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Supplementary Figure S4

Genomic studies of pediatric cancer have primarily focused on specific tumor types or high-risk disease. Here, we used a three-platform sequencing approach, including whole-genome sequencing (WGS), whole-exome sequencing (WES), and RNA sequencing (RNA-seq), to examine tumor and germline genomes from 309 prospectively identified children with newly diagnosed (85%) or relapsed/refractory (15%) cancers, unselected for tumor type. Eighty-six percent of patients harbored diagnostic (53%), prognostic (57%), therapeutically relevant (25%), and/or cancer-predisposing (18%) variants. Inclusion of WGS enabled detection of activating gene fusions and enhancer hijacks (36% and 8% of tumors, respectively), small intragenic deletions (15% of tumors), and mutational signatures revealing of pathogenic variant effects. Evaluation of paired tumor–normal data revealed relevance to tumor development for 55% of pathogenic germline variants. This study demonstrates the power of a three-platform approach that incorporates WGS to interrogate and interpret the full range of genomic variants across newly diagnosed as well as relapsed/refractory pediatric cancers.Significance:Pediatric cancers are driven by diverse genomic lesions, and sequencing has proven useful in evaluating high-risk and relapsed/refractory cases. We show that combined WGS, WES, and RNA-seq of tumor and paired normal tissues enables identification and characterization of genetic drivers across the full spectrum of pediatric cancers.This article is highlighted in the In This Issue feature, p. 2945

Supplementary Table 1 describes the clinical characteristics of patients.

Supplementary Figure from Covalent ERα Antagonist H3B-6545 Demonstrates Encouraging Preclinical Activity in Therapy-Resistant Breast Cancer

Supplementary Data from Covalent ERα Antagonist H3B-6545 Demonstrates Encouraging Preclinical Activity in Therapy-Resistant Breast Cancer

Supplementary Table 4 provides the precise description of all STAG2 mutations in Ewing sarcoma.

Supplementary Figure 1. Representative CIRCOS plots. Supplementary Figure 2. Scheme of copy number alterations. Indicates the copy number alterations in Ewing sarcoma. Supplementary Figure 3. Mutation spectrum in Ewing sarcoma. Indicates the proportion of each somatic base changes in Ewing sarcoma. Supplementary Figure 4. CDKN2A analysis across cell lines. RT-QPCR and western blot results in cell lines. Supplementary Figure 5. CDKN2A analysis across the extended cohort. QPCR analysis of the CDKN2A locus across the whole series of patients.

Supplementary Table 3. Analysis of the statistical significance of mutations.

Supplementary Table 2 provides a summary (a), list of structural variants (b), list of copy number alterations (c), list of Tier 1 single nucleotide variants (d), indels (e), and purity analyses (f).

Ewing sarcoma is a primary bone tumor initiated by EWSR1–ETS gene fusions. To identify secondary genetic lesions that contribute to tumor progression, we performed whole-genome sequencing of 112 Ewing sarcoma samples and matched germline DNA. Overall, Ewing sarcoma tumors had relatively few single-nucleotide variants, indels, structural variants, and copy-number alterations. Apart from whole chromosome arm copy-number changes, the most common somatic mutations were detected in STAG2 (17%), CDKN2A (12%), TP53 (7%), EZH2, BCOR, and ZMYM3 (2.7% each). Strikingly, STAG2 mutations and CDKN2A deletions were mutually exclusive, as confirmed in Ewing sarcoma cell lines. In an expanded cohort of 299 patients with clinical data, we discovered that STAG2 and TP53 mutations are often concurrent and are associated with poor outcome. Finally, we detected subclonal STAG2 mutations in diagnostic tumors and expansion of STAG2-immunonegative cells in relapsed tumors as compared with matched diagnostic samples.Significance: Whole-genome sequencing reveals that the somatic mutation rate in Ewing sarcoma is low. Tumors that harbor STAG2 and TP53 mutations have a particularly dismal prognosis with current treatments and require alternative therapies. Novel drugs that target epigenetic regulators may constitute viable therapeutic strategies in a subset of patients with mutations in chromatin modifiers. Cancer Discov; 4(11); 1342–53. ©2014 AACR.This article is highlighted in the In This Issue feature, p. 1243

List of supplementary tables and figures.

STAG2 mutation in three cases that show a reduction of STAG2-immunopositive cells at disease recurrence.

Nearly 30% of patients with relapsed breast cancer present activating mutations in estrogen receptor alpha (ERα) that confer partial resistance to existing endocrine-based therapies. We previously reported the development of H3B-5942, a covalent ERα antagonist that engages cysteine-530 (C530) to achieve potency against both wild-type (ERαWT) and mutant ERα (ERαMUT). Anticipating that the emergence of C530 mutations could promote resistance to H3B-5942, we applied structure-based drug design to improve the potency of the core scaffold to further enhance the antagonistic activity in addition to covalent engagement. This effort led to the development of the clinical candidate H3B-6545, a covalent antagonist that is potent against both ERαWT/MUT, and maintains potency even in the context of ERα C530 mutations. H3B-6545 demonstrates significant activity and superiority over standard-of-care fulvestrant across a panel of ERαWT and ERαMUT palbociclib sensitive and resistant models. In summary, the compelling preclinical activity of H3B-6545 supports its further development for the potential treatment of endocrine therapy–resistant ERα+ breast cancer harboring wild-type or mutant ESR1, as demonstrated by the ongoing clinical trials (NCT03250676, NCT04568902, NCT04288089). Summary: H3B-6545 is an ERα covalent antagonist that exhibits encouraging preclinical activity against CDK4/6i naïve and resistant ERαWT and ERαMUT tumors.

Decision making resides at the interface between sensory perception and movement production. Female songbirds in the context of mate choice are an excellent system to define neural circuits through which sensory perception influences production of courtship behaviors. Previous experiments by our group and others have implicated secondary auditory brain sites, including the caudal nidopallium (NC), in mediating behavioral indicators of mate choice. Here, we used anterograde tracer molecules to define projections that emerge from NC in female songbirds, identifying pathways through which NC influences downstream sites implicated in signal processing and decision making. Our results reveal that NC sends projections into the arcopallium, including the ventral intermediate arcopallium (AIV). Previous work revealed that AIV also receives input from another auditory area implicated in song preference and mate choice (caudal mesopallium, CM), suggesting that convergent input from multiple auditory areas may play important roles in initiating mate choice behaviors. In the present results, NC projects to an area implicated in postural and locomotory control (dorsal arcopallium, Ad), suggesting that NC may play a role in directing those forms of copulatory behavior. NC projections also systematically avoid a vocal motor region of the arcopallium that is innervated by CM (robust nucleus of the arcopallium, RA). These results suggest a model in which both NC and CM project to arcopallial pathways implicated in behavioral motivation. These brain regions may exert different influences on pathways through which auditory information can direct different facets of behavioral responses to information detected in those auditory signals.

Extensive production and application of magnetic minerals introduces significant amounts of magnetic wastes into the environment. Exposure to magnetic minerals could affect microbial community composition and geographic distribution. Here, we report that magnetic susceptibility is involved in determining bacterial α-diversity and community composition in surface sediment across the Bohai Sea by high-throughput sequencing analysis of the 16S rRNA gene. The results showed that environmental factors (explained 9.80%) played a larger role than spatial variables (explained 6.72%) in conditioning the bacterial community composition. Exposure to a magnetite center may shape the geographical distribution of five dissimilatory iron reducing bacteria. The microbial iron reduction ability and electroactive activity in sediment close to a magnetite center are stronger than those far away. Our study provides a novel understanding for the response of DIRB and electroactive bacteria to magnetic minerals exposure.

Background Ensovibep is a multi-specific DARPin (designed ankyrin repeat protein) antiviral in clinical development for treatment of COVID-19. In the Phase 2 EMPATHY study, ensovibep demonstrated greater viral load decline versus placebo. Here we report (1) the efficacy of ensovibep in patients with and without anti-SARS-CoV-2 antibodies at baseline and (2) SARS-CoV-2 mutation emergence data with treatment. Methods Eligible ambulatory patients with ≥2 COVID-19 symptoms (onset within 7 days) and positive SARS-CoV-2 rapid antigen test on day of dosing, were randomized (1:1:1:1) to ensovibep (600, 225 or 75 mg) or placebo as single, IV infusion. Chemiluminescent immunoassays were used for antibody detection (SARS-CoV-2 S1/S2 IgG and SARS-CoV-2 IgM). A pre-specified subgroup analysis was performed based on baseline anti-SARS-CoV-2 antibody status. Analysis of changes in viral genome from baseline to post baseline was performed to evaluate treatment-emergent mutations. Results Of the patients analyzed, 48.5% had anti-SARS-CoV-2 antibodies at baseline. Baseline log10 SARS-CoV-2 viral load (mean ±SD) was similar across groups [ensovibep (all doses) 6.5 ±1.5, placebo 6.2 ±1.5]; > 90% were infected with the Delta (B.1.617.2) variant. SARS-CoV-2 viral load reduction up to Day 8 showed similar effects in favor of ensovibep compared with placebo regardless of the presence of anti-SARS-CoV-2 antibodies (Figure 1). Patients in ensovibep 75 mg, 600 mg, and placebo groups had comparable incidences of emergent mutations, with a higher incidence in the 225 mg group. Based on analysis of 70% of the expected viral sequencing data, two mutations in the key binding residues of ensovibep were observed (Y489H and F486L) in a total of three patients treated with ensovibep. These patients either cleared virus by Day 8 or mutations were transient (occurred at a single time point but not later in the course of infection). Figure 1Forest plot of estimated treatment differences and associated 95% confidence intervals in time-weighted change from baseline in log10 SARS-CoV-2 viral load through Day 8 by subgroups for the presence of anti-SARS-CoV-2 antibodies (SARS-CoV-2 S1/S2 IgG and/or SARS-CoV-2 IgM) at baseline. Conclusion Ensovibep effectively reduces SARS-CoV-2 viral load regardless of the presence of anti-SARS-CoV-2 antibodies at baseline. Furthermore, there were no emerging mutations of concern, indicating that a single dose administration of ensovibep is associated with minimal selective pressure. Disclosures Marc Bonten, MD, PhD, Astra-Zeneca: Advisor/Consultant|Janssen: Advisor/Consultant|Merck: Advisor/Consultant|Novartis: Advisor/Consultant Richa Chandra, MD, Novartis Pharmaceuticals Corporation: Employee Damodaran Solai Elango, MD, Novartis Healthcare Pvt Ltd: Employee Pierre Fustier, PhD, Molecular Partners AG: Employee Kinfemichael Gedif, PhD, Novartis Pharmaceuticals Corporation: Employee Susana Goncalves, MD, Novartis Pharma AG: Employee Awawu Igbinadolor, MD, Novartis: Awawu Igbinadolor reports financial support from different pharmaceutical companies and organizations Jeff Kingsley, DO, MBA, CPI, FACRP, Centricity Research: Other Charles G. Knutson, PhD, Novartis Institutes for BioMedical Research: Employee Petra Kukkaro, PhD, Novartis Pharma AG: Employee Nagalingeswaran Kumarasamy, MD, Novartis: Nagalingeswaran Kumarasamy reports financial support from different pharmaceutical companies and organizations Philippe Legenne, MD, Molecular Partners AG: Employee Martha Mekebeb-Reuter, MD, Novartis: Martha Mekebeb-Reuter reports financial support from different pharmaceutical companies and organizations Krishnan Ramanathan, MD, Novartis Pharma AG: Employee Evgeniya Reshetnyak, PhD, Novartis Pharmaceuticals Corporation: Employee Michael Robinson, PhD, Novartis Institute for Tropical Disease: Employee Jennifer Rosa, MD, Novartis: Jennifer Rosa reports financial support from different pharmaceutical companies and organizations Marianne Soergel, MD, Molecular Partners AG: Employee Vaia Stavropoulou, PhD, Molecular Partners AG: Employee Nina Stojcheva, PhD, Molecular Partners AG: Employee Michael T. Stumpp, PhD, Molecular Partners AG: Employee Andreas Tietz, MD, Novartis Pharma AG: Employee Xiaojun Zhao, PhD, Novartis Institutes for BioMedical Research: Employee Zhaojie Zhang, PhD, 8. Novartis Institutes for BioMedical Research: Employee.

Developing urban functional zone classification method to study urban spatial structure is a hotspot in current research. Using the word embedding model to excavate spatial relationship of the geographic elements in urban functional zones is an important way to develop urban functional zone classification method. However, in these studies, the spatial relationship of geographic elements was regarded as their homogeneity, while the structural similarity of geographical elements was ignored, which inevitably reduces the classification accuracy of urban functional zone classification method. This paper proposes to develop an urban functional zone classification method based on Deepwalk model, which could extract homogeneity and structural similarity of nodes in graph. The proposed method uses POI data to represent geographical elements, organizes POIs into graphs, and uses Deepwalk to embedding POIs for urban functional zone classification. It was applied to classify the urban functional zones of Chaoyang district in Beijing; and the classification results were compared with those of two baseline method based on Word2vec model and Place2vec model. The experimental results show that considering both the homogeneity and structural similarity of geographical elements, the proposed model has higher accuracy than the models only considering the homogeneity of geographical elements.

Mislocalization of TAR DNA binding protein 43 kDa (TARDBP, or TDP-43) is a principal pathological hallmark identified in cases of neurodegenerative disorders such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). As an RNA binding protein, TDP-43 serves in the nuclear compartment to repress non-conserved cryptic exons to ensure the normal transcriptome. Multiple lines of evidence from animal models and human studies support the view that loss of TDP-43 leads to neuron loss, independent of its cytosolic aggregation. However, the underlying pathogenic pathways driven by the loss-of-function mechanism are still poorly defined. We employed a genetic approach to determine the impact of TDP-43 loss in pyramidal neurons of the prefrontal cortex (PFC). Using a custom-built miniscope imaging system, we performed repetitive in vivo calcium imaging from freely behaving mice for up to 7 months. By comparing calcium activity in PFC pyramidal neurons between TDP-43 depleted and TDP-43 intact mice, we demonstrated remarkably increased numbers of pyramidal neurons exhibiting hyperactive calcium activity after short-term TDP-43 depletion, followed by rapid activity declines prior to neuron loss. Our results suggest aberrant neural activity driven by loss of TDP-43 as the pathogenic pathway at early stage in ALS and FTD.

Background Low-cost raw materials such as lignocellulosic materials have been utilized in second-generation ethanol production process. However, the sequential and slow conversion of xylose into target products remains one of the main challenges for realizing efficient industrial lignocellulosic biorefinery. Results By applying different constant potentials to different microbial electrolysis cells with xylose as the sole carbon source, we analyzed the output of metabolites, microbial community structures, electron flow, and carbon flow in the process of xylose electro-fermentation by domesticated activated sludge. The bioreactors produced currents when applying positive potentials. The peak currents of the + 0.242 V, + 0.542 V and + 0.842 V reactors were 0.96 × 10–6 A, 3.36 × 10–6 A and 6.43 × 10–6 A, respectively. The application of potentials promoted the xylose consumption, and the maximum consumption rate in the + 0.542 V reactor was 95.5%, which was 34.8 times that of the reactor without applied potential. The potential application also promoted the production of ethanol and acetate. The maximum ethanol yield (0.652 mol mol−1 xylose) was obtained in the + 0.842 V reactor. The maximum acetate concentration (1,874 µmol L−1) was observed in the + 0.842 V reactor. The optimal potential for ethanol production was + 0.842 V with the maximum ethanol yield and energy saving. The application of positive potential caused the microorganisms to carry out ethanol fermentation, and the application of negative potential forced the microorganisms to carry out acetic fermentation. The potential application changed the diversity and community structure of microorganisms in the reactors, and the two most significantly changed families were Paenibacillaceae and Bacillaceae. Conclusion The constructed microbial electrolysis cells with different potentials obtained better production yield and selectivity compared with the reactor without applied potential. Our work provides strategies for the subsequent fermentation processes with different needs.

Extensive production and application of magnetic minerals produce significant amounts of magnetic wastes to the environment. These magnetic minerals exposure could affect microbial community composition and geographic distribution. Here, we reported magnetic susceptibility is involved in determining bacterial α-diversity and community composition in surface sediment across Bohai Sea. Environmental factors (explained 9.80%) played a larger role than spatial variables (explained 6.72%) in conditioning the bacterial community composition. Exposure of magnetite center may shape geographical distribution of five dissimilatory iron reducing bacteria (DIRB). Microbial iron reduction ability and electroactive activity in sediment close to magnetite center are stronger than those far away. Our study provides novel understanding for response of DIRB and electroactive bacteria to magnetic minerals exposure.

Microbial fermentation plays important roles in hydrogen production. Various methods to promote hydrogen production are being developed. Here, different magnetic field intensities (2.7 mT, 3.2 mT and 9.1 mT) were applied to the glucose fermentation system of Clostridium pasteurianum to evaluate the feasibility and effect of statistic magnetic field on hydrogen production. The results showed that the magnetic field intensity of 3.2 mT effectively enhanced the hydrogen production. The total glucose consumption reached 0.64 ± 0.010 mmol, the maximum hydrogen yield reached 2.34 ± 0.020 mol H2/mol glucose, and the maximum hydrogen production rate reached 0.065 ± 0.002 mmol/h. Compared with the control, the maximum biomass, carbon conversion efficiency and energy conversion efficiency were elevated by 366%, 114%, and 26.8%, respectively. Our results provide a new way for promotion of hydrogen production, better understanding of the interaction mechanism between magnetic field and microorganisms and for optimizing the hydrogen production.

BACKGROUND Currently, the number of severe aortic stenosis (AS) patients with a history of prior cardiac surgery (PCS) has increased. Both transcatheter aortic valve replacement (TAVR) and traditional surgical aortic valve replacement (sAVR) are effective therapy for AS. However, PCS increases the risk of adverse outcomes in patients undergoing aortic valve replacement. Thus, this meta-analysis was designed to comparatively evaluate the impact of PCS on clinical outcomes between TAVR and sAVR. METHODS A systematic search of PubMed, Embase, Cochrane Library, and Web of Science up to February 1, 2021 was conducted for relevant studies that comparing TAVR and sAVR for severe AS patients with a history of PCS. The primary outcome was the non-inferiority of TAVR and sAVR in mortality. The secondary outcomes were the other clinical outcomes. Two reviewers assessed trial quality and extracted the data independently. All statistical analyses were performed using the standard statistical procedures provided in Review Manager 5.2. RESULTS A total of 11 studies including 8852 patients were identified. The pooled results indicated that there was no difference in 30-day, and 1-year all-cause mortality between TAVR and sAVR. No significant difference was also observed in total follow-up and cardiovascular mortality between TAVR and sAVR. However, subgroup analysis revealed significantly higher 1-year all-cause mortality (OR 1.92; 95% CI 1.05-3.52; P = .04) and total follow-up mortality (OR 2.28; 95% CI 1.09-4.77; P = .03) in TAVR than sAVR for patients with a history of coronary artery bypass graft, aortic valve replacement, and mitral valve reconstruction. In addition, TAVR experienced higher pacemaker implantation than sAVR. However, compared with sAVR, TAVR experienced shorter length of stay (MD -3.18 days; 95% CI -4.78 to -1.57 days) and procedural time (MD -172.01 minutes; 95% CI -251.15 to -92.88) respectively. TAVR also lead to much less bleeding than sAVR. CONCLUSIONS Our analysis shows that TAVR as a redo procedure was equal to sAVR in mortality for severe AS patients with PCS, especially coronary artery bypass graft. We agree the advantage of TAVR as a redo procedure for patients with a history of PCS. Patients receiving TAVR experienced rapid recovery, shorter operation time and less bleeding, without increasing short and long term mortality.

Background Internet gaming disorder (IGD) is a type of behavioral addiction characterized by poorly controlled and interfering patterns of game playing. Studies have suggested that the IGD is usually accompanied by increased desire or craving for gaming, suggesting that secondary rewards related to gaming may become more salient than those for primary rewards like food. However, this hypothesis has not been formally tested and potential neural mechanisms remain unclear. Methods This is a functional magnetic resonance imaging (fMRI) study. Twenty-one IGD subjects and 23 matched individuals with recreational game use (RGU) were scanned when exposed to gaming (secondary rewards), food (primary rewards) and neutral cues. Group-by-cue-type interaction analyses and subsequent within-group analyses for fMRI data were performed and seed-based functional connectivity (FC) analyses explored further potential neural features. Results IGD subjects’ subjective craving responses to gaming cues were higher than to food cues, while the opposite was observed in RGU subjects. Group-by-cue interaction effects implicated the precuneus and precuneus-caudate FC. Simple effect analysis showed that for IGD subjects, gaming-related cues elicited higher FC in precuneus-caudate relationships than did food-related cues. In the RGU subjects, the opposite was observed. Significant correlations were found between brain features and craving scores. Conclusions These results support the hypothesis regarding imbalances in sensitivities to different types of reward in IGD, and suggest neural mechanisms by which craving for gaming may make secondary rewards more salient than primary ones, thus promoting participation in addictive patterns of gaming.

Background Real-world data (RWD) has been increasingly used in drug development. A reliable evaluation of efficacy for current treatments is challenging with very limited publication data of clinical trials available. The RWD provides a unique value and an alternative way to achieve such goal. Use data from metastatic Breast Cancer (mBC) patients in the real world clinical practice, we examine the treatment patterns and durations of different endocrine monotherapies in various clinical settings. Methods We obtained Flatiron Health subject-level mBC data set which consists a group of 20645 mBC patients. The analysis set consisted of subjects who were ER+/Her2-/(PgR+ or PgR-), received at least one prior line of CDK4/6 inhibitor (mono or combo) and one prior line of endocrine therapy (mono or combo) in the mBC settings, and had an ECOG performance score Result Out of all subjects in the mBC RWD database, 263 subjects met the inclusion criteria and were included in the analysis set. Among all 263 ER+/Her2- subjects, the median TTD of endocrine monotherapies was 3.0 months (95% CI: 2.8-3.7 months, N=263) in all subjects, 3.7 months (95% CI: 3.0-4.3 months, N=186) in PgR+ group and 2.1 months (95% CI: 1.9-2.9 months, N=77) in PgR- group. Among 186 ER+/PgR+/Her2- subjects, 1) the median TTD of endocrine monotherapies was 3.3 months (95% CI: 2.8-4.6 months, N=153) in ECOG=3 prior treatment lines group. Conclusion By investigating the RWD, we observed that the PgR status is prognostic in post CDK setting: endocrine monotherapies in PgR+ group has longer TTD compared to PgR- group in ER+/Her2- mBC subjects. By further looking into ER+/PgR+/Her2- subjects, we observed different treatment durations of endocrine therapies in various clinical scenarios, which may provide a helpful understanding of the mBC monotherapy treatments. Citation Format: Tenghui Chen, Zhaojie Zhang, Lei Gao, Catherine Scholz, Antonio Gualberto, Lihua Yu, Kun Yu. Using real-world data to evaluate the performance of endocrine therapies in ER+/Her2- metastatic breast cancer patients [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 5247.

Background Real-world data (RWD) has been increasingly used for drug development. RWD coupled with genomic data provides an opportunity to identify the association between certain genomic alterations and response to current standard of care (SOC). Such analyses may help identify predictive biomarkers to select patients who will benefit most from SOC, and/or potential therapeutic nodes that can be pharmacologically targeted to overcome resistance to SOC. Methods We obtained Flatiron CGDB Breast Cancer (as of Q3 2020 release) data set. This data set includes clinical and genomic data from 6,918 breast cancer patients. Time to treatment discontinuation (TTD) was used as real world outcome. We performed two types of genomic-outcome association analysis: 1) Use Cox proportional hazards regression model to identify which baseline mutation (mutation occurred prior to the treatment) could predict the outcome; and 2) use Fisher exact test to identify which mutations are enriched in post-treatment tumors samples, compared to pre-treatment tumor samples. Result We found TP53 mutation is associated with shorter TTD for Palbociclib + Aromatase inhibitor (AI); Palbociclib + Fulvestrant; and endocrine monotherapy. It is consistent with the reports that TP53 mutation is poor prognostic factor (ref). Interestingly, ESR1 mutation is associated with shorter TTD for Palbociclib + AI and AI monotherapy; but not associated with TTD for Palbociclib + Fulvestrant or Fulvestrant monotherapy. On the other hand, MYC amplification is associated shorter TTD for Palbociclib + Fulvestrant or Fulvestrant monotherapy. We found that genes associated with Palbociclib + Endocrine are by and large same as those associated with endocrine monotherapy; suggesting the association is largely driven by endocrine treatment. Comparison of post-treatment vs. pre-treatment analysis found that ESR1 mutation is enriched in post treatment of AI; but not Fulvestrant. Conclusion We demonstrated that real-world clinicogenomic data could identify the biologically meaningful genomic biomarkers that are associated with real world response. This study warrants the further investigation of novel genomic biomarkers identified from the analysis. Citation Format: Kun Yu, Tenghui Chen, Manav Korpal, Ping Zhu, Zhaojie Zhang, Lihua Yu, Yonghong Xiao. Real-world data to identify the genomic association with response to CDK4/6i + Endocrine therapy in ER+ breast cancer patients [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 4123.

Genomic studies of pediatric cancer have primarily focused on specific tumor types or high-risk disease. Here, we used a three-platform sequencing approach, including whole-genome sequencing (WGS), whole-exome sequencing (WES), and RNA sequencing (RNA-seq), to examine tumor and germline genomes from 309 prospectively identified children with newly diagnosed (85%) or relapsed/refractory (15%) cancers, unselected for tumor type. Eighty-six percent of patients harbored diagnostic (53%), prognostic (57%), therapeutically relevant (25%), and/or cancer-predisposing (18%) variants. Inclusion of WGS enabled detection of activating gene fusions and enhancer hijacks (36% and 8% of tumors, respectively), small intragenic deletions (15% of tumors), and mutational signatures revealing of pathogenic variant effects. Evaluation of paired tumor–normal data revealed relevance to tumor development for 55% of pathogenic germline variants. This study demonstrates the power of a three-platform approach that incorporates WGS to interrogate and interpret the full range of genomic variants across newly diagnosed as well as relapsed/refractory pediatric cancers. Significance: Pediatric cancers are driven by diverse genomic lesions, and sequencing has proven useful in evaluating high-risk and relapsed/refractory cases. We show that combined WGS, WES, and RNA-seq of tumor and paired normal tissues enables identification and characterization of genetic drivers across the full spectrum of pediatric cancers. This article is highlighted in the In This Issue feature, p. 2945

Background Anhydrobiotes, such as the yeast Saccharomyces cerevisiae, are capable of surviving almost total loss of water. Desiccation tolerance requires an interplay of multiple events, including preserving the protein function and membrane integrity, preventing and mitigating oxidative stress, maintaining certain level of energy required for cellular activities in the desiccated state. Many of these crucial processes can be controlled and modulated at the level of organelle morphology and dynamics. However, little is understood about what organelle perturbations manifest in desiccation-sensitive cells as a consequence of drying or how this differs from organelle biology in desiccation-tolerant organisms undergoing anhydrobiosis. Results In this study, electron and optical microscopy was used to examine the dynamic changes of yeast cells during the desiccation process. Dramatic structural changes were observed during the desiccation process, including the diminishing of vacuoles, decrease of lipid droplets, decrease in mitochondrial cristae and increase of ER membrane, which is likely caused by ER stress and unfolded protein response. The survival rate was significantly decreased in mutants that are defective in lipid droplet biosynthesis, or cells treated with cerulenin, an inhibitor of fatty acid synthesis. Conclusion Our study suggests that the metabolism of lipid droplets and membrane may play an important role in yeast desiccation tolerance by providing cells with energy and possibly metabolic water. Additionally, the decrease in mitochondrial cristae coupled with a decrease in lipid droplets is indicative of a cellular response to reduce the production of reactive oxygen species.

To evaluate the potential of an integrated clinical test to detect diverse classes of somatic and germline mutations relevant to pediatric oncology, we performed three-platform whole-genome (WGS), whole exome (WES) and transcriptome (RNA-Seq) sequencing of tumors and normal tissue from 78 pediatric cancer patients in a CLIA-certified, CAP-accredited laboratory. Our analysis pipeline achieves high accuracy by cross-validating variants between sequencing types, thereby removing the need for confirmatory testing, and facilitates comprehensive reporting in a clinically-relevant timeframe. Three-platform sequencing has a positive predictive value of 97–99, 99, and 91% for somatic SNVs, indels and structural variations, respectively, based on independent experimental verification of 15,225 variants. We report 240 pathogenic variants across all cases, including 84 of 86 known from previous diagnostic testing (98% sensitivity). Combined WES and RNA-Seq, the current standard for precision oncology, achieved only 78% sensitivity. These results emphasize the critical need for incorporating WGS in pediatric oncology testing., Clinical oncology is rapidly adopting next-generation sequencing technology for nucleotide variant and indel detection. Here the authors present a three-platform approach (whole-genome, whole-exome, and whole-transcriptome) in pediatric patients for the detection of diverse types of germline and somatic variants.