GAiN: An integrative tool utilizing generative adversarial neural networks for augmented gene expression analysis

Big genomic data and artificial intelligence (AI) are ushering in an era of precision medicine, providing opportunities to study previously under-represented subtypes and rare diseases rather than categorize them as variances. However, clinical researchers face challenges in accessing such novel technologies as well as reliable methods to study small datasets or subcohorts with unique phenotypes. To address this need, we developed an integrative approach, GAiN, to capture patterns of gene expression from small datasets on the basis of an ensemble of generative adversarial networks (GANs) while leveraging big population data. Where conventional biostatistical methods fail, GAiN reliably discovers differentially expressed genes (DEGs) and enriched pathways between two cohorts with limited numbers of samples (n = 10) when benchmarked against a gold standard. GAiN is freely available at GitHub. Thus, GAiN may serve as a crucial tool for gene expression analysis in scenarios with limited samples, as in the context of rare diseases, under-represented populations, or limited investigator resources.

Does Chemo-Radiotherapy Improve Survival Outcomes vs. Radiotherapy Alone for High-Grade cT1 Urothelial Carcinoma of the Bladder?

BACKGROUND

Non-muscle invasive bladder cancer (non-MIBC) that is high-grade and confined to the lamina propria (HGT1) often has an aggressive clinical course. Currently, there is limited data on the comparative effectiveness of RT vs. CRT for HGT1 non-MIBC. We hypothesized that CRT would be associated with improved overall survival (OS) vs. RT in HGT1 bladder cancer.

METHODS

Patients diagnosed with HGT1 non-MIBC, and treated with transurethral resection of bladder tumor followed by either treatment with RT alone or CRT, were identified in the National Cancer Database. Inverse probability of treatment weighting (IPTW) was employed and weight-adjusted multivariable analysis (MVA) using Cox regression modeling was used to compare overall survival (OS) hazard ratios. OS was the primary endpoint, and was estimated using the Kaplan-Meier method and log-rank tests.

RESULTS

A total of 259 patients with HGT1 UC were treated with: (i) RT alone (n = 123) or (ii) CRT (n = 136). Propensity-weighted MVA showed that combined modality treatment with CRT was associated with improved OS relative to radiation alone (Hazard Ratio [HR]: 0.62, 95% Confidence Interval (95% CI): 0.44-0.88, P = .007). Four-year OS for the CRT vs. RT alone was 36% and 19%, respectively (log-rank P <.008).

CONCLUSION

For patients with HGT1 bladder cancer, concurrent CRT was associated with improved OS compared with radiation alone in a retrospective cohort. These results are hypothesis-generating. The NRG is currently developing a phase II randomized clinical trial comparing CRT to other novel, bladder preservation strategies.

Unlocking the Power of ChatGPT, Artificial Intelligence, and Large Language Models: Practical Suggestions for Radiation Oncologists

Recent advances in artificial intelligence (AI), such as generative AI and large language models (LLMs), have generated significant excitement about the potential of AI to revolutionize our lives, work, and interaction with technology. This article explores the practical applications of LLMs, particularly ChatGPT, in the field of radiation oncology. We offer a guide on how radiation oncologists can interact with LLMs like ChatGPT in their routine clinical and administrative tasks, highlighting potential use cases of the present and future. We also highlight limitations and ethical considerations, including the current state of LLMs in decision making, protection of sensitive data, and the important role of human review of AI-generated content.

Genomic Characterization of Cervical Tumors Driven by Rare High-Risk HPV Subtypes Utilizing a Deep Learning Framework

PURPOSE/OBJECTIVE(S)

As many as 30-50% of patients with locally advanced cervical cancer (LACC) experience recurrence after chemoradiation therapy (CRT). More sophisticated prognostic schemes and targeted therapeutic options are urgently needed. Human papillomavirus (HPV) is responsible for the majority of invasive cervical carcinomas, most commonly HPV 16 and 18 subtypes. In large part due to their rarity, little is known about the biologic behavior of LACC driven by non-16/18 HPV genotypes. We hypothesized that rare HPV subtypes drive distinct gene expression patterns. To aid in the common dilemma of limited sample procurement, we developed a tool which leverages population data and generative adversarial neural network (GAN) modelling to exploit patterns of gene expression of small phenotypic groups for downstream analysis. Here, we employed a deep learning approach to identify gene expression patterns unique to tumors caused by rare HPV subtypes.

MATERIALS/METHODS

Whole transcriptome analysis of tumor biopsies from an institutional LACC tumor bank were employed including 130 HPV16/18 positive, and at least 3 each of rare HPV subtypes 31, 33, 39, 45, 52, 58, and 59. A Wasserstein GAN model (WGAN) was trained for each rare HPV subtype, and used to generate augmented rare HPV population data for downstream differential expression testing between rare HPV subtypes and HPV16/18. K-means clustering analysis was performed using R stats package. Differential gene expression testing between rare HPV subtype populations was performed using the EdgeR R-package. Pathway Enrichment analysis was conducted using EnrichR software.

RESULTS

By minimizing intergroup clustering distance, 3 clusters of HPV driven disease were demonstrated. The first cluster demonstrated biology similar to HPV16 and HPV18. Namely, pathway enrichment analysis performed on lists of differentially expressed genes between GAN augmented rare HPV subtypes (HPV45, HPV52, and HPV58) and classical HPV subtypes 16 and 18, yielded no significant statistical differences. The second cluster demonstrated enriched gene expression in proinflammatory IL-1 and IL-6 family cytokines and focal adhesion signaling (HPV31, HPV33, HPV39) (IL-1 regulation of extracellular matrix, p = 5.0e-6; Oncostatin M signaling, p = 2.0e-7; Integrin Signaling, 2.5e-7). The last cluster demonstrated an increased Th2/myeloid signature (HPV59) (T helper cell surface molecules 1.2e-7, myeloid cell signature 8.5e-9).

CONCLUSION

Utilizing a deep learning architecture to model gene expression of rare HPV subtypes we demonstrate 3 groups of HPV driven cervical cancer biology. These groups include a classical subtype, a high IL-1/IL-6 high subtype, and a myeloid associated subtype. Knowledge of such tumor heterogeneity can aid in the future development of targeted treatment plans and patient prognosis.

Development of a Radiomic Signature from Pre-Treatment FDG-PET for Recurrence Prediction in Cervical Cancer

PURPOSE/OBJECTIVE(S)

As many as 30-50% of patients with locally advanced cervical cancer (LACC) experience recurrence after standard-of-care chemoradiation therapy (CRT), creating a critical need to identify pre-treatment biomarkers of treatment failure. The purpose of this study is to identify whether radiomic features derived from pre-treatment FDG-PET imaging can be used to construct a predictive signature useful for assessing risk of recurrence during treatment planning.

MATERIALS/METHODS

Standardized uptake values (SUV) were obtained from within the physician-defined metabolic tumor volumes (MTV) delineated on FDG-PET scans acquired for 90 LACC patients at our institution prior to standard of care curative-intent CRT. Clinical outcome data of these patients has a median follow-up time of 85 months. The clinical endpoint was local recurrence within 3 years of treatment. 851 quantitative radiomic features describing intensity, shape, texture and high and low frequency spatial filters of the MTV were extracted for each patient. Low information features, defined by pairwise correlation > 0.85 with another feature or a maximum deviation within 20% of the mean, were discarded, leaving 146 features. Predictive signatures were constructed from features using multiple techniques, including multivariate Cox modelling, a set of machine learning models (random forest (RF), support vector classifier (SVC), ridge regression, LASSO regression, and elastic net regression), and a deep neural network (DNN) classifier.

RESULTS

The DNN classifier had the best overall performance, predicting a patient's recurrence group with an F1 score of 0.917 ± 0.028 under 5-fold cross-validation. By contrast, the Cox model classifier yielded an F1 score of 0.604 ± 0.085 and the best performing of the alternative machine learning models, elastic net, yielded F1 score of 0.868 ± 0.018. A set of textural features contributed the most to the output of the DNN classifier, including Large Area Low Gray Level Emphasis of the gray level size zone matrix (GLSZM) and coarseness and busyness of the neighboring gray tone difference matrix (NGTDM), reflecting the important role patterns of tumor heterogeneity play in post-treatment recurrence.

CONCLUSION

In this pilot study, we investigated multiple techniques to construct predictive radiomic signatures for local recurrence in LACC, determining that a DNN classifier is most capable of stratifying patients by risk of early recurrence. Future work will seek to validate this result on additional PET imaging data sets and to integrate radiomic features with gene expression data from matched tumor samples to establish radiogenomic biomarkers for recurrence.

Mutational Landscape of ER Receptor Negative Endometrial Cancer Patients Categorized as No Specific Molecular Profile (NSMP)

PURPOSE/OBJECTIVE(S)

The endometrial cancer (EC) molecular classification introduced by The Cancer Genome Atlas (TCGA) has initiated molecular-based classification with clear prognostic value. Four major tumor subtypes exist: 1) TP53 mutation (p53abn); 2) POLE mutation (POLEmut); 3) mismatch repair protein deficient (MMRd); and 4) no specific molecular profile (NSMP). Of these subtypes, p53abn patients exhibited the worst prognosis. Recently, a prognostic refinement of NSMP EC using estrogen receptor (ER) status, from PORTEC-III trial data, showed that (ER-) NSMP patients had a strikingly poor prognosis, similar to p53abn patients. Currently, drivers of NSMP (ER-) disease are unknown and require genomic characterization. In this study, we perform an integrated molecular analysis to characterize this aggressive and poorly understood cohort.

MATERIALS/METHODS

RNAseq and mutational data was downloaded from the TCGA, PanCancer Atlas, Uterine Endometrial Carcinoma dataset via the genomic data commons (GDC). All patients in this cohort demonstrated endometrioid histology. P53abn, and POLE mutated patients were filtered using mutational data. MMRd and NSMP ESR1 gene low expressors (ER Low) were filtered using Z-score cutoffs of RNAseq expression data. Survival analysis was performed using the Survival R-package. Gene expression testing was performed using the EdgeR R-package. Pathway Enrichment analysis was conducted using EnrichR software.

RESULTS

Forty-two patients out of 529 samples met our GDC NSMP (ER low) filtering criteria (7%), similar to the 5% of PORTEC-III patients classified as NSMP (ER -). Strikingly 83% percent of GDC NSMP (ER low) patients harbored a mutation in the PI3K-AKT-mTOR signaling pathway, with 48% of GDC NSMP (ER low) patients carrying a mutation in the p110 alpha (PIK3CA) gene. Interestingly, of the patients with PIK3CA mutant tumors, 2/20 patients died in 5 years (10%), compared to 9/22 patients whose tumors were PIK3CA WT (41%) (p = 0.02). Among GDC NSMP (ER low) patients with PIK3CA WT tumors gene expression signatures were enriched for MYC target genes (p = 1.1e-51), DNA replication (p = 4.3e-30), cell cycle (p = 9.32e-20), and cell cycle checkpoints (p = 6.4e-20) pathways. Additionally, strongly in PIK3CA WT tumors are mitochondrial membrane proteins (p = 1.63e-37) and ribosomal proteins (2.9e-24).

CONCLUSION

In this analysis, we show that GDC NSMP (ER low) tumors nearly all harbor a mutation in the PI3K-AKT-mTOR signaling pathway. Further we demonstrate that the most common gene mutation in the cohort, PIK3CA, is counterintuitively a marker of improved survival. Additionally, we show that within that this subpopulation, PIK3CA WT patients exhibit robustly upregulated gene expression programs dedicated to energy production, cell cycling, and division.

Clinical Efficacy and Safety of Once-Weekly Fractionation in Stereotactic Body Radiotherapy for Pulmonary Oligometastatic Lesions

PURPOSE/OBJECTIVE(S)

As the oligometastatic disease paradigm has become more widely accepted, further investigation is needed to risk-stratify patients within this spectrum of disease and define optimal treatment methods. Stereotactic Body Radiotherapy (SBRT) has emerged as an efficacious and safe modality to control individual lesions and improve clinical outcomes in the setting of oligometastatic disease. There is scant literature describing ideal SBRT inter-fraction time intervals or their impact on clinical outcomes, especially for treating pulmonary oligometastases. Most institutions appear to offer treatments on consecutive days or every other day. In this abstract, we sought to evaluate the efficacy and safety of delivering SBRT treatments in a once-weekly fractionation scheme.

MATERIALS/METHODS

The study was undertaken via retrospective review at a single institution. We included patients with pulmonary metastatic lesions treated with SBRT at our institution between 2015 and 2019. Patients with oligometastatic disease were included, defined as patients with 5 or fewer total metastatic lesions. Treatments were delivered between 3 and 5 fractions and using at least 5 Gy per fraction. Per institutional protocol, all treatments were delivered 7 days apart.

RESULTS

From a single institution, 204 lesions from 111 patients were included. Median follow-up was 16.5 months [IQR 7 - 36.3]. Median dose was 40 Gy [IQR 30 - 50], median BED was 80 Gy [IQR 60-100], median dose per fraction was 10 Gy [IQR 8-11]. Median internal target volume (ITV) was 18.5 cc [IQR 9.3 - 45.8]. The most common tumor histologies were lung adenocarcinoma (38.2%), colorectal adenocarcinoma (15.6%), lung squamous cell carcinoma (12.7%), renal cell carcinoma (5.9%), breast invasive ductal carcinoma (5.4%), small cell lung cancer (3.9%), and melanoma (2.9%). 2-year local control (LC) rate was 85.7% and 5-year LC rate was 84.3%. 2-year regional control (RC) rate was 53.9% and 5-year RC was 49%. Median overall survival (OS) was 20 months [IQR 9 - 37.3]. Cox regression analysis revealed biologically effective dose (BED) (HR 0.99 [0.98 - 0.99] p = 0.001) as well as dose per fraction (HR 0.92 [0.86 - 0.97] p = 0.003) were both associated with improved OS. Longest tumor dimension was associated with worse OS independent of BED and dose per fraction (HR 1.26 [1.1 - 1.4] p = 0.001). Total toxicity incidence was 7.3%, which consisted only of G1-G2 cough, dyspnea, and fatigue.

CONCLUSION

Treatment of pulmonary oligometastatic lesions with SBRT delivered via once-weekly fractionation is associated with excellent local control and minimal toxicity. Larger studies are warranted to directly compare clinical outcomes of weekly SBRT fractionation to other conventional SBRT treatment schedules.

Yin Yang 1 controls cerebellar astrocyte maturation

Diverse subpopulations of astrocytes tile different brain regions to accommodate local requirements of neurons and associated neuronal circuits. Nevertheless, molecular mechanisms governing astrocyte diversity remain mostly unknown. We explored the role of a zinc finger transcription factor Yin Yang 1 (YY1) that is expressed in astrocytes. We found that specific deletion of YY1 from astrocytes causes severe motor deficits in mice, induces Bergmann gliosis, and results in simultaneous loss of GFAP expression in velate and fibrous cerebellar astrocytes. Single cell RNA-seq analysis showed that YY1 exerts specific effects on gene expression in subpopulations of cerebellar astrocytes. We found that although YY1 is dispensable for the initial stages of astrocyte development, it regulates subtype-specific gene expression during astrocyte maturation. Moreover, YY1 is continuously needed to maintain mature astrocytes in the adult cerebellum. Our findings suggest that YY1 plays critical roles regulating cerebellar astrocyte maturation during development and maintaining a mature phenotype of astrocytes in the adult cerebellum.

Pre-Younger Dryas megafaunal extirpation at Rancho La Brea linked to fire-driven state shift

The cause, or causes, of the Pleistocene megafaunal extinctions have been difficult to establish, in part because poor spatiotemporal resolution in the fossil record hinders alignment of species disappearances with archeological and environmental data. We obtained 172 new radiocarbon dates on megafauna from Rancho La Brea in California spanning 15.6 to 10.0 thousand calendar years before present (ka). Seven species of extinct megafauna disappeared by 12.9 ka, before the onset of the Younger Dryas. Comparison with high-resolution regional datasets revealed that these disappearances coincided with an ecological state shift that followed aridification and vegetation changes during the Bølling-Allerød (14.69 to 12.89 ka). Time-series modeling implicates large-scale fires as the primary cause of the extirpations, and the catalyst of this state shift may have been mounting human impacts in a drying, warming, and increasingly fire-prone ecosystem.

p38MAPKα Stromal Reprogramming Sensitizes Metastatic Breast Cancer to Immunotherapy

Metastatic breast cancer is an intractable disease that responds poorly to immunotherapy. We show that p38MAPKα inhibition (p38i) limits tumor growth by reprogramming the metastatic tumor microenvironment in a CD4+ T cell-, IFNγ-, and macrophage-dependent manner. To identify targets that further increased p38i efficacy, we utilized a stromal labeling approach and single-cell RNA sequencing. Thus, we combined p38i and an OX40 agonist that synergistically reduced metastatic growth and increased overall survival. Intriguingly, patients with a p38i metastatic stromal signature had better overall survival that was further improved by the presence of an increased mutational load, leading us to ask if our approach would be effective in antigenic breast cancer. The combination of p38i, anti-OX40, and cytotoxic T-cell engagement cured mice of metastatic disease and produced long-term immunologic memory. Our findings demonstrate that a detailed understanding of the stromal compartment can be used to design effective antimetastatic therapies.

SIGNIFICANCE

Immunotherapy is rarely effective in breast cancer. We dissected the metastatic tumor stroma, which revealed a novel therapeutic approach that targets the stromal p38MAPK pathway and creates an opportunity to unleash an immunologic response. Our work underscores the importance of understanding the tumor stromal compartment in therapeutic design. This article is highlighted in the In This Issue feature, p. 1275.

Late Pleistocene osseous projectile point from the Manis site, Washington-Mastodon hunting in the Pacific Northwest 13,900 years ago

Bone fragments embedded in a rib of a mastodon (Mammut americanum) from the Manis site, Washington, were digitally excavated and refit to reconstruct an object that is thin and broad, has smooth, shaped faces that converge to sharp lateral edges, and has a plano-convex cross section. These characteristics are consistent with the object being a human-made projectile point. The 13,900-year-old Manis projectile point is morphologically different from later cylindrical osseous points of the 13,000-year-old Clovis complex. The Manis point, which is made of mastodon bone, shows that people predating Clovis made and used osseous weapons to hunt megafauna in the Pacific Northwest during the Bølling-Allerød.

Effect of histology on stereotactic body radiotherapy for non-small cell lung cancer oligometastatic pulmonary lesions

Background

Stereotactic body radiotherapy (SBRT) is commonly used to provide targeted treatment to metastatic lung disease. Investigation is needed to understand the influence of histology on treatment outcomes. We report how tumor histology affects local control (LC) in a cohort of patients with non-small cell lung cancer (NSCLC) receiving SBRT for oligometastatic and recurrent pulmonary lesions.

Methods

Patients who received SBRT to recurrent or oligometastatic NSCLC pulmonary lesions from 2015-2019 at our institution were included in this retrospective cohort study. Minimum follow-up was 2 months. Kaplan-Meier (KM) analysis was performed to assess local progression-free survival (LPFS). Local failure cumulative incidence curves using death as a competing risk factor were also generated.

Results

A total of 147 treated lesions from 83 patients were included: 95 lesions from 51 patients with lung adenocarcinoma and 52 lesions from 32 patients with lung squamous cell carcinoma (SqCC). Median follow-up was 23 [interquartile range (IQR): 9.5-44.5] months for adenocarcinoma, and 11.5 (6-32.25) months for SqCC. Two-year LC was 89% for adenocarcinoma and 77% for SqCC (P=0.04). Median overall survival (OS) was 24.5 (10-46.25) months for adenocarcinoma and 14.5 (7.75-23.25) months for SqCC. Adenocarcinoma had improved LPFS over SqCC (P=0.014). SqCC was associated with increased local failure risk that approached statistical significance (P=0.061) with death as a competing risk. Overall toxicity incidence was 8.2% with no G3+ toxicities.

Conclusions

For SBRT-treated oligometastatic or recurrent NSCLC pulmonary lesions, adenocarcinoma histology is associated with improved 2-year LC and LPFS compared to SqCC and reduced incidence of local recurrence (LR) with death as a competing risk.

The Association of Radiation Dose With Overall Survival for Patients Treated With Prostate Stereotactic Body Radiation Therapy

Introduction Stereotactic body radiation therapy (SBRT) for prostate adenocarcinoma (PCa) has demonstrated excellent biochemical recurrence-free survival, with studies showing improved BRFS with higher-dose SBRT. However, current studies have been underpowered to evaluate the relationship of SBRT dose to overall survival (OS). In this retrospective study using the National Cancer Database (NCDB), we hypothesize that, given the low alpha/beta ratio of PCa, a relatively small increase in the dose-per-fraction would be associated with improved survival outcomes for intermediate-risk PCa (IR-PCa) comparing 36.25 Gy/5 fx [biologically equivalent dose (BEDα/β = 1.5 = 211.46 Gy vs. 35 Gy (BED1.5 = 198.33 Gy)]. Materials and methods We queried records from the NCDB from 2005 to 2015 for men receiving prostate SBRT for IR-PCa (n=2673). 82% were treated using either 35 Gy/5 fx or 36.25 Gy/5 fx. We compared OS in men receiving 35 Gy versus 36.25 Gy. Inverse probability of treatment weighting (IPTW) was used to adjust for covariable imbalances. Unweighted- and weighted-multivariable analysis (MVA) using Cox regression was used to compare OS hazard ratios, accounting for age, race, Charlson-Deyo comorbidity score, treatment facility type, prostate-specific antigen (PSA), clinical T-stage, Gleason Score, and use of androgen deprivation therapy (ADT). Kaplan-Meier analysis was performed. Results Seven hundred and eighty men (35%) were treated with 35 Gy/5 fx and 1434 men (65%) were treated with 36.25 Gy/5 fx (n=2214). Compared to 35 Gy, treatment with 36.25 Gy was associated with significantly improved OS (hazard ratio [HR]: 0.61 [95% CI: 0.43-0.89], P=0.009) on MVA. On Kaplan-Meier analysis, 36.25 Gy was associated with improved survival (p=0.034), with a five-year OS of 92% and 88%, respectively. Conclusions In a multi-institutional retrospective database of 2,214 IR patients treated with prostate SBRT, a prescription dose of 36.25 Gy/5 fx was associated with improved OS vs. 35 Gy/5 fx. Results are hypothesis-generating but do lend support to the current National Comprehensive Cancer Network (NCCN) guidelines that the minimum recommended dose for prostate SBRT is 36.25 Gy/5 fx.

Abstract 3475: An 18-gene expression model predicts resistance to standard of care therapy on 3-month follow up 18FDG-PET in locally advanced cervical cancer

Introduction: As many as 30-50% of patients with locally advanced cervical cancer (LACC) experience recurrence after chemoradiation therapy (CRT), and five-year survival rates for these patients is only ~10%. While local recurrence and overall survival are useful metrics for analyzing genomic risk factors in LACC, such time to event analysis can be complicated by confounding variables which impede the elucidation of biologically relevant signals. Our group previously reported upregulation of genes from the PI3K pathway in cervical tumors with residual abnormal 18F-Fluoro-deoxy-glucose (FDG) uptake on positron emission tomography (PET) performed 3 months after CRT. Here, we analyzed whole transcriptome data using RNASeq from N=86 prospectively collected pretreatment cervix tumor biopsies to identify novel gene expression signatures associated with persistent or new FDG uptake on 3 month post-therapy FDG-PET.

Objective: To identify and validate a predictive gene expression signature able to distinguish primary tumors likely to be resistant to standard of care CRT as assessed by PET scan obtained 3-months following completion of therapy.

Methods: Whole tumor RNA-seq analysis was performed on 86 pre-treatment tumor specimens and compared with associated 3-month post-CRT FDG-PET. Response was dichotomized into metabolic complete response (mCR) and persistent/new disease (mP/N) defined as persistent or new areas of FDG-uptake on post-CRT PET per the nuclear medicine report. Differential expression analysis was conducted using the EdgeR R-package. Pathway enrichment analysis was conducted using reference libraries as specified and EnrichR software. Decision tree modeling, hyperparameter optimization, and k-fold cross-validation was performed using the sci-kitlearn python package.

Results: We identified an 18-gene expression signature predictive for mCR vs. mP/N in patients treated with definitive CRT with an overall prospective accuracy of 0.92. This model reliably identified both classes of patients (mCR F1=0.95, precision = 0.90, recall =1.0 ; mP/N F1=0.80, precision 0.67, recall =1.0). Crowd source enrichment analysis using EnrichR identified an NRF2 driven expression program (p=0.0006), and an altered inflammatory response (0.000006) within the predictive 18 gene signature.

Conclusions: We generated an 18-gene model to predict response to CRT as assessed by 3 month PET imaging. This novel expression signature further identified the NRF2 transcription factor as an important marker for resistance to CRT, consistent with previous studies showing NRF2 promotes cervical cancer growth. Our findings highlight the need for further elucidation of the NRF2 pathway in LACC, and can be used to accurately assess high risk patients who would benefit from treatment escalation.

Citation Format: Michael R. Waters, Matthew Inkman, Perry W. Grigsby, Stephanie Markovina, Julie K. Schwarz, Jin Zhang. An 18-gene expression model predicts resistance to standard of care therapy on 3-month follow up 18FDG-PET in locally advanced cervical cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3475.

Integrating imaging and RNA-seq improves outcome prediction in cervical cancer

Approaches using a single type of data have been applied to classify human tumors. Here we integrate imaging features and transcriptomic data using a prospectively collected tumor bank. We demonstrate that increased maximum standardized uptake value on pretreatment 18F-fluorodeoxyglucose-positron emission tomography correlates with epithelial-to-mesenchymal transition (EMT) gene expression. We derived and validated 3 major molecular groups, namely squamous epithelial, squamous mesenchymal, and adenocarcinoma, using prospectively collected institutional (n = 67) and publicly available (n = 304) data sets. Patients with tumors of the squamous mesenchymal subtype showed inferior survival outcomes compared with the other 2 molecular groups. High mesenchymal gene expression in cervical cancer cells positively correlated with the capacity to form spheroids and with resistance to radiation. CaSki organoids were radiation-resistant but sensitive to the glycolysis inhibitor, 2-DG. These experiments provide a strategy for response prediction by integrating large data sets, and highlight the potential for metabolic therapy to influence EMT phenotypes in cervical cancer.

Stereotactic body radiation therapy for spinal metastases: a novel local control stratification by spinal region

OBJECTIVE

This study evaluated a large cohort of patients treated with stereotactic body radiation therapy for spinal metastases and investigated predictive factors for local control, local progression-free survival (LPFS), overall survival, and pain response between the different spinal regions.

METHODS

The study was undertaken via retrospective review at a single institution. Patients with a tumor metastatic to the spine were included, while patients with benign tumors or primary spinal cord cancers were excluded. Statistical analysis involved univariate analysis, Cox proportional hazards analysis, the Kaplan-Meier method, and machine learning techniques (decision-tree analysis).

RESULTS

A total of 165 patients with 190 distinct lesions met all inclusion criteria for the study. Lesions were distributed throughout the cervical (19%), thoracic (43%), lumbar (19%), and sacral (18%) spines. The most common treatment regimen was 24 Gy in 3 fractions (44%). Via the Kaplan-Meier method, the 24-month local control was 80%. Sacral spine lesions demonstrated decreased local control (p = 0.01) and LPFS (p < 0.005) compared with those of the thoracolumbar spine. The cervical spine cases had improved local control (p < 0.005) and LPFS (p < 0.005) compared with the sacral spine and trended toward improvement relative to the thoracolumbar spine. The 36-month local control rates for cervical, thoracolumbar, and sacral tumors were 86%, 73%, and 44%, respectively. Comparably, the 36-month LPFS rates for cervical, thoracolumbar, and sacral tumors were 85%, 67%, and 35%, respectively. A planning target volume (PTV) > 50 cm3 was also predictive of local failure (p = 0.04). Fewer cervical spine cases had disease with PTV > 50 cm3 than the thoracolumbar (p = 5.87 × 10−8) and sacral (p = 3.9 × 10−3) cases. Using decision-tree analysis, the highest-fidelity models for predicting pain-free status and local failure demonstrated the first splits as being cervical and sacral location, respectively.

CONCLUSIONS

This study presents a novel risk stratification for local failure and LPFS by spinal region. Patients with metastases to the sacral spine may have decreased local control due to increased PTV, especially with a PTV of > 50 cm3. Multidisciplinary care should be emphasized in these patients, and both surgical intervention and radiotherapy should be strongly considered.

A single institutional experience with central lung stereotactic body radiation therapy demonstrating encouraging results with increased inter-fraction time

Background

Stereotactic body radiation therapy (SBRT) is an effective treatment modality for non-small cell lung cancer (NSCLC); however, there are concerns regarding potential toxicity for centrally located tumors.

Methods

This retrospective study considered patients with SBRT for central lung NSCLC (defined as a tumor within 2 cm of any mediastinal critical structure). The institutional protocol was that patients with central tumors received SBRT less frequently than daily—generally once or twice weekly.

Results

A total of 115 patients with 148 lesions were treated with SBRT to a median 45 [5–60] Gy in 4 [1–5] fractions over a median 5.3 [0–18] days. Many patients treated with this method presented with advanced disease: 58 treatments involved nodal targets, and 42 had stage 3 disease. 52% of patients had chronic obstructive pulmonary disease (COPD), and only 49% had a biopsy, often due to concerns regarding other medical comorbidities. Rates of prior chemotherapy, thoracic surgery, and thoracic radiotherapy were 32%, 21%, and 49%, respectively. Via the Kaplan-Meier method, 2-year overall survival was 65%, and 2-year local control was 77%. Two-year local-progression free survival was 53%, and 2-year progression-survival was 48%. Treatments for stage 3 disease had an impressive 82% 2-year local control that was comparable to early stage treatments. Patients with stage 3 disease had a 2-year overall survival of 59%, which trended towards decreased overall survival compared to early stage patients. There were 13 grade 1 (9%) and 14 grade 2 (9%) toxicities. There were no reported grade ≥3 acute or late toxicities and only 3 cases of pneumonitis.

Conclusions

Our series demonstrates encouraging local control with low rates of toxicity for central lung SBRT, including many stage 3 patients. This may be the result of the relatively large inter-fraction interval. This interval may allow for greater tumor effects (such as reoxygenation) and improved tolerance from normal tissues.

Stereotactic body radiation therapy for empirically treated hypermetabolic lung lesions: a single-institutional experience identifying the Charlson score as a key prognostic factor

Background

Though pathologic evidence for non-small cell lung cancer (NSCLC) is preferred, many patients do not receive a biopsy prior to treatment with stereotactic body radiation therapy (SBRT). This study seeks to analyze the overall survival (OS), local control, and toxicity rates for such patients.

Methods

This retrospective review included patients empirically treated with SBRT for presumed non-metastatic NSCLC at a single institution. Inclusion criteria included a hypermetabolic pulmonary lesion noted on positron emission tomography (PET) imaging but no pathological evidence of NSCLC. Patients with another known metastatic tumor were excluded. Statistical analysis was conducted with Cox proportional hazards analysis, univariate analysis, and the Kaplan-Meier method.

Results

Ninety-one treatments in 90 unique patients met inclusion criteria. Patients were a median 77.9 years at the start of treatment and had a median Charlson score of 7. Pre-treatment standardized uptake value (SUV) was a median 4.5 and 1.5 after treatment. At a median follow-up of 12.9 months, 36-month local control of 91.3% was achieved. Twenty-four-month OS and progression-free survival were 65.4% and 44.8%, respectively. On univariate analysis, biologically effective dose (BED) ≥120 Gy was predictive of improved OS (P=0.001), with 36-month OS of 50.5% for patients with BED ≥120 Gy and only 31.6% for patients with BED <120 Gy. On Kaplan-Meier analysis, Charlson score ≥9 was predictive of decreased OS (P=0.04), and BED ≥120 Gy trended towards improved OS (P=0.08). Thirty-two cases of grade <3 toxicity were reported, and only two cases of grade 3 morbidity (fatigue) were noted.

Conclusions

Local control rates for empiric SBRT treatment for hypermetabolic, non-metastatic NSCLC are similar to those for biopsied NSCLC. OS is primarily dependent on a patient’s overall health status, which can be accurately assessed with the Charlson score. BED ≥120 Gy may also contribute to improved OS.

The age of Clovis-13,050 to 12,750 cal yr B.P

Thirty-two radiocarbon ages on bone, charcoal, and carbonized plant remains from 10 Clovis sites range from 11,110 ± 40 to 10,820 ± 10 ¹⁴C years before the present (yr B.P.). These radiocarbon ages provide a maximum calibrated (cal) age range for Clovis of ~13,050 to ~12,750 cal yr B.P. This radiocarbon record suggests that Clovis first appeared at the end of the Allerød and is one of at least three contemporary archaeological complexes in the Western Hemisphere during the terminal Pleistocene. Stemmed projectile points in western North America are coeval and even older than Clovis, and the Fishtail point complex is well established in the southern cone of South America by ~12,900 cal yr B.P. Clovis disappeared ~12,750 cal yr B.P. at the beginning of the Younger Dryas, coincident with the extinction of the remaining North American megafauna (Proboscideans) and the appearance of multiple North American regional archaeological complexes.

Rapid range shifts and megafaunal extinctions associated with late Pleistocene climate change

Large-scale changes in global climate at the end of the Pleistocene significantly impacted ecosystems across North America. However, the pace and scale of biotic turnover in response to both the Younger Dryas cold period and subsequent Holocene rapid warming have been challenging to assess because of the scarcity of well dated fossil and pollen records that covers this period. Here we present an ancient DNA record from Hall’s Cave, Texas, that documents 100 vertebrate and 45 plant taxa from bulk fossils and sediment. We show that local plant and animal diversity dropped markedly during Younger Dryas cooling, but while plant diversity recovered in the early Holocene, animal diversity did not. Instead, five extant and nine extinct large bodied animals disappeared from the region at the end of the Pleistocene. Our findings suggest that climate change affected the local ecosystem in Texas over the Pleistocene-Holocene boundary, but climate change on its own may not explain the disappearance of the megafauna at the end of the Pleistocene.

The impact of late Pleistocene climate change on ecosystems has been hard to assess. Here, the authors sequence ancient DNA from Hall’s Cave, Texas and find that both plant and vertebrate diversity decreased with cooling, and though plant diversity recovered with rewarming, megafauna went extinct.

Low-dose hilar and mediastinal stereotactic body radiation therapy for non-small cell lung cancer: Analysis of outcomes in patients receiving one or multiple courses of treatment

Background

This study reports the outcomes of a single institutional experience treating non‐small cell lung cancer (NSCLC) involving the pulmonary hilum with low‐dose stereotactic body radiation therapy (SBRT). The authors also present a series of repeat hilar SBRT.

Methods

Inclusion criteria required treatment with SBRT for NSCLC involving regional lymph nodes of the: (i) hilum, (ii) mediastinum, (iii) aortopulmonary window (station 5), or (iv) mainstem bronchus. At least one clinical follow‐up with imaging was required, unless the patient had a prior documented death from cancer.

Results

A total of 32 patients with 44 treatments were included, and 37 treatments targeted the hilum directly, with seven concerning the mediastinum, AP window, or mainstem bronchus. Median dose was 28 Gy in four fractions with once‐weekly fractionation. At a median clinical follow‐up of 23 months, local control was 64%. Median overall survival was 24 months, and median progression‐free survival was 15 months. A total of 48% of treatments resulted in complete radiographic response on last imaging follow‐up, and no cases of grade ≥ 3 toxicity were reported. For repeat SBRT (after prior hilar SBRT), local control was 92%. Median overall survival was 20 months, and median progression‐free survival was 19 months. Complete radiographic response was noted after 58% of treatments, with 0 instances of progressive response and no reported side effects.

Conclusions

Low‐dose hilar SBRT was efficacious and well‐tolerated, with impressive overall survival and no grade ≥ 3 toxicity. Repeat treatments with SBRT were feasible and effective, demonstrating overall survival, local control, and toxicity comparable to primary treatments.

Key points

Stereotactic Body Radiation Therapy for Salvage Treatment of Recurrent Non-Small Cell Lung Cancer

PURPOSE

This study analyzes the outcomes and toxicity of stereotactic body radiation therapy (SBRT) as salvage treatment for recurrent non-small cell lung cancer (NSCLC).

METHODS AND MATERIALS

This retrospective analysis considered patients treated with thoracic SBRT and a history of prior external beam radiation therapy (EBRT), SBRT, or surgical resection for NSCLC. Follow-up included positron emission tomography and computed tomography imaging at 2- to 3-month intervals. Key outcomes were presented with the Kaplan-Meier method.

RESULTS

Forty patients with 52 treatments were included at a mean of 11.82 months after treatment with EBRT (n = 21), SBRT (n = 15), surgical resection (n = 9), and SBRT after EBRT (n = 7). Median imaging and clinical follow-up were 13.39 and 19.01 months, respectively. SBRT delivered a median dose of 40 Gy in 4 fractions. Median biologically effective dose (BED) was 79.60 Gy. Median gross tumor volume and planning target volume were 10.80 and 26.25 cm³, respectively. Local control was 65%, with a median time to local failure of 13.52 months. Local control was 87% after previous SBRT but only 33% after surgery. Median overall survival was 24.46 months, and median progression-free survival (PFS) was 14.11 months. Patients presenting after previous SBRT had improved local control (P = .021), and the same result was obtained including patients with SBRT after EBRT (P = .0037). Treatments after surgical resection trended toward worse local control (P = .061). Patients with BED ≥80 Gy had improved local PFS (P = .032), PFS (P = .021), time without any treatment failure (P = .033), and time to local failure (P = .041). Using the Kaplan-Meier method, BED ≥80 Gy was predictive of improved local PFS (P = .01) and PFS (P < .005). Toxicity consisted of 10 instances of grade <3 toxicity (16%) and no grade ≥3 toxicity.

CONCLUSIONS

Salvage treatment for recurrent NSCLC with SBRT was effective and well tolerated, particularly after initial treatment with SBRT. When possible, salvage SBRT should aim to achieve a BED of ≥80 Gy.

Stereotactic body radiation therapy in the treatment of ovarian cancer

BACKGROUND

This study evaluates the outcomes and toxicity of stereotactic body radiation therapy (SBRT) in ovarian cancer.

METHODS

This retrospective analysis considered all patients treated with SBRT from 2009 to 2018 with a primary ovarian tumor. Follow-up included PET-CT and CT scans at 2-3 month intervals. Statistical analysis primarily consisted of univariate analysis, Cox proportional hazards analysis, and the Kaplan-Meier method.

RESULTS

The study included 35 patients with 98 treatments for lymph nodes (51), local recurrence (21), and de novo solid metastases (26). Median biologically effective dose (BED), gross tumor volume, and planning target volume were 38.40 Gy, 10.41 cc, and 25.21 cc, respectively. 52 lesions showed complete radiographic response, and two-year local control was 80%. Median overall survival (OS) was 35.2 months, and two-year progression-free survival (PFS) was 12%. On univariate analysis, Eastern Cooperative Oncology Group performance status > 0 was predictive of decreased OS (p = 0.0024) and PFS (p = 0.044). Factors predictive of local failure included lower BED (p = 0.016), treatment for recurrence (p = 0.029), and higher pre-treatment SUV (p = 0.026). Kaplan-Meier analysis showed BED ≤35 Gy (p < 0.005) and treatment for recurrence (p = 0.01) to be predictive of local failure. On Cox proportional hazards analysis, treatment of lymph nodes was predictive of complete radiographic response (hazard ratio (HR) = 4.95), as was higher BED (HR = 1.03). Toxicity included 27 cases of grade < 3 toxicity, and one grade 5 late toxicity of GI bleed from a radiation therapy-induced duodenal ulcer.

CONCLUSIONS

SBRT provides durable local control with minimal toxicity in ovarian cancer, especially with BED > 35 Gy and treatment for lymph nodes.

Late Pleistocene exploration and settlement of the Americas by modern humans

North and South America were the last continents to be explored and settled by modern humans at the end of the Pleistocene. Genetic data, derived from contemporary populations and ancient individuals, show that the first Americans originated from Asia and after several population splits moved south of the continental ice sheets that covered Canada sometime between ~17.5 and ~14.6 thousand years (ka) ago. Archaeological evidence shows that geographically dispersed populations lived successfully, using biface, blade, and osseous technologies, in multiple places in North and South America between ~15.5 and ~14 ka ago. Regional archaeological complexes emerged by at least ~13 ka ago in North America and ~12.9 ka ago in South America. Current genetic and archaeological data do not support an earlier (pre-17.5 ka ago) occupation of the Americas.

A comparison of stereotactic body radiation therapy for metastases to the sacral spine and treatment of the thoracolumbar spine

Background: This study compares the outcomes of stereotactic body radiation therapy (SBRT) for sacral and thoracolumbar spine metastases. Methods: This analysis considered each sacral spine SBRT treatment at a single institution and a cohort of consecutive thoracolumbar treatments. Results: 28 patients with 35 sacral treatments and 41 patients with 49 thoracolumbar treatments were included. Local control was 63% and 90%, respectively. The sacral cohort contained more lesions with ≥2 vertebrae and epidural and paraspinal involvement. Sacral patients had larger treatment volumes, increased rates of subsequent SBRT, decreased propensity for pain improvement, and decreased local control (p=0.02 on Kaplan-Meier analysis). Multivariate analysis demonstrated that PTV > 50 cc and epidural involvement were correlated with decreased local control. No cases had grade ≥3 toxicity. Conclusion: SBRT for sacral spine metastases is a distinct disease process than metastases to the thoracolumbar spine, resulting in lower rates of local control and pain improvement.

Micro Methods for Megafauna: Novel Approaches to Late Quaternary Extinctions and Their Contributions to Faunal Conservation in the Anthropocene

Drivers of Late Quaternary megafaunal extinctions are relevant to modern conservation policy in a world of growing human population density, climate change, and faunal decline. Traditional debates tend toward global solutions, blaming either dramatic climate change or dispersals of Homo sapiens to new regions. Inherent limitations to archaeological and paleontological data sets often require reliance on scant, poorly resolved lines of evidence. However, recent developments in scientific technologies allow for more local, context-specific approaches. In the present article, we highlight how developments in five such methodologies (radiocarbon approaches, stable isotope analysis, ancient DNA, ancient proteomics, microscopy) have helped drive detailed analysis of specific megafaunal species, their particular ecological settings, and responses to new competitors or predators, climate change, and other external phenomena. The detailed case studies of faunal community composition, extinction chronologies, and demographic trends enabled by these methods examine megafaunal extinctions at scales appropriate for practical understanding of threats against particular species in their habitats today.

RelB acts as a molecular switch driving chronic inflammation in glioblastoma multiforme

Glioblastoma multiforme (GBM) is a primary brain tumor characterized by extensive necrosis and immunosuppressive inflammation. The mechanisms by which this inflammation develops and persists in GBM remain elusive. We identified two cytokines interleukin-1β (IL-1) and oncostatin M (OSM) that strongly negatively correlate with patient survival. We found that these cytokines activate RelB/p50 complexes by a canonical NF-κB pathway, which surprisingly drives expression of proinflammatory cytokines in GBM cells, but leads to their inhibition in non-transformed astrocytes. We discovered that one allele of the gene encoding deacetylase Sirtuin 1 (SIRT1), needed for repression of cytokine genes, is deleted in 80% of GBM tumors. Furthermore, RelB specifically interacts with a transcription factor Yin Yang 1 (YY1) in GBM cells and activates GBM-specific gene expression programs. As a result, GBM cells continuously secrete proinflammatory cytokines and factors attracting/activating glioma-associated microglia/macrophages and thus, promote a feedforward inflammatory loop.

RelB controls adaptive responses of astrocytes during sterile inflammation

In response to brain injury or infections, astrocytes become reactive, undergo striking morphological and functional changes, and secrete and respond to a spectrum of inflammatory mediators. We asked whether reactive astrocytes also display adaptive responses during sterile IL-1β-induced neuroinflammation, which may limit tissue injury associated with many disorders of the central nervous system. We found that astrocytes display days-to-weeks long specific tolerance of cytokine genes, which is coordinated by NF-κB family member, RelB. However, in contrast to innate immune cells, astrocytic tolerance does not involve epigenetic silencing of the cytokine genes. Establishment of tolerance depends on persistent higher levels of RelB in tolerant astrocytes and its phosphorylation on serine 472. Mechanistically, this phosphorylation prevents efficient removal of RelB from cytokine promoters by IκBα and helps to establish tolerance. Importantly, ablation of RelB from astrocytes in mice abolishes tolerance during experimental neuroinflammation in vivo.

STAT3 suppresses Wnt/β-catenin signaling during the induction phase of primary Myf5+ brown adipogenesis

Thermogenic fat is a promising target for new therapies in diabetes and obesity. Understanding how thermogenic fat develops is important to develop rational strategies to treat obesity. Previously, we have shown that Tyk2 and STAT3, part of the JAK-STAT pathway, are necessary for proper development of classical brown fat. Using primary preadipocytes isolated from newborn mice we demonstrate that STAT3 is required for differentiation and robust expression of Uncoupling Protein 1 (UCP1). We also confirm that STAT3 is necessary during the early induction stage of differentiation and is dispensable during the later terminal differentiation stage. The inability of STAT3^-/- preadipocytes to differentiate can be rescued using Wnt ligand secretion inhibitors when applied during the induction stage. Through chemical inhibition and RNAi, we show that it is the canonical β-catenin pathway that is responsible for the block in differentiation; inhibition or knockdown of β-catenin can fully rescue adipogenesis and UCP1 expression in the STAT3^-/- adipocytes. During the induction stage, Wnts 1, 3a, and 10b have increased expression in the STAT3^-/- adipocytes, potentially explaining the increased levels and activity of β-catenin. Our results for the first time point towards an interaction between the JAK/STAT pathway and the Wnt/β-catenin pathway during the early stages of in-vitro adipogenesis.

Sphingosine kinase 1 activation by estrogen receptor α36 contributes to tamoxifen resistance in breast cancer

In breast cancer, 17β-estradiol (E2) plays critical roles mainly by binding to its canonical receptor, estrogen receptor (ER) α66, and eliciting genomic effects. E2 also triggers rapid, nongenomic responses. E2 activates sphingosine kinase 1 (SphK1), increasing sphingosine-1-phosphate (S1P) that binds to its receptors, leading to important breast cancer signaling. However, the E2 receptor responsible for SphK1 activation has not yet been identified. Here, we demonstrate in triple-negative breast cancer cells, which lack the canonical ERα66 but express the novel splice variant ERα36, that ERα36 is the receptor responsible for E2-induced activation of SphK1 and formation and secretion of S1P and dihydro-S1P, the ligands for S1PRs. Tamoxifen, the first-line endocrine therapy for breast cancer, is an antagonist of ERα66, but an agonist of ERα36, and, like E2, activates SphK1 and markedly increases secretion of S1P. A major problem with tamoxifen therapy is development of acquired resistance. We found that tamoxifen resistance correlated with increased SphK1 and ERα36 expression in tamoxifen-resistant breast cancer cells, in patient-derived xenografts, and in endocrine-resistant breast cancer patients. Our data also indicate that targeting this ERα36 and SphK1 axis may be a therapeutic option to circumvent endocrine resistance and improve patient outcome.

Pre-Clovis projectile points at the Debra L. Friedkin site, Texas-Implications for the Late Pleistocene peopling of the Americas

Lanceolate projectile points of the Clovis complex and stemmed projectile points of the Western Stemmed Tradition first appeared in North America by ~13 thousand years (ka) ago. The origin, age, and chronological superposition of these stemmed and lanceolate traditions are unclear. At the Debra L. Friedkin site, Texas, below Folsom and Clovis horizons, we find stemmed projectile points dating from ~13.5 to ~15.5 ka ago, with a triangular lanceolate point form appearing ~14 ka ago. The sequential relationship of stemmed projectile points followed by lanceolate forms suggests that lanceolate points are derived from stemmed forms or that they originated from two separate migrations into the Americas.

ABCC1-Exported Sphingosine-1-phosphate, Produced by Sphingosine Kinase 1, Shortens Survival of Mice and Patients with Breast Cancer

Sphingosine-1-phosphate (S1P), a bioactive sphingolipid mediator, has been implicated in regulation of many processes important for breast cancer progression. Previously, we observed that S1P is exported out of human breast cancer cells by ATP-binding cassette (ABC) transporter ABCC1, but not by ABCB1, both known multidrug resistance proteins that efflux chemotherapeutic agents. However, the pathologic consequences of these events to breast cancer progression and metastasis have not been elucidated. Here, it is demonstrated that high expression of ABCC1, but not ABCB1, is associated with poor prognosis in breast cancer patients. Overexpression of ABCC1, but not ABCB1, in human MCF7 and murine 4T1 breast cancer cells enhanced S1P secretion, proliferation, and migration of breast cancer cells. Implantation of breast cancer cells overexpressing ABCC1, but not ABCB1, into the mammary fat pad markedly enhanced tumor growth, angiogenesis, and lymphangiogenesis with a concomitant increase in lymph node and lung metastases as well as shorter survival of mice. Interestingly, S1P exported via ABCC1 from breast cancer cells upregulated transcription of sphingosine kinase 1 (SPHK1), thus promoting more S1P formation. Finally, patients with breast cancers that express both activated SPHK1 and ABCC1 have significantly shorter disease-free survival. These findings suggest that export of S1P via ABCC1 functions in a malicious feed-forward manner to amplify the S1P axis involved in breast cancer progression and metastasis, which has important implications for prognosis of breast cancer patients and for potential therapeutic targets.Implication: Multidrug resistant transporter ABCC1 and activation of SPHK1 in breast cancer worsen patient's survival by export of S1P to the tumor microenvironment to enhance key processes involved in cancer progression. Mol Cancer Res; 16(6); 1059-70. ©2018 AACR.

Abstract P5-03-05: Sphingosine-1-phosphate produced by sphingosine kinase 1 and exported via ABCC1 shortens survival of mice and humans with breast cancer

Background: Sphingosine-1-phosphate (S1P), a bioactive sphingolipid mediator that is generated by sphingosine kinase 1 (SphK1) when it is phosphorylated (pSphK1) inside cells, has been implicated in regulation of many process important for breast cancer progression. Previously we have shown that S1P is exported out of human breast cancer cells by ATP-binding cassette (ABC) transporter ABCC1, but not by ABCB1, both known multidrug resistance proteins that efflux chemotherapeutic agents. However, the pathological consequences of these events to breast cancer progression and metastasis have not been elucidated. Here, we report that high expression of ABCC1, but not ABCB1, is associated with poor prognosis in breast cancer patients via exporting S1P.

Materials and methods: Microarray based gene expression data of 2509 patients associated with their survival were obtained from METABRIC database. Single gene survival analysis based on expressin of SphK1, and dual ABCC1 or ABCB1 and SphK1 survival analyses were perfomerd. For protein analyses, tissues were obrained from 275 patients with stage 1-3 breast cancers treated in Yokohama City University Medical Center in Japan between 2006 and 2008. The expression of pSphK1 was analyzed by immunohistochemistry and investigate the relationship with clinicopathological findings. For in vitro and in vivo experiments, breast cancer cell lines were transfected by ABCB1, ABCC1 or vector transiently or stably. BALB/c nu/nu mice and BALB/c mice were used for in vivo experiments. S1P was measured by LC-ESI-MS/MS.

Results: SphK1 expression significantly associate with worse overall survival (median survival of 124 months with high SphK1 expression compared to 163 months for patients with low SphK1 expression, p=0.0014). Although patients with high ABCC1 expression had only a slightly worse overall survival of 150 months, those with high levels of both SphK1 and ABCC1 had much worse prognosis with median overall survival of 114 months (p &lt; 0.0068). Such association was not observed with ABCB1 expression. The frequency of strong pSphK1 protein expression was higher in HER2 enrhiched or TNBC than in Luminal. pSphK1 was more prevalent and increased in a larger tumors and in tumors from patients with lymph node metastases. Patients with breast cancers that express both pSphK1 and ABCC1 proteins have significantly shorter disease free survival. Overexpression of ABCC1, but not ABCB1, in human MCF7 and murine 4T1 cells enhanced S1P secretion, proliferation and migration of breast cancer cells. Implantation of breast cancer cells overexpressing ABCC1, but not ABCB1, into the mammary pad markedly enhanced tumor growth, angiogenesis and lymphangiogenesis with concomitant increases in lymph node and lung metastases as well as shorter survival of mice. Interestingly, S1P exported via ABCC1 from breast cancer cells upregulated transcription of SphK1 and its own formation.

Conclusions: Our findings suggest that production and export of S1P via ABCC1, but not ABCB1, is associated with worse overall and disease free survival of breast cancer patients and that S1P axis play a role in aggressive biology of breast cancer progression and metastasis.

Citation Format: Yamada A, Nagahashi M, Aoyagi T, Huang W-C, Lima S, Miyazaki H, Narui K, Ishikawa T, Endo I, Waters MR, Milstien S, Spiegel S, Takabe K. Sphingosine-1-phosphate produced by sphingosine kinase 1 and exported via ABCC1 shortens survival of mice and humans with breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P5-03-05.

Interleukin-13 receptor alpha 2 cooperates with EGFRvIII signaling to promote glioblastoma multiforme

The interleukin-13 receptor alpha2 (IL-13Rα2) is a cancer-associated receptor overexpressed in human glioblastoma multiforme (GBM). This receptor is undetectable in normal brain which makes it a highly suitable target for diagnostic and therapeutic purposes. However, the pathological role of this receptor in GBM remains to be established. Here we report that IL-13Rα2 alone induces invasiveness of human GBM cells without affecting their proliferation. In contrast, in the presence of the mutant EGFR (EGFRvIII), IL-13Rα2 promotes GBM cell proliferation in vitro and in vivo. Mechanistically, the cytoplasmic domain of IL-13Rα2 specifically binds to EGFRvIII, and this binding upregulates the tyrosine kinase activity of EGFRvIII and activates the RAS/RAF/MEK/ERK and STAT3 pathways. Our findings support the "To Go or To Grow" hypothesis whereby IL-13Rα2 serves as a molecular switch from invasion to proliferation, and suggest that targeting both receptors with STAT3 signaling inhibitor might be a therapeutic approach for the treatment of GBM.

Pre-Clovis occupation 14,550 years ago at the Page-Ladson site, Florida, and the peopling of the Americas

Stone tools and mastodon bones occur in an undisturbed geological context at the Page-Ladson site, Florida. Seventy-one radiocarbon ages show that ~14,550 calendar years ago (cal yr B.P.), people butchered or scavenged a mastodon next to a pond in a bedrock sinkhole within the Aucilla River. This occupation surface was buried by ~4 m of sediment during the late Pleistocene marine transgression, which also left the site submerged. Sporormiella and other proxy evidence from the sediments indicate that hunter-gatherers along the Gulf Coastal Plain coexisted with and utilized megafauna for ~2000 years before these animals became extinct at ~12,600 cal yr B.P. Page-Ladson expands our understanding of the earliest colonizers of the Americas and human-megafauna interaction before extinction.

Sphingosine-1-phosphate inhibits IL-1-induced expression of C-C motif ligand 5 via c-Fos-dependent suppression of IFN-β amplification loop

The neuroinflammation associated with multiple sclerosis involves activation of astrocytes that secrete and respond to inflammatory mediators such as IL-1. IL-1 stimulates expression of many chemokines, including C-C motif ligand (CCL) 5, that recruit immune cells, but it also stimulates sphingosine kinase-1, an enzyme that generates sphingosine-1-phosphate (S1P), a bioactive lipid mediator essential for inflammation. We found that whereas S1P promotes IL-1-induced expression of IL-6, it inhibits IL-1-induced CCL5 expression in astrocytes. This inhibition is mediated by the S1P receptor (S1PR)-2 via an inhibitory G-dependent mechanism. Consistent with this surprising finding, infiltration of macrophages into sites of inflammation increased significantly in S1PR2(-/-) animals. However, activation of NF-κB, IFN regulatory factor-1, and MAPKs, all of which regulate CCL5 expression in response to IL-1, was not diminished by the S1P in astrocytes. Instead, S1PR2 stimulated inositol 1,4,5-trisphosphate-dependent Ca(++) release and Elk-1 phosphorylation and enhanced c-Fos expression. In our study, IL-1 induced the IFNβ production that supports CCL5 expression. An intriguing finding was that S1P induced c-Fos-inhibited CCL5 directly and also indirectly through inhibition of the IFN-β amplification loop. We propose that in addition to S1PR1, which promotes inflammation, S1PR2 mediates opposing inhibitory functions that limit CCL5 expression and diminish the recruitment of immune cells.

POPULATION GENETICS. Genomic evidence for the Pleistocene and recent population history of Native Americans

How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we found that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (ka) and after no more than an 8000-year isolation period in Beringia. After their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 ka, one that is now dispersed across North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative "Paleoamerican" relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.

RelB/p50 complexes regulate cytokine-induced YKL-40 expression

The secreted protein, YKL-40, has been proposed as a biomarker of a variety of human diseases characterized by ongoing inflammation, including chronic neurologic pathologies such as multiple sclerosis and Alzheimer's disease. However, inflammatory mediators and the molecular mechanism responsible for enhanced expression of YKL-40 remained elusive. Using several mouse models of inflammation, we now show that YKL-40 expression correlated with increased expression of both IL-1 and IL-6. Furthermore, IL-1 together with IL-6 or the IL-6 family cytokine, oncostatin M, synergistically upregulated YKL-40 expression in both primary human and mouse astrocytes in vitro. The robust cytokine-driven expression of YKL-40 in astrocytes required both STAT3 and NF-κB binding elements of the YKL-40 promoter. In addition, YKL-40 expression was enhanced by constitutively active STAT3 and inhibited by dominant-negative IκBα. Surprisingly, cytokine-driven expression of YKL-40 in astrocytes was independent of the p65 subunit of NF-κB and instead required subunits RelB and p50. Mechanistically, we show that IL-1-induced RelB/p50 complex formation was further promoted by oncostatin M and that these complexes directly bound to the YKL-40 promoter. Moreover, we found that expression of RelB was strongly upregulated during inflammation in vivo and by IL-1 in astrocytes in vitro. We propose that IL-1 and the IL-6 family of cytokines regulate YKL-40 expression during sterile inflammation via both STAT3 and RelB/p50 complexes. These results suggest that IL-1 may regulate the expression of specific anti-inflammatory genes in nonlymphoid tissues via the canonical activation of the RelB/p50 complexes.

Pre-Clovis mastodon hunting 13,800 years ago at the Manis site, Washington

The tip of a projectile point made of mastodon bone is embedded in a rib of a single disarticulated mastodon at the Manis site in the state of Washington. Radiocarbon dating and DNA analysis show that the rib is associated with the other remains and dates to 13,800 years ago. Thus, osseous projectile points, common to the Beringian Upper Paleolithic and Clovis, were made and used during pre-Clovis times in North America. The Manis site, combined with evidence of mammoth hunting at sites in Wisconsin, provides evidence that people were hunting proboscideans at least two millennia before Clovis.

The Buttermilk Creek complex and the origins of Clovis at the Debra L. Friedkin site, Texas

Compelling archaeological evidence of an occupation older than Clovis (~12.8 to 13.1 thousand years ago) in North America is present at only a few sites, and the stone tool assemblages from these sites are small and varied. The Debra L. Friedkin site, Texas, contains an assemblage of 15,528 artifacts that define the Buttermilk Creek Complex, which stratigraphically underlies a Clovis assemblage and dates between ~13.2 and 15.5 thousand years ago. The Buttermilk Creek Complex confirms the emerging view that people occupied the Americas before Clovis and provides a large artifact assemblage to explore Clovis origins.

The late Pleistocene dispersal of modern humans in the Americas

When did humans colonize the Americas? From where did they come and what routes did they take? These questions have gripped scientists for decades, but until recently answers have proven difficult to find. Current genetic evidence implies dispersal from a single Siberian population toward the Bering Land Bridge no earlier than about 30,000 years ago (and possibly after 22,000 years ago), then migration from Beringia to the Americas sometime after 16,500 years ago. The archaeological records of Siberia and Beringia generally support these findings, as do archaeological sites in North and South America dating to as early as 15,000 years ago. If this is the time of colonization, geological data from western Canada suggest that humans dispersed along the recently deglaciated Pacific coastline.

Redefining the age of Clovis: implications for the peopling of the Americas

The Clovis complex is considered to be the oldest unequivocal evidence of humans in the Americas, dating between 11,500 and 10,900 radiocarbon years before the present (14C yr B.P.). Adjusted 14C dates and a reevaluation of the existing Clovis date record revise the Clovis time range to 11,050 to 10,800 14C yr B.P. In as few as 200 calendar years, Clovis technology originated and spread throughout North America. The revised age range for Clovis overlaps non-Clovis sites in North and South America. This and other evidence imply that humans already lived in the Americas before Clovis.

Geochronology: age of Mexican ash with alleged 'footprints'

A report of human footprints preserved in 40,000-year-old volcanic ash near Puebla, Mexico (http://www.royalsoc.ac.uk/exhibit.asp?id=3616&tip=1), was the subject of a press conference that stirred international media attention. If the claims (http://www.mexicanfootprints.co.uk) of Gonzalez et al. are valid, prevailing theories about the timing of human migration into the Americas would need significant revision. Here we show by 40Ar/39Ar dating and corroborating palaeomagnetic data that the basaltic tuff on which the purported footprints are found is 1.30+/-0.03 million years old. We conclude that either hominid migration into the Americas occurred very much earlier than previously believed, or that the features in question were not made by humans on recently erupted ash.

The archaeology of Ushki Lake, Kamchatka, and the Pleistocene peopling of the Americas

The Ushki Paleolithic sites of Kamchatka, Russia, have long been thought to contain information critical to the peopling of the Americas, especially the origins of Clovis. New radiocarbon dates indicate that human occupation of Ushki began only 13,000 calendar years ago-nearly 4000 years later than previously thought. Although biface industries were widespread across Beringia contemporaneous to the time of Clovis in western North America, these data suggest that late-glacial Siberians did not spread into Beringia until the end of the Pleistocene, perhaps too recently to have been ancestral to proposed pre-Clovis populations in the Americas.

Diring Yuriakh: A lower paleolithic site in central Siberia

Lower Paleolithic artifacts have been recovered from a single occupation surface within stratified deposits at Diring Yuriakh, an archaeological site in central Siberia. Thermoluminescence age estimates from eolian sediments indicate that the cultural horizon is greater than 260,000 years old. Diring Yuriakh is an order of magnitude older than documented Paleolithic sites in Siberia and is important for understanding the timing of human expansion into the far north, early adaptations to cold climates, and the peopling of the Americas.