bluuebunny/crossref_metadata_2025 huggingface dataset:
Exploring the Mechanism of Ling-Gui-Zhu-Gan Decoction in Ventricular Remodeling after Acute Myocardial Infarction Based on UPLC and In Vivo Experiments
Authors: Zhou Peng , Zhang Meng , Zhao Xiao-ni , Tang Tong-juan , Wang Xiang , Huang Lu-lu , Kong Qi , Wang Liang , Huang Jin-ling
Published: May 2022

Ventricular remodeling (VR) after acute myocardial infarction (AMI) is an important pathophysiological basis for the development of chronic heart failure (CHF). At present, Ling-Gui-Zhu-Gan decoction (LGZGD) has been widely reported in the clinical treatment and basic research of cardiovascular diseases (CVDs), such as myocardial infarction, heart failure, and angina pectoris. However, the mechanism of LGZGD against VR after AMI remains unclear. Ultra-performance liquid chromatography (UPLC) was applied to investigate the major constituents of LGZGD, and molecular docking was used to predict the targets on the NLRP3/Caspase-1/GSDMD signaling pathway. In vivo, histological changes in the myocardium were visualized using HE staining and Masson staining, and cardiomyocyte apoptosis was detected using TUNEL. IL-1β activity in rat serum was determined by ELISA. Finally, NLRP3, Caspase-1, and GSDMD expressions were analyzed through RT-qPCR and Western blotting. The results showed that 8 authentic reference substances have been detected in LGZGD. Molecular docking showed that the major chemical constituents of LGZGD had a good binding activity with NLRP3, Caspase-1, and GSDMD. Our results showed that LGZGD treatment markedly improved cardiac pathology, decreased cardiomyocyte apoptosis, reduced IL-1β activity, and regulated the expression of genes and proteins related to the NLRP3/Caspase-1/GSDMD signal pathway. These results suggest that LGZGD protects against VR after AMI through NLRP3/Caspase-1/GSDMD signal pathway.
HSP90 Mediates IFNγ-Induced Adaptive Resistance to Anti-PD-1 Immunotherapy
Authors: Liu Ke , Huang Jun , Liu Jiao , Li Changfeng , Kroemer Guido , Tang Daolin , Kang Rui
Published: May 2022

Constitutive or acquired resistance is a major problem limiting the clinical success of anticancer immunotherapies targeting the PD-1/PD-L1 interaction. Here, we report that the molecular chaperone HSP90 is a key mediator of IFNγ-induced adaptive immune resistance. An unbiased screen of 17 cancer cell lines or primary cancer cells identified novel metabolic agents, especially HSP90 inhibitors, that blocked the upregulation of immune checkpoints (IDO1 and PD-L1) induced by IFNγ. Subsequent quantitative mass spectrometry combined with functional rescue analysis revealed that IFNγ-induced immune checkpoint expression requires increased protein stability of the transcription factor STAT1, mediated by the HSP90–SUGT1 chaperone complex. Expression of dominant-negative HSP90 (D88N) resulted in inhibition of STAT1-mediated IFNγ signaling. The upregulation of IDO1 in cancer cells acted as an immunosuppressive feedback mechanism to limit the proliferation and function of cytotoxic CD8+ T lymphocytes through iron-dependent kynurenine production and subsequent TSPAN5-mediated kynurenine secretion. The effectiveness and safety of combinations of anti-PD-1 immunotherapy with iron chelation or pharmacologic inhibitors of HSP90 or IDO1 was confirmed in xenograft, orthotopic, and transgenic mouse models of pancreatic cancer. These findings support the rationale for future clinical trials in which widely used immunotherapies are combined with additional molecules that intercept resistance by iron chelation, IDO1 inhibition, or HSP90 neutralization.

Significance:

This study reveals an HSP90-centric, iron-modulated mechanism that confers immunosuppression, offering potential therapeutic targets for interfering with acquired resistance to the most prevalent anticancer immunotherapies.
Plasticity Enables Cooperation among Heterogeneous Cancer Cell Populations to Support Metastatic Fitness
Authors: LeBleu Valerie S.
Published: May 2022

The invasive progression of cancer known as metastasis remains strongly associated with morbidity and lethality. New meaningful therapeutic interventions could be derived from a better understanding of the underlying processes driving cancer cell seeding and proliferation at secondary sites. Emerging findings regarding the heterogeneity of cancer cells observed in metastases have led us to revisit concepts surrounding metastatic fitness. Novel model systems to study the markers of cancer stem cell plasticity and their evolution during metastatic growth have uncovered that dynamic and heterogeneous cancer cell populations are observed during metastatic disease progression. Heinz and colleagues studied the heterogeneity of colorectal carcinomas, where primary tumors evolve alongside an epithelium well characterized for its self-renewing stem cell population. Their work revealed a functional dynamic interplay in the organization of the metastatic lesions as they transition from stagnating to expanding nodules, wherein the heterogeneous mixture of cancer cell stem cells with more differentiated cancer cells is essential for metastatic outgrowth. Their work supports that dynamic YAP signaling enables the growth-permissive heterogeneous composition of the metastatic nodule, in contrast with growth-restricted homogeneous compositions.

See related article by Heinz et al., p. 1953
Telaglenastat plus Everolimus in Advanced Renal Cell Carcinoma: A Randomized, Double-Blinded, Placebo-Controlled, Phase II ENTRATA Trial
Authors: Lee Chung-Han , Motzer Robert , Emamekhoo Hamid , Matrana Marc , Percent Ivor , Hsieh James J. , Hussain Arif , Vaishampayan Ulka , Liu Sandy , McCune Steven , Patel Vijay , Shaheen Montaser , Bendell Johanna , Fan Alice C. , Gartrell Benjamin A. , Goodman Oscar B. , Nikolinakos Petros G. , Kalebasty Arash Rezazadeh , Zakharia Yousef , Zhang Zhentao , Parmar Hema , Akella Lalith , Orford Keith , Tannir Nizar M.
Published: May 2022

Purpose:

Glutaminase is a key enzyme, which supports elevated dependency of tumors on glutamine-dependent biosynthesis of metabolic intermediates. Dual targeting of glucose and glutamine metabolism by the mTOR inhibitor everolimus plus the oral glutaminase inhibitor telaglenastat showed preclinical synergistic anticancer effects, which translated to encouraging safety and efficacy findings in a phase I trial of 2L+ renal cell carcinoma (RCC). This study evaluated telaglenastat plus everolimus (TelaE) versus placebo plus everolimus (PboE) in patients with advanced/metastatic RCC (mRCC) in the 3L+ setting (NCT03163667).

Patients and Methods:

Eligible patients with mRCC, previously treated with at least two prior lines of therapy [including ≥1 VEGFR-targeted tyrosine kinase inhibitor (TKI)] were randomized 2:1 to receive E, plus Tela or Pbo, until disease progression or unacceptable toxicity. Primary endpoint was investigator-assessed progression-free survival (PFS; one-sided α <0.2).

Results:

Sixty-nine patients were randomized (46 TelaE, 23 PboE). Patients had a median three prior lines of therapy, including TKIs (100%) and checkpoint inhibitors (88%). At median follow-up of 7.5 months, median PFS was 3.8 months for TelaE versus 1.9 months for PboE [HR, 0.64; 95% confidence interval (CI), 0.34–1.20; one-sided P = 0.079]. One TelaE patient had a partial response and 26 had stable disease (SD). Eleven patients on PboE had SD. Treatment-emergent adverse events included fatigue, anemia, cough, dyspnea, elevated serum creatinine, and diarrhea; grade 3 to 4 events occurred in 74% TelaE patients versus 61% PboE.

Conclusions:

TelaE was well tolerated and improved PFS versus PboE in patients with mRCC previously treated with TKIs and checkpoint inhibitors.
Detection of Occult Recurrence Using Circulating Tumor Tissue Modified Viral HPV DNA among Patients Treated for HPV-Driven Oropharyngeal Carcinoma
Authors: Berger Barry M. , Hanna Glenn J. , Posner Marshall R. , Genden Eric M. , Lautersztain Julio , Naber Stephen P. , Del Vecchio Fitz Catherine , Kuperwasser Charlotte
Published: May 2022

Purpose:

Despite generally favorable outcomes, 15% to 25% of patients with human papillomavirus (HPV)-driven oropharyngeal squamous cell carcinoma (OPSCC) will have recurrence. Current posttreatment surveillance practices rely on physical examinations and imaging and are inconsistently applied. We assessed circulating tumor tissue modified viral (TTMV)-HPV DNA obtained during routine posttreatment surveillance among a large population of real-world patients.

Experimental Design:

This retrospective clinical case series included 1,076 consecutive patients across 108 U.S. sites who were ≥ 3 months posttreatment for HPV-driven OPSCC and who had one or more TTMV-HPV DNA tests (NavDx, Naveris Laboratories) obtained during surveillance between February 6, 2020, and June 29, 2021. Test results were compared with subsequent clinical evaluations.

Results:

Circulating TTMV-HPV DNA was positive in 80 of 1,076 (7.4%) patients, with follow-up available on all. At first positive surveillance testing, 21 of 80 (26%) patients had known recurrence while 59 of 80 (74%) patients were not known to have recurrent disease. Among these 59 patients, 55 (93%) subsequently had a confirmed recurrence, 2 patients had clinically suspicious lesions, and 2 had clinically “no evidence of disease” (NED) at last follow-up. To date, the overall positive predictive value of TTMV-HPV DNA testing for recurrent disease is 95% (N = 76/80). In addition, the point-in-time negative predictive value is 95% (N = 1,198/1,256).

Conclusions:

These findings highlight the clinical potential for circulating TTMV-HPV DNA testing in routine practice. As a surveillance tool, TTMV-HPV DNA positivity was the first indication of recurrence in the majority of cases, pre-dating identification by routine clinical and imaging exams. These data may inform future clinical and guideline-endorsed strategies for HPV-driven malignancy surveillance.

See related commentary by Colevas, p. 4171
PD-1 Inhibition—Trouble for Subsequent TIL Therapy in Patients with Melanoma?
Authors: Blass Eryn , Ott Patrick A.
Published: May 2022

To explore the lower efficacy of adoptive cell transfer (ACT) therapy in patients with anti–PD-1 experienced melanoma, tumor mutational burden (TMB), predicted neoantigen frequencies, and tumor-infiltrating lymphocyte (TIL) neoantigen reactivity were assessed. Reduced neoantigen-specific TIL frequencies correlated with lower ACT response even in patients with similar TMB, suggesting a potentially harmful effect of PD-1 inhibition on T-cell outgrowth.

See related article by Levi et al., p. 3042
Abstract A012: Advanced melanoma exhibits a diversity of evolutionary routes to lethality
Authors: Coulton Alexander , Lobon Irene , Spain Lavinia , Rowan Andrew , Shnidrig Desiree , Shepherd Scott , Shum Ben , Byrne Fiona , Au Lewis , Edmonds Kim , Carlyle Ellie , Renn Alexandra , Messiou Christina , Spencer Charlotte , Schmidt Andreas M. , Tippu Zayd , Rogiers Aljosja , Emmerich Max , Gerard Camille , Pallikonda Husayn , Naceur-Lombardelli Cristina , Foijer Floris , van den Bos Hilda , Wardenaar René , Spierings Diana , Young Kate , Pickering Lisa , Furness Andrew , Borg Elaine , Mitchison Miriam , Moore David , Falzon Mary , Proctor Ian , Stewart Ruby , Mahadeva Ula , Green Anna , Larkin James , Swanton Charles , Jamal-Hanjani Mariam , Litchfield Kevin , Turajlic Samra
Published: May 2022

This abstract is being presented as a short talk in the scientific program. A full abstract is available in the Proffered Abstracts section (PR002) of the Conference Proceedings.

Citation Format: Alexander Coulton, Irene Lobon, Lavinia Spain, Andrew Rowan, Desiree Shnidrig, Scott Shepherd, Ben Shum, Fiona Byrne, Lewis Au, Kim Edmonds, Ellie Carlyle, Alexandra Renn, Christina Messiou, Charlotte Spencer, Andreas M. Schmidt, Zayd Tippu, Aljosja Rogiers, Max Emmerich, Camille Gerard, Husayn Pallikonda, Cristina Naceur-Lombardelli, Floris Foijer, Hilda van den Bos, René Wardenaar, Diana Spierings, Kate Young, Lisa Pickering, Andrew Furness, Elaine Borg, Miriam Mitchison, David Moore, Mary Falzon, Ian Proctor, Ruby Stewart, Ula Mahadeva, Anna Green, James Larkin, Charles Swanton, Mariam Jamal-Hanjani, Kevin Litchfield, Samra Turajlic. Advanced melanoma exhibits a diversity of evolutionary routes to lethality [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr A012.
Abstract A016: Mapping of subclonal events in multi-region multi-omics oncogenomics studies
Authors: Tran Mark , McGranahan Nicholas , Barnes Chris , Herrero Javier
Published: May 2022

Advanced cancer genomics relies on multi-region sequencing to detect intra-tumor heterogeneity. These data allow for backtracking tumor’s evolutionary history by inferring its clonal population structure (Roth et al. 2014) and reconstructing a phylogenetic tree (Malikic et al. 2015). However, methods for mapping subclonal copy number changes onto tumor evolutionary trees are still lacking. McGranahan et al. 2017 presented LOHHLA, a tool for estimation of allele-specific HLA loss from sequencing data, which demonstrated the effects of loss of heterozygosity of HLA on early-stage non-small-cell lung cancer. Here, we present MAPping SubClonal Events (MAPSCE), a tool for mapping subclonal copy number events on the tumor evolutionary trees. Similar to LOHHLA, MAPSCE uses Quadratic Programming for the branch test, where copy-number states before and after a branch are estimated, one branch at a time. Additionally, it relies on the Bayesian Information Criterion from bootstrapped samples to compare the results for each branch and the null hypothesis (H0 = no subclonal event). While mapping loss of heterozygosity events of HLA allele in TRACERx 100 cohort (Jamal-Hanjani et al. 2017) MAPSCE pre-empts the need for manual review on LOHHLA’s initial results, can take into account multiple possible solutions and maintains high accuracy of the results. Using simulated data sets we tested the robustness of MAPSCE to the addition of noise to the cluster CCFs that define each tumor clone. MAPSCE outperforms LOHHLA’s mapping of subclonal LOH events when adding noise up to ±25% CCF. Sub-clonal LOH affecting larger clones are easier to detect and both LOHHLA and MAPSCE produce similar results. However, only MAPSCE maintains high accuracy in detecting events affection smaller clones. In data sets with simulated amplification and duplication events, MAPSCE can also identify duplication and amplification events with at least 70% accuracy up to ±20% CCF noise range. In the future, we are planning to extend this approach to other data types such as gene expression and methylation data, a combination of which would allow us to identify the biological events underlying the formation of new tumor clones, to ultimately integrate these in a comprehensive model of cancer evolution.

Citation Format: Mark Tran, Nicholas McGranahan, Chris Barnes, Javier Herrero. Mapping of subclonal events in multi-region multi-omics oncogenomics studies [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr A016.
Abstract A017: In vivo tracking of clonal dynamics during UV-induced skin carcinogenesis
Authors: Avdieiev Stanislav , Tordesillas Leticia , Chiang Omar Chavez , Chen Zhihua , Simoes Luiza Silva , Chen Y. Ann , Andor Noemi , Gatenby Robert , Flores Elsa R. , Brown Joel S. , Tsai Kenneth Y.
Published: May 2022

This abstract is being presented as a short talk in the scientific program. A full abstract is available in the Proffered Abstracts section (PR004) of the Conference Proceedings.

Citation Format: Stanislav Avdieiev, Leticia Tordesillas, Omar Chavez Chiang, Zhihua Chen, Luiza Silva Simoes, Y. Ann Chen, Noemi Andor, Robert Gatenby, Elsa R. Flores, Joel S. Brown, Kenneth Y. Tsai. In vivo tracking of clonal dynamics during UV-induced skin carcinogenesis [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr A017.
Abstract A022: Effects of chemotherapy on the peripheral immune-cellome in patients with pancreatic cancer
Authors: Svensson Maja , Petersson Alexandra , Sincic Viktor , Hau Sofie Olsson , Eberhard Jakob , Nord David Gisselsson , Leandersson Karin , Lundberg Kristina , Jirström Karin
Published: May 2022

Pancreatic cancer (PC) has become one of the leading causes of cancer related deaths. Late detection and resistance to therapy are two reasons for the dismal prognosis of this disease. Hence, there is an immense need for novel treatment options as well as predictive biomarkers, to prolong the life of these patients. The Chemotherapy, Host Response and Molecular Dynamics in Periampullary Cancer, the CHAMP study (clinical trial nr NCT03724994), is an ongoing observational, prospective clinical study that includes newly diagnosed patients with PC or other periampullary cancers receiving adjuvant or first-line palliative chemotherapy. The present study aims to investigate the peripheral immune-cellome in serial blood samples obtained during treatment from 24 patients, of whom 8 had resectable tumors. Buffy coat was isolated from blood samples taken at baseline (before treatment), after one month and after three to four months of treatment. Flow cytometry with two panels of antibodies was applied to detect major immune populations in both the innate and the adaptive immune system, as well as subpopulations of T cells. Immune cell frequencies were compared between patients with progression and no progression during treatment, and the associations of different immune cell subsets with overall survival were examined. As B cells have been highlighted as being of particular clinical relevance, single-cell transcriptomics and proteomics will be applied to further delineate the dynamics and prognostic impact of individual subtypes within this lineage. The results will provide important real-world data on the longitudinal dynamics of circulating immune cells under the pressure of chemotherapy in patients with PC. These results will in the future be related to analyses of circulating tumor DNA in matched blood samples, and together they will provide a foundation for forthcoming adaptive treatment trials based on results from the CHAMP study.

Citation Format: Maja Svensson, Alexandra Petersson, Viktor Sincic, Sofie Olsson Hau, Jakob Eberhard, David Gisselsson Nord, Karin Leandersson, Kristina Lundberg, Karin Jirström. Effects of chemotherapy on the peripheral immune-cellome in patients with pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr A022.
Abstract A025: Agency of the Cell: Convergence between Origin of Life, Evolution, Cognition and Cancer
Authors: Marshall Perry S.
Published: May 2022

All cells exhibit agency and evolve purposefully. This is why cancer has outwitted doctors for 100 years and why Stage 3-4 patients are no better in 2022 than in 1930. Evolution was presumed to be random and purposeless, yet all cells possess cognition (Shapiro 2020). Cell behavior is normally algorithmic, but uniquely responds to novel situations. This is what makes evolution (and cancer) possible. Cognition—sensing and responding to the environment—is the unifying principle behind the genetic code, origin of life, evolution, consciousness, artificial intelligence, and cancer. Thus the central question in biology is: What is the nature and origin of cognition? A solution to the origin of the genetic code, for which the presenter’s organization offers a $10 million prize (announced at the Royal Society in 2019) is an unsolved cognition problem. This choice is a non-deterministic action of a free agent with sensory capacity and memory. It is not computable from prior states. As well as reading and reacting to its environment, it anticipates future threats, chooses goals and reasons inductively. Computers do none of these things. This new model explains the futility of reducing cancer to a single random or algorithmic component, and suggests we should treat cancer as an autonomous purposeful agent with unique identity and capacity to choose.

Citation Format: Perry S. Marshall. Agency of the Cell: Convergence between Origin of Life, Evolution, Cognition and Cancer [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr A025.
Abstract A032: Integrating spatial analysis and agent-based modeling for studies of stroma sheltering effects in NSCLC
Authors: Miti Tatiana , Miller Anna , Myroshnychenko Daria , Desai Bina , Marusyk Andriy , Basanta David
Published: May 2022

Background: Stroma plays a crucial role in shaping tumor growth dynamics, invasion, and metastasis. High stroma to tumor ratio in the clinic is associated with poor outcomes and shorter remission periods for lung cancer patients. Recent studies suggest that stroma shelters tumor cells during drug administration, but the precise mechanisms to confer this protection remain unclear. We hypothesize that stroma secretes paracrine factors that enhance tumor cells' proliferation rate in proximity, hence outcompeting the death rate due to therapies. In this context, the residual disease is an inherent stage in tumors' eco-evolutionary dynamics under treatment. Therefore, understanding the nature of stroma-tumor cell interactions is crucial for designing effective therapies. Methods: The spatial relationship between the stroma and proliferating tumor cells was interrogated via spatial analysis of 2D samples from mouse xenograft models and subsequent spatial agent-based modeling (ABM). Results: First, we built a pipeline to quantify the spatial extent and amplitude of stroma shielding the presence or absence of treatment. The spatial distributions of tumor cells, their proliferating rates, and the spatial extent of stroma protective effects are used to parametrize the ABM and simulate the spatio-temporal dynamics of tumor growth with and without treatment. Our preliminary results show moderately higher clustering of proliferating and stroma cells than stroma and non-proliferating cells or random distribution in the absence of treatment. In contrast, during therapy, stroma-proliferating tumor cell clustering is considerably higher than stroma-non proliferating tumor cells and stroma-random distribution. Moreover, stroma's protective effect during treatment seems limited to cells either in direct contact with stromal cells or in their immediate proximity. Conclusions: We expect our results to lead to novel therapeutic interventions that aim to shift eco-evolutionary dynamics rather than maximize short-term tumor cell killing efficiency.

Citation Format: Tatiana Miti, Anna Miller, Daria Myroshnychenko, Bina Desai, Andriy Marusyk, David Basanta. Integrating spatial analysis and agent-based modeling for studies of stroma sheltering effects in NSCLC [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr A032.
Abstract B011: P300 histone acetyltransferase mediates glioma stem cell adaptive response to therapeutic stress
Authors: Muthukrishnan Sree Deepthi , Kawaguchi Riki , Nair Pooja , Alvarado Alvaro , Kornblum Harley
Published: May 2022

Glioma stem-like and tumor cells exhibit phenotypic plasticity in response to environmental and therapeutic stress leading to tumor recurrence, but the underlying mechanisms remain largely unknown. In this study, we employed single-cell and whole transcriptomic analyses to uncover that radiation-stress induces a dynamic shift in functional states of glioma cells allowing for acquisition of vascular endothelial-like and pericyte-like cell phenotypes. These vascular-like cells provide trophic support to promote proliferation of tumor cells, and their selective depletion results in reduced tumor growth post-treatment in vivo. Mechanistically, the acquisition of vascular-like phenotype is driven by increased chromatin accessibility and H3K27 acetylation in specific vascular gene regions allowing for their increased expression post-treatment. Blocking P300 histone acetyltransferase activity using a small molecule inhibitor C646 or gene knockdown reverses the epigenetic changes induced by radiation, inhibits the adaptive conversion of GSC into vascular-like cells, reduces tumor growth and enhances animal survival. Our findings highlight an important role for P300 in mediating adaptive response of glioma stem cells to therapeutic-stress, and opens a new therapeutic avenue for preventing glioma recurrence.

Citation Format: Sree Deepthi Muthukrishnan, Riki Kawaguchi, Pooja Nair, Alvaro Alvarado, Harley Kornblum. P300 histone acetyltransferase mediates glioma stem cell adaptive response to therapeutic stress [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr B011.
Abstract B013: Dissecting cell states that enable multi-stressor resistance in cancer
Authors: Schaff Dylan L. , Fasse Aria J. , Shaffer Sydney M.
Published: May 2022

In this work, we investigate how single-cell differences in melanoma lead to resistance to multiple diverse and therapeutically relevant stressors. Targeted small-molecule inhibitors and immunotherapy have shown incredible success in the clinic. However, most patients still only partially respond to a given treatment, succumbing to recurrent, treatment-resistant tumors. As a result, oncologists must resort to sequentially treating tumors with new drugs or co-treating with multiple drugs from the beginning. Despite such a complex clinical paradigm, researchers are still studying the root of treatment resistance one drug at a time. We believe that by more broadly studying how certain cells adapt to and survive a multitude of stressful conditions, we can identify treatment strategies that more effectively overcome many resistant behaviors at once. Here, we use lentiviral cell barcoding to simultaneously trace cells that survive stress from microenvironmental factors (extracellular acidosis and hypoxia), inhibition of specific signaling pathways (with Dabrafenib and Trametinib), and chemotherapy (Cisplatin and Doxorubicin) back to their cells of origin and characterize them by scRNA-seq. Strikingly, we have found that there is a rare population of stress-naïve cells that is resistant to our entire panel of stressors. We are exploring two complementary approaches for overcoming this multi-stressor resistance. First, we have combined cell barcoding and scRNA-seq to identify the initial differences in gene expression that allow certain lineages of cells to survive across stressful conditions. Our goal is to use small-molecule inhibitors and genetic knockouts to target these differences in gene expression in stress-naïve cells, eliminating multi-stressor resistance at its source. Second, we are tracking lineages of cells as they undergo a series of cellular changes needed to ultimately survive our panel of stressors. Using scRNA-seq and cell barcoding, we are identifying these crucial changes as cells reprogram into full resistance. We will look to prevent this reprogramming by simultaneously stressing cells and targeting core reprogramming genes and pathways. Overall, this work uncovers single-cell gene expression differences that allow cancer cells to survive under many stressful conditions. We will work to overcome this resistance by directly eliminating the multi-stressor resistant cells and disrupting their ability to reprogram.

Citation Format: Dylan L. Schaff, Aria J. Fasse, Sydney M. Shaffer. Dissecting cell states that enable multi-stressor resistance in cancer [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr B013.
Abstract B017: Homotypic cell-cell fusion in TNBC cells downregulates cancer testis antigen MAGEC2 and increases therapeutic sensitivity to paclitaxel and doxorubicin
Authors: Gardner Andrea , Zheng Lan , Howland Kennedy , Iloegbunam Chisom , Barrera Patrik , De Santiago Carolina , Brock Amy
Published: May 2022

This abstract is being presented as a short talk in the scientific program. A full abstract is available in the Proffered Abstracts section (PR007) of the Conference Proceedings.

Citation Format: Andrea Gardner, Lan Zheng, Kennedy Howland, Chisom Iloegbunam, Patrik Barrera, Carolina De Santiago, Amy Brock. Homotypic cell-cell fusion in TNBC cells downregulates cancer testis antigen MAGEC2 and increases therapeutic sensitivity to paclitaxel and doxorubicin [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr B017.
Abstract B026: Simulations of cancer evolution predict relative benefits of synergistic and non-synergistic drug combinations for combating different landscapes of drug-resistance
Authors: Saputra Elysia , Tucker-Kellogg Lisa
Published: May 2022

Cancer therapies often have short duration of success due to the development of drug-resistance, which motivates research into anti-evolutionary therapies. A popular strategy is to combine two drugs, particularly if they have synergistic (greater-than-additive) efficacy. However, therapies that cause synergistic suppression of drug-sensitive cells will also suffer from synergistic release of drug-resistant cells, when drug-resistance arises. Not yet understood is the impact of partial drug-resistance and semi-resistant phenotypes on the speed of clonal expansion under combination therapy. In this work, we perform computational modeling to compare the growth rates of heterogeneous populations of cells, when drug-resistance is a binary (all-or-nothing) phenotype, versus when it is a spectrum of partially-sensitive phenotypes. We ask whether the type and granularity of drug-resistance levels in the drug-resistance landscape affects the relative outcome of using synergistic versus non-synergistic drug combinations. We observe that if drug-resistance can develop via rapid, “plastic” phenotypic transitions, then synergistic drugs provide long-lasting suppression of resistance than additive drugs (when dosed to have equal initial efficacy). Conversely, if drug-resistance develops via slow acquisition of phenotypic changes (e.g., requiring multiple genomic lesions), then synergistic drugs promote faster evolution of drug-resistance than additive drugs. When studying how synergism affects evolution, we found that cells escaping a synergistic treatment would be more likely to develop “asymmetric resistance” toward one drug (with greater sensitivity toward the other drug). In contrast, cells escaping antagonistic treatments would be more likely to develop symmetric resistance (equal levels of resistance) toward both drugs. Our findings suggest that after a synergistic treatment, a post-relapse tumor would be more likely to retain sensitivity to one of the drugs used, compared with equivalent relapse after non-synergistic combination treatment. Thus, theoretical modeling can provide testable predictions that complement the hypotheses arising from experiments.

Citation Format: Elysia Saputra, Lisa Tucker-Kellogg. Simulations of cancer evolution predict relative benefits of synergistic and non-synergistic drug combinations for combating different landscapes of drug-resistance [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr B026.
Abstract B031: Metabolism-epigenetics interplay drives cancer cell persistence during receptor tyrosine kinase inhibition
Authors: El-Kenawi Asmaa , Berglund Anders , Brown Joel , Gatenby Robert
Published: May 2022

Receptor tyrosine kinase inhibitors (TKI) are effective anti-cancer treatments. However, evolution of resistance almost inevitably occurs due to pre-existing mutations or development of therapy-tolerant persister cells. Here, we combined time-lapse imaging with longitudinal DNA/RNA sequencing, metabolomics and genome-wide DNA methylation profiling to decipher mechanisms of TKI-induced persisters. Whole exome sequencing demonstrated that persisters were genetically indistinguishable from their parental counterparts, suggesting non-genetic mechanisms were involved. Using untargeted metabolomics, we uncovered that persisters were deficient in methionine metabolism intermediates, including S-(5'-adenosyl)-L-homocysteine (SAH), a major determinant DNA methylation. Examining the consumption of a panel of isotope labeled extracellular amino acids indicated that persisters don’t exhibit deregulation in methionine and cysteine transport. Instead, persisters preferentially consume methionine and cystine to support their survival. Profiling of wide-genome DNA methylation suggested that these metabolic changes was associated with a unique global DNA hypermethylation. We then discovered that promotor regions of genes encoding a range of trace element transporters were uniquely hypermethylated. Through further functional analysis, we then unraveled that these metabolic and epigenetic changes collectively facilitate emergence of a phenotype characterized by methionine/cystine-dependent resistance to osmotic stress. Thus, evolution of TKI resistance can develop by metabolism-dependent epigenetic modifications. Unraveling the detailed mechanisms of these metabolic and epigenetic strategies in cancer cell persisters is crucial to prevent cancer recurrence.

Citation Format: Asmaa El-Kenawi, Anders Berglund, Joel Brown, Robert Gatenby. Metabolism-epigenetics interplay drives cancer cell persistence during receptor tyrosine kinase inhibition [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr B031.
Abstract B038: Blockade of c-met signaling to circumvent radioresistance-associated metastasis in head and neck cancer
Authors: Dou Juan , Lang Liwei , Chen Georgia , Saba Nabil F. , Teng Yong
Published: May 2022

One of the significant clinical challenges in head and neck cancer (HNC) treatment is a high rate of recurrence and metastasis after radiotherapy. Once tumor metastasis occurs following radiotherapy, the prognosis of HNC patients is extremely poor. However, the failure of radiotherapy for cancers is closely related to various factors, and the underlying mechanism remains unclear. We report here that c-Met is the most activated receptor tyrosine kinases in HNC cells once they develop radioresistance. Inactivation of c-Met dramatically attenuates the increased metastatic potential gained in HNC radioresistant cells, leading to tumor regression. Cancer stem cells (CSC) have been confirmed to be in a quiescent state in most established tumors. Mechanistically, the quiescent CSC population can be “awakened” by hyperactive c-Met signaling in radiation, which in turn initiates proliferation and differentiation to potentiate a series of malignant phenotypes. Most importantly, knockdown c-Met by shRNAs or inactivating it by c-Met inhibitor SU11274 reduces the population of “awakened” CSCs and suppresses metastasis, leading to increased sensitivity of HNC radioresistant cells to radiation. These novel findings highlight the importance of additional c-Met blockade in radiotherapy and suggest that combined targeting of c-Met and radiotherapy could be a promising strategy to improve the care for patients with HNC.

Citation Format: Juan Dou, Liwei Lang, Georgia Chen, Nabil F. Saba, Yong Teng. Blockade of c-met signaling to circumvent radioresistance-associated metastasis in head and neck cancer [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr B038.
Abstract IA004: Tracking population heterogeneity and chemoresistance with functionalized cell barcodes
Authors: Brock Amy
Published: May 2022

Heterogeneity across individual cancer cells and clonal populations impacts growth rate, tumor composition, and response to therapy. To improve treatment, new tools are required to measure and control the contributions of diverse cell subpopulations. Our team has developed a high-complexity expressed barcode system, ClonMapper, that integrates expressed cell barcoding with single-cell RNA-sequencing and clonal isolation to characterize and track subpopulation trajectories. Using this approach, we uncovered subsets of cells from cell models with distinct transcriptional signatures and chemotherapy survivorship trajectories. To gain a deeper understanding of the process of clonal diversification, we profiled clones and retrieved sub-clones over the course of expansion and treatment. Supervised learning indicated that clonal subpopulations have characteristic transcriptomic signatures that are well-conserved under a variety of therapeutic perturbations. By providing the capability for systematic dissection of complex clonal dynamics, ClonMapper enables the delineation of an underlying engine of clonal diversification in cancer cell populations and refines our understanding of clonal identity.

Citation Format: Amy Brock. Tracking population heterogeneity and chemoresistance with functionalized cell barcodes [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr IA004.
Successful Enucleation of Intra-Nipple Recurrence of Breast Cancer
Authors: Yasuda Koji , Oura Shoji , Makimoto Shinichiro
Published: May 2022

A 36-year-old unmarried woman had undergone nipple-preserving mastectomy and immediate breast reconstruction using extended latissimus dorsi muscle flap for her left breast cancer. During adjuvant endocrine therapy, the patient sometimes developed faint bloody nipple discharge with negative cytological results. More than 9 years after operation, the patient developed left nipple swelling with evident bloody nipple discharge. A small tissue, spouted from the single duct orifice of the nipple by manual compression, showed atypical cells growing in papillary fashion, leading to the diagnosis of intra-nipple recurrence. Based on both the strong request from the patient and high probability of noninvasive nature of the recurrent cancer, we tried to enucleate the intra-nipple recurrence. In the operation, we first threaded the nipple skin at the affected duct orifice of the nipple, second incised the nipple with horizontal skin incision between the bilateral edges of the left areola via a small spindle skin resection just around the affected duct orifice, third threaded the intact lateral nipple skin for countertraction, and finally enucleated the intra-nipple recurrence. After completely enucleating the recurrent focus without any macroscopic cancer residuals in the nipple, we reproduced the nipple into the original shape, resulting in excellent cosmesis without any nipple necrosis. Histological study showed the intra-nipple recurrence to be noninvasive papillary cancer. Approximately a quarter of the main tumor and a small part of one ductal spread focus were pathologically exposed but were present without any missing boarders, suggesting complete resection of the intra-nipple recurrence. This is the first case of intra-nipple recurrence of breast cancer successfully enucleated without any complications.
Mechanism of circHIPK3-miRNA-124-3p/miRNA-148b-3p-Mediated Inflammatory Responses and Cell Senescence in Candida albicans-Induced Septic Acute Kidney Injury
Authors: Han Jing , Li Wanli , Zhang Jie , Guan Yulin , Huang Ying , Li Xiaoyue
Published: May 2022

Introduction: Sepsis is a life-threatening inflammatory state that can result in septic acute kidney injury (SAKI). Circular RNAs (circRNAs) are implicated in various inflammatory diseases including SAKI. This study investigated the effect of circHIPK3 on inflammatory responses and cell senescence in Candida albicans-induced SAKI. Methods: circHIPK3 expression and inflammatory factors in the serum of SAKI patients and healthy volunteers were detected. The murine and cell models of SAKI were established by C. albicans and lipopolysaccharide induction, respectively. The effect of circHIPK3 on SAKI inflammatory responses and cell senescence was measured using ELISA, SA-β-gal staining, CCK-8, RT-qPCR, and Western blot. The binding relationships among circHIPK3, miR-124-3p, or miR-148b-3p and KLF6 or DNMT1/3a were confirmed. The binding of KLF6 and NLRP3 was determined, and the methylation level of the Klotho promoter was detected. Functional rescue experiments were performed to verify the effect of miR-124-3p or miR-148b-3p on SAKI. Results: circHIPK3 was highly expressed in SAKI. circHIPK3 silencing alleviated kidney injury in SAKI mice and enhanced SAKI cell viability by alleviating inflammatory responses and cell senescence. Mechanically, circHIPK3 upregulated KLF6 expression by competitively binding to miR-124-3p, thereby promoting the binding of KLF6 and NLRP3, activating NLRP3/caspase-1-mediated pyroptosis, and eventually aggravating SAKI inflammatory responses. circHIPK3 upregulated DNMT1/3a expression by competitively binding to miR-148b-3p, thus elevating the methylation level of Klotho promoter and accelerating SAKI cell senescence. Downregulation of miR-124-3p or miR-148b-3p attenuated the protective effect of circHIPK3 silencing on SAKI. Conclusion: circHIPK3 aggravated SAKI inflammatory responses via miR-124-3p/KLF6 and accelerated SAKI cell senescence via miR-148b-3p/DNMT1/3a.
Tubular IL-1β Induces Salt Sensitivity in Diabetes by Activating Renal Macrophages
Authors: Veiras Luciana C. , Bernstein Ellen A. , Cao DuoYao , Okwan-Duodu Derick , Khan Zakir , Gibb David R. , Roach Arantxa , Skelton Rachel , Williams Ryan M. , Bernstein Kenneth E. , Giani Jorge F.
Published: May 2022

Background:

Chronic renal inflammation has been widely recognized as a major promoter of several forms of high blood pressure including salt-sensitive hypertension. In diabetes, IL (interleukin)-6 induces salt sensitivity through a dysregulation of the epithelial sodium channel. However, the origin of this inflammatory process and the molecular events that culminates with an abnormal regulation of epithelial sodium channel and salt sensitivity in diabetes are largely unknown.

Methods:

Both in vitro and in vivo approaches were used to investigate the molecular and cellular contributors to the renal inflammation associated with diabetic kidney disease and how these inflammatory components interact to develop salt sensitivity in db/db mice.

Results:

Thirty-four-week-old db/db mice display significantly higher levels of IL-1β in renal tubules compared with nondiabetic db/+ mice. Specific suppression of IL-1β in renal tubules prevented salt sensitivity in db/db mice. A primary culture of renal tubular epithelial cells from wild-type mice releases significant levels of IL-1β when exposed to a high glucose environment. Coculture of tubular epithelial cells and bone marrow-derived macrophages revealed that tubular epithelial cell-derived IL-1β promotes the polarization of macrophages towards a proinflammatory phenotype resulting in IL-6 secretion. To evaluate whether macrophages are the cellular target of IL-1β in vivo, diabetic db/db mice were transplanted with the bone marrow of IL-1R1 (IL-1 receptor type 1) knockout mice. db/db mice harboring an IL-1 receptor type 1 knockout bone marrow remained salt resistant, display lower renal inflammation and lower expression and activity of epithelial sodium channel compared with db/db transplanted with a wild-type bone marrow.

Conclusions:

Renal tubular epithelial cell-derived IL-1β polarizes renal macrophages towards a proinflammatory phenotype that promotes salt sensitivity through the accumulation of renal IL-6. When tubular IL-1β synthesis is suppressed or in db/db mice in which immune cells lack the IL-1R1, macrophage polarization is blunted resulting in no salt-sensitive hypertension.
Predicting Residual Angina After Chronic Total Occlusion Percutaneous Coronary Intervention: Insights from the OPEN‐CTO Registry
Authors: Butala Neel M. , Tamez Hector , Secemsky Eric A. , Grantham J. Aaron , Spertus John A. , Cohen David J. , Jones Philip , Salisbury Adam C. , Arnold Suzanne V. , Harrell Frank , Lombardi William , Karmpaliotis Dimitrios , Moses Jeffrey , Sapontis James , Yeh Robert W.
Published: May 2022

Background

Given that percutaneous coronary intervention (PCI) of a chronic total occlusion (CTO) is indicated primarily for symptom relief, identifying patients most likely to benefit is critically important for patient selection and shared decision‐making. Therefore, we identified factors associated with residual angina frequency after CTO PCI and developed a model to predict postprocedure anginal burden.

Methods and Results

Among patients in the OPEN‐CTO (Outcomes, Patient Health Status, and Efficiency in Chronic Total Occlusion Hybrid Procedures) registry, we evaluated the association between patient characteristics and residual angina frequency at 6 months, as assessed by the Seattle Angina Questionnaire Angina Frequency Scale. We then constructed a prediction model for angina status after CTO PCI using ordinal regression. Among 901 patients undergoing CTO PCI, 28% had no angina, 31% had monthly angina, 30% had weekly angina, and 12% had daily angina at baseline. Six months later, 53% of patients had a ≥20‐point increase in Seattle Angina Questionnaire Angina Frequency Scale score. The final model to predict residual angina after CTO PCI included baseline angina frequency, baseline nitroglycerin use frequency, dyspnea symptoms, depressive symptoms, number of antianginal medications, PCI indication, and presence of multiple CTO lesions and had a C index of 0.78. Baseline angina frequency and nitroglycerin use frequency explained 71% of the predictive power of the model, and the relationship between model components and angina improvement at 6 months varied by baseline angina status.

Conclusions

A 7‐component OPEN‐AP (OPEN‐CTO Angina Prediction) score can predict angina improvement and residual angina after CTO PCI using variables commonly available before intervention. These findings have implications for appropriate patient selection and counseling for CTO PCI.