bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figure S10 from Safety and Preliminary Efficacy of Pembrolizumab Following Transarterial Chemoembolization for Hepatocellular Carcinoma: The PETAL Phase Ib Study
Authors: Pinato David J. , D'Alessio Antonio , Fulgenzi Claudia Angela Maria , Schlaak Alexandra Emilia , Celsa Ciro , Killmer Saskia , Blanco Jesus Miguens , Ward Caroline , Stikas Charalampos-Vlasios , Openshaw Mark R. , Acuti Nicole , Nteliopoulos Georgios , Balcells Cristina , Keun Hector C. , Goldin Robert D. , Ross Paul J. , Cortellini Alessio , Thomas Robert , Young Anna-Mary , Danckert Nathan , Tait Paul , Marchesi Julian R. , Bengsch Bertram , Sharma Rohini
Published: June 2024

Supplementary Figure S10.
Bar graphs showing the absence of association between entropy and response prior to the start of pembrolizumab (A) and at the end of treatment (B). Abbreviations: ICI, immune checkpoint inhibitor; ns, not significant; EOT, end of treatment.
Supplementary Figure 5 from Measurement of ctDNA Tumor Fraction Identifies Informative Negative Liquid Biopsy Results and Informs Value of Tissue Confirmation
Authors: Rolfo Christian D. , Madison Russell W. , Pasquina Lincoln W. , Brown Derek W. , Huang Yanmei , Hughes Jason D. , Graf Ryon P. , Oxnard Geoffrey R. , Husain Hatim
Published: June 2024

Supplementary Figure 5: Above 1%, concordance of paired tissue and liquid biopsy specimens was universally high across ctDNA TF ranges.
Supplementary Figure 3 from Measurement of ctDNA Tumor Fraction Identifies Informative Negative Liquid Biopsy Results and Informs Value of Tissue Confirmation
Authors: Rolfo Christian D. , Madison Russell W. , Pasquina Lincoln W. , Brown Derek W. , Huang Yanmei , Hughes Jason D. , Graf Ryon P. , Oxnard Geoffrey R. , Husain Hatim
Published: June 2024

Supplementary Figure 3: Positive percent agreement (PPA) and negative predictive value (NPV) of liquid biopsy collected no more than 60 days after tissue biopsy.
Supplementary Figure 2 from Measurement of ctDNA Tumor Fraction Identifies Informative Negative Liquid Biopsy Results and Informs Value of Tissue Confirmation
Authors: Rolfo Christian D. , Madison Russell W. , Pasquina Lincoln W. , Brown Derek W. , Huang Yanmei , Hughes Jason D. , Graf Ryon P. , Oxnard Geoffrey R. , Husain Hatim
Published: June 2024

Supplementary Figure 2: Positive percent agreement (PPA) and negative predictive value (NPV) of liquid biopsy collected no more than 30 days after tissue biopsy.
Data from Upfront Neck Dissection for Treatment Selection and Improvement in Quality of Life as a Novel Treatment Paradigm for Deintensification in HPV+ OPSCC
Authors: Swiecicki Paul L. , Bellile Emily , Dragovic Aleksandar F. , McHugh Jonathan , Udager Aaron , Mierzwa Michelle Lynn , Shah Jennifer , Heft-Neal Molly , Rosko Andrew , Malloy Kelly M. , Casper Keith , Chinn Steven Bennett , Shuman Andrew G. , Stucken Chaz , Chepeha Douglas B. , Wolf Gregory T. , Bradford Carol Rossier , Eisbruch Avraham , Prince Mark E. , Worden Francis P. , Spector Matthew E.
Published: June 2024

AbstractPurpose:
Locoregionally advanced HPV+ oropharyngeal squamous cell carcinoma (OPSCC) has excellent cure rates, although current treatment regimens are accompanied by acute and long-term toxicities. We designed a phase II deescalation trial for patients with HPV+ OPSCC to evaluate the feasibility of an upfront neck dissection to individualize definitive treatment selection to improve the quality of life without compromising survival.
Patients and Methods:
Patients with T1–3, N0–2 HPV+ OPSCC underwent an upfront neck dissection with primary tumor biopsy. Arm A included patients with a single lymph node less than six centimeters, with no extracapsular spread (ECS) and no primary site adverse features underwent transoral surgery. Arm B included patients who had two or more positive lymph nodes with no ECS, or those with primary site adverse features were treated with radiation alone. Arm C included patients who had ECS in any lymph node and were treated with chemoradiation. The primary endpoint was quality of life at 1 year compared with a matched historical control.
Results:
Thirty-four patients were enrolled and underwent selective neck dissection. On the basis of pathologic characteristics, 14 patients were assigned to arm A, 10 patients to arm B, and 9 to arm C. A significant improvement was observed in Head and Neck Quality of Life (HNQOL) compared with historical controls (−2.6 vs. −11.9, P = 0.034). With a median follow-up of 37 months, the 3-year overall survival was 100% and estimated 3-year estimated progression-free survival was 96% [95% confidence interval (CI), 76%–99%].
Conclusions:
A neck dissection–driven treatment paradigm warrants further research as a deintensification strategy.
Data from IRX4204 Induces Senescence and Cell Death in HER2-positive Breast Cancer and Synergizes with Anti-HER2 Therapy
Authors: Moyer Cassandra L. , Lanier Amanda , Qian Jing , Coleman Darian , Hill Jamal , Vuligonda Vidyasagar , Sanders Martin E. , Mazumdar Abhijit , Brown Powel H.
Published: June 2024

AbstractPurpose:
Rexinoids, agonists of nuclear retinoid X receptor (RXR), have been used for the treatment of cancers and are well tolerated in both animals and humans. However, the usefulness of rexinoids in treatment of breast cancer remains unknown. This study examines the efficacy of IRX4204, a highly specific rexinoid, in breast cancer cell lines and preclinical models to identify a biomarker for response and potential mechanism of action.
Experimental Design:
IRX4204 effects on breast cancer cell growth and viability were determined using cell lines, syngeneic mouse models, and primary patient-derived xenograft (PDX) tumors. In vitro assays of cell cycle, apoptosis, senescence, and lipid metabolism were used to uncover a potential mechanism of action. Standard anti-HER2 therapies were screened in combination with IRX4204 on a panel of breast cancer cell lines to determine drug synergy.
Results:
IRX4204 significantly inhibits the growth of HER2-positive breast cancer cell lines, including trastuzumab and lapatinib–resistant JIMT-1 and HCC1954. Treatment with IRX4204 reduced tumor growth rate in the MMTV-ErbB2 mouse and HER2-positive PDX model by 49% and 44%, respectively. Mechanistic studies revealed IRX4204 modulates lipid metabolism and induces senescence of HER2-positive cells. In addition, IRX4204 demonstrates additivity and synergy with HER2-targeted mAbs, tyrosine kinase inhibitors, and antibody–drug conjugates.
Conclusions:
These findings identify HER2 as a biomarker for IRX4204 treatment response and demonstrate a novel use of RXR agonists to synergize with current anti-HER2 therapies. Furthermore, our results suggest that RXR agonists can be useful for the treatment of anti-HER2 resistant and metastatic HER2-positive breast cancer.
Data from Phase I Trial of Viral Vector-Based Personalized Vaccination Elicits Robust Neoantigen-Specific Antitumor T-Cell Responses
Authors: D'Alise Anna Morena , Leoni Guido , Cotugno Gabriella , Siani Loredana , Vitale Rosa , Ruzza Valentino , Garzia Irene , Antonucci Laura , Micarelli Elisa , Venafra Veronica , Gogov Sven , Capone Alessia , Runswick Sarah , Martin‐Liberal Juan , Calvo Emiliano , Moreno Victor , Symeonides Stefan N. , Scarselli Elisa , Bechter Oliver
Published: June 2024

AbstractPurpose:
Personalized vaccines targeting multiple neoantigens (nAgs) are a promising strategy for eliciting a diversified antitumor T-cell response to overcome tumor heterogeneity. NOUS-PEV is a vector-based personalized vaccine, expressing 60 nAgs and consists of priming with a nonhuman Great Ape Adenoviral vector (GAd20) followed by boosts with Modified Vaccinia Ankara. Here, we report data of a phase Ib trial of NOUS-PEV in combination with pembrolizumab in treatment-naïve patients with metastatic melanoma (NCT04990479).
Patients and Methods:
The feasibility of this approach was demonstrated by producing, releasing, and administering to 6 patients 11 of 12 vaccines within 8 weeks from biopsy collection to GAd20 administration.
Results:
The regimen was safe, with no treatment-related serious adverse events observed and mild vaccine-related reactions. Vaccine immunogenicity was demonstrated in all evaluable patients receiving the prime/boost regimen, with detection of robust neoantigen-specific immune responses to multiple neoantigens comprising both CD4 and CD8 T cells. Expansion and diversification of vaccine-induced T-cell receptor (TCR) clonotypes was observed in the posttreatment biopsies of patients with clinical response, providing evidence of tumor infiltration by vaccine-induced neoantigen-specific T cells.
Conclusions:
These findings indicate the ability of NOUS-PEV to amplify and broaden the repertoire of tumor-reactive T cells to empower a diverse, potent, and durable antitumor immune response. Finally, a gene signature indicative of the reduced presence of activated T cells together with very poor expression of the antigen-processing machinery genes has been identified in pretreatment biopsies as a potential biomarker of resistance to the treatment.
Data from KRT17high/CXCL8+ Tumor Cells Display Both Classical and Basal Features and Regulate Myeloid Infiltration in the Pancreatic Cancer Microenvironment
Authors: Carpenter Eileen S. , Kadiyala Padma , Elhossiny Ahmed M. , Kemp Samantha B. , Li Jay , Steele Nina G. , Nicolle Rémy , Nwosu Zeribe C. , Freeman Julia , Dai Henry , Paglia Daniel , Du Wenting , Donahue Katelyn , Morales Jacqueline , Medina-Cabrera Paola I. , Bonilla Monica E. , Harris Lindsey , The Stephanie , Gunchick Valerie , Peterson Nicole , Brown Kristee , Mattea Michael , Espinoza Carlos E. , McGue Jake , Kabala Sarah M. , Baliira Rachel K. , Renollet Nur M. , Mooney Ayden G. , Liu Jianhua , Bhalla Sean , Farida Jeremy P. , Ko Christopher , Machicado Jorge D. , Kwon Richard S. , Wamsteker Erik-Jan , Schulman Allison , Anderson Michelle A. , Law Ryan , Prabhu Anoop , Coulombe Pierre A. , Rao Arvind , Frankel Timothy L. , Bednar Filip , Shi Jiaqi , Sahai Vaibhav , Pasca Di Magliano Marina
Published: June 2024

AbstractPurpose:
Pancreatic ductal adenocarcinoma (PDAC) is generally divided in two subtypes, classical and basal. Recently, single-cell RNA sequencing has uncovered the coexistence of basal and classical cancer cells, as well as intermediary cancer cells, in individual tumors. The latter remains poorly understood; here, we sought to characterize them using a multimodal approach.
Experimental Design:
We performed subtyping on a single-cell RNA sequencing dataset containing 18 human PDAC samples to identify multiple intermediary subtypes. We generated patient-derived PDAC organoids for functional studies. We compared single-cell profiling of matched blood and tumor samples to measure changes in the local and systemic immune microenvironment. We then leveraged longitudinally patient-matched blood to follow individual patients over the course of chemotherapy.
Results:
We identified a cluster of KRT17-high intermediary cancer cells that uniquely express high levels of CXCL8 and other cytokines. The proportion of KRT17high/CXCL8+ cells in patient tumors correlated with intratumoral myeloid abundance, and, interestingly, high protumor peripheral blood granulocytes, implicating local and systemic roles. Patient-derived organoids maintained KRT17high/CXCL8+ cells and induced myeloid cell migration in a CXCL8-dependent manner. In our longitudinal studies, plasma CXCL8 decreased following chemotherapy in responsive patients, while CXCL8 persistence portended worse prognosis.
Conclusions:
Through single-cell analysis of PDAC samples, we identified KRT17high/CXCL8+ cancer cells as an intermediary subtype, marked by a unique cytokine profile and capable of influencing myeloid cells in the tumor microenvironment and systemically. The abundance of this cell population should be considered for patient stratification in precision immunotherapy.

See related commentary by Faraoni and McAllister, p. 2297
Data from A Phase I Trial of Enzalutamide Plus Selective Glucocorticoid Receptor Modulator Relacorilant in Patients with Metastatic Castration-Resistant Prostate Cancer
Authors: Desai Kunal B. , Serritella Anthony V. , Stadler Walter M. , O'Donnell Peter H. , Sweis Randy F. , Szmulewitz Russell Z.
Published: June 2024

AbstractPurpose:
The majority of patients with metastatic prostate cancer who receive androgen-deprivation therapy and androgen receptor (AR) signaling inhibitors (ARSI) progress. Activation of the glucocorticoid receptor (GR) is associated with ARSI resistance. This single-arm phase I trial assessed safety and pharmacokinetic (PK) feasibility of a combined AR antagonist (enzalutamide) and selective GR modulator (relacorilant) in patients with metastatic castration-resistant prostate cancer (mCRPC).
Patients and Methods:
This was a phase I trial (NCT03674814) of relacorilant and enzalutamide in patients with refractory mCRPC enrolled using a 6+3 design. The enzalutamide dose was kept constant at 120 mg/d with escalating doses of relacorilant based on safety and PK measures in cohorts of ≥6 patients. The primary objective was safety and establishment of pharmacologically active doses. Secondary objectives were related to antitumor activity.
Results:
Thirty-five patients with mCRPC were enrolled. Twenty-three were accrued across three dose cohorts in the dose-escalation phase, and 12 enrolled at the recommended phase II dose. The combination was generally well tolerated, safe, and achieved desirable enzalutamide PK. RP2D of 120 + 150 mg/d, respectively, was established. Median time on study was 2.2 months with four patients remaining on study for longer than 11 months. Four of 12 evaluable patients had a prostate-specific antigen (PSA) partial response.
Conclusions:
This is the first prospective trial combining an AR antagonist and a nonsteroidal selective GR modulator. The combination was safe and well tolerated with PSA response and prolonged disease control observed in a limited subset of patients. Further prospective trials are justified to evaluate efficacy and identify predictive biomarkers of response.
Data from Preclinical Efficacy of a PSMA-Targeted Actinium-225 Conjugate (225Ac-Macropa-Pelgifatamab): A Targeted Alpha Therapy for Prostate Cancer
Authors: Schatz Christoph A. , Zitzmann-Kolbe Sabine , Moen Ingrid , Klotz Monika , Nair Shankari , Stargard Stefan , Bjerke Roger M. , Wickstrøm Biseth Katrine , Feng Yuan Zeng , Indrevoll Bård , Cruciani Veronique , Karlsson Jenny , Haendler Bernard , Nielsen Carsten H. , Alfsen Maria Z. , Hammer Stefanie , Hennekes Hartwig , Cuthbertson Alan , Hagemann Urs B. , Larsen Åsmund
Published: June 2024

AbstractPurpose:
Initially, prostate cancer responds to hormone therapy, but eventually resistance develops. Beta emitter-based prostate-specific membrane antigen (PSMA)-targeted radionuclide therapy is approved for the treatment of metastatic castration-resistant prostate cancer. Here we introduce a targeted alpha therapy (TAT) consisting of the PSMA antibody pelgifatamab covalently linked to a macropa chelator and labeled with actinium-225 and compare its efficacy and tolerability with other TATs.
Experimental Design:
The in vitro characteristics and in vivo biodistribution, antitumor efficacy, and tolerability of 225Ac-macropa-pelgifatamab (225Ac-pelgi) and other TATs were investigated in cell line– and patient-derived prostate cancer xenograft models. The antitumor efficacy of 225Ac-pelgi was also investigated in combination with the androgen receptor inhibitor darolutamide.
Results:
Actinium-225-labeling of 225Ac-pelgi was efficient already at room temperature. Potent in vitro cytotoxicity was seen in PSMA-expressing (LNCaP, MDA-PCa-2b, and C4-2) but not in PSMA-negative (PC-3 and DU-145) cell lines. High tumor accumulation was seen for both 225Ac-pelgi and 225Ac-DOTA-pelgi in the MDA-PCa-2b xenograft model. In the C4-2 xenograft model, 225Ac-pelgi showed enhanced antitumor efficacy with a T/Cvolume (treatment/control) ratio of 0.10 compared with 225Ac-DOTA-pelgi, 225Ac-DOTA-J591, and 227Th-HOPO-pelgifatamab (227Th-pelgi; all at 300 kBq/kg) with T/Cvolume ratios of 0.37, 0.39, and 0.33, respectively. 225Ac-pelgi was less myelosuppressive than 227Th-pelgi. 225Ac-pelgi showed dose-dependent treatment efficacy in the patient-derived KuCaP-1 model and strong combination potential with darolutamide in both cell line– (22Rv1) and patient-derived (ST1273) xenograft models.
Conclusions:
These results provide a strong rationale to investigate 225Ac-pelgi in patients with prostate cancer. A clinical phase I study has been initiated (NCT06052306).
Data from Solid Organ Transplant Recipients Exhibit More TET2-Mutant Clonal Hematopoiesis of Indeterminate Potential Not Driven by Increased Transplantation Risk
Authors: Silver Alexander J. , Vlasschaert Caitlyn , Mack Taralynn , Sharber Brian , Xu Yaomin , Bick Alexander G. , Pinson C. Wright , Savona Michael R.
Published: June 2024

AbstractPurpose:
Solid organ transplant recipients comprise a unique population of immunosuppressed patients with increased risk of malignancy, including hematologic neoplasms. Clonal hematopoiesis of indeterminate potential (CHIP) represents a known risk factor for hematologic malignancy and this study describes the prevalence and patterns of CHIP mutations across several types of solid organ transplants.
Experimental Design:
We use two national biobank cohorts comprised of >650,000 participants with linked genomic and longitudinal phenotypic data to describe the features of CHIP across 2,610 individuals who received kidney, liver, heart, or lung allografts.
Results:
We find individuals with an allograft before their biobank enrollment had an increased prevalence of TET2 mutations (OR, 1.90; P = 4.0e−4), but individuals who received transplants post-enrollment had a CHIP mutation spectrum similar to that of the general population, without enrichment of TET2. In addition, we do not observe an association between CHIP and risk of incident transplantation among the overall population (HR, 1.02; P = 0.91). And in an exploratory analysis, we do not find evidence for a strong association between CHIP and rates of transplant complications such as rejection or graft failure.
Conclusions:
These results demonstrate that recipients of solid organ transplants display a unique pattern of clonal hematopoiesis with enrichment of TET2 driver mutations, the causes of which remain unclear and are deserving of further study.
Data from Safety and Preliminary Efficacy of Pembrolizumab Following Transarterial Chemoembolization for Hepatocellular Carcinoma: The PETAL Phase Ib Study
Authors: Pinato David J. , D'Alessio Antonio , Fulgenzi Claudia Angela Maria , Schlaak Alexandra Emilia , Celsa Ciro , Killmer Saskia , Blanco Jesus Miguens , Ward Caroline , Stikas Charalampos-Vlasios , Openshaw Mark R. , Acuti Nicole , Nteliopoulos Georgios , Balcells Cristina , Keun Hector C. , Goldin Robert D. , Ross Paul J. , Cortellini Alessio , Thomas Robert , Young Anna-Mary , Danckert Nathan , Tait Paul , Marchesi Julian R. , Bengsch Bertram , Sharma Rohini
Published: June 2024

AbstractPurpose:
Transarterial chemoembolization (TACE) may prime adaptive immunity and enhance immunotherapy efficacy. PETAL evaluated safety, preliminary activity of TACE plus pembrolizumab and explored mechanisms of efficacy.
Patients and Methods:
Patients with liver-confined hepatocellular carcinoma (HCC) were planned to receive up to two rounds of TACE followed by pembrolizumab 200 mg every 21 days commencing 30 days post-TACE until disease progression or unacceptable toxicity for up to 1 year. Primary endpoint was safety, with assessment window of 21 days from pembrolizumab initiation. Secondary endpoints included progression-free survival (PFS) and evaluation of tumor and host determinants of response.
Results:
Fifteen patients were included in the safety and efficacy population: 73% had nonviral cirrhosis; median age was 72 years. Child-Pugh class was A in 14 patients. Median tumor size was 4 cm. Ten patients (67%) received pembrolizumab after one TACE; 5 patients after two (33%). Pembrolizumab yielded no synergistic toxicity nor dose-limiting toxicities post-TACE. Treatment-related adverse events occurred in 93% of patients, most commonly skin rash (40%), fatigue, and diarrhea (27%). After a median follow-up of 38.5 months, objective response rate 12 weeks post-TACE was 53%. PFS rate at 12 weeks was 93% and median PFS was 8.95 months [95% confidence interval (CI): 7.30–NE (not estimable)]. Median duration of response was 7.3 months (95% CI: 6.3–8.3). Median overall survival was 33.5 months (95% CI: 11.6–NE). Dynamic changes in peripheral T-cell subsets, circulating tumor DNA, serum metabolites, and in stool bacterial profiles highlight potential mechanisms of action of multimodal therapy.
Conclusions:
TACE plus pembrolizumab was tolerable with no evidence of synergistic toxicity, encouraging further clinical development of immunotherapy alongside TACE.
Data from Maintenance Pembrolizumab Therapy in Patients with Metastatic HER2-negative Breast Cancer with Prior Response to Chemotherapy
Authors: Iwase Toshiaki , Cohen Evan N. , Gao Hui , Alexander Angela , Kai Megumi , Chiv Vivian , Wang Xiaoping , Krishnamurthy Savitri , Liu Diane , Shen Yu , Kida Kumiko , Reuben Alexandre , Layman Rachel M. , Ramirez David L. , Tripathy Debasish , Moulder Stacy L. , Yam Clinton , Valero Vicente , Lim Bora , Reuben James M. , Ueno Naoto T.
Published: June 2024

AbstractPurpose:
Accumulating toxicities hinder indefinite chemotherapy for many patients with metastatic/recurrent HER2-negative breast cancer. We conducted a phase II trial of pembrolizumab monotherapy following induction chemotherapy to determine the efficacy of maintenance immunotherapy in patients with metastatic HER2-negative inflammatory breast cancer (IBC) and non-IBC triple-negative breast cancer (TNBC) and a biomarker study.
Patients and Methods:
Patients with a complete response, partial response, or stable disease (SD) after at least three cycles of chemotherapy for HER2-negative breast cancer received pembrolizumab, regardless of programmed death-ligand 1 expression. Pembrolizumab (200 mg) was administered every 3 weeks until disease progression, intolerable toxicity, or 2 years of pembrolizumab exposure. The endpoints included the 4-month disease control rate (DCR), progression-free survival (PFS), overall survival, and response biomarkers in the blood.
Results:
Of 43 treated patients, 11 had metastatic IBC and 32 non-IBC TNBC. The 4-month DCR was 58.1% [95% confidence interval (CI), 43.4–72.9]. For all patients, the median PFS was 4.8 months (95% CI, 3.0–7.1 months). The toxicity profile was similar to the previous pembrolizumab monotherapy study. Patients with high T-cell clonality at baseline had a longer PFS with pembrolizumab treatment than did those with low T-cell clonality (10.4 vs. 3.6 months, P = 0.04). Patients who achieved SD also demonstrated a significant increase in T-cell clonality during therapy compared with those who did not achieve SD (20% vs. 5.9% mean increase, respectively; P = 0.04).
Conclusions:
Pembrolizumab monotherapy achieved durable treatment responses. Patients with a high baseline T-cell clonality had prolonged disease control with pembrolizumab.
Supplementary Tables S4 and S5 from Overcoming Clinical Resistance to EZH2 Inhibition Using Rational Epigenetic Combination Therapy
Authors: Kazansky Yaniv , Cameron Daniel , Mueller Helen S. , Demarest Phillip , Zaffaroni Nadia , Arrighetti Noemi , Zuco Valentina , Kuwahara Yasumichi , Somwar Romel , Ladanyi Marc , Qu Rui , de Stanchina Elisa , Dela Cruz Filemon S. , Kung Andrew L. , Gounder Mrinal M. , Kentsis Alex
Published: June 2024

Supplementary Table S4: List of mutations found in all MRT and ES cell lines used in this study as determined by targeted MSK-IMPACT sequencing. Related to Figure 3A.
Supplementary Table S5: List of PDX models used in this study, with clinical characteristics of the original tumor specimens, followed by a list of mutations found in all PDX models, as determined by targeted MSK-IMPACT sequencing.
Supplementary Table S6 from Overcoming Clinical Resistance to EZH2 Inhibition Using Rational Epigenetic Combination Therapy
Authors: Kazansky Yaniv , Cameron Daniel , Mueller Helen S. , Demarest Phillip , Zaffaroni Nadia , Arrighetti Noemi , Zuco Valentina , Kuwahara Yasumichi , Somwar Romel , Ladanyi Marc , Qu Rui , de Stanchina Elisa , Dela Cruz Filemon S. , Kung Andrew L. , Gounder Mrinal M. , Kentsis Alex
Published: June 2024

Supplementary Table S6: List of endogenous transposable elements whose expression is up- or downregulated by TAZ treatment. Related to Supplementary Figure S12.
Supplementary Table S3 from Overcoming Clinical Resistance to EZH2 Inhibition Using Rational Epigenetic Combination Therapy
Authors: Kazansky Yaniv , Cameron Daniel , Mueller Helen S. , Demarest Phillip , Zaffaroni Nadia , Arrighetti Noemi , Zuco Valentina , Kuwahara Yasumichi , Somwar Romel , Ladanyi Marc , Qu Rui , de Stanchina Elisa , Dela Cruz Filemon S. , Kung Andrew L. , Gounder Mrinal M. , Kentsis Alex
Published: June 2024

Supplementary Table S3: List of Hallmark gene sets identified by Gene Set Enrichment Analysis (GSEA) up- and down-regulated by TAZ treatment. Related to Supplementary Figure S2C.
Figure 5 from Spatial Architecture of Myeloid and T Cells Orchestrates Immune Evasion and Clinical Outcome in Lung Cancer
Authors: Enfield Katey S.S. , Colliver Emma , Lee Claudia , Magness Alastair , Moore David A. , Sivakumar Monica , Grigoriadis Kristiana , Pich Oriol , Karasaki Takahiro , Hobson Philip S. , Levi Dina , Veeriah Selvaraju , Puttick Clare , Nye Emma L. , Green Mary , Dijkstra Krijn K. , Shimato Masako , Akarca Ayse U. , Marafioti Teresa , Salgado Roberto , Hackshaw Allan , Jamal-Hanjani Mariam , van Maldegem Febe , McGranahan Nicholas , Glass Benjamin , Pulaski Hanna , Walk Eric , Reading James L. , Quezada Sergio A. , Hiley Crispin T. , Downward Julian , Sahai Erik , Swanton Charles , Angelova Mihaela
Published: June 2024

Neutrophil-rich TMEs are associated with activating mutations in PI3K and tumor-intrinsic CXCL8 upregulation. A, Representative crops of tumor-level H&E images with low TAN scores in the tumor nest and stroma (left) and high TAN scores in the tumor nest and stroma (right), inferred as the proportion of the neutrophil area in tumor/stroma from the total tumor/stroma tissue area. Scale bar, 50 μm; 400× magnification. B, Neutrophil cell density as defined by IMC compared between region-level TAN-low versus TAN-high tumor cores based on H&E scores in LUAD and LUSC. C and D, Proportion of tumor cores with (mut) and without (wt) PIK3CA driver mutations compared between TS:Neutrophil high versus other TME classes combined (C) and region-level TAN-High versus TAN-Low cores (D) in LUSC. P values were derived from a Chi-square test. E, Neutrophil cell density by PIK3CA mutation status, points colored by TME class assignment. F and G, TMM expression values for CXCL8 compared by PIK3CA mutation status (F) and between TME classes (G) in LUSC. H, Immunofluorescence images of CXCL8 RNAscope multiplexed with antibody staining of pancytokeratin (panCK) or MPO in an LUSC tumor region with a TS:Neutrophil high TME and subclonal PIK3CA mutation, and an LUSC patient with multiple TAN-high tumor regions and a clonal PIK3CA mutation. panCK and MPO examples for CRUK0075:R2 illustrate the same region of interest, whereas different regions of interest are shown for CRUK0468:R6. Scale bar, 100 μm. P values for B and E were calculated in a linear mixed-effects model with patient as the random-effect covariate. P values in F and G were derived from a limma–voom differential expression analysis correcting for multiple regions per tumor. ·, P < 0.1; *, P < 0.05; **, P < 0.01; ***, P < 0.001; LUAD, lung adenocarcinoma; LUSC, lung squamous cell carcinoma; TMM, trimmed mean of M-values; TS, tumor/stroma; TIL, tumor-infiltrating lymphocyte; MΦ, macrophage; TAN, tumor-associated neutrophils; H&E, hematoxylin and eosin; mt, mutant; wt, wild-type.
Table S1 from Early Changes in Tumor-Naive Cell-Free Methylomes and Fragmentomes Predict Outcomes in Pembrolizumab-Treated Solid Tumors
Authors: Stutheit-Zhao Eric Y. , Sanz-Garcia Enrique , Liu Zhihui (Amy) , Wong Derek , Marsh Kayla , Abdul Razak Albiruni R. , Spreafico Anna , Bedard Philippe L. , Hansen Aaron R. , Lheureux Stephanie , Torti Dax , Lam Bernard , Yang Shih Yu Cindy , Burgener Justin , Luo Ping , Zeng Yong , Cheng Nicholas , Awadalla Philip , Bratman Scott V. , Ohashi Pamela S. , Pugh Trevor J. , Siu Lillian L.
Published: June 2024

CMC and CSM early kinetics discordant cases
Supplementary Figure 9 from Early Changes in Tumor-Naive Cell-Free Methylomes and Fragmentomes Predict Outcomes in Pembrolizumab-Treated Solid Tumors
Authors: Stutheit-Zhao Eric Y. , Sanz-Garcia Enrique , Liu Zhihui (Amy) , Wong Derek , Marsh Kayla , Abdul Razak Albiruni R. , Spreafico Anna , Bedard Philippe L. , Hansen Aaron R. , Lheureux Stephanie , Torti Dax , Lam Bernard , Yang Shih Yu Cindy , Burgener Justin , Luo Ping , Zeng Yong , Cheng Nicholas , Awadalla Philip , Bratman Scott V. , Ohashi Pamela S. , Pugh Trevor J. , Siu Lillian L.
Published: June 2024

Multivariable analysis of survival using cancer-specific methylation (CSM) scores at baseline and cycle 3 of pembrolizumab. We computed CSM scores across the trial cohort. At both baseline and cycle 3, patients were split into above- or below-median groups. Survival outcomes are shown in a multivariable analysis including cohort, PD-L1 expression, and tumor mutation burden (TMB).
Supplementary Figure 4 from Early Changes in Tumor-Naive Cell-Free Methylomes and Fragmentomes Predict Outcomes in Pembrolizumab-Treated Solid Tumors
Authors: Stutheit-Zhao Eric Y. , Sanz-Garcia Enrique , Liu Zhihui (Amy) , Wong Derek , Marsh Kayla , Abdul Razak Albiruni R. , Spreafico Anna , Bedard Philippe L. , Hansen Aaron R. , Lheureux Stephanie , Torti Dax , Lam Bernard , Yang Shih Yu Cindy , Burgener Justin , Luo Ping , Zeng Yong , Cheng Nicholas , Awadalla Philip , Bratman Scott V. , Ohashi Pamela S. , Pugh Trevor J. , Siu Lillian L.
Published: June 2024

Validation of the 200 CpG signature using publicly available WGBS data. A 200 CpG signature was generated using 450K array data from TCGA PanCanAtlas. We validated this signature in publicly available data from WGBS of esophageal squamous cell carcinoma and adjacent normal tissue (GSE149608), as well as breast cancers (GSE186747). (A) A heatmap of methylation beta values of our signature sites demonstrates that the methylation signature demonstrated hypermethylation in both esophageal and breast cancers relative to adjacent normal esophageal tissue. (B) A scatter plot of mean beta values, with one point for each signature window is shown. This confirms that any differentially methylated windows were generally hypermethylated in tumor relative to normal. (C) Methylation signature scores were computed by summing the beta values across all sites for each sample. This verified that tumors demonstrated higher scores than adjacent normal tissue.
Supplementary Figure 11 from Early Changes in Tumor-Naive Cell-Free Methylomes and Fragmentomes Predict Outcomes in Pembrolizumab-Treated Solid Tumors
Authors: Stutheit-Zhao Eric Y. , Sanz-Garcia Enrique , Liu Zhihui (Amy) , Wong Derek , Marsh Kayla , Abdul Razak Albiruni R. , Spreafico Anna , Bedard Philippe L. , Hansen Aaron R. , Lheureux Stephanie , Torti Dax , Lam Bernard , Yang Shih Yu Cindy , Burgener Justin , Luo Ping , Zeng Yong , Cheng Nicholas , Awadalla Philip , Bratman Scott V. , Ohashi Pamela S. , Pugh Trevor J. , Siu Lillian L.
Published: June 2024

Multivariable analysis of OS and PFS using cancer mutation concentration (CMC) at baseline and cycle 3 of pembrolizumab. CMC was determined using a bespoke targeted approach across the trial cohort. At both baseline and cycle 3, patients were split into above- or below-median groups. Survival outcomes are shown in a multivariable analysis including cohort, PD-L1 expression, and tumor mutation burden (TMB).
Supplementary Figure 10 from Early Changes in Tumor-Naive Cell-Free Methylomes and Fragmentomes Predict Outcomes in Pembrolizumab-Treated Solid Tumors
Authors: Stutheit-Zhao Eric Y. , Sanz-Garcia Enrique , Liu Zhihui (Amy) , Wong Derek , Marsh Kayla , Abdul Razak Albiruni R. , Spreafico Anna , Bedard Philippe L. , Hansen Aaron R. , Lheureux Stephanie , Torti Dax , Lam Bernard , Yang Shih Yu Cindy , Burgener Justin , Luo Ping , Zeng Yong , Cheng Nicholas , Awadalla Philip , Bratman Scott V. , Ohashi Pamela S. , Pugh Trevor J. , Siu Lillian L.
Published: June 2024

Predicting survival outcomes using cancer mutation concentration (CMC) at baseline and cycle 3 of pembrolizumab. CMC was determined using a tumor-informed bespoke approach across the trial cohort. At both baseline and cycle 3, patients were split into above- or below-median groups. Survival outcomes are shown, with hazard ratios and p-values adjusted for cohort using a Cox model. PFS analysis at cycle 3 excludes one patient who progressed before the collection of cycle 3 sample.
Supplementary_Table_S4 from Glioblastoma-Infiltrating CD8+ T Cells Are Predominantly a Clonally Expanded GZMK+ Effector Population
Authors: Wang Anthony Z. , Mashimo Bryce L. , Schaettler Maximilian O. , Sherpa Ngima D. , Leavitt Lydia A. , Livingstone Alexandra J. , Khan Saad M. , Li Mao , Anzaldua-Campos Markus I. , Bradley Joseph D. , Leuthardt Eric C. , Kim Albert H. , Dowling Joshua L. , Chicoine Michael R. , Jones Pamela S. , Choi Bryan D. , Cahill Daniel P. , Carter Bob S. , Petti Allegra A. , Johanns Tanner M. , Dunn Gavin P.
Published: June 2024

Gene markers for Xenium in situ cell type identification.
Supplementary_Table_S3 from Glioblastoma-Infiltrating CD8+ T Cells Are Predominantly a Clonally Expanded GZMK+ Effector Population
Authors: Wang Anthony Z. , Mashimo Bryce L. , Schaettler Maximilian O. , Sherpa Ngima D. , Leavitt Lydia A. , Livingstone Alexandra J. , Khan Saad M. , Li Mao , Anzaldua-Campos Markus I. , Bradley Joseph D. , Leuthardt Eric C. , Kim Albert H. , Dowling Joshua L. , Chicoine Michael R. , Jones Pamela S. , Choi Bryan D. , Cahill Daniel P. , Carter Bob S. , Petti Allegra A. , Johanns Tanner M. , Dunn Gavin P.
Published: June 2024

Antibody markers and respective clone numbers.
Supplementary_Fig_S9 from Glioblastoma-Infiltrating CD8+ T Cells Are Predominantly a Clonally Expanded GZMK+ Effector Population
Authors: Wang Anthony Z. , Mashimo Bryce L. , Schaettler Maximilian O. , Sherpa Ngima D. , Leavitt Lydia A. , Livingstone Alexandra J. , Khan Saad M. , Li Mao , Anzaldua-Campos Markus I. , Bradley Joseph D. , Leuthardt Eric C. , Kim Albert H. , Dowling Joshua L. , Chicoine Michael R. , Jones Pamela S. , Choi Bryan D. , Cahill Daniel P. , Carter Bob S. , Petti Allegra A. , Johanns Tanner M. , Dunn Gavin P.
Published: June 2024

Comparison of CD8+ GZMK+ TIL from IDH-WT GBM and IDH-mut G4A samples.
Supplementary_Fig_S6 from Glioblastoma-Infiltrating CD8+ T Cells Are Predominantly a Clonally Expanded GZMK+ Effector Population
Authors: Wang Anthony Z. , Mashimo Bryce L. , Schaettler Maximilian O. , Sherpa Ngima D. , Leavitt Lydia A. , Livingstone Alexandra J. , Khan Saad M. , Li Mao , Anzaldua-Campos Markus I. , Bradley Joseph D. , Leuthardt Eric C. , Kim Albert H. , Dowling Joshua L. , Chicoine Michael R. , Jones Pamela S. , Choi Bryan D. , Cahill Daniel P. , Carter Bob S. , Petti Allegra A. , Johanns Tanner M. , Dunn Gavin P.
Published: June 2024

Gating strategy of GBM and PBMC T cells.
Supplementary Table 7 from Single-Cell Chromatin Accessibility Analysis Reveals the Epigenetic Basis and Signature Transcription Factors for the Molecular Subtypes of Colorectal Cancers
Authors: Liu Zhenyu , Hu Yuqiong , Xie Haoling , Chen Kexuan , Wen Lu , Fu Wei , Zhou Xin , Tang Fuchou
Published: June 2024

Supplementary Table 7. Specifically gained promoter peaks of CIMP-High subtype.
Supplementary Table 6 from Single-Cell Chromatin Accessibility Analysis Reveals the Epigenetic Basis and Signature Transcription Factors for the Molecular Subtypes of Colorectal Cancers
Authors: Liu Zhenyu , Hu Yuqiong , Xie Haoling , Chen Kexuan , Wen Lu , Fu Wei , Zhou Xin , Tang Fuchou
Published: June 2024

Supplementary Table 6. Chromatin accessibility at CGIs related to known markers of CIMP subtypes.
Supplementary_Fig_S3 from Glioblastoma-Infiltrating CD8+ T Cells Are Predominantly a Clonally Expanded GZMK+ Effector Population
Authors: Wang Anthony Z. , Mashimo Bryce L. , Schaettler Maximilian O. , Sherpa Ngima D. , Leavitt Lydia A. , Livingstone Alexandra J. , Khan Saad M. , Li Mao , Anzaldua-Campos Markus I. , Bradley Joseph D. , Leuthardt Eric C. , Kim Albert H. , Dowling Joshua L. , Chicoine Michael R. , Jones Pamela S. , Choi Bryan D. , Cahill Daniel P. , Carter Bob S. , Petti Allegra A. , Johanns Tanner M. , Dunn Gavin P.
Published: June 2024

Analysis of RNA Tirosh exhaustion and inhibitory scores expressed by T cells from cohort 1.
Supplementary Table 4 from Single-Cell Chromatin Accessibility Analysis Reveals the Epigenetic Basis and Signature Transcription Factors for the Molecular Subtypes of Colorectal Cancers
Authors: Liu Zhenyu , Hu Yuqiong , Xie Haoling , Chen Kexuan , Wen Lu , Fu Wei , Zhou Xin , Tang Fuchou
Published: June 2024

Supplementary Table 4. NMF identification of malignant clusters and association with iCMS classification.
Supplementary Table 3 from Single-Cell Chromatin Accessibility Analysis Reveals the Epigenetic Basis and Signature Transcription Factors for the Molecular Subtypes of Colorectal Cancers
Authors: Liu Zhenyu , Hu Yuqiong , Xie Haoling , Chen Kexuan , Wen Lu , Fu Wei , Zhou Xin , Tang Fuchou
Published: June 2024

Supplementary Table 3. Differentially accessibility peaks of adenoma and healthy colon epithelial cells.
Supplementary_Fig_S12 from Glioblastoma-Infiltrating CD8+ T Cells Are Predominantly a Clonally Expanded GZMK+ Effector Population
Authors: Wang Anthony Z. , Mashimo Bryce L. , Schaettler Maximilian O. , Sherpa Ngima D. , Leavitt Lydia A. , Livingstone Alexandra J. , Khan Saad M. , Li Mao , Anzaldua-Campos Markus I. , Bradley Joseph D. , Leuthardt Eric C. , Kim Albert H. , Dowling Joshua L. , Chicoine Michael R. , Jones Pamela S. , Choi Bryan D. , Cahill Daniel P. , Carter Bob S. , Petti Allegra A. , Johanns Tanner M. , Dunn Gavin P.
Published: June 2024

Harmony integration of TIL from many cancer types.
Supplementary_Fig_S11 from Glioblastoma-Infiltrating CD8+ T Cells Are Predominantly a Clonally Expanded GZMK+ Effector Population
Authors: Wang Anthony Z. , Mashimo Bryce L. , Schaettler Maximilian O. , Sherpa Ngima D. , Leavitt Lydia A. , Livingstone Alexandra J. , Khan Saad M. , Li Mao , Anzaldua-Campos Markus I. , Bradley Joseph D. , Leuthardt Eric C. , Kim Albert H. , Dowling Joshua L. , Chicoine Michael R. , Jones Pamela S. , Choi Bryan D. , Cahill Daniel P. , Carter Bob S. , Petti Allegra A. , Johanns Tanner M. , Dunn Gavin P.
Published: June 2024

Heatmap of top differentially expressed genes by CD8+ T cell states from cohorts 1 and 2.
Supplementary_Fig_S1 from Glioblastoma-Infiltrating CD8+ T Cells Are Predominantly a Clonally Expanded GZMK+ Effector Population
Authors: Wang Anthony Z. , Mashimo Bryce L. , Schaettler Maximilian O. , Sherpa Ngima D. , Leavitt Lydia A. , Livingstone Alexandra J. , Khan Saad M. , Li Mao , Anzaldua-Campos Markus I. , Bradley Joseph D. , Leuthardt Eric C. , Kim Albert H. , Dowling Joshua L. , Chicoine Michael R. , Jones Pamela S. , Choi Bryan D. , Cahill Daniel P. , Carter Bob S. , Petti Allegra A. , Johanns Tanner M. , Dunn Gavin P.
Published: June 2024

MAIT clonotype occurrence in T cells from cohort 1.
Supplementary Figure 14 from Single-Cell Chromatin Accessibility Analysis Reveals the Epigenetic Basis and Signature Transcription Factors for the Molecular Subtypes of Colorectal Cancers
Authors: Liu Zhenyu , Hu Yuqiong , Xie Haoling , Chen Kexuan , Wen Lu , Fu Wei , Zhou Xin , Tang Fuchou
Published: June 2024

Supplementary Figure 14. Module-trait association identified key TFs for CRC heterogeneities.
Supplementary Figure 13 from Single-Cell Chromatin Accessibility Analysis Reveals the Epigenetic Basis and Signature Transcription Factors for the Molecular Subtypes of Colorectal Cancers
Authors: Liu Zhenyu , Hu Yuqiong , Xie Haoling , Chen Kexuan , Wen Lu , Fu Wei , Zhou Xin , Tang Fuchou
Published: June 2024

Supplementary Figure 13. Network construction and module detection based on TF activities.
Supplementary Figure 12 from Single-Cell Chromatin Accessibility Analysis Reveals the Epigenetic Basis and Signature Transcription Factors for the Molecular Subtypes of Colorectal Cancers
Authors: Liu Zhenyu , Hu Yuqiong , Xie Haoling , Chen Kexuan , Wen Lu , Fu Wei , Zhou Xin , Tang Fuchou
Published: June 2024

Supplementary Figure 12. Differential accessible peaks and TF regulators of CIMP subtypes.
Supplementary Figure 11 from Single-Cell Chromatin Accessibility Analysis Reveals the Epigenetic Basis and Signature Transcription Factors for the Molecular Subtypes of Colorectal Cancers
Authors: Liu Zhenyu , Hu Yuqiong , Xie Haoling , Chen Kexuan , Wen Lu , Fu Wei , Zhou Xin , Tang Fuchou
Published: June 2024

Supplementary Figure 11. Identification of CIMP subtypes.
Supplementary Figure 1 from Single-Cell Chromatin Accessibility Analysis Reveals the Epigenetic Basis and Signature Transcription Factors for the Molecular Subtypes of Colorectal Cancers
Authors: Liu Zhenyu , Hu Yuqiong , Xie Haoling , Chen Kexuan , Wen Lu , Fu Wei , Zhou Xin , Tang Fuchou
Published: June 2024

Supplementary Figure 1. Quality control, cell type annotation, and FACS validation of scATAC-seq atlas.
Data from Spatial Architecture of Myeloid and T Cells Orchestrates Immune Evasion and Clinical Outcome in Lung Cancer
Authors: Enfield Katey S.S. , Colliver Emma , Lee Claudia , Magness Alastair , Moore David A. , Sivakumar Monica , Grigoriadis Kristiana , Pich Oriol , Karasaki Takahiro , Hobson Philip S. , Levi Dina , Veeriah Selvaraju , Puttick Clare , Nye Emma L. , Green Mary , Dijkstra Krijn K. , Shimato Masako , Akarca Ayse U. , Marafioti Teresa , Salgado Roberto , Hackshaw Allan , Jamal-Hanjani Mariam , van Maldegem Febe , McGranahan Nicholas , Glass Benjamin , Pulaski Hanna , Walk Eric , Reading James L. , Quezada Sergio A. , Hiley Crispin T. , Downward Julian , Sahai Erik , Swanton Charles , Angelova Mihaela
Published: June 2024

Abstract
Understanding the role of the tumor microenvironment (TME) in lung cancer is critical to improving patient outcomes. We identified four histology-independent archetype TMEs in treatment-naïve early-stage lung cancer using imaging mass cytometry in the TRACERx study (n = 81 patients/198 samples/2.3 million cells). In immune-hot adenocarcinomas, spatial niches of T cells and macrophages increased with clonal neoantigen burden, whereas such an increase was observed for niches of plasma and B cells in immune-excluded squamous cell carcinomas (LUSC). Immune-low TMEs were associated with fibroblast barriers to immune infiltration. The fourth archetype, characterized by sparse lymphocytes and high tumor-associated neutrophil (TAN) infiltration, had tumor cells spatially separated from vasculature and exhibited low spatial intratumor heterogeneity. TAN-high LUSC had frequent PIK3CA mutations. TAN-high tumors harbored recently expanded and metastasis-seeding subclones and had a shorter disease-free survival independent of stage. These findings delineate genomic, immune, and physical barriers to immune surveillance and implicate neutrophil-rich TMEs in metastasis.
Significance:
This study provides novel insights into the spatial organization of the lung cancer TME in the context of tumor immunogenicity, tumor heterogeneity, and cancer evolution. Pairing the tumor evolutionary history with the spatially resolved TME suggests mechanistic hypotheses for tumor progression and metastasis with implications for patient outcome and treatment.

This article is featured in Selected Articles from This Issue, p. 897
Data from Single-Cell Chromatin Accessibility Analysis Reveals the Epigenetic Basis and Signature Transcription Factors for the Molecular Subtypes of Colorectal Cancers
Authors: Liu Zhenyu , Hu Yuqiong , Xie Haoling , Chen Kexuan , Wen Lu , Fu Wei , Zhou Xin , Tang Fuchou
Published: June 2024

Abstract
Colorectal cancer is a highly heterogeneous disease, with well-characterized subtypes based on genome, DNA methylome, and transcriptome signatures. To chart the epigenetic landscape of colorectal cancers, we generated a high-quality single-cell chromatin accessibility atlas of epithelial cells for 29 patients. Abnormal chromatin states acquired in adenomas were largely retained in colorectal cancers, which were tightly accompanied by opposite changes of DNA methylation. Unsupervised analysis on malignant cells revealed two epigenetic subtypes, exactly matching the iCMS classification, and key iCMS-specific transcription factors (TFs) were identified, including HNF4A and PPARA for iCMS2 tumors and FOXA3 and MAFK for iCMS3 tumors. Notably, subtype-specific TFs bind to distinct target gene sets and contribute to both interpatient similarities and diversities for both chromatin accessibilities and RNA expressions. Moreover, we identified CpG-island methylator phenotypes and pinpointed chromatin state signatures and TF regulators for the CIMP-high subtype. Our work systematically revealed the epigenetic basis of the well-known iCMS and CIMP classifications of colorectal cancers.
Significance:
Our work revealed the epigenetic basis of the well-known iCMS and CIMP classifications of colorectal cancers. Moreover, interpatient minor similarities and major diversities of chromatin accessibility signatures of TF target genes can faithfully explain the corresponding interpatient minor similarities and major diversities of RNA expression signatures of colorectal cancers, respectively.

This article is featured in Selected Articles from This Issue, p. 897
TABLE 1 from Molecular Landscape and Clinical Implication of CCNE1-amplified Esophagogastric Cancer
Authors: Rustgi Naryan , Wu Sharon , Samec Timothy , Walker Phillip , Xiu Joanne , Lou Emil , Goel Sanjay , Saeed Anwaar , Moy Ryan H.
Published: June 2024

Patient demographic data and frequency of CCNE1 amplification by EGC subtype
Supplementary Table S1 from Molecular Landscape and Clinical Implication of CCNE1-amplified Esophagogastric Cancer
Authors: Rustgi Naryan , Wu Sharon , Samec Timothy , Walker Phillip , Xiu Joanne , Lou Emil , Goel Sanjay , Saeed Anwaar , Moy Ryan H.
Published: June 2024

Supplementary Table S1. Frequency of CCNE1 amplifications in EGC by primary tumor or metastatic site.
Supplementary Figure S7 from Molecular Landscape and Clinical Implication of CCNE1-amplified Esophagogastric Cancer
Authors: Rustgi Naryan , Wu Sharon , Samec Timothy , Walker Phillip , Xiu Joanne , Lou Emil , Goel Sanjay , Saeed Anwaar , Moy Ryan H.
Published: June 2024

Supplementary Figure S7 shows treatment outcomes and survival analysis of CCNE1-amplified vs. non-amplified esophageal adenocarcinoma and esophagogastric junction carcinoma
Supplementary Figure S3 from Molecular Landscape and Clinical Implication of CCNE1-amplified Esophagogastric Cancer
Authors: Rustgi Naryan , Wu Sharon , Samec Timothy , Walker Phillip , Xiu Joanne , Lou Emil , Goel Sanjay , Saeed Anwaar , Moy Ryan H.
Published: June 2024

Supplementary Figure S3 shows frequently occurring molecular co-alterations in EA and GA with CCNE1 CN amplification or gain
FIGURE 2 from Molecular Landscape and Clinical Implication of CCNE1-amplified Esophagogastric Cancer
Authors: Rustgi Naryan , Wu Sharon , Samec Timothy , Walker Phillip , Xiu Joanne , Lou Emil , Goel Sanjay , Saeed Anwaar , Moy Ryan H.
Published: June 2024

Frequently occurring molecular coalterations in CCNE1-amplified EGC. Frequency of comutated genes among all CCNE1-amplified and nonamplified EG adenocarcinoma by WES and NGS (A). CNAs co-occurring with CCNE1 amplification (B). LOH with CCNE1 amplification (C). HER2 overexpression or ERBB2 amplification in CCNE1-amplified EG adenocarcinoma by CISH assays, IHC, or NGS (D). Statistical significance is displayed as the following: *, q < 0.05; **, q < 0.01; ***, q < 0.001; ****, q < 0.0001.