bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inferred Immune-Cell Activity Is an Independent Predictor of HER2-Negative Breast Cancer Prognosis and Response to Paclitaxel-Based Therapy in the GeparSepto Trial
Authors: Fasching Peter A. , Szeto Christopher , Denkert Carsten , Benz Stephen , Weber Karsten , Spilman Patricia , Budczies Jan , Schneeweiss Andreas , Stickeler Elmar , Schmatloch Sabine , Jackisch Christian , Karn Thomas , Sinn Hans Peter , Warm Mathias , van Mackelenbergh Marion , Rabizadeh Shahrooz , Schem Christian , Heinmöller Ernst , Mueller Volkmar , Marmé Frederik , Soon-Shiong Patrick , Nekljudova Valentina , Untch Michael , Loibl Sibylle 
Published: April 2023

Abstract

Purpose:
Tumor microenvironment (TME) immune markers have been correlated with both response to neoadjuvant therapy and prognosis in patients with breast cancer. Here, immune-cell activity of breast cancer tumors was inferred by expression-based analysis to determine if it is prognostic and/or predictive of response to neoadjuvant paclitaxel-based therapy in the GeparSepto (G7) trial (NCT01583426).

Experimental Design:
Pre-study biopsies from 279 patients with HER2-negative breast cancer in the G7 trial underwent RNA-seq-based profiling of 104 immune-cell-specific genes to assess inferred Immune Cell Activity (iICA) of 23 immune-cell types. Hierarchical clustering was used to classify tumors as iICA “hot,” “warm,” or “cold” by comparison of iICA in the G7 cohort relative to that of 1,467 samples from a tumor database established by Nantomics LLC. Correlations between iICA cluster, pathology-assessed tumor-infiltrating lymphocytes (TIL), and hormone receptor (HR) status for pathologic complete response (pCR), disease-free survival (DFS), and overall survival (OS) were determined.

Results:
iICA cluster correlated with TIL levels. The highest pCR rates were observed in hot cluster tumors, and those with relatively higher TILs. Greater inferred activity of several T-cell types was significantly associated with pCR and survival. DFS and OS were prolonged in patients with hot or warm cluster tumors, the latter particularly for HR negative tumors, even if TILs were relatively low.

Conclusions:
Overall, TIL level better predicted pCR, but iICA cluster better predicted survival. Differences in associations between TILs, cluster, pCR, and survival were observed for HR-positive tumors versus HR-negative tumors, suggesting expanded study of the implication of these findings is warranted.
The Negative Influence of Baseline Cell-free DNA on Long-term Survival in DLBCL Depends on Frontline Treatment Intensity
Authors: Desmots Fabienne , Rossille Delphine , Roussel Mikael , Pangault Céline , Louarn Laetitia , De Saint Jore Mylène , Le Gouill Steven , Bouabdallah Krimo , Delwail Vincent , Gressin Remy , Cornillon Jérôme , Damaj Gandhi , Maisonneuve Hervé , Damotte Diane , Kraeber-Bodere Françoise , Lamy Thierry , Parrens Marie-Cécile , Milpied Noël , Fest Thierry 
Published: April 2023

Abstract

Purpose:
This study aims to investigate the relationship between the intensity of the initial treatment given to patients with de novo diffuse large B-cell lymphoma (DLBCL) and the impact of their baseline cell-free DNA (cfDNA) levels on their long-term survival.

Experimental Design:
The GOELAMS 075 randomized clinical trial compared rituximab plus cyclophosphamide, doxorubicin, vincristine and prednisone (R-CHOP) with high-dose R-chemotherapy plus autologous stem cell transplantation (R-HDT) for patients aged ≤60. An interim PET assessment was used to refer patients for salvage therapy. With a median follow-up of more than 5.8 years, we analyzed the effects of the treatment arm, salvage therapy, and cfDNA level at diagnosis on overall survival (OS).

Results:
In a representative group of 123 patients, a high cfDNA concentration (&gt;55 ng/mL) at diagnosis was associated with poor clinical prognostic factors and constituted a prognostic marker, independently of the age-adjusted International Prognostic Index. A cfDNA level above a threshold value of 55 ng/mL at diagnosis was associated with significantly worse OS. In an intention-to-treat analysis, high-cfDNA R-CHOP patients (but not high-cfDNA R-HDT patients) had worse OS [HR (95% confidence interval), 3.99 (1.98–10.74); P = 0.006]. In patients with high cfDNA levels, salvage therapy and transplantation were associated with a significantly higher OS rate. Among 50 patients with complete response 6 months after the end of treatment, for 11 of 24 R-CHOP patients, the cfDNA did not fall back to normal values.

Conclusions:
In this randomized clinical trial, intensive regimens mitigated the negative influence of high cfDNA levels in de novo DLBCL, relative to R-CHOP.
Abstract 1065: Cancer-specific molecular subtypes of cholangiocarcinoma reveal unique molecular dependency with clinical relevance
Authors: Kwon Woo Young , LEE Sung Hwan 
Published: April 2023

Abstract
Introduction: Cholangiocarcinoma is a heterogeneous tumor entity harboring distinct tumor biology and clinical phenotype according to their unique tumor microenvironment (TME), especially anatomic location in terms of intrahepatic, peri-hilar, and distal extrahepatic portion. Therefore, there is a clear unmet need for the precision strategy based on cancer-specific genomic features rather than previous molecular subtypes from bulk RNA sequencing.
Methods: Comprehensive analyses were performed using the dataset from the cancer dependency map (DepMap) project, including cancer-specific molecular characterization with multi-omics data, genome-wide loss-of-function screening with CRISPR-Cas9 system, and drug sensitivity with compound screening to uncover cancer-specific molecular subtypes showing clinical relevance. The cancer-specific molecular signatures were validated in independent translational cohorts (TCGA-CHOL; n=45, ICGC-BTC; n=181, GSE132305; n=220).
Results: Integrative profiling of transcriptome from bile duct cancer cell lines (n=39) from the Cancer Cell Line Encyclopedia (CCLE) revealed a total of three cancer-specific molecular subtypes showing distinct tumor biology through all omics layer as well as clinical relevance with prognostic significance. Major molecular features of each subtype were reproducible in the validation cohorts. Subtype-specific molecular biomarkers, including mutational signature and metabolites, were identified. Finally, the target drug with subtype-specific genetic dependency was analyzed to provide precision strategy according to distinct subtypes’ molecular characterization.
Conclusions: Comprehensive analysis using a multi-omics dataset revealed precision strategies based on cancer-specific molecular subtypes of cholangiocarcinoma in terms of tumor classification and discriminative therapeutic chances. Prospective translational studies companion with clinical trials based on cancer-specific molecular subtypes is mandatory to establish the precision strategy for managing cholangiocarcinoma.
Citation Format: Woo Young Kwon, Sung Hwan LEE. Cancer-specific molecular subtypes of cholangiocarcinoma reveal unique molecular dependency with clinical relevance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1065.
Abstract 1076: Targeting EGFR and PI3K pathways with KRASG12D inhibitor overcomes oncogenic dependence in pancreatic cancer
Authors: Bhavar Prashant Kashinath , Surampudi Uday Kumar , Gandham Adilakshmi , Sarma Partha Pratim 
Published: April 2023

Abstract
In the U.S., pancreatic cancer is 9th most commonly diagnosed cancer (depending on gender), but the fourth leading cause of cancer death in men and women. FOLFIRINOX or gemcitabine plus nab-paclitaxel have been the standard of care for pancreatic cancer, but late stage prognosis often leads to disease progression of disease, with an overall 5 year survival of 11.5%, in the US, and 9% in Japan. KRASG12D mutant isoform is found in 36% of pancreatic adenocarcinoma patients and hence targeting this major mutation that appear early in the disease may help overcome cancer progression. Several signaling pathways are known to converge on the MAPK and PI3K pathways as effectors of cellular response within the cell. Pancreatic cancer is driven by activating mutations in KRAS, which in turn is expected to activate PI3K signalling through the p110α subunit, indicating that a large proportion of patients could benefit from effective targeting of this pathway. Role of EGFR on the other hand in KRAS-dependent pancreatic cancer progression is not well understood, and cetuximab as single agent has not provided benefit in PDAC patients. Recent studies of KRASG12C inhibitors in combination with EGFR inhibitors have shown clinical benefit in colorectal cancer possibly due to enhanced inhibition of KRAS-dependent signaling or overcoming adaptive feedback mechanisms. This opens an opportunity to investigate combinations of KRASG12D inhibitors with other inhibitors of MAPK and PI3K pathways. Here we report a data for 40-point combination dose response matrix combining VRTX153, a novel and highly selective inhibitor of KRASG12D with Alpelisib (a p110α inhibitor) and an EGFR inhibitor using MTT assay. Effect on downstream markers such as pERK, pEGFR and pAKT is being investigated. In vivo pharmacological effect of these agents will be investigated in the due course of development.
Citation Format: Prashant Kashinath Bhavar, Uday Kumar Surampudi, Adilakshmi Gandham, Partha Pratim Sarma. Targeting EGFR and PI3K pathways with KRASG12D inhibitor overcomes oncogenic dependence in pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1076.
Abstract 1132: Exploiting MGMT loss using a new class of DNA modifiers which selectively target tumor DNA and overcome therapy resistance mechanisms across multiple tumor types
Authors: Ruggeri Bruce , Tarantino Kyle , Sundaram Ranjini , Lin Kingson , Herzon Seth , Park Joseph , Johnson Spenser , Gueble Susan , Bindra Ranjit S. 
Published: April 2023

Abstract
DNA damage response (DDR) defects are common in cancer, and it is well established that these tumor-associated DNA repair vulnerabilities can be exploited for a therapeutic gain. Small molecule inhibitors of DDR proteins have been developed to target these cancers, which are now FDA-approved and/or currently being tested in clinical trials. Our team recently reported on an entirely new approach to exploit DDR defects in cancer, via DNA modification, eliminating the need to target proteins (Lin et al., Science 2022). In this recent study, we demonstrated that our new class of “DNA modifiers (DMs)” can be engineered to exploit loss of O6-methylguanine methyltransferase (MGMT), which leads to robust and selective killing of MGMT-deficient glioma tumors, both in vivo and in vitro. We also found that our approach could overcome acquired and intrinsic defects in another DDR pathway, mismatch repair (MMR), which is a known resistance mechanism to standard-of-care cytotoxic therapies in glioma, including TMZ.
Here, we sought to determine the extent to which our approach can be expanded to selectively target a wide range of cancers beyond glioma in which loss of MGMT, as well as acquired and intrinsic MMR defect, are commonly seen at various frequencies. To this end, we profiled over 900 cell line models, as well as several collections of patient-derived cultures derived from several tumor types for sensitivity to our DMs based on MGMT and MMR status in vitro. We then validated our findings in cell line xenograft and patient-derived xenograft models, in vivo. In parallel, we compared the activity of DMs to commonly used, standard-of-care cytotoxic drugs, in vitro and in vivo. Our data indicate that DMs can effectively target MGMT loss, as well as intrinsic and acquired MMR defects, in multiple non-CNS tumor types. Taken together, the findings reported here support an entirely new approach to selectively exploit DDR defects via direct DNA modification. This new approach has the potential to overcome known resistance mechanisms to currently used small molecule inhibitors of DDR proteins, across a broad range of cancers.
Citation Format: Bruce Ruggeri, Kyle Tarantino, Ranjini Sundaram, Kingson Lin, Seth Herzon, Joseph Park, Spenser Johnson, Susan Gueble, Ranjit S. Bindra. Exploiting MGMT loss using a new class of DNA modifiers which selectively target tumor DNA and overcome therapy resistance mechanisms across multiple tumor types [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1132.
Abstract 1170: Scalable co-sequencing of RNA and DNA from individual nuclei
Authors: Olsen Timothy R. , Talla Pranay , Furnari Julia , Zha Shan , Canoll Peter , Bruce Jeffrey , Sims Peter 
Published: April 2023

Abstract
A scalable co-assay for single cell mRNA and gDNA sequencing could potentially harmonize the identification of rare cell populations and cell states with corresponding cell-lineage relationships, drug sensitivities, and genetic mutations. Such an assay would provide new insights into the relationship between genetic alterations and tumor cell phenotype. However, simultaneously measuring the genomic and transcriptomic content of individual cells at high throughput remains challenging. Here we present single-cell lithium assisted nucleosome depleted sequencing (scLAND-seq), a scalable method for co-sequencing RNA and DNA from single nuclei that uses the widely available 10x Genomics microfluidics platform. In scLAND-seq, nuclei are treated with a mild detergent, lithium diiodosalicylate, which denatures protein and renders gDNA free of nucleosome packing while preserving the nuclear membrane. The nuclei are then tagmented with Tn5 transposase, which randomly fragments gDNA and integrates universal sequencing adapters. Tagmented nuclei are loaded into a microfluidic droplet generator which co-encapsulates nuclei with beads containing barcoded primers for reverse transcription of mRNA and replication of gDNA. Ultimately two libraries are created: one for nuclear mRNA and one for gDNA. Each library contains barcodes linking it to its nuclei of origin, thus allowing simultaneous analysis of the transcriptome and genome of each nucleus. Once nuclei have been depleted of nucleosomes, all steps can be performed using a 10x Genomics Chromium Controller and 10x Multiome Kit without further experimental modification. We characterize LAND-seq with BJ fibroblasts, a human diploid cell line, and demonstrate the detection of rare subpopulations with copy number variants (CNVs) associated with specific transcriptional clusters. Analysis of transcription start site enrichment indicates near-complete disruption of chromatin structure, resulting in high-complexity libraries that could not be sequenced to saturation even with &gt;1M reads/cell. The corresponding gene expression library is of high-quality, containing ~20,000 gene counts per nuclei. Finally, to demonstrate scLAND-seq’s compatibility with primary cells, we applied scLAND-seq to cryopreserved, human glioblastoma (GBM) surgical specimens, enabling direct investigation into the relationship between phenotype and genotype in thousands of individual cells.
Character limit: 2,600
Citation Format: Timothy R. Olsen, Pranay Talla, Julia Furnari, Shan Zha, Peter Canoll, Jeffrey Bruce, Peter Sims. Scalable co-sequencing of RNA and DNA from individual nuclei [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1170.
Abstract 1190: Mimicking CAFs, pial cells support leptomeningeal metastasis
Authors: Snyder Jenna , Remsik Jan , Prescott Nicholas , Boire Adrienne 
Published: April 2023

Abstract
Leptomeningeal metastasis (LM), the spread of cancer into cerebrospinal fluid (CSF)-filled coverings of the brain and spinal cord, is a dismal complication of cancer leading to rapid neurologic disability and death. While a diverse array of primary tumors may result in LM, recent work from our laboratory (Chi Y et al 2020 Science) demonstrates a conserved transcriptional signature, independent of primary tumor, suggesting that tumor-microenvironmental interactions play a dominant role in this pathology. We have proteomically interrogated CSF collected from breast (n = 45), lung (n = 30), and melanoma (n = 27) patients with and without LM. We detect robust expression of inflammatory cytokines in all LM+ samples, 15 of these cytokines including IL8, IL6, and CXCL1 are conserved across tumor types in the presence of LM. Because cancer cells in the CSF do not express mRNA associated with these cytokines, we hypothesized that these inflammatory cytokines may originate from the microenvironment. Within the leptomeninges, LM cells adhere to and interact with the innermost layer of the meninges, the pia mater, which contains fibroblast-like cells. Co-culture of cancer cells with pial cells induced changes in the pial cell transcriptome and secretome, leading to increased IL8, IL6, and CXCL1 production. This communication between cancer cells and pial cells is preserved in the absence of direct cell-cell contact. To identify cancer cell signal(s) responsible for these pial cell changes, we subjected cancer cell conditioned media to gel filtration, and uncovered TGFBI as a key secreted factor inducing pial cell transcriptional changes. These pial cells support cancer cell growth in vivo, as measured by co-implantation experiments. In autopsy samples, we detect IL8, IL6, and CXCL1 expression in the pia of patients harboring LM. Taken together, these observations support a cancer-associated-fibroblast like role for pial cells in the setting of LM. We are currently carrying out single cell RNA sequencing of both human and mouse LM samples to capture heterogeneity in both cancer and pial cell responses, and to place these cells in the larger context of the CAF knowledgebase. Our work extends the CAF phenotype beyond classical fibroblasts to include pial cells, suggesting novel therapeutic opportunities within CNS malignancies.
Citation Format: Jenna Snyder, Jan Remsik, Nicholas Prescott, Adrienne Boire. Mimicking CAFs, pial cells support leptomeningeal metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1190.
Abstract 1218: Mercury(II)-induced abnormalities in processing of topoisomerase I-mediated DNA damage
Authors: Ursu Giorgiana Madalina , Cyran Anna M. , Zhitkovich Anatoly 
Published: April 2023

Abstract
Mercury (Hg) is a persistent environmental pollutant that has long been associated with neurotoxic and other noncancer health effects in exposed populations. Recent large epidemiological studies using different internal indices of Hg exposure have found significantly elevated risks for skin cancers in both men and women. To understand potential carcinogenic mechanisms for Hg(II), we examined its mutagenicity and impact on processing of different types of DNA damage. In agreement with its lack of DNA reactivity, we found that Hg(II) was not mutagenic at the mammalian Hprt locus and did not change DNA incorporation of rNMPs which are the most abundant endogenous nucleotide abnormalities in the genome. We next tested the impact of Hg(II) at nontoxic or only mildly toxic concentrations on sensitivity of cells to several genotoxicants producing specific classes of DNA damage. We found that even nontoxic concentrations of Hg(II) impaired cellular resistance to topoisomerase I-mediated DNA damage in human epidermal keratinocytes. Hg(II) had no significant effect on cytotoxicity of topoisomerase II-mediated DNA lesions and examination of numerous components of DNA damage response activated by topoisomerase II-targeting drugs showed no major differences between control and Hg(II)-exposed cells. In contrast, Hg(II)-treated keratinocytes displayed a distorted DNA damage response to topoisomerase I-produced DNA damage, manifested in a misbalanced activation of ATM and ATR targets. Consistent with their lower survival, Hg(II)-treated cells accumulated higher levels of toxic DNA double-strand breaks (DSBs). Further analyses indicated that Hg(II) caused impartment of DNA repair of replication-associated DSBs. Thus, although Hg(II) is not directly genotoxic, it can increase genomic instability by interfering with accurate processing of endogenous DNA damage produced by topoisomerase I.
Citation Format: Giorgiana Madalina Ursu, Anna M. Cyran, Anatoly Zhitkovich. Mercury(II)-induced abnormalities in processing of topoisomerase I-mediated DNA damage [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1218.
Abstract 1227: Esophageal cancer shows spontaneous plasticity between epithelial and mesenchymal status
Authors: Tsuchihashi Kenji , Hirata Yuki , Yamasaki Juntaro , Suina Kentaro , Tanoue Kenro , Yae Toshifumi , Masuda Kenta , Baba Eishi , Akashi Koichi , Kitagawa Yuko , Saya Hideyuki , Nagano Osamu 
Published: April 2023

Abstract
Epithelial-mesenchymal transition (EMT) is one of essential processes in cancer progression. Plasticity between epithelial and mesenchymal status is referred as epithelial-mesenchymal plasticity (EMP). The significance of spontaneous change of EMP is under investigation in the field of EMT. To date, spontaneous EMP is reported in breast and prostate cancer, which leads to the acquisition of stem-cell properties and chemoresistance. On the other hand, the presence of spontaneous EMP is still not examined in other cancer including esophageal cancer. In the present study, we tackled the question of whether esophageal cancer have the potency of spontaneous EMP. We screened eleven esophageal squamous cancer cell (ESCC) cell lines with CD44 isoform expression, which is known to reflect epithelial and mesenchymal status. Interestingly, KYSE520 was found to comprise heterogenous populations consisting of CD44v+ and CD44v- subpopulations. CD44v+ and CD44v- cells showed the expression of epithelial and mesenchymal markers, respectively. Single-cell sorting of CD44v+ and CD44v- cells revealed both cells gave rise to cell populations consisting of CD44v+ and CD44v- cells, indicating CD44v+ epithelial-like and CD44v- mesenchymal-like cells can generate counterparts, respectively. This EMP was maintained in next generation. Further, we found the generation of counterparts between CD44v+ and CD44v- cells in vivo. Epithelial splicing regulatory protein 1 (ESRP1) is reported as the regulator of CD44 mRNA splicing. The role of ESRP1 in EMP is not well understood in esophageal cancer. The inhibition of ESRP1 shifted CD44v+ to CD44v- cells in KYSE520. However, the expression of epithelial-mesenchymal transition (EMT)-related markers or transcriptional factors were almost not affected, suggesting ESRP1 functions downstream of EMP. Our results firstly revealed the presence of spontaneous EMP in esophageal cancer and give a new insight in the field of EMT.
Citation Format: Kenji Tsuchihashi, Yuki Hirata, Juntaro Yamasaki, Kentaro Suina, Kenro Tanoue, Toshifumi Yae, Kenta Masuda, Eishi Baba, Koichi Akashi, Yuko Kitagawa, Hideyuki Saya, Osamu Nagano. Esophageal cancer shows spontaneous plasticity between epithelial and mesenchymal status [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1227.