bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figure 12 from Podoplanin drives amoeboid invasion in canine and human mucosal melanoma
Authors: Shinada Masahiro , Kato Daiki , Motegi Tomoki , Tsuboi Masaya , Ikeda Namiko , Aoki Susumu , Iguchi Takaaki , Li Toshio , Kodera Yuka , Ota Ryosuke , Hashimoto Yuko , Takahashi Yosuke , Chambers James , Uchida Kazuyuki , Kato Yukinari , Nishimura Ryohei , Nakagawa Takayuki
Published: September 2024

Human mucosal melanomas with PDPN high expression demonstrate enrichment of gene signatures associated with amoeboid invasion.
Figure S2 from USP1 expression driven by EWS::FLI1 transcription factor stabilizes Survivin and mitigates replication stress in Ewing sarcoma
Authors: Mallard Halle J. , Wan Shibiao , Nidhi Prakriti , Hanscom-Trofy Yvan D. , Mohapatra Bhopal , Woods Nicholas T. , Lopez-Guerrero Jose Antonio , Llombart-Bosch Antonio , Machado Isidro , Scotlandi Katia , Kreiling Natasha F. , Perry Megan C. , Mirza Sameer , Coulter Donald W. , Band Vimla , Band Hamid , Ghosal Gargi
Published: September 2024

Figure S2 shows USP1 knockdown or inhibition decreases cell growth.
Table S9 from CBF-beta mitigates PI3K-alpha-specific inhibitor killing through PIM1 in PIK3CA mutant gastric cancer
Authors: Stanland Lyla J. , Ang Hazel X. , Hoj Jacob P. , Chu Yunqiang , Tan Patrick , Wood Kris C. , Luftig Micah A.
Published: September 2024

Quantification of Human Phospho-Proteome Array
Supplementary Figure Legends 1-7 from CBF-beta mitigates PI3K-alpha-specific inhibitor killing through PIM1 in PIK3CA mutant gastric cancer
Authors: Stanland Lyla J. , Ang Hazel X. , Hoj Jacob P. , Chu Yunqiang , Tan Patrick , Wood Kris C. , Luftig Micah A.
Published: September 2024

S1. BYL719 and DMSO beta scores
S2. Ribbon plots of non-gastric cancer cell lines included in screen.
S3. Dasatinib renders AGS cells hyper-sensitive to BYL719
S4. Loss of BCL-XL induces cell death in BYL719 treated MKN1
S5. BCL-XL inhibitor A-1331852 is the only inhibitor capable of increasing BYL719-induced cell death and inhibiting cell growth.
S6. CBFB binding co-factor RUNX1 is down-regulated at protein and mRNA level in BYL719 resistant clones.
S7. Pan-PIM inhibition or PIM1 KO re-sensitizes CBFB KO and resistant clones to BYL719.
Figure S2 from CBF-beta mitigates PI3K-alpha-specific inhibitor killing through PIM1 in PIK3CA mutant gastric cancer
Authors: Stanland Lyla J. , Ang Hazel X. , Hoj Jacob P. , Chu Yunqiang , Tan Patrick , Wood Kris C. , Luftig Micah A.
Published: September 2024

Figure S2 shows ribbon plots generated for non-gastric cancer cell lines included in the screen
Supplementary Figure S2 from Precision cut lung slices as a preclinical model for non-small cell lung cancer chemoprevention
Authors: Sompel Kayla , Smith Alex J. , Hauer Caroline , Elango Alamelu P. , Clambey Eric T. , Keith Robert L. , Tennis Meredith A.
Published: September 2024

Supplementary Figure S2 shows a dot blot for Figure 4C.
Supplementary Table S4 from Phase II Trial of Nelipepimut-S Peptide Vaccine in Women with Ductal Carcinoma in Situ
Authors: O'Shea Anne E. , Clifton Guy T. , Qiao Na , Heckman-Stoddard Brandy M. , Wojtowicz Malgorzata , Dimond Eileen , Bedrosian Isabelle , Weber Diane , Garber Judy E. , Husband Alexander , Pastorello Ricardo , Lee J. Jack , Hernandez Mike , Liu Diane D. , Vornik Lana A. , Brown Powel H. , Alatrash Gheath , Peoples George E. , Mittendorf Elizabeth A.
Published: September 2024

Supplementary Table S4: Lymphocyte infiltration
Supplementary Table 11 from Associations between physical activity and incidence of cancer among overweight adults in Korea: Results from the Health Examinees-G study
Authors: Choi Jaesung , Park JooYong , Kim Ji-Eun , Lee Miyoung , Kang Daehee , Shin Aesun , Choi Ji-Yeob
Published: September 2024

Supplementary Table 11 shows the association of physical activity with lung cancer incidence
Supplementary Methods S1 from EXAMINING THE BARRIERS AND OPPORTUNITIES FOR HUMAN PAPILLOMAVIRUS VACCINE DELIVERY IN CANCER CARE SETTINGS: A MIXED-METHODS STUDY
Authors: Garcia Melany A. , Schlecht Nicolas F. , Rokitka Denise A. , Attwood Kristopher M. , Rodriguez Elisa M.
Published: September 2024

Supplementary Methods S1 contains the survey questionnaire items discussed in section 2 of the main text.
Data from Risk Factors for Early Onset Sporadic Colorectal Cancer in Male Veterans
Authors: Imperiale Thomas F. , Myers Laura J. , Barker Barry C. , Larson Jason , Stump Timothy E. , Daggy Joanne K.
Published: September 2024

Abstract
Identifying risk factors for early onset colorectal cancer (EOCRC) could help reverse its rising incidence through risk factor reduction and/or early screening. We sought to identify EOCRC risk factors that could be used for decisions about early screening.
Using electronic databases and medical record review, we compared male veterans aged 35-49 years diagnosed with sporadic EOCRC (2008-2015) matched 1:4 to clinic and colonoscopy controls without CRC, excluding those with established inflammatory bowel disease, high-risk polyposis and non-polyposis syndromes, prior bowel resection, and high-risk family history. We ascertained sociodemographic and lifestyle factors, family and personal medical history, physical measures, vital signs, medications, and laboratory values 6-18 months prior to case diagnosis. In the derivation cohort (75% of the total sample), univariate and multivariate logistic regression models were used to derive a full model and a more parsimonious model. Both models were tested using a validation cohort.
Among 600 cases of sporadic EOCRC (mean [SD] age 45.2 [3.5] years; 66% White), 1200 primary care clinic controls (43.4 [4.2] years; 68% White), and 1200 colonoscopy controls (44.7 [3.8] years; 63% White), independent risk factors included age, cohabitation and employment status, BMI, comorbidity, CRC or other visceral cancer in a first- or second-degree relative; alcohol use; exercise; hyperlipidemia; use of statins, NSAIDs, and multivitamins. Validation c-statistics were 0.75-0.76 for the full model and 0.74-0.75 for the parsimonious model, respectively.
These independent risk factors for EOCRC may identify veterans for whom CRC screening prior to age 45 or 50 years should be considered.
Figure S6 from Type I Interferon Signaling via the EGR2 Transcriptional Regulator Potentiates CAR T cell-intrinsic Dysfunction
Authors: Jung In-Young , Bartoszek Robert L. , Rech Andrew J. , Collins Sierra M. , Ooi Soon-Keat , Williams Erik F. , Hopkins Caitlin R. , Narayan Vivek , Haas Naomi B. , Frey Noelle V. , Hexner Elizabeth O. , Siegel Donald L. , Plesa Gabriela , Porter David L. , Cantu Adrian , Everett John K. , Guedan Sonia , Berger Shelley L. , Bushman Frederic D. , Herbst Friederike , Fraietta Joseph A.
Published: September 2024

Pathways regulated by EGR2 in CD8+ CAR T-cells. (A-C) Top pathways differentially expressed in EGR2 knockout CD8+ CAR-T cells compared to AAVS1 knockout CAR T-cells. Libraries used in this enrichment analysis: A, Reactome 2016. B, NCI-Nature Pathway Interaction Database 2015. C, ARCHS4 transcription factor (TF) co-expression.
Figure S3 from Type I Interferon Signaling via the EGR2 Transcriptional Regulator Potentiates CAR T cell-intrinsic Dysfunction
Authors: Jung In-Young , Bartoszek Robert L. , Rech Andrew J. , Collins Sierra M. , Ooi Soon-Keat , Williams Erik F. , Hopkins Caitlin R. , Narayan Vivek , Haas Naomi B. , Frey Noelle V. , Hexner Elizabeth O. , Siegel Donald L. , Plesa Gabriela , Porter David L. , Cantu Adrian , Everett John K. , Guedan Sonia , Berger Shelley L. , Bushman Frederic D. , Herbst Friederike , Fraietta Joseph A.
Published: September 2024

Impact of EGR2 knockout on different T-cell subsets and CD28-based CAR T-cells. A, Naive, central memory, effector memory, and effector T-cells were magnetically isolated. PSMA CAR-T cells with AAVS1 and EGR2 knockout (KO) were then generated from the T-cell subsets and restimulation experiments were conducted to examine the development of exhaustion and memory. B, Expression of exhaustion markers (TIM3+LAG3+), C, cytotoxicity and D, expression of early memory markers (CD45RO+CD27+) after chronic CAR stimulation. (E-H) EGR2 was deleted in PSMA-CD28 based CAR T-cells, and the immunophenotype of CAR T-cells was assessed during the restimulation assay. E, Expression of exhaustion markers (TIM3+LAG3+), F, cytotoxicity, G, expression of early memory markers (CD45RO+CD27+) after chronic CAR stimulation and H, CAR T-cell expansion capacity during restimulation. All experiments were conducted using T-cells from two independent healthy donors, and panels (A-H) are representative data from one donor. (Mann-Whitney test, n = 4). *P < 0.05, **P < 0.01, ***P < 0.001, ns.: not significant.
Supplementary Table S2 from C/EBPa confers dependence to fatty acid anabolic pathways and vulnerability to lipid oxidative stress-induced ferroptosis in FLT3-mutant leukemia
Authors: Sabatier Marie , Birsen Rudy , Lauture Laura , Mouche Sarah , Angelino Paolo , Dehairs Jonas , Goupille Lea , Boussaid Ismael , Heiblig Mael , Boet Emeline , Sahal Ambrine , Saland Estelle , Santos Juliana C. , Armengol Marc , Fernandez-Serrano Miranda , Farge Thomas , Cognet Guillaume , Simonetta Federico , Pignon Corentin , Graffeuil Antoine , Mazzotti Celine , Avet-Loiseau Herve , Delos Oceane , Bertrand-Michel Justine , Chedru Amelie , Dembitz Vilma , Gallipoli Paolo , Anstee Natasha S. , Loo Sun , Wei Andrew H. , Carroll Martin , Goubard Armelle , Castellano Remy , Collette Yves , Vergez Francois , Mansat-De Mas Veronique , Bertoli Sarah , Tavitian Suzanne , Picard Muriel , Recher Christian , Bourges-Abella Nathalie , Granat Fanny , Kosmider Olivier , Sujobert Pierre , Colsch Benoit , Joffre Carine , Stuani Lucille , Swinnen Johannes V. , Guillou Herve , Roue Gael , Hakim Nawad , Dejean Anne S. , Tsantoulis Petros , Larrue Clement , Bouscary Didier , Tamburini Jerome , Sarry Jean-Emmanuel
Published: September 2024

Table S2: EnrichR analysis of FLT3 gene signatures
Table S3 from An African-specific variant of TP53 reveals PADI4 as a regulator of p53-mediated tumor suppression
Authors: Indeglia Alexandra , Leung Jessica C. , Miller Sven A. , Leu Julia I-Ju , Dougherty James F. , Clarke Nicole L. , Kirven Nicole A. , Shao Chunlei , Ke Lei , Lovell Scott , Barnoud Thibaut , Lu David Y. , Lin Cindy , Kannan Toshitha , Battaile Kevin P. , Yang Tyler Hong Loong. , Batista Oliva Isabela , Claiborne Daniel T. , Vogel Peter , Liu Lijun , Liu Qin , Nefedova Yulia , Cassel Joel , Auslander Noam , Kossenkov Andrew V. , Karanicolas John , Murphy Maureen E.
Published: September 2024

Oligos for ChIP-qPCR and qPCR used in this study
Figure S2 from Distinct assemblies of heterodimeric cytokine receptors govern stemness programs in leukemia
Authors: Kan Winnie L. , Dhagat Urmi , Kaufmann Kerstin B. , Hercus Timothy R. , Nero Tracy L. , Zeng Andy GX. , Toubia John , Barry Emma F. , Broughton Sophie E. , Gomez Guillermo A. , Benard Brooks A. , Dottore Mara , Cheung Tung Shing Karen S. , Boutzen Helena , Samaraweera Saumya E. , Simpson Kaylene J. , Jin Liqing , Goodall Gregory J. , Begley C. Glenn , Thomas Daniel , Ekert Paul G. , Tvorogov Denis , D'Andrea Richard J. , Dick John E. , Parker Michael W. , Lopez Angel F.
Published: September 2024

Key interactions between distinct residues in the IL-3R ternary complex crystal structure.
Supplementary Video S1 from Dynamic glycoprotein hyposialylation promotes chemotherapy evasion and metastatic seeding of quiescent circulating tumor cell clusters in breast cancer
Authors: Dashzeveg Nurmaa K. , Jia Yuzhi , Zhang Youbin , Gerratana Lorenzo , Patel Priyam , Shajahan Asif , Dandar Tsogbadrakh , Ramos Erika K. , Almubarak Hannah F. , Adorno-Cruz Valery , Taftaf Rokana , Schuster Emma J. , Scholten David , Sokolowski Michael T. , Reduzzi Carolina , El-Shennawy Lamiaa , Hoffmann Andrew D. , Manai Maroua , Zhang Qiang , D'Amico Paolo , Azadi Parastoo , Colley Karen J. , Platanias Leonidas C. , Shah Ami N. , Gradishar William J. , Cristofanilli Massimo , Muller William A. , Cobb Brian A. , Liu Huiping
Published: September 2024

Supplementary Video S1 shows the clustering video of SNA high cells presented in Fig.2A.
Supplementary Tables S1-S2 from Dynamic glycoprotein hyposialylation promotes chemotherapy evasion and metastatic seeding of quiescent circulating tumor cell clusters in breast cancer
Authors: Dashzeveg Nurmaa K. , Jia Yuzhi , Zhang Youbin , Gerratana Lorenzo , Patel Priyam , Shajahan Asif , Dandar Tsogbadrakh , Ramos Erika K. , Almubarak Hannah F. , Adorno-Cruz Valery , Taftaf Rokana , Schuster Emma J. , Scholten David , Sokolowski Michael T. , Reduzzi Carolina , El-Shennawy Lamiaa , Hoffmann Andrew D. , Manai Maroua , Zhang Qiang , D'Amico Paolo , Azadi Parastoo , Colley Karen J. , Platanias Leonidas C. , Shah Ami N. , Gradishar William J. , Cristofanilli Massimo , Muller William A. , Cobb Brian A. , Liu Huiping
Published: September 2024

Supplementary Table S1 shows clinical characteristics and multivariable Cox regression model analysis of patients.
Supplementary Table S2 shows the clinical characteristics of patients with breast cancer.
Table S9 from Dual immune checkpoint blockade induces analogous alterations in the dysfunctional CD8+ T cell and activated Treg compartment
Authors: van der Leun Anne M. , Traets Joleen J.H. , Vos Joris L. , Elbers Joris B.W. , Patiwael Sanne , Qiao Xiaohang , Machuca-Ostos Mercedes , Thommen Daniela S. , Haanen John B.A.G. , Schumacher Ton N.M. , Zuur Charlotte L.
Published: September 2024

Genes correlating with the dysfunctional CD8+ T cell trajectory.
Table S3 from Dual immune checkpoint blockade induces analogous alterations in the dysfunctional CD8+ T cell and activated Treg compartment
Authors: van der Leun Anne M. , Traets Joleen J.H. , Vos Joris L. , Elbers Joris B.W. , Patiwael Sanne , Qiao Xiaohang , Machuca-Ostos Mercedes , Thommen Daniela S. , Haanen John B.A.G. , Schumacher Ton N.M. , Zuur Charlotte L.
Published: September 2024

Number of cells per cell state in individual patients per timepoint.
Figure S5 from Dual immune checkpoint blockade induces analogous alterations in the dysfunctional CD8+ T cell and activated Treg compartment
Authors: van der Leun Anne M. , Traets Joleen J.H. , Vos Joris L. , Elbers Joris B.W. , Patiwael Sanne , Qiao Xiaohang , Machuca-Ostos Mercedes , Thommen Daniela S. , Haanen John B.A.G. , Schumacher Ton N.M. , Zuur Charlotte L.
Published: September 2024

Dual ICB-induced changes in activation state of Tregs.
Figure S2 from The origin of highly elevated cell-free DNA in healthy individuals and patients with pancreatic, colorectal, lung, or ovarian cancer
Authors: Mattox Austin K. , Douville Christopher , Wang Yuxuan , Popoli Maria , Ptak Janine , Silliman Natalie , Dobbyn Lisa , Schaefer Joy , Lu Steve , Pearlman Alexander H. , Cohen Joshua D. , Tie Jeanne , Gibbs Peter , Lahouel Kamel , Bettegowda Chetan , Hruban Ralph H. , Tomasetti Cristian , Jiang Peiyong , Chan K.C. Allen , Lo Yuk Ming Dennis , Papadopoulos Nickolas , Kinzler Kenneth W. , Vogelstein Bert
Published: September 2024

Supplemental Figure 2. The concentration of plasma cfDNA in previous described patients with cancer according to stage. (A) The concentration of cfDNA in patients of all cancer types (9). The concentration of cfDNA in patients with Stage III cancers was significantly higher than that of patients with Stage I cancers (p < 0.01). (B) The concentration of cfDNA in individual cancer types. Stage was classified according to AJCC 7th edition. The concentration of cfDNA in patients with Stage III breast cancer was significantly higher than that of patients with Stage I breast cancer (p < 0.05). For both panels, data were derived from the previously published CancerSEEK study (9).
Figure S10 from The origin of highly elevated cell-free DNA in healthy individuals and patients with pancreatic, colorectal, lung, or ovarian cancer
Authors: Mattox Austin K. , Douville Christopher , Wang Yuxuan , Popoli Maria , Ptak Janine , Silliman Natalie , Dobbyn Lisa , Schaefer Joy , Lu Steve , Pearlman Alexander H. , Cohen Joshua D. , Tie Jeanne , Gibbs Peter , Lahouel Kamel , Bettegowda Chetan , Hruban Ralph H. , Tomasetti Cristian , Jiang Peiyong , Chan K.C. Allen , Lo Yuk Ming Dennis , Papadopoulos Nickolas , Kinzler Kenneth W. , Vogelstein Bert
Published: September 2024

Supplemental Figure 10. In silico mixing experiments (N = 10) of buffy coat bisulfite sequencing data with liver (A), lung (B), colon epithelial cell (C), and left atrium (D) bisulfite sequencing data deconvoluted using the Moss et al. (43) reference matrix and quadratic programming shows excellent agreement between predicted and actual fractional contribution.
Table S5 from Clinical efficacy of ONC201 in H3K27M-mutant diffuse midline gliomas is driven by disruption of integrated metabolic and epigenetic pathways
Authors: Venneti Sriram , Kawakibi Abed Rahman , Ji Sunjong , Waszak Sebastian M. , Sweha Stefan R. , Mota Mateus , Pun Matthew , Deogharkar Akash , Chung Chan , Tarapore Rohinton S. , Ramage Samuel , Chi Andrew , Wen Patrick Y. , Arrillaga-Romany Isabel , Batchelor Tracy T. , Butowski Nicholas A. , Sumrall Ashley , Shonka Nicole , Harrison Rebecca A. , de Groot John , Mehta Minesh , Hall Matthew D. , Daghistani Doured , Cloughesy Timothy F. , Ellingson Benjamin M. , Beccaria Kevin , Varlet Pascale , Kim Michelle M. , Umemura Yoshie , Garton Hugh , Franson Andrea , Schwartz Jonathan , Jain Rajan , Kachman Maureen , Baum Heidi , Burant Charles F. , Mottl Sophie L. , Cartaxo Rodrigo T. , John Vishal , Messinger Dana , Qin Tingting , Peterson Erik , Sajjakulnukit Peter , Ravi Karthik , Waugh Alyssa , Walling Dustin , Ding Yujie , Xia Ziyun , Schwendeman Anna , Hawes Debra , Yang Fusheng , Judkins Alexander R. , Wahl Daniel , Lyssiotis Costas A. , de la Nava Daniel , Alonso Marta M. , Eze Augustine , Spitzer Jasper , Schmidt Susanne V. , Duchatel Ryan J. , Dun Matthew D. , Cain Jason E. , Jiang Li , Stopka Sylwia A. , Baquer Gerard , Regan Michael S. , Filbin Mariella G. , Agar Nathalie Y.R. , Zhao Lili , Kumar-Sinha Chandan , Mody Rajen , Chinnaiyan Arul , Kurokawa Ryo , Pratt Drew , Yadav Viveka N. , Grill Jacques , Kline Cassie , Mueller Sabine , Resnick Adam , Nazarian Javad , Allen Joshua E. , Odia Yazmin , Gardner Sharon L. , Koschmann Carl
Published: September 2024

VST-transformed gene expression values for all samples and protein-coding genes.
Fig. S1 from Senescent CAFs Mediate Immunosuppression and Drive Breast Cancer Progression
Authors: Ye Jiayu , Baer John M. , Faget Douglas V. , Morikis Vasilios A. , Ren Qihao , Melam Anupama , Delgado Ana Paula , Luo Xianmin , Bagchi Satarupa Mullick , Belle Jad I. , Campos Edward , Friedman Michael , Veis Deborah J. , Knudsen Erik S. , Witkiewicz Agnieszka K. , Powers Scott , Longmore Gregory D. , DeNardo David G. , Stewart Sheila A.
Published: September 2024

Supplementary figure S1 shows scRNA-Seq analyses of ER+, HER2+, and TNBC focusing on CAFs.
Data from Analysis of donor pancreata defines the transcriptomic signature and microenvironment of early neoplastic lesions.
Authors: Carpenter Eileen S. , Elhossiny Ahmed M. , Kadiyala Padma , Li Jay , McGue Jake , Griffith Brian D. , Zhang Yaqing , Edwards Jacob , Nelson Sarah , Lima Fatima , Donahue Katelyn L. , Du Wenting , Bischoff Allison C. , Alomari Danyah , Watkoske Hannah R. , Mattea Michael , The Stephanie , Espinoza Carlos E. , Barrett Meredith , Sonnenday Christopher J. , Olden Nicholas , Chen Chin-Tung , Peterson Nicole , Gunchick Valerie , Sahai Vaibhav , Rao Arvind , Bednar Filip , Shi Jiaqi , Frankel Timothy L. , Pasca di Magliano Marina
Published: September 2024

Abstract
The adult healthy human pancreas has been poorly studied given lack of indication to obtain tissue from the pancreas in the absence of disease and rapid postmortem degradation. We obtained pancreata from brain dead donors thus avoiding any warm ischemia time. The 30 donors were diverse in age and race and had no known pancreas disease. Histopathological analysis of the samples revealed PanIN lesions in most individuals irrespective of age. Using a combination of multiplex immunohistochemistry, single cell RNA sequencing, and spatial transcriptomics, we provide the first ever characterization of the unique microenvironment of the adult human pancreas and of sporadic PanIN lesions. We compared healthy pancreata to pancreatic cancer and peritumoral tissue and observed distinct transcriptomic signatures in fibroblasts, and, to a lesser extent, macrophages. PanIN epithelial cells from healthy pancreata were remarkably transcriptionally similar to cancer cells, suggesting that neoplastic pathways are initiated early in tumorigenesis.
Data from GABA regulates electrical activity and tumor initiation in melanoma
Authors: Tagore Mohita , Hergenreder Emiliano , Perlee Sarah C. , Cruz Nelly M. , Menocal Laura , Suresh Shruthy , Chan Eric , Baron Maayan , Melendez Stephanie , Dave Asim , Chatila Walid K. , Nsengimana Jeremie , Koche Richard P. , Hollmann Travis J. , Ideker Trey , Studer Lorenz , Schietinger Andrea , White Richard M.
Published: September 2024

Abstract
Oncogenes can only initiate tumors in certain cellular contexts, which is referred to as oncogenic competence. In melanoma, whether cells in the microenvironment can endow such competence remains unclear. Using a combination of zebrafish transgenesis coupled with human tissues, we demonstrate that GABAergic signaling between keratinocytes and melanocytes promotes melanoma initiation by BRAFV600E. GABA is synthesized in melanoma cells, which then acts on GABA-A receptors on keratinocytes. Electron microscopy demonstrates specialized cell-cell junctions between keratinocytes and melanoma cells, and multi-electrode array analysis shows that GABA acts to inhibit electrical activity in melanoma/keratinocyte co-cultures. Genetic and pharmacologic perturbation of GABA synthesis abrogates melanoma initiation in vivo. These data suggest that GABAergic signaling across the skin microenvironment regulates the ability of oncogenes to initiate melanoma.
AMG 193, a Clinical Stage MTA-Cooperative PRMT5 Inhibitor, Drives Antitumor Activity Preclinically and in Patients with MTAP-Deleted Cancers
Authors: Belmontes Brian , Slemmons Katherine K. , Su Chun , Liu Siyuan , Policheni Antonia N. , Moriguchi Jodi , Tan Hong , Xie Fang , Aiello Daniel Andrew , Yang Yajing , Lazaro Raul , Aeffner Famke , Rees Matthew G. , Ronan Melissa M. , Roth Jennifer A. , Vestergaard Mikkel , Cowland Sanne , Andersson Jan , Sarvary Ian , Chen Qing , Sharma Pooja , Lopez Patricia , Tamayo Nuria , Pettus Liping H. , Ghimire-Rijal Sudipa , Mukund Susmith , Allen Jennifer R. , DeVoss Jason , Coxon Angela , Rodon Jordi , Ghiringhelli François , Penel Nicolas , Prenen Hans , Glad Sanne , Chuang Chen-Hua , Keyvanjah Kiana , Townsley Danielle M. , Butler John R. , Bourbeau Matthew P. , Caenepeel Sean , Hughes Paul E.
Published: September 2024

One of the most robust synthetic lethal interactions observed in multiple functional genomic screens has been the dependency on protein arginine methyltransferase 5 (PRMT5) in cancer cells with MTAP deletion. We report the discovery of the clinical stage MTA-cooperative PRMT5 inhibitor AMG 193, which preferentially binds PRMT5 in the presence of MTA and has potent biochemical and cellular activity in MTAP-deleted cells across multiple cancer lineages. In vitro, PRMT5 inhibition induces DNA damage, cell cycle arrest, and aberrant alternative mRNA splicing in MTAP-deleted cells. In human cell line and patient-derived xenograft models, AMG 193 induces robust antitumor activity and is well tolerated with no impact on normal hematopoietic cell lineages. AMG 193 synergizes with chemotherapies or the KRAS G12C inhibitor sotorasib in vitro and combination treatment in vivo substantially inhibits tumor growth. AMG 193 is demonstrating promising clinical activity, including confirmed partial responses in patients with MTAP-deleted solid tumors from an ongoing phase 1/2 study.

Significance: AMG 193 preferentially inhibits the growth of MTAP-deleted tumor cells by inhibiting PRMT5 when in complex with MTA, thus sparing MTAP wild-type normal cells. AMG 193 shows promise as a targeted therapy in a clinically defined patient population.
Supplementary figures from The immunopeptidome from a genomic perspective: Establishing the non-canonical landscape of MHC class I–associated peptides
Authors: Bedran Georges , Gasser Hans-Christof , Weke Kenneth , Wang Tongjie , Bedran Dominika , Laird Alexander , Battail Christophe , Zanzotto Fabio Massimo , Pesquita Catia , Axelson Håkan , Rajan Ajitha , Harrison David J. , Palkowski Aleksander , Pawlik Maciej , Parys Maciej , O'Neill J Robert. , Brennan Paul M. , Symeonides Stefan N. , Goodlett David R. , Litchfield Kevin , Fahraeus Robin , Hupp Ted R. , Kote Sachin , Alfaro Javier A.
Published: September 2024

Supplementary Figures S1 to S7.
Supplementary Table 3 from Regional variation in the tumor microenvironment, immune escape and prognostic factors in breast cancer in sub-Saharan Africa
Authors: Bauer Marcus , Vetter Martina , Stückrath Kathrin , Yohannes Meron , Desalegn Zelalem , Yalew Tewodros , Bekuretsion Yonas , Kenea Tariku W. , Joffe Maureen , Van Den Berg Eunice J. , Nikulu Julien Ilunga. , Bakarou Kamaté , Manraj Shyam S. , Ogunbiyi Olufemi J. , Ekanem Ima-Obong , Igbinoba Festus , Diomande Mohenou , Adebamowo Clement , Dzamalala Charles P. , Anele Angelica A. , Zietsman Annelle , Galukande Moses , Foerster Milena , dos-Santos-Silva Isabel , Liu Biying , Santos Pablo , Jemal Ahmedin , Abebe Tamrat , Wickenhauser Claudia , Seliger Barbara , McCormack Valerie , Kantelhardt Eva J.
Published: September 2024

Supplementary Table 3
Supplementary Figures and Tables from Feasibility and Safety of Personalized, Multi-Target, Adoptive Cell Therapy (IMA101): First-In-Human Clinical Trial in Patients with Advanced Metastatic Cancer
Authors: Tsimberidou Apostolia M. , Guenther Kerstin , Andersson Borje S. , Mendrzyk Regina , Alpert Amir , Wagner Claudia , Nowak Anna , Aslan Katrin , Satelli Arun , Richter Fabian , Kuttruff-Coqui Sabrina , Schoor Oliver , Fritsche Jens , Coughlin Zoe , Mohamed Ali S. , Sieger Kerry , Norris Becky , Ort Rita , Beck Jennifer , Vo Henry Hiep. , Hoffgaard Franziska , Ruh Manuel , Backert Linus , Wistuba Ignacio I. , Fuhrmann David , Ibrahim Nuhad K. , Morris Van Karlyle. , Kee Bryan K. , Halperin Daniel M. , Nogueras-González Graciela M. , Kebriaei Partow , Shpall Elizabeth J. , Vining David , Hwu Patrick , Singh-Jasuja Harpreet , Reinhardt Carsten , Britten Cedrik M. , Hilf Norbert , Weinschenk Toni , Maurer Dominik , Walter Steffen
Published: September 2024

Supplementary Figure Legends and Tables
Supplemental Figure 9 from Feasibility and Safety of Personalized, Multi-Target, Adoptive Cell Therapy (IMA101): First-In-Human Clinical Trial in Patients with Advanced Metastatic Cancer
Authors: Tsimberidou Apostolia M. , Guenther Kerstin , Andersson Borje S. , Mendrzyk Regina , Alpert Amir , Wagner Claudia , Nowak Anna , Aslan Katrin , Satelli Arun , Richter Fabian , Kuttruff-Coqui Sabrina , Schoor Oliver , Fritsche Jens , Coughlin Zoe , Mohamed Ali S. , Sieger Kerry , Norris Becky , Ort Rita , Beck Jennifer , Vo Henry Hiep. , Hoffgaard Franziska , Ruh Manuel , Backert Linus , Wistuba Ignacio I. , Fuhrmann David , Ibrahim Nuhad K. , Morris Van Karlyle. , Kee Bryan K. , Halperin Daniel M. , Nogueras-González Graciela M. , Kebriaei Partow , Shpall Elizabeth J. , Vining David , Hwu Patrick , Singh-Jasuja Harpreet , Reinhardt Carsten , Britten Cedrik M. , Hilf Norbert , Weinschenk Toni , Maurer Dominik , Walter Steffen
Published: September 2024

Supplemental Figure 9
Data from SWI/SNF complex genomic alterations as a predictive biomarker for response to immune checkpoint inhibitors in multiple cancers
Authors: Wang Di , Wang Jianchao , Zhou Dongmei , Wu Zhixian , Liu Wei , Chen Yanping , Chen Gang , Zhang Jing
Published: September 2024

Abstract
Whether there is an association between SWI/SNF genomic alterations in tumors and response to immune checkpoint inhibitors (ICIs) remains unclear because prior studies have focused on either an individual gene or a predefined set of genes. Herein, using mutational and clinical data from 832 ICI-treated patients who underwent whole-exome sequencing, including sequencing of all 31 genes of the SWI/SNF complex, we found that SWI/SNF complex alterations were associated with significantly improved overall survival (OS) in melanoma, clear cell renal cell carcinoma, and gastrointestinal cancer, as well as improved progression-free survival (PFS) in non-small cell lung cancer. Including tumor mutational burden as a variable, the multivariate Cox regression analysis showed SWI/SNF genomic alterations had prognostic value in melanoma (HR 0.63 [95% CI 0.47–0.85], p = 0.003), clear cell renal cell carcinoma (HR 0.62 [95% CI 0.46–0.85], p = 0.003) and gastrointestinal cancer (HR 0.42 [95% CI 0.18–1.01], p = 0.053). Further, we used the random forest method for variable screening, identifying 14 genes as a SWI/SNF signature for potential clinical application. Significant correlations were observed between SWI/SNF signature alterations and improved OS and PFS in all cohorts. This suggests that SWI/SNF gene alterations are associated with better clinical outcomes in ICI-treated patients and may serve as a predictive marker for ICI therapy in multiple cancers.
Data from Single-Cell Profiling of CD8+ T Cells in Acute Myeloid Leukemia Reveals a Continuous Spectrum of Differentiation and Clonal Hyperexpansion
Authors: Desai Poonam N. , Wang Bofei , Fonseca Andre , Borges Pamella , Jelloul Fatima Zahra. , Reville Patrick K. , Lee Eric , Ly Christopher , Basi Akshay , Root Jessica , Baran Natalia , Post Sean M. , Deng Qing , Sun Hanxiao , Harmanci Arif O. , Burks Jared K. , Gomez Javier A. , DiNardo Courtney D. , Daver Naval G. , Alatrash Gheath , Konopleva Marina , Green Michael R. , Antunes Dinler A. , Futreal Andrew , Hao Dapeng , Abbas Hussein A.
Published: September 2024

Abstract
Comprehensive investigation of CD8+ T cells in acute myeloid leukemia (AML) is essential for developing immunotherapeutic strategies beyond immune checkpoint blockade. Herein, we performed single-cell RNA profiling of CD8+ T cells from 3 healthy bone marrow donors and 23 newly diagnosed (NewlyDx) and 8 relapsed/refractory (RelRef) AML patients. Cells co-expressing canonical exhaustion markers formed a cluster constituting <1% of all CD8+ T cells. We identified two effector CD8+ T cell subsets characterized by distinct cytokine and metabolic profiles that were differentially enriched in NewlyDx and RelRef patients. We refined a 25-gene CD8-derived signature correlating with therapy resistance, including genes associated with activation, chemoresistance, and terminal differentiation. Pseudotemporal trajectory analysis supported enrichment of a terminally differentiated state in CD8+ T cells with high CD8-derived signature expression at relapse or refractory disease. Higher expression of the 25-gene CD8 AML signature correlated with poorer outcomes in previously untreated AML patients, suggesting that the bona fide state of CD8+ T cells and their degree of differentiation are clinically relevant. Immune clonotype tracking revealed more phenotypic transitions in CD8 clonotypes in NewlyDx than in RelRef patients. Furthermore, CD8+ T cells from RelRef patients had a higher degree of clonal hyperexpansion associated with terminal differentiation and higher CD8-derived signature expression. Clonotype-derived antigen prediction revealed that most previously unreported clonotypes were patient-specific, suggesting significant heterogeneity in AML immunogenicity. Thus, immunologic reconstitution in AML is likely to be most successful at earlier disease stages when CD8+ T cells are less differentiated and have greater capacity for clonotype transitions.
Fritillaria cirrhosa D. Don Alleviates Inflammatory Progression and Suppresses M1 Polarization of Macrophages in Chronic Obstructive Pulmonary Disease
Authors: Li Lei , Sun Jihui , Li Qian , Sun Kexin , Jiang Jianhua
Published: September 2024

Introduction: Chronic obstructive pulmonary disease (COPD) is a progressive and largely irreversible disease. Current therapeutic approaches for COPD are limited in terms of slowing disease progression and suppressing pulmonary inflammation. Therefore, this study aimed to identify a method for alleviating inflammation in COPD. Methods: A COPD-like mouse model was established and treated with or without Fritillaria cirrhosa D. Don (hereinafter referred to as Fritillaria). The expression levels of inflammatory cytokines in mouse serum were detected by using enzyme-linked immunosorbent assay (ELISA). Additionally, lung tissue was analyzed by hematoxylin-eosin staining and immunohistochemistry analysis, respectively. MLE-12 cells were exposed to cigarette smoke extract (CSE) and treated with or without Fritillaria. The MTT assay was conducted to assess cell viability. The activation of NF-κB p65 was determined by Western blotting (WB). Finally, flow cytometry was applied to analyze the M1 macrophage percentage. Results: The results displayed that Fritillaria downregulated the levels of IL-1β, IL-6, IL-8, and TNF-α in the COPD-like mouse serum and MLE-12 cells. Fritillaria alleviated the inflammatory response in lung tissue of COPD-like mice. The cell viability of MLE-12 cells considerably decreased when exposed to CSE, which could be restored by adding Fritillaria. The Fritillaria reduced the activation of the pro-inflammatory factor NF-κB p65 and inhibited M1 polarization of macrophages, thereby mitigating the inflammatory response. Conclusion: In conclusion, Fritillaria exhibits beneficial effects in suppressing pulmonary infection-related inflammation in both the COPD-like mouse model and in vitro cell experiments.
Impact of Diabetes Mellitus and Obesity Comorbidities on Survival Outcomes after Hepatocellular Carcinoma Resection: A Multicenter Retrospective Study
Authors: Shinkawa Hiroji , Kaibori Masaki , Ueno Masaki , Yasuda Satoshi , Ikoma Hisashi , Aihara Tsukasa , Nakai Takuya , Kinoshita Masahiko , Kosaka Hisashi , Hayami Shinya , Matsuo Yasuko , Morimura Ryo , Nakajima Takayoshi , Nobori Chihoko , Ishizawa Takeaki
Published: September 2024

Introduction: This study aimed to evaluate the association of obesity and diabetes mellitus (DM) comorbidity with hepatocellular carcinoma (HCC) recurrence and survival. Methods: We investigated 1,644 patients who underwent hepatic resection for solitary HCC without vascular invasion using computed tomography. Patients were categorized into four groups according to the combination of obesity and DM comorbidities: OB (+) or (−) and DM (+) or (−). Postoperative cumulative recurrence rates within and beyond 2 years and beyond 5 years were assessed. Results: Multivariate Cox proportional hazard regression analysis revealed that the adjusted hazard ratios (HRs) of reduced recurrence-free survival was 1.10 (95% confidence interval [CI]: 0.91–1.33; p = 0.31), 0.94 (95% CI: 0.78–1.12; p = 0.48), and 1.24 (95% CI: 1.01–1.54; p = 0.045) in the OB(+)DM(−), OB(−)DM(+), and OB(+)DM(+) groups compared with the OB(−)DM(−) group, respectively. Additionally, the corresponding adjusted HRs of reduced overall survival were 0.93 (p = 0.57), 0.97 (p = 0.76), and 1.38 (p = 0.013) for OB(+)DM(−), OB(−)DM(+), and OB(+)DM(+) groups, respectively. No significant difference in the early recurrence rate was determined among the four groups. The OB(+)DM(+) group demonstrated an increased risk for late recurrence beyond 2 years and 5 years postoperatively compared with the OB(−)DM(−) group (HR: 1.51; p = 0.024 and HR: 2.53; p = 0.046, respectively). The OB(+)DM(−) and OB(−)DM(+) groups demonstrated an increased risk for late recurrence beyond 5 years postoperatively (HR: 3.83; p < 0.001 and HR: 1.95; p = 0.037, respectively). Conclusions: Obesity and DM coexistence increased late recurrence and worsened prognosis in patients with HCC undergoing hepatic resection. The results help surgeons develop possible different surveillance protocol and need to focus on diabetes/obesity control during life-long surveillance for patients with HCC.
The Tribute to G.M. Andreeva: the Role of Technological Innovations in Social Change
Authors: Vinokurov Fedor N. , Panov Kirill A. , Sadovskaia Ekaterina D.
Published: September 2024

Background. Technological innovations have become an important agent of social change, creating new socio-psychological meaning. In this context, G.M. Andreeva's idea that social psychology should help people adapt to changing environments remains relevant. Objectives. This paper aims to highlight the socio-psychological perspective on the role of innovative technologies in social change. We present two empirical studies that demonstrate emerging socio-psychological patterns in the context of open-source software development (study 1) and the use of virtual assistants (VA) for economic decision-making (study 2). Study Participants. Study (1): 900 posts from a collaborative development platform. Study (2): 200 users of the VA popular in Russia, residents of Russian cities with a population of more than 500,000 people. Methods. Study (1): Content analysis using large language models. Study (2): Quantitative online survey assessed users' perception of their VA and previously unknown VA across 15 characteristics, subjective trust levels, and economic trust through scenarios involving monetary transactions. Results. Study (1): A pre-configured GPT-4 turbo model with an instruction consisting of two examples achieved 56% accuracy in classification. Using a fine-tuned model of the previous generation, DeBERTa-v3-Small, increased the efficiency of classifying developer messages by up to 70%. This allowed the model to be used to encode developer interactions in order to identify the factors that contribute to effective collaboration. Study (2): Both forms of trust (declared and economic) are significantly related to components of social representations (SR) of VA. Individual components of these perceptions correlate with both declared and economic trust at the level of r > 0.3, p < 0.05. However, there is a difference in the strength of these relationships for familiar and unfamiliar VAs. An assumption can be made about the possible influence of the duration of use of VA on the strength of connections between SR and trust in VA. Thus, SR formed through interaction with VA contributes to a trusting attitude towards it and, accordingly, to decision-making processes involving its use. Conclusions. Socio-psychological knowledge about the changing socio-psychological meaning can form the foundation for the development of human-centered technologies. As a part of professional work, a developer can improve current tools for the creation, management, and optimization of collaborative activities. In everyday life, it is also important to establish a level of trust that is appropriate for the situation in which a Virtual Assistant is used.
A Physics-Informed Auto-Learning Framework for Developing Stochastic Conceptual Models for ENSO Diversity
Authors: Zhang Yinling , Chen Nan , Vialard Jérôme , Fang Xianghui
Published: September 2024

Understanding El Niño–Southern Oscillation (ENSO) dynamics has tremendously improved over the past few decades. The ENSO diversity in spatial pattern, peak intensity, and temporal evolution is, however, still poorly represented in conceptual ENSO models. In this paper, a physics-informed auto-learning framework is applied to derive ENSO stochastic conceptual models with varying degrees of freedom. The framework is computationally efficient and easy to apply. Once the state vector of the target model is set, causal inference is exploited to build the right-hand side of the equations based on a mathematical function library. Fundamentally different from standard nonlinear regression, the auto-learning framework provides a parsimonious model by retaining only terms that improve the dynamical consistency with observations. It can also identify crucial latent variables and provide physical explanations. This methodology successfully reconstructs the equations of a realistic six-dimensional reference ENSO model based on the recharge oscillator theory from its data. A hierarchy of lower-dimensional models is derived, and their representation of ENSO (including its diversity) is systematically assessed. The minimum model that represents ENSO diversity is four-dimensional, with three interannual variables describing the western Pacific thermocline depth, the eastern and central Pacific sea surface temperatures (SSTs), and one intraseasonal variable for westerly wind events. Without the intraseasonal variable, the resulting three-dimensional model underestimates extreme events and is too regular. A limited number of weak nonlinearities in the model are essential in reproducing the observed extreme El Niño events and the observed nonlinear relationship between eastern and western Pacific SSTs.

Significance Statement

This study develops a physics-informed auto-learning approach to improve the modeling and understanding of El Niño–Southern Oscillation (ENSO), a major climate phenomenon influencing global weather and climate. The auto-learning framework explores the causality between key processes to systematically produce stochastic conceptual models with different climate factors that simulate the diversity of observed ENSO events. The key finding is that the minimal model for characterizing the ENSO diversity (with the least number of climate factors) is a four-variable model capturing thermocline depth, sea surface temperatures, and wind bursts that can reproduce intensity and spatial pattern variation. This advancement provides an interpretable tool to identify the minimum sufficient processes governing ENSO behavior for improved predictability.
Sibling Bereavement Among Young Indian Adults
Authors: Kolte Akash , Mohan Miriam Priti
Published: September 2024

This qualitative study explores the bereavement experiences of 12 surviving siblings in India, focusing on familial, societal, and cultural influences. Six themes emerged: “The Demanding Familial Role,” “Isolation That Accompanies the Grief,” “Damaging Impact of Society,” “Positive Role of Friends and Family,” “Support Systems,” and “Continuing Bonds.” Participants often felt the burden of supporting their parents, leading to personal grief suppression and isolation, exacerbated by societal stigmas. Conversely, empathetic friends, supportive extended family, and professional resources like therapy provided crucial coping mechanisms. Continuing bonds with the deceased offered comfort and connection. The study highlights the need for comprehensive support systems tailored to cultural and societal contexts. It emphasizes the importance of public awareness and education to foster a supportive response to bereavement. Further research with larger, more diverse samples is recommended.
Carrot or Stick? The Efficacy of Incentives and Sanctions for Improving Probation Supervision Outcomes
Authors: Wodahl Eric J. , Schweitzer Kimberly , Heck Cary
Published: September 2024

The current study examined the role of sanctions and incentives in improving community supervision outcomes, utilizing data collected from 300 individuals under probation supervision by the Denver Adult Probation Department. The research expanded the current literature by addressing two important existing gaps. First, we included supervision failure due to absconding as a unique dependent variable. Second, we controlled for client behavior to enhance our confidence in study findings. Findings revealed no evidence in support of the use of sanctions to improve supervision outcomes. Incentives, however, were associated with both an increased likelihood of supervision completion and a lower incidence of criminal offending. Study findings suggest a need to prioritize efforts to integrate incentive use into everyday supervision practices, as well as a need to increase funding to support the research and development of incentive programs to guide agencies in creating and sustaining programs that will have the greatest impact.
Multidisciplinary treatment of a patient with TMJ ankylosis and a severe dentofacial discrepancy: A case report
Authors: Khan Sara , Nazir Rozina , Hanif Maidah
Published: September 2024

Introduction:

Temporomandibular joint (TMJ) ankylosis is a debilitating condition characterised by the fusion of bony or fibrous tissues in the TMJ, resulting in restricted mouth opening, functional challenges and facial deformities. This report highlights the complexity and multifaceted nature of TMJ ankylosis and emphasises the significance of early intervention and a multidisciplinary approach. Distraction osteogenesis has emerged as a successful method for managing TMJ ankylosis and associated facial asymmetry. Post-distraction orthodontic management is essential to address occlusal changes, including posterior open bite and crossbite.

Diagnosis and treatment plan:

A 17-year-old boy with unilateral right-sided TMJ ankylosis presented with restricted mouth opening, facial asymmetry and functional difficulties. Multidisciplinary treatment planning involved distraction osteogenesis, condylectomy, coronoidectomy and orthodontic correction to achieve proper occlusion and facial aesthetics.

Results:

The treatment significantly improved facial aesthetics, mouth opening, occlusion and the patient’s confidence and self-esteem.

Conclusion:

This case report underscores the complexity of TMJ ankylosis and the need for a comprehensive approach, including surgical and orthodontic interventions. Collaboration among healthcare professionals and ongoing research is vital to refine treatment approaches and improve the quality of life for patients with TMJ ankylosis.
Research on a new method for the degree of freedom analysis of parallel mechanism
Authors: Luo Jianguo , Li Siyu , Zhang Min
Published: September 2024

At present, traditional analysis methods sometimes show incompatibility when analyzing the degree of freedom (DOF) of parallel mechanisms. In this research, a new DOF analysis method (MV-DOF method) based on primary-ancillary motion theory is developed. The 4PPRRR series-parallel mechanism is taken as an example, the analysis results by using the MV-DOF method are compared with those of traditional inverse helix theory and modified Grübler-Kutzbach formula, respectively. The comparison shows that this MV-DOF method can always analyze the DOF of the 4PPRRR series-parallel mechanism accurately, while the other two traditional methods show inapplicability sometimes. During the analysis, an important rule is also found that the ancillary motion is equivalent to local constraint helix motion, but it is not always true in turn. Based on this MV-DOF method, a DOF cutting analysis way is also suggested. Any output point on a complex mechanism can be taken as a cutting point, along which the mechanism can be cut into two independent sub-mechanisms. The output DOF of each sub-mechanism can be analyzed separately by using the MV-DOF method, then the intersection can be obtained as the DOF of the whole mechanism at this output point. This research provides a new and effective analytical way for DOF analysis of parallel mechanisms.