bluuebunny/crossref_metadata_2025 huggingface dataset:
OMRT-5. Therapy-induced reprogramming drives glioma vascular transdifferentiation and recurrence
Authors: Muthukrishnan Sree Deepthi , Kawaguchi Riki , Nair Pooja , Prasad Rachna , Qin Yue , Condro Michael , Wang Qing , Alvarado Alvaro , Kornblum Harley
Published: July 2021

Therapy-resistant glioma cells elicit remarkable phenotypic plasticity leading to aggressive tumor recurrence. Here, we used single-cell and whole transcriptomic sequencing to uncover that radiation treatment induces a dynamic shift in functional states of glioma cells allowing for acquisition of either stem-like, mesenchymal-like or vascular-like phenotypes. The predominant phenotype switch induced by radiation in surviving tumor cells is the vascular-like cell state, resulting in transdifferentiation to endothelial-like and pericyte-like cells in distinct cell clusters. The transdifferentiated endothelial-like and pericyte-like cells secrete trophic factors to support proliferation of tumor cells, and their selective ablation results in reduced tumor growth and recurrence post-treatment. Mechanistically, the acquisition of vascular-like phenotype is driven by increased acetylation and chromatin accessibility in vascular genes and in regions for binding of vascular specification transcription factors. Blocking histone acetylation using a small molecule inhibitor targeting P300 histone acetyltransferase activity prior to radiation treatment inhibits the vascular-like transdifferentiation of glioma cells and tumor growth. Our findings indicate that radiation therapy-induces rewiring of glioma cells that promotes vascular cell-like transdifferentiation, tumor growth and recurrence.
OMRT-6. Optimizing MDM2 inhibition for the treatment of high-grade glioma
Authors: Rendo Veronica , Lupien Leslie , Khuu Nicholas , Pelton Kristine , Lu Sophie , Khadka Prasidda , Langhnoja Jaldeep , Phoenix Timothy , Ligon Keith , Bandopadhayay Pratiti , Beroukhim Rameen
Published: July 2021

Over 80% of high-grade gliomas have alterations in members of the p53 pathway, a central regulator of cell cycle progression and apoptosis that becomes activated in response to cellular stress and DNA damage. For tumors that retain wild-type p53, pathway deregulation frequently occurs through the amplification of negative regulators of p53, including the E3 ubiquitin ligase MDM2. The p53/MDM2 interaction axis has served as basis for the development of several classes of MDM2 inhibitors, with AMG232 being the most potent molecule currently undergoing clinical evaluation. As the effects of MDM2 inhibition (MDM2i) remain poorly understood in high-grade glioma, we performed genomic and transcriptomic analyses in patient-derived models to better characterize sensitive tumors and identify putative biomarkers of drug response. Treatment with AMG232 impaired the growth of cell lines with wild-type p53 status, particularly in tumors with additional amplification of MDM4 or PPM1D activating mutations. Treatment with AMG232 upregulated both cell cycle arrest and apoptotic cellular responses, as measured by annexin V/PI staining and immunoblotting. Interestingly, the dynamics of these two downstream p53 signaling axis were dependent on treatment duration across models. In addition to p53 pathway activation and apoptotic induction, RNA-sequencing revealed MDM2i to be associated with the activation of oncogenic MAPK and KRAS signaling as well as epithelial to mesenchymal transition markers. In most solid tumors, resistance to MDM2i is mainly mediated by acquisition of p53 inactivating mutations. We hypothesized that resistance mechanisms in glioma may be partially driven by transcriptional changes, as these tumors consist of subpopulations with diverse cell differentiation states. By chronic AMG232 treatment, we have developed in vitro and in vivo models of acquired MDM2i resistance that are not mediated by p53 inactivation. Ongoing work is focused on characterizing the transcriptional profile of these cells to identify transcriptional changes leading to decreased drug response.
OMRT-7. Angiogenesis inhibitors strongly synergize with therapeutics targeting tumor metabolism
Authors: Khadka Sunada
Published: July 2021

Angiogenesis inhibition has become a mainstay of oncology despite having fallen short of its early promise. As originally envisioned, angiogenesis inhibition would cut off the blood supply, deprive tumor cells of key nutrients, leading to their death. In practice, while there is evidence that tumors under angiogenesis treatment do in fact exhibit some degree of metabolic stress, this is stress is not sufficient to induce significant cancer cell death. We posit that the full potential of angiogenesis inhibition can be realized by the combination of angiogenesis inhibition with emerging tumor metabolism targeting therapies. Because tumors under angiogenesis inhibition are already in a state of nutrient stress, the effects of metabolically targeted therapies such as amino acid depletion (e.g. asparginase, methionine restriction), inhibitors of stress adaption (AMPK and GCN2 inhibitors) or energy metabolism (e.g. IACS-010759, Metformin, POMHEX) stand to dramatically increase in potency whilst remaining selective for (angiogenic) tumor versus (non-angiogenic) normal tissue. Here, we provide proof-of-principal for this thesis. First, we performed metabolomic profiling of angiogenesis-inhibited tumors, which corroborates a state of nutrient stress in angiogenesis-inhibited tumors. Second, we demonstrate dramatic anti-neoplastic synergy (effectively curing of xenografted tumor-bearing mice, irrespective of initial tumor size), without enhanced adverse toxicities, between the OxPhos inhibitor IACS-010759 and the angiogenesis tyrosine kinase inhibitor, Tivozanib. The same results were recapitulated with the anti-VEGFA antibody, Avastin, and the OxPhos inhibitor could be substituted with the Enolase inhibitor HEX, with similar effects. The synergy was observed in a broad range of tumor types, even those without clear genetic susceptibilities. Together, these results suggest that angiogenesis inhibitors synergize broadly with cancer therapies targeting metabolism, allowing the realization of the full potential of these previously disappointing drugs. Our results warrant systematic combination clinical trials between angiogenesis inhibitors and established, as well as emerging anti-metabolic cancer therapies.
OMRT-9. Effect of Pre-Operative Stereotactic Radiosurgery on Brain Metastasis: Analysis of DNA and RNA Genomic Profiles from Phase-II Clinical Trial NCT03398694
Authors: Shireman Jack , Huff Wei , Monaco Gina , Agrawal Namita , Watson Gordon , Dey Mahua
Published: July 2021

Background

With improved systemic therapy that has limited impact on the intracranial compartment, the incidence of brain metastasis (BM) from solid cancers is rising and negatively impacting patient’s overall survival (OS). Treatment varies based on presentation, however, for patients with <4 symptomatic BMs current clinical practice involves surgical resection followed by stereotactic radiosurgery (SRS) to the resection cavity. Post-operative SRS is associated with increased risk of leptomeningeal disease (LMD) and local recurrence in the follow-up period. We hypothesize that pre-operative SRS will decrease the incidence of LMD as well as local recurrence and increase patient’s OS by delivering a lethal dose of radiation to tumor cells before they are disturbed by surgical resection. In a Phase II clinical trial (NCT03398694) we are treating patients with 1–4 symptomatic BMs with pre-operative SRS while collecting DNA and RNA sequencing data from core and peripheral edges of the resected tumor to examine the genomic effects of SRS on tumor.

Methods

Post-SRS resected tumor specimens were divided into two groups: ‘center’ and ‘periphery’ with respect to the center of SRS treatment with periphery within 50% isodose line. Previously resected untreated BMs were used as control. DNA and RNA were isolated from all samples for sequencing.

Conclusions

Our initial analyses show that pre-treatment with SRS, results in significant genomic changes at DNA and RNA levels throughout the tumor, in both center as well as periphery. Furthermore, significant transcriptomic differences were noted among matched samples between the central and peripheral SRS locations implicating differential effect of SRS dosing within a tumor. Initial gene ontological analysis on non-small cell lung cancer samples demonstrated an overexpression of WNT and BMP signaling pathways (p <.001, p<.01). These pathways are typically involved in neuronal development, hinting that adaptation to the brain microenvironment was occurring post SRS treatment.
OMRT-15. Multidisciplinary management of non-small cell lung cancer patients with leptomeningeal metastasis in the TKI era
Authors: Chen Kuan-Yu , Huang Abel Po-Hao
Published: July 2021

Background

leptomeningeal metastasis (LM) is a devastating scenario in patients with non-small cell lung cancer (NSCLC), with an estimated median overall survival (OS) of 4–6 months from diagnosis. Several studies have clarified the prognosis of treatment modalities after LM. However, just a few studies have clarified the prognosis of LM patterns. We evaluate the prognosis based on various patterns of LM under multidisciplinary treatment (MDT).

Method

This retrospective study evaluated NSCLC patients treated at National Taiwan University Hospital between 2007–2019 with brain metastases (BM) and LM. LM was classified into LM only, LM concurrent with BM, and LM after BM. Treatments including systemic therapy, whole-brain radiotherapy (WBRT), stereotactic radiosurgery (SRS), and intrathecal chemotherapy with Methotrexate (IT MTX) were recorded. BM excision was done by a neurosurgeon using minimally invasive neurosurgery. The MDT was done according to patients’ clinical situations. Kaplan-Meier methodology was used to describe overall survival OS. Multivariate Cox regression model was used to access prognostic factors.

Result

One hunderd patients with NSCLC CNS metastasis was included in this study. Median OS in patients with single, oligo and multiple BM was 42.0 months (95% CI= 0.12–83.89), 58.1 months (95% CI= 13.00–103.26), and 21.3 months (95% CI= 16.93–25.73), respectively. The median OS of all LM patients was 9.8 months. The median OS of LM after BM, concurrent BMLM, and LM only was 8 months (95% CI= 2.58–13.56), 41.5 months (95% CI= 0.00–94.36), and 18.5 months (95% CI=3.68–33.32), respectively. Multivariate Cox regression analysis showed only IT MTX (p= 0.010, HR= 0.392, 95%CI= 0.19–0.80) was associated with survival.

Conclusion

MDT in the TKI era has led to a dramatic improvement of OS in patients with LM (4–6 months vs. 9.8 months). NSCLC patients with LM only and concurrent BM LM has a better prognosis and longer survival, and thus are worth receiving intensive MDT care.
OTME-5. Meningioma liquid biopsy specimens exhibit contrasting immune-cell landscapes across methylation-subtypes and estimated recurrence risk subgroups
Authors: Herrgott Grayson , She Ruicong , Sabedot Thais , Wells Michael , Asmaro Karam , Malta Tathiane , Mosella Maritza , Nelson Kevin , deCarvalho Ana , Poisson Laila , Mukherjee Abir , Cazacu Simona , Robin Adam , Lee Ian , Snyder James , Walbert Tobias , Rosenblum Mark , Mikkelsen Tom , Kalkanis Steven , Rock Jack , Noushmehr Houtan , Castro Ana Valeria
Published: July 2021

Background

Tumor-infiltrating immune cell compositions have been previously correlated to encouragement or inhibition of tumor growth. This association highlights immune-landscape profiling through non-invasive methods as a crucial step in approaches to treatment of patients with meningioma (MNG), a prevalent primary intracranial tumor. Genome-wide DNA methylation patterns can aid in definition and assessment of cell compositions in liquid biopsy serum specimens, and allow for development of machine-learning models with predictive capabilities.

Methods

We profiled the cfDNA methylome (EPIC array) in liquid biopsy specimens from patients with MNG (n = 63) and nontumor controls (n = 6). We conducted both unsupervised epigenome-wide and supervised analyses of the meningioma methylome. Estimation of immune cell composition was conducted using Python-based methodology, where a reference methylome atlas of chosen cell types (B-cells, CD4- and CD8T-cells, neutrophils, natural killer cells, monocytes, cortical neuron, vascular endothelial cells, and healthy meninge) was used to deconvolute the MNG samples. Recurrence risk was estimated using an existing methylation-based Random-Forest classifier previously reported and validated, adapted to our serum-based cohort through employment of translatable meningioma subgroup-specific methylation markers (differentially methylated probes).

Results

We identified four distinct genome-wide methylation subgroups (k-clusters) of MNG which presented differential tumor micro-environments across all cell types investigated. Application of the DNA methylation-based Random-Forest classifier allowed for categorization of primary MNG serum samples into estimated recurrence-risk subgroups. Significantly contrasting micro-environments for the subgroups were observed across several cell-types, with those MNG more likely to recur displaying depletion in cell types reported to improve anti-tumoral response in many tumors (e.g. T-Cells).

Conclusions

DNA methylation based deconvolution allowed for detection of contrasting tumor microenvironment compositions across MNG methylation subtypes and recurrence-risk estimation subgroups. These results suggest that microenvironment profiling can be informative of probable tumor behavior and prognostic outcomes, helping guide therapeutic approaches towards treatment of patients with MNG.
OTME-7. Cancer - immune cell interactions drive transitions to mesenchymal-like state in glioblastoma
Authors: Hara Toshiro , Chanoch-Myers Rony , Mathewson Nathan , Myskiw Chad , Atta Lyla , Bussema Lillian , Eichhorn Stephen , Kinker Gabriela , Rodman Christopher , Gonzalez Nicolas , Wakimoto Hiroaki , Rozenblatt-Rosen Orit , Zhuang Xiaowei , Fan Jean , Hunter Tony , Verma Inder , Wucherpfennig Kai , Regev Aviv , Suvà Mario , Tirosh Itay
Published: July 2021

Communication between cancer cells and immune cells is a key determinant of the glioblastoma ecosystem and its response to therapies, but remains poorly understood. Here we leveraged single-cell RNA-sequencing (scRNA-seq) of human samples and mouse models, deconvolution analysis of bulk specimen from The Cancer Genome Atlas (TCGA) and functional approaches, to dissect cellular cross-talks in glioblastoma. We demonstrate that macrophages induce a transition of glioblastoma cells into mesenchymal-like (MES-like) states. This effect is mediated, both in vitro and in vivo, by macrophage-derived Oncostatin M (OSM) and its cognate receptor OSMR on glioblastoma cells. We show that MES-like glioblastoma states are also associated with increased expression of a mesenchymal program in macrophages and with increased cytotoxicity of T cells, highlighting extensive alterations of the immune microenvironment with potential therapeutic implications.
OTME-13. Integration of metabolic and transcriptional signatures of glioblastoma invasion reveals extracellular matrix reorganization and vasculature remodeling
Authors: Cudalbu Cristina , Bady Pierre , Lai Marta , Xin Lijing , Gusyatiner Olga , Hamou Marie-France , Lepore Mario , Brouland Jean-Philippe , Daniel Roy , Hottinger Andreas , Hegi Monika
Published: July 2021

Background

The invasive behavior of glioblastoma is considered highly relevant for recurrence. However, the invasion zone is difficult to visualize, typically lies outside the resected and irradiated area, and is protected by the blood brain barrier, posing a particular challenge for treatment. We present biological features of invasive growth accompanying tumor progression and invasion based on associated metabolic and transcriptomic changes in patient derived orthotopic xenografts (PDOX) and corresponding patients.

Methods

Patients with suspected glioblastoma were enrolled (NCT02904525) and underwent 1H-MR spectroscopy and imaging (1H-MRS/I, 7T). Tissue obtained at surgery was transplanted orthotopically into immune-compromised mice. Longitudinal follow-up was performed by 1H-MRS/I (14.1T) on the injected and the contralateral side. The PDOX, the corresponding contralateral side, and the original human tumors underwent RNA-sequencing.

Results

The temporal changes of the metabolite profiles characterized the kinetics of invasive growth of PDOX, and were patient specific. Comparison of 1H-MRS derived metabolite signatures, reflecting temporal changes of tumor development and invasion in PDOX, revealed high similarity to spatial metabolite signatures of combined multi-voxel analyses of the patients’ tumors. Associations between the metabolite profiles and the combined transcriptome of the xenografts and the host, reflected molecular signatures of invasion, comprising extracellular matrix degradation and reorganization, growth factor binding, and vascular remodeling.

Conclusion

Integrating metabolic profiles and gene expression of highly invasive PDOX allows in vivo monitoring of progression in the non-enhancing tumor infiltration zone and provides insights into the remodeling of the extracellular matrix that is essential for cell-cell communication and regulation of cellular processes. The changes of the structural and biochemical properties of the extracellular matrix are of importance for the biological behavior of the tumors and may be subjected to therapeutic targeting.
OTME-14. TGF-beta signaling in microtube formation of glioblastoma
Authors: Storevik Simon , Joseph Justin , Magaut Capucine , Henrique Luiz , Mathivet Thomas , Latif Md Abdul , Rudewicz Justine , Guyon Joris , Gambaretti Matteo , Haukås Frida , Trones Amalie , Ystaas Lars Andreas Rømo , Hossain Jubayer , Ninzima Sandra , Zhou Wenjing , Tomar Tushar , Winkler Frank , Kruyt Frank , Bikfalvi Andreas , Bjerkvig Rolf , Daubon Thomas , Miletic Hrvoje
Published: July 2021

Microtubes (MTs) are cytoplasmic extensions of glioma cells serving as important cell communication structures while also promoting invasion and treatment resistance through network formation. MTs are abundant in chemoresistant gliomas, in particular glioblastomas, while they are uncommon in chemosensitive IDH mutated and 1p/19q co-deleted oligodendrogliomas.

By performing a bioinformatics analysis on data from The Cancer Genome Atlas (TCGA) we identified the TGF-b pathway as being distinctly upregulated in glioblastomas compared to oligodendrogliomas, making this a signaling pathway potentially involved in MT formation. Based on patient-derived GBM stem cell line models we demonstrated that stimulation of TGF-b increased MT formation, while inhibition of TGF-b reduced MT formation. MT formation was verified by expression of GAP43 and nestin, which have previously been shown to be important structural proteins of MTs.

Interestingly, we also observed a responder/non-responder relationship between GBM cell lines P3 and GG16/ GG6 regarding MT formation upon TGF-b stimulation. To determine downstream signaling mediators of the TGF-b pathway crucial for MT formation, we subsequently performed RNA sequencing of these cell lines. From the 34 initial candidates common to responders, but absent in non-responders, only 3 genes were left after filtering through TCGA data and in vivo RNA sequencing data of a GBM xenograft model derived from P3.

Thrombospondin 1 (TSP1) emerged as the most interesting candidate as we have previously shown that transcription of this gene is activated by TGF-b/SMAD signaling and TSP1 also promotes invasiveness of GBM. TSP1 was upregulated by TGFB1 stimulation in responder cells and promoted MT formation. Transcriptional activation of TSP1 was absent in the non-responder cell line GG6 and could be reversed in the responder cell line P3 by TSP1 shRNAs in vitro and in vivo. Thus, TSP1 was experimentally verified as an important mediator of microtube formation downstream of TGF-b signaling.
Transcriptome Dynamics of Epidermal Reprogramming during Direct Shoot Regeneration inTorenia fournieri
Authors: Morinaka Hatsune , Mamiya Akihito , Tamaki Hiroaki , Iwamoto Akitoshi , Suzuki Takamasa , Kawamura Ayako , Ikeuchi Momoko , Iwase Akira , Higashiyama Tetsuya , Sugimoto Keiko , Sugiyama Munetaka
Published: July 2021

abstract

Shoot regeneration involves reprogramming of somatic cells and de novo organization of shoot apical meristems (SAMs). In the best-studied model system of shoot regeneration using Arabidopsis, regeneration is mediated by the auxin-responsive pluripotent callus formation from pericycle or pericycle-like tissues according to the lateral root development pathway. In contrast, shoot regeneration can be induced directly from fully differentiated epidermal cells of stem explants of Torenia fournieri (Torenia), without intervening the callus mass formation in culture with cytokinin; yet, its molecular mechanisms remain unaddressed. Here, we characterized this direct shoot regeneration by cytological observation and transcriptome analyses. The results showed that the gene expression profile rapidly changes upon culture to acquire a mixed signature of multiple organs/tissues, possibly associated with epidermal reprogramming. Comparison of transcriptomes between three different callus-inducing cultures (callus induction by auxin, callus induction by wounding and protoplast culture) of Arabidopsis and the Torenia stem culture identified genes upregulated in all the four culture systems as candidates of common factors of cell reprogramming. These initial changes proceeded independently of cytokinin, followed by cytokinin-dependent, transcriptional activations of nucleolar development and cell cycle. Later, SAM regulatory genes became highly expressed, leading to SAM organization in the foci of proliferating cells in the epidermal layer. Our findings revealed three distinct phases with different transcriptomic and regulatory features during direct shoot regeneration from the epidermis in Torenia, which provides a basis for further investigation of shoot regeneration in this unique culture system.
Impact of Left Ventricular Systolic Function After Moderate-to-Severe Isolated Traumatic Brain Injury: A Systematic Review and Meta-Analysis
Authors: Okuya Yoshiyuki , Gohil Kavita , Moussa Issam D.
Published: July 2021

Traumatic brain injury (TBI) can result in left ventricular dysfunction, which can lead to hypotension and secondary brain injuries. However, the association between left ventricular systolic dysfunction (LVSD) and in-hospital mortality in patients with moderate-to-severe isolated TBI is controversial. Therefore, we conducted a systematic review and meta-analysis to identify the prevalence of LVSD and evaluate whether LVSD following moderate-to-severe isolated TBI increases the in-hospital mortality. We searched PubMed, EMBASE, and the Cochrane Library database from January 1, 2010, through June 30, 2020. Meta-analysis was performed to determine the incidence of LVSD and related mortality in patients with moderate-to-severe isolated TBI. A systematic review identified 5 articles appropriate for meta-analysis. The total number of patients pooled was 256. LVSD was reported in 4 studies, of which the estimated incidence of patients with LVSD was 18.7% (95% confidence interval, 11.9–26.6). Five studies reported on in-hospital mortality, and the estimated in-hospital mortality was 14.1% (95% confidence interval, 5.3–25.6). Finally, 3 studies were eligible for analyzing the association of LVSD and in-hospital mortality. On meta-analysis, in-hospital mortality was significantly higher in patients with LVSD (risk ratio, 6.57; 95% confidence interval, 3.71–11.65; P < 0.001). In conclusion, LVSD after moderate-to-severe TBI is common and may be associated with worse in-hospital outcomes.
Testing Katharine Kolcaba Theory of Comfort
Authors: Sharma Mukesh Chandra , Kalia Raman
Published: July 2021

The aim of this study was to test Katharine Kolcaba's theory of comfort by evaluating the effectiveness of integrative comfort care interventions on discomfort experienced by children (aged 5–10 years) during the postoperative period. An experimental approach, pretest-and-posttest control group design, was used for evaluating the effectiveness of integrative comfort care interventions on discomfort experienced by children. Sample was composed of 200 children, selected using purposive sampling technique with random assignment to experimental and control groups. Kolcaba's Comfort Theory was used to assess the child's condition and then plan and deliver integrative comfort care interventions. The steps that followed for data collection, planning, and implementing effective care were based on the presuppositions of the theory. The tools used for data collection were demographics, a Comfort Behaviors Checklist, and the Comfort Daisies tool. Comfort care interventions were delivered through nursing process approach. These interventions were addressed across physical, psychological, social, spiritual, and environmental aspects. After the application of theory, the analysis revealed improvement in the comfort level of the subjects. Mann–Whitney U test was used to find out the significant difference in posttest postoperative discomfort scores among subjects in the experimental and control groups. Findings were significant at <.001. The findings revealed that subjects who received integrative comfort care interventions using the comfort theory experienced more comfort as compared with the subjects in the control group.
Virtual Surgical Planning for Intracranial Intraosseous Meningioma Reconstruction
Authors: Shah Rema , Lu Xiaona , Dinis Jacob , Junn Alexandra , Alperovich Michael
Published: July 2021

Objective:

To assess the use of custom-made intracranial implants and three-dimensional cutting guides to direct the intracranial, intraorbital, and temporal reconstruction process for intraosseous meningioma.

Methods:

A retrospective analysis was conducted on 6 patients who were operated on by the senior author for intraosseous meningioma between 2017 and 2020. Three-dimensional models of the maxillofacial skeleton were created from preoperative virtual planned reconstruction and postoperative computed tomography scan images in the Mimics and 3-Matics software. Orbital reconstruction and temporal implant accuracy assessments were performed through the Materialise Mimics software.

Results:

Orbital cone volume had a mean discrepancy between the planned and actual orbital volume of 1.5% ± 1.6%. The reconstructed postoperative orbital volume was within 1.3% ± 2.0% of the unaffected orbit. Temporal bone reconstructions had a mean implant accuracy of 81.0%.

Conclusions:

Our results show that the postextirpative intracranial applications of virtual surgical planning are particularly suited for high fidelity reconstructions such as orbital reconstructions, as well as temporal reconstructions with intraoperative adjustments. Custom implants and virtual three-dimensional planning is particularly ideal and promising for intraosseous meningiomas given the involvement of complex intracranial and intraorbital bony structures.
Proof-of-concept pilot study on comprehensive spatiotemporal intra-patient heterogeneity for colorectal cancer with liver metastasis
Authors: Kyrochristos Ioannis D. , Glantzounis Georgios K. , Goussia Anna , Eliades Alexia , Achilleos Achilleas , Tsangaras Kyriakos , Hadjidemetriou Irene , Elpidorou Marilena , Ioannides Marios , Koumbaris George , Mitsis Michail , Patsalis Philippos C. , Roukos Dimitrios H.
Published: July 2021

Purpose

The mechanisms underlying high drug resistance and relapse rates after multi-modal treatment in patients with colorectal cancer (CRC) and liver metastasis (LM) remain poorly understood. We evaluate the potential translational implications of intra-patient heterogeneity (IPH) comprising primary and matched metastatic intratumor heterogeneity (ITH) coupled with circulating tumor DNA (ctDNA) variability.

Patients and methods

According to our IPH-based protocol, 18 eligible patients with CRC-LM, who underwent complete tumor resection after neo-adjuvant treatment, with a total of 122 multi-regional tumor and perioperative liquid biopsies were analyzed via next-generation sequencing (NGS) of a custom 77-gene panel. The primary endpoints were the extent of IPH and the frequency of actionable mutations.

Results

The proportion of patients with ITH were 53% and 56% in primary CRC and LM respectively, while 35% of patients harbored de novo mutations in LM indicating spatiotemporal tumor evolution and the necessity of multiregional analysis. Among the 56% of patients with alterations in liquid biopsies, de novo mutations in cfDNA were identified in 25% of patients, which were undetectable in both CRC and LM. All 17 patients with driver alterations harbored actionable mutations, with an average of 3.2 oncogenic events per patient, for molecularly targeted drugs either approved or under evaluation in ongoing clinical trials or in pre-clinical studies.

Conclusions

Our proof-of-concept prospective study provides initial evidence and warrants the conduction of precision oncology trials to test the potential clinical utility of IPH-driven matched therapy.
An Approach for Open Multivariate Analysis of Integrated Clinical and Environmental Exposures Data
Authors: Fecho Karamarie , Haaland Perry , Krishnamurthy Ashok , Lan Bo , Ramsey Stephen A. , Schmitt Patrick L. , Sharma Priya , Sinha Meghamala , Xu Hao
Published: July 2021

The Integrated Clinical and Environmental Exposures Service (ICEES) provides regulatory-compliant open access to sensitive patient data that have been integrated with public exposures data. ICEES was designed initially to support dynamic cohort creation and bivariate contingency tests. The objective of the present study was to develop an open approach to support multivariate analyses using existing ICEES functionalities and abiding by all regulatory constraints. We first developed an open approach for generating a multivariate table that maintains contingencies between clinical and environmental variables using programmatic calls to the open ICEES application programming interface. We then applied the approach to data on a large cohort (N = 22,365) of patients with asthma or related conditions and generated an eight-feature table. Due to regulatory constraints, data loss was incurred with the incorporation of each successive feature variable, from a starting sample size of N = 22,365 to a final sample size of N = 4,556 (20.5%), but data loss was < 10% until the addition of the final two feature variables. We then applied a generalized linear model to the subsequent dataset and focused on the impact of seven select feature variables on asthma exacerbations, defined as annual emergency department or inpatient visits for respiratory issues. We identified five feature variables—sex, race, obesity, prednisone, and airborne particulate exposure—as significant predictors of asthma exacerbations. We discuss the advantages and disadvantages of ICEES open multivariate analysis and conclude that, despite limitations, ICEES can provide a valuable resource for open multivariate analysis and can serve as an exemplar for regulatory-compliant informatics solutions to open patient data, with capabilities to explore the impact of environmental exposures on health outcomes.
Prevalence and Correlates of Parosmia and Phantosmia among Smell Disorders
Authors: Pellegrino Robert , Mainland Joel D. , Kelly Christine E. , Parker Jane K. , Hummel Thomas
Published: July 2021

Among those many individuals who suffer from a reduced odor sensitivity (hyposmia/anosmia) some individuals also experience disorders that lead to odor distortion, such as parosmia (i.e., distorted odor with a known source), or odor phantoms (i.e., odor sensation without an odor source). We surveyed a large population with at least one olfactory disorder (N = 2031) and found that odor distortions were common (46%), with respondents reporting either parosmia (19%), phantosmia (11%), or both (16%). In comparison to respondents with hyposmia or anosmia, respondents with parosmia were more likely to be female, young, and suffered from post-viral olfactory loss (p < 0.001), while phantosmia occurred most frequently in middle-aged respondents (p < 0.01) and was more likely to be caused by head trauma than parosmia (p < 0.01). A higher prevalence of odor distortion was observed 3 months to a year after their olfactory symptom onset (p < 0.001), which coincides with the timeline of physiological recovery. Additionally, we observed that the frequency and duration of distortions negatively affects quality of life, with parosmia showing a higher range of severity than phantosmia (p < 0.001). Previous research often grouped these distortions together, but our results show that they have distinct patterns of demographics, medical history, and loss in quality of life.
Analysis of feature influence on Covid-19 Death Rate Per Country Using a Novel Orthogonalization Technique
Authors: Gonnet Gaston , Stewart John , Lafleur Joseph , Keith Stephen , McLellan Mark , Jiang-Gorsline David , Snider Tim
Published: July 2021

We have developed a new technique of Feature Importance, a topic of machine learning, to analyze the possible causes of the Covid-19 pandemic based on country data. This new approach works well even when there are many more features than countries and is not affected by high correlation of features. It is inspired by the Gram-Schmidt orthogonalization procedure from linear algebra. We study the number of deaths, which is more reliable than the number of cases at the onset of the pandemic, during Apr/May 2020. This is while countries started taking measures, so more light will be shed on the root causes of the pandemic rather than on its handling.

The analysis is done against a comprehensive list of roughly 3,200 features. We find that globalization is the main contributing cause, followed by calcium intake, economic factors, environmental factors, preventative measures, and others. This analysis was done for 20 different dates and shows that some factors, like calcium, phase in or out over time. We also compute row explainability, i.e. for every country, how much each feature explains the death rate. Finally we also study a series of conditions, e.g. comorbidities, immunization, etc. which have been proposed to explain the pandemic and place them in their proper context. While there are many caveats to this analysis, we believe it sheds light on the possible causes of the Covid-19 pandemic.

One-Sentence Summary

We use a novel feature importance technique to find that globalization, followed by calcium intake, economic factors, environmental factors, and some aspects of societal quality are the main country-level data that explain early Covid-19 death rates.
RAFFT: Efficient prediction of RNA folding pathways using the fast Fourier transform
Authors: Opuu Vaitea , Merleau Nono S. C. , Messow Vincent , Smerlak Matteo
Published: July 2021

We propose a novel heuristic to predict RNA secondary structure formation pathways that has two components: (i) a folding algorithm and (ii) a kinetic ansatz. This heuristic is inspired by the kinetic partitioning mechanism, by which molecules follow alternative folding pathways to their native structure, some much faster than others. Similarly, our algorithm RAFFT starts by generating an ensemble of concurrent folding pathways ending in multiple metastable structures, which is in contrast with traditional thermodynamic approaches that find single structures with minimal free energies. When we constrained the algorithm to predict only 50 structures per sequence, nearnative structures were found for RNA molecules of length ≤ 200 nucleotides. Our heuristic has been tested on the coronavirus frameshifting stimulation element (CFSE): an ensemble of 68 distinct structures allowed us to produce complete folding kinetic trajectories, whereas known methods require evaluating millions of sub-optimal structures to achieve this result. Thanks to the fast Fourier transform on which RAFFT is based, these computations are efficient, with complexity 𝒪(L2 log L).
Comprehensive evaluation of machine learning models and gene expression signatures for prostate cancer prognosis using large population cohorts
Authors: Li Ruidong , Zhu Jianguo , Zhong Wei-De , Jia Zhenyu
Published: July 2021

Overtreatment remains the pervasive problem in prostate cancer (PCa) management due to the highly variable and often indolent course. Molecular signatures derived from gene expression profiling have played critical roles in PCa treatment decision-making. Many gene expression signatures have been developed to improve the risk stratification of PCa and some of them have already been translationally applied to clinical practice, however, no comprehensive evaluation was performed to compare the performances of the signatures. In this study, we conducted a systematic and unbiased evaluation of 15 machine learning (ML) algorithms and 30 published PCa gene expression-based prognostic signatures leveraging 10 transcriptomics datasets with 1,558 primary PCa patients from public data repositories. The results revealed that survival analysis models outperformed binary classification models for risk assessment, and the performances of the survival analysis methods - Cox model regularized with ridge penalty (Cox-Ridge) and partial least squares regression for Cox model (Cox-PLS) – were generally more robust than the other methods. Based on the Cox-Ridge algorithm, a few top prognostic signatures that have comparable or even better performances than the commercial panels have been identified. The findings from the study will greatly facilitate the identification of existing prognostic signatures that are promising for further validations in prospective studies and promote the development of robust prognostic models to guide clinical decision-making. Moreover, the study provided a valuable data resource from large primary PCa cohorts, which can be used to develop, validate, and evaluate novel statistical methodologies and molecular signatures to improve PCa management.
Association of preoperative plasma suPAR levels with intraoperative sublingual microvascular perfusion in patients undergoing major non-cardiac surgery
Authors: Chalkias Athanasios , Papagiannakis Nikolaos , Saugel Bernd , Flick Moritz , Kolonia Konstantina , Angelopoulou Zacharoula , Ragias Dimitrios , Papaspyrou Dimitra , Ntalarizou Nicoletta , Bouzia Aikaterini , Stamoulis Konstantinos , Kyriakaki Aikaterini , Eugen-Olsen Jesper , Laou Eleni , Arnaoutoglou Eleni
Published: July 2021

INTRODUCTION

The plasma suPAR level has previously been associated with postoperative complications and has been shown to be an independent predictor of coronary microvascular function and flow reserve. We investigated the association between preoperative suPAR levels and intraoperative sublingual microvascular perfusion in patients undergoing elective major non-cardiac surgery.

Methods

This study included 100 patients undergoing major non-cardiac surgery between February 2019 and September 2020. The primary objective was to investigate the association between preoperative suPAR and intraoperative sublingual De Backer score, Consensus Proportion of Perfused Vessels (Consensus PPV), and Consensus PPV (small). Secondary objectives were to investigate the associations between these sublingual microcirculatory variables and (1) complications and (2) mean arterial pressure. EDTA blood was collected before induction of anesthesia and plasma suPAR levels were determined using the suPARnostic® quick triage lateral flow assay. Sublingual microcirculation was monitored with Sidestream DarkField (SDF+) imaging technique at 20 minutes after induction of anesthesia before surgical incision (baseline) and then every 30 minutes until emergence from anesthesia.

Results

A decrease of 0.7 mm-1 in the De Backer score, 2.5% in the Consensus PPV, and 2.8% in the Consensus PPV (small) from baseline measurement was observed for every 1 ng/ml increase of suPAR or 1 additional minute of intraoperative time. De Baker score did not change significantly from baseline (p=0.404), while Consensus PPV and Consensus PPV (small) decreased significantly from baseline (p<0.001 in both cases). The De Backer score, the Consensus PPV, and the Consensus PPV (small) correlated with postoperative complications. Mean arterial pressure correlated with De Backer score (p=0.487) but not with Consensus PPV (p=0.506) or Consensus PPV (small) (p=0.697) during the intraoperative period.

Conclusion

Preoperative suPAR levels and prolonged operative duration were associated with intraoperative impairment of sublingual microvascular perfusion in patients undergoing elective major non-cardiac surgery.
PHENOTYPIC CHARACTERIZATION OF TWO NOVEL CELL LINE MODELS OF CASTRATION RESISTANT PROSTATE CANCER
Authors: Haffner Michael C. , Bhamidipati Akshay , Tsai Harrison K. , Esopi David M. , Vaghasia Ajay M. , Low Jin-Yih , Patel Radhika A. , Guner Gunes , Pham Minh-Tam , Castagna Nicole , Hicks Jessica , Wyhs Nicolas , Aebersold Ruedi , De Marzo Angelo M. , Nelson William G. , Guo Tiannan , Yegnasubramanian Srinivasan
Published: July 2021

BACKGROUND

Resistance to androgen deprivation therapies is a major driver of mortality in advanced prostate cancer. Therefore, there is a need to develop new pre-clinical models that allow the investigation of resistance mechanisms and the assessment of drugs for the treatment of castration resistant prostate cancer.

METHODS

We generated two novel cell line models (LAPC4-CR and VCaP-CR) which were derived by passaging LAPC4 and VCaP cells in vivo and in vitro under castrate conditions. We performed detailed transcriptomic (RNA-seq) and proteomic analyses (SWATH-MS) to delineate expression differences between castration-sensitive and castration-resistant cell lines. Furthermore, we characterized the in vivo and in vitro growth characteristics of the novel cell line models.

RESULTS

The two cell line derivatives LAPC4-CR and VCaP-CR showed castration resistant growth in vitro and in vivo which was only minimally inhibited by AR antagonists, enzalutamide and bicalutamide. High-dose androgen treatment resulted in significant growth arrest of VCaP-CR but not in LAPC4-CR cells. Both cell lines maintained AR expression, but exhibited distinct expression changes on the mRNA and protein level. Integrated analyses including data from LNCaP and the previously described castration resistant LNCaP-abl cells revealed an expression signature of castration resistance.

CONCLUSIONS

The two novel cell line models LAPC4-CR and VCaP-CR and their comprehensive characterization on the RNA and protein level represent important resources to study the molecular mechanisms of castration resistance.
ECM-integrin signalling instructs cellular position-sensing to pattern the early mouse embryo
Authors: Kim Esther Jeong Yoon , Sorokin Lydia , Hiiragi Takashi
Published: July 2021

Development entails patterned emergence of diverse cell types within the embryo. In mammals, cells positioned inside the embryo gives rise to the inner cell mass (ICM) that eventually forms the embryo proper. Yet the molecular basis of how these cells recognise their ‘inside’ position to instruct their fate is unknown. Here we show that cells perceive their position through extracellular matrix (ECM) and integrin-mediated adhesion. Provision of ECM to isolated embryonic cells induces ICM specification and alters subsequent spatial arrangement between epiblast (EPI) and primitive endoderm (PrE) cells that emerge within the ICM. Notably, this effect is dependent on integrin β1 activity and involves apical to basal conversion of cell polarity. We demonstrate that ECM-integrin activity is sufficient for ‘inside’ positional signalling and it is required for proper sorting of EPI/PrE cells. Our findings thus highlight the significance of ECM-integrin adhesion in enabling position-sensing by cells to achieve tissue patterning.
Coding of interceptive saccades in parietal cortex of macaque monkeys
Authors: Churan Jan , Kaminiarz Andre , Schwenk Jakob C. B. , Bremmer Frank
Published: July 2021

The oculomotor system can initiate remarkably accurate saccades towards moving targets (interceptive saccades) the processing of which is still under debate. The generation of these saccades requires the oculomotor centers to have information about the motion parameters of the target that then must be extrapolated to bridge the inherent processing delays. We investigated to what degree the information about motion of a saccade target is available in the lateral intra-parietal area (area LIP) of macaque monkeys for generation of accurate interceptive saccades. When a multi-layer neural network was trained based on neural discharges from area LIP around the time of saccades towards stationary targets it was also able to predict the end points of saccades directed towards moving targets. This prediction, however, lagged behind the actual post-saccadic position of the moving target by ~80 ms when the whole neuronal sample of 105 neurons was used. We further found that single neurons differentially code for the motion of the target. Selecting neurons with the strongest representation of target motion reduced this lag to ~30 ms which represents the position of the moving target approximately at the onset of the interceptive saccade. We conclude that - similarly to recent findings from the Superior Colliculus (Goffart et al., 2017) – there is a continuum of contributions of individual LIP neurons to the accuracy of interceptive saccades. A contribution of other gaze control centers (like the cerebellum or the frontal eye field) that further increase the saccadic accuracy is, however, likely.
A new transgene mouse model using an extravesicular EGFP tag to elucidate the in vivo function of extracellular vesicles
Authors: Ø. Nørgård Mikkel , Steffensen Lasse B. , Hansen Didde R. , Füchtbauer Ernst-Martin , Engelund Morten B. , Dimke Henrik , Jensen Boye L. , Andersen Ditte C. , Svenningsen Per
Published: July 2021

The in vivo function of cell-derived extracellular vesicles (EVs) is challenging to establish since cell-specific EVs are difficult to isolate. We therefore created an EV reporter using CD9 to display enhanced green fluorescent protein (EGFP) on the EV surface. CD9-EGFP expression in cells did not affect EV size and concentration, but allowed for co-precipitation of EV markers TSG101 and ALIX from cell-conditioned medium by anti-GFP immunoprecipitation. We created a transgenic mouse where CD9-EGFP was inserted in the inverse orientation and double-floxed, ensuring Cre recombinase-dependent EV reporter expression. We crossed the EV reporter mice with mice expressing Cre ubiquitously (CMV- Cre), in cardiomyocytes (AMHC-Cre) and kidney epithelium (Pax8-Cre), respectively. The mice showed tissue-specific EGFP expression, and plasma and urine samples were used to immunoprecipitate EVs. CD9-EGFP EVs was detected in plasma samples from CMV-Cre/CD9-EGFP and AMHC-Cre/CD9-EGFP mice, but not in PAX8-Cre/CD9-EGFP mice. On the other hand, CD9-EGFP EVs were detected in urine samples from CMV-Cre/CD9-EGFP and PAX8-Cre/CD9-EGFP mice, but not AMHC-Cre/CD9-EGFP, indicating that plasma EVs are not filtered to the urine. In conclusion, our EV reporter mouse model enables Cre-dependent EV labeling, providing a new approach to study cell-specific EVs in vivo and gain new insight into their physiological and pathophysiological function.