We comment on the evolving nature of predictive molecular events used to select patients who will most benefit clinically from treatment. We also discuss advances in the development of strategic treatment regimens for combination therapies, rational drug design of small-molecule inhibitors, and structurally informed drug repurposing.
Supplementary Figure 2 from Dynamic Evolution of Fibroblasts Revealed by Single-Cell RNA Sequencing of Human Pancreatic Cancer
Authors: Dimitrieva Slavica , Harrison Jon M. , Chang Jonathan , Piquet Michelle , Mino-Kenudson Mari , Gabriel Millicent , Sagar Vivek , Horn Heiko , Lage Kasper , Kim Julie , Li Gang , Weng Shaobu , Harris Cynthia , Kulkarni Anupriya S. , Ting David T. , Qadan Motaz , Fagenholz Peter J. , Ferrone Cristina R. , Grauel Angelo L. , Laszewski Tyler , Raza Alina , Riester Markus , Somerville Tim , Wagner Joel P. , Dranoff Glenn , Engelman Jeffrey A. , Kauffmann Audrey , Leary Rebecca , Warshaw Andrew L. , Lillemoe Keith D. , Fernández-del Castillo Carlos , Ruddy David A. , Liss Andrew S. , Cremasco Viviana
Published: December 2024

Supplementary Figure 2
Figure 5 from Dynamic Evolution of Fibroblasts Revealed by Single-Cell RNA Sequencing of Human Pancreatic Cancer
Authors: Dimitrieva Slavica , Harrison Jon M. , Chang Jonathan , Piquet Michelle , Mino-Kenudson Mari , Gabriel Millicent , Sagar Vivek , Horn Heiko , Lage Kasper , Kim Julie , Li Gang , Weng Shaobu , Harris Cynthia , Kulkarni Anupriya S. , Ting David T. , Qadan Motaz , Fagenholz Peter J. , Ferrone Cristina R. , Grauel Angelo L. , Laszewski Tyler , Raza Alina , Riester Markus , Somerville Tim , Wagner Joel P. , Dranoff Glenn , Engelman Jeffrey A. , Kauffmann Audrey , Leary Rebecca , Warshaw Andrew L. , Lillemoe Keith D. , Fernández-del Castillo Carlos , Ruddy David A. , Liss Andrew S. , Cremasco Viviana
Published: December 2024

Integration of single-cell and spatial transcriptomics reveals spatially defined fibroblast populations. A, Marker gene expression for fibroblast clusters overlayed on untreated PDAC sample HTB2779. Black box corresponds to that in whole mount image in B. B, Whole mount image and progressively higher magnifications of H&E-stained section of HTB2779. Scale bars, 2 mm (left), 300 μm (middle), and 60 μm (right). The locations of histologically defined cancer glands are indicated by black arrows. C, Marker gene expression for fibroblast clusters overlayed on NAT-PDAC sample HTB2903. Black box corresponds to that in whole mount image in D. D, Whole mount image and progressively higher magnifications of H&E-stained section of HTB2903. Scale bars, 2 mm (left), 300 μm (middle), and 60 μm (right). The locations of histologically defined cancer glands are indicated by black arrows. H&E, hematoxylin and eosin.
Molecular Recognition of Polyaromatic Hydrocarbons (PAHs) by Naphthalene Dioxygenase through the Action of Rhamnolipid
Authors: Azhary Nabihah , Abdul Hamid Azzmer Azzar , Mohd Ashaari Mardiana
Published: December 2024

Rhamnolipids are a type of glycolipid biosurfactant that has garnered significant attention in various industries, including healthcare and petroleum. Their remarkable properties, such as highly biodegradable and good emulsification, have propelled extensive research on their potential role in the biodegradation of polycyclic aromatic hydrocarbons (PAHs). While numerous empirical studies have focused on PAH biodegradation, the molecular interactions between biosurfactants and PAHs remain elusive. This study aims to provide insights into the molecular recognition of PAHs by naphthalene dioxygenase (NDO) in the presence of rhamnolipid by molecular docking and molecular dynamics (MD) simulations. The results indicated that selected PAH compounds, phenanthrene (PHE), fluoranthene (FLU), and benzo[a]pyrene (BAP), interact with NDO’s active site mostly through hydrophobic interactions. The presence of rhamnolipid changes NDO’s structural conformation, which leads to a more stable binding between PAHs and NDO, as demonstrated during simulation runs. In addition, the MD simulation analysis by using root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), solvent accessible surface area (SASA), and minimum distance parameters for the systems with rhamnolipid provided better results compared to the system without rhamnolipid, especially for NDO-BAP complex. Moreover, the number of consensuses interacting residues (Phe224, His195, Leu307) for the NDO-BAP complex with rhamnolipid presence was higher compared to without rhamnolipid (Val209, Leu253). Phe224 was identified as a consensus interacting residue for the NDO-BAP complex with rhamnolipid; assuming its important role for substrate binding when rhamnolipid is present. Hence, this study offers molecular insights into the role of biosurfactants during hydrocarbon degradation, especially for high molecular weight PAHs.
Genome-wide investigation and characterization of heat shock transcription factors in papaya (Carica papaya)
Authors: Le Thi Man , Azar Sahar , Thi Thanh Tran Huyen , Chu Ha Duc , Vu Quyen Thi Xuan , Tran Lan Thi Mai , La Hong Viet , Le Chi Toan , Cao Phi Bang
Published: December 2024

Heat shock transcription factors (Hsf-s) have been considered one of the major regulatory proteins that play important roles in various biological processes during the growth and development of plants. Unfortunately, no comprehensive studies of the Hsf family in papaya (Carica papaya), a popular tropical fruit crop, have been performed, even the papaya genome assembly has been released recently. In this study, a total of 18 members of the Hsf family, namely CpHsf-s have been identified in papaya. Based on various computational tools, a systematic characterization of the CpHsf family, such as gene structure, physic-chemical features, categorization, and protein-protein interaction, has been conducted. We found that the physic-chemical properties of the CpHsf proteins were highly variable, while all proteins were hydrophilic and localized in the nucleus. Our classification indicated that the CpHsf proteins could be categorized into three groups, including HsfA, HsfB, and HsfC, and members in the same clade share similar gene structure. According to the previous RNA-Seq datasets, our re-analysis revealed that the CpHsf genes exhibited different expressions in various major organs or tissues during fruit ripening and under the ultra-low temperature stress. Taken together, our study could provide a list of candidate genes for further functional characterization towards the improvement of stress tolerance in papaya.
Expression of TAD1 (Tillering & Dwarf1) Gene in Hawara Bunar and IR64 Rice Cultivars
Authors: Sindiya Vita , Fendiyanto Miftahul Huda , Hamim Hamim , Miftahudin Miftahudin
Published: December 2024

Rice cv. Hawara Bunar is a local rice cultivar tolerant to aluminum (Al) and drought stress. However, the cultivar has inferior characteristics, such as a tall habitus and a small number of tillers, making the cultivar agronomically unattractive. Many genes control plant height and tiller number; one is the TAD1 gene. Analysis of gene expression in two contrasting rice cultivars for both characters is a prerequisite for selecting certain genes for gene editing targets. This study aimed to analyze the gene expression of the TAD1 in rice cv. IR64 and Hawara Bunar, and to construct a phylogenetic tree of genes that regulate rice plant height and tiller number. Gene expression analysis was conducted using the qRT-PCR technique, while the phylogenetic tree was constructed based on the Neighbor-Joining method using PAUP4 software. The results showed TAD1 gene expression in the tillering phase of rice cv. Hawara Bunar is higher than the cv. IR64. The gene expression level in both cultivars corresponds to the plant height and tiller number characters in both rice cultivars. Phylogenetic analysis showed that the TAD1 gene clustered with genes that cause the rice to have a tall habitus with few tillers. The results of a transcriptome meta-analysis reinforced the phylogenetic tree, which shows that the TAD1 gene was found in a group of downregulated genes based on the volcano plots. Therefore, the TAD1 gene can be selected as a target gene for editing in rice cv. Hawara Bunar to obtain superior characters.
Battra: The Traditional Knowledge Holder on Medicinal Plant among People of East Lampung, Indonesia
Authors: Yudiyanto Yudiyanto , Wakhidah Anisatu Z. , Abdullah Irwan , Indiyanto Agus
Published: December 2024

Local knowledge continues to experience two fundamental problems that cause its existence to be marginalized and cannot be widely passed on. Externally, local knowledge has always been questioned for its relevance to the times. Internally, it has become elitist, making it difficult for other groups to access it. Gradually, local knowledge is alienated in people's lives. To date, ethnobotany studies have focused on identifying plants and their properties for policy and business purposes. This study was carried out in four old villages near the Way Kambas National Park, East Lampung, which were selected using the purposive sampling method. The key respondents were selected using the snowball sampling method, while data were collected from respondents through semi-structured interviews. Selected medicinal plants were observed, and the data were analyzed qualitatively and descriptively. Interviews with parties interested in medicinal plant knowledge show the monopolistic mastery of knowledge by all parties and their interests. The study shows a great need for synergy between parties for the preservation of medicinal plant knowledge, starting with the opening of access to knowledge for all. The openness of the battras  (traditional healers) to share sources of knowledge, the dedication of researchers/scientists in transforming knowledge into the public domain, the willingness of the private sector to share the value of medicinal plants benefits, and a pro-people policy framework will be key to the sustainability of medicinal plant knowledge for the development of fair and dignified public health.
Distoseptispora motuoensis (Distoseptisporaceae), a new freshwater hyphomycetous species from Xizang Autonomous Prefecture, China
Authors: LI JIA-NING , XU RONG-JU , XU KE , ZHAO QI , ZHU YING-AN
Published: December 2024

During an investigation of lignicolous freshwater fungi in Xizang Autonomous Prefecture, China, two collections were obtained from submerged wood in freshwater stream. This study reported a novel species within the genus Distoseptispora, namely Distoseptispora motuoensis, based on phylogenetic results from combined sequence data (ITS, LSU and tef1-α) and morphologies. Distoseptispora motuoensis is characterized by conidia with 7–12-distoseptate, sometimes with percurrent proliferation, which forms another conidium from the conidial apex. Phylogenetic analysis revealed that this species forms a distinct clade with strong support (88% ML, 1.00 PP), and it is also morphologically different from the other species of Distoseptispora.
Spegazzinia cryptica sp. nov. (Didymosphaeriaceae) from the western Pacific monsoon region
Authors: LU LIANG-TING , SUGITA RYOSUKE , SATO MISAKI , TANAKA KAZUAKI , KIRSCHNER ROLAND
Published: December 2024

A new species of Spegazzinia on dead leaves of Cyperaceae and Poaceae from Taiwan and Japan is described and illustrated as S. cryptica. By the four to eight cells comprising the body of the α conidia, the species differs from other species of Spegazzinia. Although this fungus could hardly be distinguished from S. musae by morphology, it is revealed as a new species by diagnostic bases and phylogenetic analyses of nucrDNA and translation elongation factor 1-α gene (ITS/LSU and TEF) sequences.
Rediscovery of the Endangered Pseudophilotes fatma (Oberthür, 1890) (Lepidoptera: Lycaenidae) in Algeria after 71 years, with an update on its distribution and designation of a lectotype
Authors: BOUAM IDRISS , TENNENT W. JOHN , ABDENNEBI AHMED , BENMOKHTAR ELALMI
Published: December 2024

Pseudophilotes fatma (Oberthür, 1890) is a Palearctic butterfly species endemic to the Maghreb region, characterised by a highly restricted distribution and “Endangered” conservation status. Recent field observations in Batna Province, northeastern Algeria, have documented new localities for P. fatma, marking its rediscovery after a 71-year absence. We updated the global distribution map for this species and highlight the urgent need for conservation actions to ensure its persistence. A lectotype is designated for Lycæna bavius var. fatma Oberthür, 1890.
Guidelines for species descriptions of free-living aquatic nematodes: characters, measurements and their presentation in taxonomic publications
Authors: MOKIEVSKY VADIM , BEZERRA TANIA NARA , DECRAEMER WILFRIDA , EISENDLE URSULA , HODDA MIKE , HOLOVACHOV OLEKSANDR , LEDUC DANIEL , MILJUTIN DMITRY , PEÑA-SANTIAGO REYES , SHARMA JYOTSNA , SMOL NIC , TCHESUNOV ALEXEI , VENEKEY VIRÁG , ZHAO ZENGQI , PÉREZ-GARCÍA JOSÉ ANDRÉS , PŮŽA VLADIMÍR , ZULLINI ALDO , VANREUSEL ANN
Published: December 2024

Free-living aquatic nematodes are abundant, diverse and of general environmental importance. However, knowledge of species distributions of both marine and freshwater nematodes is sparse. Species distribution data are crucial for evaluating environmental impacts from human activities and to conduct integrated nematode community assessments. Basic knowledge on taxonomy and species descriptions is lacking for many regions due to decreasing taxonomic expertise, yet it is essential for biodiversity research and for building molecular sequence libraries for the application of methods such as environmental DNA. In order to encourage and facilitate taxonomic and descriptive work on this understudied group, we present here a framework for nematode species description. We begin by providing a brief overview of nematology history, then provide suggestions of microscopic methods that should be used and provide a list of characters essential for morphometric species descriptions. Finally, we briefly discuss common molecular sequencing approaches that are commonly used in nematode taxonomic literature.
Who decides whether two lacewing populations (Neuroptera, Chrysopidae) are two different species, them or us?
Authors: DUELLI PETER , KOCH BÄRBEL , HENRY CHARLES S.
Published: December 2024

Most insects were dead when they were named by taxonomists, and predominantly morphological criteria have been used for more than two centuries. But in nature there are populations with individuals looking identical, that turn out to represent two or more different species, and others that look different but are single biological species. Coastal and several continental populations of the green lacewing Chrysoperla mediterranea (Hölzel 1972) had been considered to be one species, based on identical precopulatory “song patterns” (Henry et al. 1999) and viable hybrid production. More than 20 years later, Canard & Thierry (2020) described Chrysoperla europaea Canard and Thierry, 2020 as a new species, based on continental specimens, which they decided were morphologically different enough from the coastal morph of C. mediterranea. Here, we test in free choice experiments whether virgin males and females of coastal and continental populations can detect a difference between sexual partners of their own population versus members of the other morph. No reproductive separation between three populations were found, although they show significant morphological differences in claw shape and size. We conclude that all three tested populations from Southern France, Southern Switzerland, and Central Switzerland are the same biological species, and that C. europaea is therefore a junior synonym of C. mediterranea. We suggest the future use of behavioral tests in closely related allopatric species to see whether they are in fact the same species.
UNDER THE LAW: The (mis)education of Indigenous students
Authors: Kim Robert
Published: December 2024

Indigenous students in the U.S. — including American Indian, Alaska Native, and Native Hawaiian children — have faced a history of serious educational mistreatment. Today, the abusive boarding school program has ended, but Indigenous children still experience formidable challenges. Robert Kim describes laws related to schools funded by the Bureau of Indian Education, studies showing how the federal government has fallen short of its responsibilities, and a recent case attempting to hold the government accountable.
Hic Sunt Dracones: On the Risks of Comparing the ITCV With Control Variable Correlations
Authors: Lonati Sirio , Wulff Jesper N.
Published: December 2024

To examine the robustness of their results against omitted variable bias, management researchers often compare the Impact Threshold of a Confounding Variable (ITCV) with control variable correlations. This paper describes three issues with this approach. First, the ITCV and control variable correlations are measured on mathematically different scales. As a result, their direct comparison is inappropriate. Second, a fair comparison requires a rescaled version of the ITCV known as “the unconditional ITCV.” Third, even the interpretation of the unconditional ITCV is complicated by the presence of multiple omitted variables, numerous control variables, and correlations between the omitted and control variables. We illustrate these issues with simple computer-generated data, a Monte Carlo simulation, and a practical application based on a published dataset. These results suggest that rules of thumb based on ITCV and control variable correlations are misleading and call for alternative ways of running, interpreting, and reporting the ITCV.
An empirical study of factors influencing usage intention for generative artificial intelligence products: A case study of China
Authors: Cao Zhenxiang , Peng Liqing
Published: December 2024

The rapid advancement of generative artificial intelligence technologies has sparked widespread interest, yet understanding of user adoption patterns for these tools remains limited. While the unified theory of acceptance and use of technology model has been widely applied to various technologies, its applicability to generative artificial intelligence products, which present unique challenges and opportunities, has not been thoroughly explored. This gap in knowledge hinders the development of effective strategies for promoting user acceptance and optimising the design of generative artificial intelligence tools. This study extends the unified theory of acceptance and use of technology model to investigate the factors influencing usage intention for generative artificial intelligence products. The study incorporates additional variables such as digital literacy, perceived risk and perceived trust to provide a more comprehensive framework. Using structural equation modelling to analyse survey data, the study found that effort expectancy, performance expectancy, social influence, and perceived trust significantly and positively impact usage intention. In addition, digital literacy indirectly enhances usage intention through effort expectancy, while perceived risk negatively influences usage intention through reduced trust. Notably, facilitating conditions did not exhibit a significant effect on usage intention. These findings offer valuable insights for developers and researchers in the field of generative artificial intelligence, highlighting the importance of user-friendly design, performance optimisation, and trust-building measures. By identifying key factors that drive user adoption, this study contributes to a more nuanced understanding of technology acceptance in the context of advanced artificial intelligence systems, paving the way for more effective development and implementation strategies in this rapidly evolving field.
Political Reform as Regime Survival Strategy in the Hashemite Kingdom of Jordan After the Arab Uprisings
Authors: Csicsmann László
Published: December 2024

Jordan has recently celebrated its centennial in a volatile region. The Jordanian regime has an experience in dealing with mass protests; however, the recent decade with a surmounting socio-economic challenge aggravated by the mass influx of Syrian refugees has pushed the Kingdom towards a “boiling point.” The narrative of political reform has been dominated the daily political life of the monarchy; however, citizens have disillusioned with the pace of political liberalization in the Kingdom. Constitutional amendments mainly empowered the King authority with new rights, and the new election law adopted in 2016 failed to meet with the demands of the protesters. Jordan is not a country in political transition as the regime has remained intact from a genuine structural reform aimed at reaching a constitutional democracy. The introduction of economic liberalization process as well as the austerity measures dictated by the International Monetary Fund has led to an eroding social base of the monarchy. The rise of the new businessmen elite and the growing socio-economic problems in the tribal South made the society restructured in a way, which provoked more protest waves. Until now Jordan has managed to tackle with all difficulties; however, the pandemic and the shifting regional order have been aggravating the situation. The reforms mainly serve as a regime survival strategy; however, the ones launched in 2021 show that the monarch understands the situation. It has yet to be seen whether the new reforms will last and satisfy the citizens.
People, Platforms, and Places: The Conditional Effects of Psychological Distances on Livestream Viewership
Authors: Goh Zhang Hao , Hou Minzheng , Tandoc Edson C.
Published: December 2024

Reducing the social distance between livestreamers and viewers is known to enhance viewership as well as generate desirable psychosocial and economic outcomes. However, apart from the social dimension, scholars have not explored other distance dimensions that may induce the same benefits. Leveraging the construal level theory, the current study explicates the concept of distance in the form of three different perceived psychological distance dimensions (i.e., perceived response latency, heterophily, and spatialization) to examine how it can induce viewership in the context of livestreaming. A survey conducted in Singapore ( n = 401) found that the effect of perceived heterophily affecting viewership in livestream was moderated by viewers’ chronic construal tendencies, demonstrating a construal fit. The current study provides insights into how chronic differences in viewers’ construal can influence viewership.
Cancer-associated fibroblasts derived-exosomal circ_0076535 promotes esophageal squamous cell carcinoma progression
Authors: Kang Ningning , Ge Wei , Hu Jinxiu , Zhao Yuan , Zheng Hao , Lu Xuan
Published: December 2024

Background

Esophageal cancer (EC) is a common malignant tumor of the digestive tract and an important health-related problem in many developing countries. Esophageal squamous cell carcinoma (ESCC) is the most common subtype of EC. The cancer-associated fibroblasts (CAFs) are the major stromal cells in ESCC microenvironment. They play important role in ESCC proliferation, metastasis, angiogenesis and chemotherapy resistance through paracrine processes. However, the roles of circRNAs enriched in CAF-derived exosmes have not been reported.

Objective

To explore the mechanisms of how CAF affects ESCC proliferation and metastasis through paracrine processes and to investigate the role of circRNAs enriched in CAF-derived exosomes.

Methods

Exosomes were isolated from the conditional medium of CAF using differential ultracentrifugation, and then validated by Nanosight analysis. Exosome secretion inhibitor-GW4869 validates the pro-carcinogenic role of exosomes. The qRT-PCR showed the highest expression of circ_0076535 in the exosomal CircRNA, and knockdown of it confirmed its function. Online bioinformatics tool was utilized to predict the potential target gene of circ_0076535, and captured miR-145-5p as the target gene with high predictive value. The targeting association between miR-145-5p and circ_0076535 is further confirmed by the dual luciferase reporter experiment. The stimulation of tumour development and EMT by the CAF-derived exosome circ_0076535 is further validated in vivo.

Results

In our research, we found that CAF-derived exosomes increased proliferation, migration, invasion and EMT in ESCC cells. Circ_0076535 was highly enriched in CAF-exosomes and transferred into ESCC cells directly depend on internalization of exosomes. CAF-exosomal circ_0076535 increased the level of circ_0076535 in ESCC cells and induced EMT. Mechanistic experiments revealed circ_0076535 acted as a sponge to absorb miR-145-5p and activated NF-κB signaling pathway.

Conclusions

Conclusively, CAF-exosomal circ_0076535 promoted the ESCC progression via miR-145-5p/NF-κB axis and expected to be a potential biomarker for early diagnosis and treatment of ESCC.
Supporting Talent Development Among Low-Income, High-Ability Students: Camp Launch
Authors: Kim Mihyeon , Cross Jennifer Riedl
Published: December 2024

The Center for Gifted Education (Center) at William & Mary has provided diverse enrichment programs for high-ability students since 1988. With an aspiration to serve financially disadvantaged students, the Center developed and hosted a summer residential enrichment program in STEM areas. Camp Launch, for low-income, high-ability middle school students started in 2012. The program expanded to serve up to 10th-grade students. Follow-up surveys and interviews of alumni provide evidence of the program’s impact on their academic and career planning.