bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generalizable FGFR prediction across tumor types using self supervised learning.
Authors: Parmar Chaitanya , Ramon Albert Juan , Stone Nicole L. , Triantos Spyros , Greshock Joel , Standish Kristopher 
Published: June 2023

e15057 Background: Deep Learning models have demonstrated the ability to detect tumors, classify disease state, or infer genetic biomarkers from digital whole slide images (WSI) of Hematoxylin and Eosin (H&E)-stained tissue. Such models can be deployed to improve clinical practice or efficiently recruit for clinical trials. However, the data to train these models is often very limited and image capture protocols vary between labs. We propose to use Self Supervised Learning (SSL) on large unlabeled histopathology data sets to improve generalizability and predictive performance of deep learning models on unseen data. Methods: We pre-trained a Convolutional Neural Network (CNN) using SSL on 25,120 unlabeled, digital WSIs from various sources (multiple scanners, hospital systems, labs, diseases, tissue sites). We then fine-tuned the pre-trained CNN to infer the presence or absence of select FGFR alterations in Muscle Invasive Bladder Cancer (MIBC) from the digital WSI. We applied this model (FGFRSSL) to WSIs of biopsies from other data sources and tumor types and compared with a model (FGFRTRAD) that was trained exclusively on MIBC samples without self-supervised learning. Results: The FGFRSSL model achieved an Area Under ROC Curve (AUC = 0.80) on MIBC WSIs and maintained performance on images from an independent lab (AUC=0.82). We further show that the model generalizes to Non-Muscle Invasive Bladder Cancer (NMIBC) samples with (AUC = 0.76) and Pan-Tumor WSIs (AUC: 0.83). The FGFRTRAD model trained without SSL-based pre-training achieved an Area Under ROC Curve (AUC: 0.76) on MIBC WSIs was less generalizable, showing lower performance for independent data (AUC = 0.72), NMIBC samples (AUC = 0.72), and Pan-Tumor samples (AUC = 0.64). Conclusions: We leveraged SSL pretraining to improve the reliability and generalizability of AI-based models across multiple data sources. We also demonstrate our model’s ability to infer FGFR status across multiple solid tumor types after training on only MIBC samples, suggesting the cell morphology conferred by FGFR alteration in cancer may be shared across diverse tumor types. These models represent a means for efficiently screening patients for actionable clinical biomarkers in a robust manner to guide clinical decisions and inform drug development efforts. [Table: see text]
RNA sequencing as a confirmatory assay and its impact on patient care in multiple cancer types.
Authors: Kasi Pashtoon Murtaza , Smirnova Sofia , Nikulin Vladislav , Brown Jessica H. , Almog Nava , Ogloblina Anna , Yam Clinton , Peguero Julio Antonio , Pandya Devesh Mahesh , Kerr Daniel , Fowler Nathan 
Published: June 2023

e15058 Background: Increasing evidence shows the ability of RNA sequencing (RNA-seq) to detect expression of multiple biomarkers with improved sensitivity and scalability, offering a more objective and reproducible interpretation of data compared to pathological assessment methods by immunohistochemistry (IHC). Further, ongoing research demonstrating strong correlation between RNA-seq gene expression values and IHC values suggests the utility of RNA-seq as an objective diagnostic approach. Here, we highlight 4 cases where discordance in expression levels measured by IHC and RNA-seq resulted in re-evaluation of IHC values and a subsequent change in the clinical course. Methods: All patients underwent RNA and DNA sequencing of tumor tissue as part of a standard-of-care workflow. Sequencing was performed and reported with the BostonGene Tumor Portrait test, utilizing whole-exome sequencing (WES) and transcriptome sequencing data for tumor analysis. Gene expression levels were evaluated by comparison to a reference cohort of patients with a similar diagnosis. Results: In one case, a 53-year-old female was diagnosed with metastatic cholangiocarcinoma. While IHC of her biopsy reported positive HER2 (+3) expression, RNA-seq revealed low expression. A repeated IHC assay confirmed negative HER2 expression, leading to a change in therapy options. Another 61-year-old female was diagnosed with triple negative breast cancer (TNBC) (IHC: ER 0%, PR 0%, HER2 1+). Integrated WES and RNA-seq analysis detected HER2 amplification (+8 copies), ERBB2-activating mutation, high ERBB2 (HER2) expression and a HER2-enriched PAM50 subtype. IHC was repeated, now showing positive HER2 (+3) expression. In order to target HER2, systemic treatment was changed to a combination containing trastuzumab and pertuzumab, resulting in pathological complete response. In the third case of an 85-year-old female with relapsed TNBC, IHC demonstrated 1% PDL-1 staining. In contrast, RNA-seq detected high PD-L1 expression leading the treating physician to repeat IHC. Staining showed high PDL-1 (CPS50), prompting a change in therapy to an anti-PDL-1 (pembrolizumab) therapy. Lastly, while IHC of a 21-year-old female diagnosed with diffuse large B-cell lymphoma (DLBCL) showed negative CD30, subsequent RNA-seq detected relatively high CD30 expression that prompted a second IHC evaluation confirming positive CD30 expression. Eventually, the diagnosis was changed to primary mediastinal B-cell lymphoma and DA-EPOCH was selected as the therapy. Conclusions: RNA-seq is emerging as an objective tool to evaluate key diagnostic and targetable events in multiple cancer types. The use of RNA-seq can also add value as an objective measurement to confirm critical IHC findings, potentially changing clinical care.
The role of MIBG scan in the diagnosis of pheochromocytoma.
Authors: Ghomari Cherifa Fazila , Medjahedi Abdelkader 
Published: June 2023

e15064 Background: Pheochromocytoma is an uncommon adrenal medulla tumor. Metaiodobenzylguanidine (MIBG) scintigraphy is the current gold standard functional imaging method for evaluating pheochromocytoma, due to its excellent 100% specificity, 80% sensitivity, and general availability. In addition to establishing an extension evaluation and monitoring medication efficacy, MIBG scintigraphy is essential to confirm the diagnosis of suspected pheochromocytoma, especially when there is a tumor-like adrenal mass whose etiology is to be determined and biopsy is contraindicated given the risk of catecholamine discharge with hypertensive flare and the risk of bleeding. Our aims are to determine the efficacy of scintigraphy in the diagnosis of pheochromocytoma by examining the epidemiological characteristic and uptake patterns of the disease. Methods: In a retrospective analysis from January 2010 to December 2020, we examined pheochromocytoma patients medical records who had been referred for MIBG scintigraphy to the regional western Algerian Nuclear Medicine department at the University Hospital Center of Tlemcen. Prior to a progressive intravenous injection of 40–80 MBq of l-MIBG, patients underwent preparation (discontinuation of interfering drugs with I-MIBG especially antihypertensive treatment, thyroid blocking, and hydration). Imaging acquisition was carried out 48 and 72 hours later. Results: Fifty patients with probable pheochromocytoma (sex ratio = 0,78; mean age = 43 [17-74] years) completed I-MIBG scintigraphy prior to adrenalectomy. The MIBG scan has a high specificity and positive predictive value (100%). It confirms the presence of pheochromocytoma in 21 cases (42%), even if the metanephrine is normal in a patient with a non-secreting pheochromocytoma. In 18 cases, the main pattern is a single, homogenous, and intense intra-abdominal uptake. For the three remaining patients, a voluminous and heterogeneous uptake with a photopenic center that was associated to a necrotic adrenal mass larger than 10 cm in size, seen on abdominal Computerized Tomography (CT). In this retrospective analysis, no cases of metastatic or multiple diseases were documented. The sensitivity and negative predictive value are 84% and 86%, respectively. In 29 patients (58%), the scan reveals no abnormalities in uptake. This is attributed, in part, to 30% false positive biology (sampling conditions of urinary and/or plasmatic metanephrines and/or normetanephrines), 20% false positive CT imaging (differential diagnosis of adrenal mass: benign or malignant adrenal nodule), and 8% false negative MIBG scintigraphy (subcentimetric, cystic and necrotic lesion). Conclusions: Due to its exceptional specificity, robust sensitivity, and whole-body staging, MIBG scintigraphy—along with biology and morphology imaging—is a crucial noninvasive diagnostic method for the management of pheochromocytoma prior to adrenalectomy.
Interim analysis examining the feasibility of incorporating laser microdissection enrichment of tumor specimens and reverse phase protein array analysis with next generation sequencing into a molecular tumor board.
Authors: Cannon Timothy Lewis , Randall Jamie , Hunt Allison L. , Nutcharoen Aratara , Deeken John F. , Bateman Nicholas W. , Corgiat Brian , Davis Justin B , Petricoin Emanuel , Conrads Thomas P. 
Published: June 2023

e15068 Background: Since next generation sequencing (NGS) based profiling does not provide measures of protein abundance or activation state, clinical integration of reverse phase protein array (RPPA) with NGS could be useful for improving selection of targeted cancer therapy. We incorporated biopsy testing and proteogenomic analyses in an institutional Molecular Tumor Board (MTB) for cancer patients using CLIA-certified commercially available multi-omic platforms, including a commercially available CLIA RPPA functional protein drug target activation mapping platform. We present an interim analysis of our experience integrating functional phosphoprotein/protein based drug target activity data with NGS from 117 patients with metastatic solid tumors. Methods: Formalin-fixed, paraffin-embedded (FFPE) tumor biopsy specimens (n = 166) were obtained prospectively from patients as part of an IRB approved MTB. A representative H&E-stained tissue section for each specimen was reviewed by a board-certified surgical pathologist. Specimens with sufficient total tumor cellularity to achieve protein lysate input requirements for RPPA were thin sectioned onto laser microdissection (LMD) membrane slides for selective harvest of tumor epithelium by LMD and RPPA analysis. In parallel, specimens from each case were also submitted for NGS analysis. The multi-omic data for each patient was reviewed by a panel of clinicians and scientists as part of the Inova Institutional MTB for clinical decision-making. Results: Patient tissue specimens (median = 1 per patient; range 1-5) were reviewed to assess feasibility of enriching tumor areas via LMD prior to RPPA analysis. Specimens from 64/117 patients were used for LMD, RPPA, and NGS. 48/117 patients were dropped due to inadequate tumor cellularity, patient death, or referral cases with inadequate specimen. At this time, 7/117 patients remained in the consenting-LMD-RPPA workflow. The median time from patient consent to RPPA analysis completion was 47.4 days. During this period, specimens were outside of the standard hospital-NGS workflow (ie, utilized for sectioning and review for LMD-RPPA) for ~10 days (median). Integrated review of the RPPA and NGS data by the MTB supported a clinical recommendation change for 34/64 patients (53%) overall, with some dependency by primary disease site. Clinical trial information: U20-11-4308.Conclusions: Incorporation of RPPA analysis of LMD enriched tumor samples with NGS was feasible in this pan-cancer cohort, with the mean time to results being less than 7 weeks. RPPA data provided additional treatment considerations for 59% of patients, the outcomes for whom continue to be monitored. [Table: see text]
MOSAIC: Multi-Omic Spatial Atlas in Cancer, effect on precision oncology.
Authors: Lehar Joseph , Madissoon Elo , Chevallier Jerome , Schiratti Jean Baptiste , Kamburov Atanas , Barnes Rodrigo , Haignere Carla , Joy Anna , Dodacki Agnès , Hoffmann Caroline , Lopez Lastra Silvia , Espin Perez Almudena , Bayard Quentin , von Loga Katharina , Chaperon Hubert , Vert Jean-Philippe , Durand Eric , Soumelis Vassili , Wainrib Gilles , Clozel Thomas ,   MOSAIC Consortium
Published: June 2023

e15076 Background: Precision oncology aims to first break diagnoses into biologically distinct subtypes, then pursue personalized therapies for each group of patients ( Garraway et al, J Clin Onc, 2013). This strategy is enabled by recent advances in technologies for medical imaging, molecular profiling, and artificial intelligence. Spatially resolved molecular profiling (“spatial omics”) is an emerging technology that harnesses all three of these advances ( Navarro et al, Science, 2016; Rao et al, Nature, 2021). Cancer is driven by localized interactions between tumor cells, immune and non-immune stromal components. Methods: Spatial omics studies have revealed specific cell types and pathways that control those tumor-microenvironment crosstalks ( Hunter et al, Nat Comm, 2021; Alon et al, Science, 2021), involving both innate and adaptive immunity ( Binnewies et al, Nat Med, 2018). Identifying new cancer subtypes based on the spatially localized tumor-host interactions across many patients have the potential to revolutionize immuno-oncology. The advances in utilizing AI-based methods have so far been unattainable due to a small number of patients in spatial omics studies. Results: Here we present the MOSAIC project - a collaborative initiative across industry and top oncology hospitals to build the largest collection of spatial omics data in cancer. We combine comprehensive clinical annotation with new deep profiling methods to both discover cancer subtypes and identify drug targets and biomarkers within them. MOSAIC aims to generate multimodal data for a total of 7,000 patients in seven cancer indications. Data modalities will include spatial and single cell transcriptomics and proteomics, bulk molecular profiling, pathology images, and curated clinical information. This collaboration harnesses the strengths of academia and industry to provide patient samples, generate high-quality data, develop AI-based analytical tools, and compile a resource that will eventually be made widely available for medical research. Conclusions: Here we present the workflow of the MOSAIC study, demonstrate the data processing pipelines and show spatial distributions of transcripts within the tumor microenvironment. Building upon these initial datasets, we discuss how the MOSAIC parties will collaborate to build an unprecedented database for research and discovery of new immuno-oncology therapeutic approaches.
Association of encapsulation of CDK12 inhibitor with anti-tumour activity in colon cancer cell lines.
Authors: Pérez-Segura Pedro , Diaz-Tejeiro Cristina , Ocana Alberto , Sanvicente Adrián , Arenas-Moreira María , Moreno Carlos Alonso , Nieto Jiménez Cristina 
Published: June 2023

e15077 Background: Colorectal cancer (CRC) is the third most common cancer worldwide. Unfortunately, despite the incorporation of new therapeutic options, the metastatic setting is still an incurable disease. Cyclin-dependent kinases (CDKs) are a large family of proteins involved in cell cycle and transcriptional regulation, and are highly expressed in colon cancer, such as CDK12. Here, we explore the antitumor activity of a novel CDK12 inhibitor (CDK12-IN-E9) in preclinical models of colon cancer, and its liposomal formulation (LP-CDK12-IN-E9). Methods: Expression of CDK12 at a genomic level was assessed using web tools such as the Colonomics database. CDK12-IN-E9 was encapsulated in a liposomal formulation to evaluate differences between the free and the liposome form. The effect of compounds on cell viability was assessed with MTT assays. Matrigel assays were performed to study invasiveness and wound assays for migration. In addition, cell cycle and apoptosis studies were carried out by flow cytometry with 7-AAD, annexin V staining, and western-blot for specific protein expression. DNA damage and caspase degradation assays were performed by immunofluorescence. Results: Genomic mapping of CDK12 showed a higher expression in CRC than in normal tissue ( p−value = 1.424e−43). The CDK12 inhibitor was formulated in liposomes LP-CDK12-IN-E9 with the following characteristics: a polydispersity index of 0.11 ±0.02, a hydrodynamic radius of 62.98 ±10.29 nm and a zeta potential of -27.12±1.65 mV. CDK12-IN-E9 induced an antiproliferative effect in SW620, SW480 and HCT116 colon cancer cell lines. LP-CDK12-IN-E9 displayed an EC50 two times higher compared to CDK12-IN-E9 and a higher reduction of invasiveness between free inhibitor and its liposomal formulation mainly in HCT116 ( p-value < 0.001). Cell cycle studies showed no significant differences between CDK12-IN-E9 and LP-CDK12-IN-E9, but there was a profound induction of cell death at the highest doses through apoptosis mediated largely by caspases. In parallel to the effect on cell death, an increase in histone H2AX phosphorylation and an increase in cleaved caspase-3 was observed, which also implies a large increase in DNA damage in tumor cells. In vivo studies are ongoing. Conclusions: In summary, LP- CDK12-IN-E9 showed more antitumoral activity than its free formulation in CRC cell lines mainly through a caspase-dependent induction of apoptosis. This data suggests that liposomal formulation of novel chemical entities can augment its antitumoral properties.
Transformation of tissue-resident, very small embryonic-like stem cells (VSELs) into cancer stem cells (CSCs) and its role in cancer initiation via epigenetic changes.
Authors: Bhartiya Deepa , Singh Pushpa , Kaushik Ankita 
Published: June 2023

e15084 Background: CSCs are postulated to initiate cancer but still no consensus on their surface markers and origin. Pluripotent VSELs exist in adult tissues, express receptors for steroid and gonadotropin hormones and are possible ‘embryonic remnants’ that could initiate cancer. Methods: Neonatal exposure to diethylstilbestrol (DES) or estradiol (E2) resulted in tumor-like changes in uterus and testes of 100 days old mice. Various studies included histological changes, VSELs enumeration by flow cytometry, and a carefully selected panel of transcripts by qRT-PCR to delineate various cellular events. Mice neonatally exposed to endocrine disruption were administered XAR (a nano-formulation of resveratrol) or transplanted niche-providing mesenchymal stromal cells on D60 and studied later on D100 for reversal/prevention of cancer phenotype. Results: Both E2 and DES resulted in increased numbers of VSELs in testis (Ctrl:0.2%; E2:0.4%; DES:1.3%) and uterus (Ctrl:18.52%; E2:35.42%; DES:40.57%). An up-regulation of pluripotent transcripts ( Oct-4, Sox-2, Nanog) was detected. Oct4A (specific marker for pluripotent VSELs) was upregulated after both DES (testis > 8 folds; uterus > 15 folds) and E2 (testis > 3 folds and uterus > 10 folds) treatment. Excessive self-renewal of VSELs was associated with dysregulated expression of DNA methyltransferases (Dnmts). Dnmt1 was downregulated while Dnmt3a, Dnmt3b, and Dnmt3L were upregulated in the testis. In the uterus, Dnmts showed increased expression after both E2 and DES treatment. Marked reduction of 5mC suggested global hypomethylation and increased Igf2 and Dlk-1 suggested affected/loss of imprinting at IGF2/H19 and DLK-1/MEG3 loci. VSELs acquired CSCs phenotype with increased expression of CD166 and ALDH1. Genomic instability in CSCs was suggested by dysregulated mismatch repair axis (DNMT-1/NP95/PCNA) and repair enzymes ( Brca-1, Rad-51, Mlh-1). Reduced expression of Pten and p53 was associated with blocked differentiation. Both reversal strategies resulted in normalization of stem cells compartment, improved differentiation (spermatogenesis/adenogenesis), reduced CSC markers, and increased p53, Pten, Np95, Sirt-1 expression. Interestingly, XAR treatment resulted in downregulation of Igf2 and Dlk1. Stem cells niche was also improved as evident by increased expression of SOX9 in testis and CD90, VIMENTIN in endometrium. Conclusions: Only immortal VSELs can transmit developmental insults to adult cells. Altered epigenetic state of VSELs resulted in cancer initiation and it was possible to prevent/reverse cancer by normalizing epigenetic state of VSELs and their niche. Targeting CSCs and pushing them back into quiescent VSELs and facilitating their normal differentiation offers novel method to win the war against cancer.
Safety and feasibility of the addition of a radiosensitizing methionine-restricted diet to radiation therapy.
Authors: Mattes Malcolm David , Leung Calvin N. , Koturbash Igor , Wen Sijin , Jacobson Geraldine M. 
Published: June 2023

e15087 Background: Methionine is an amino acid necessary for cell growth and survival. Normal cells can tolerate methionine deficiency, but most cancer cells are methionine auxotrophs, requiring dietary intake since they cannot synthesize it. In vitro, methionine deficiency causes cancer cells to undergo cell cycle arrest and cell death, and in vivo a methionine restricted diet (MRD) enhances radiosensitization without significant adverse effects. Combining a MRD and radiation therapy (RT) for human malignancies has never been evaluated. The hypothesis of this Phase I study was that a MRD would be safe, and feasible to administer concurrently with curative-intent RT. Methods: Eligible patients included adults with any non-skin cancer malignancy undergoing standard RT without concurrent cytotoxic chemotherapy. The MRD consisted of low-protein cereals, grains, and breads; fruits; vegetables; margarines and oils; and simple carbohydrates. A clinical dietician developed a personalized meal plan with each subject to reduce methionine consumption to 5-10 mg/kg body weight/day, while maintaining adequate protein and caloric intake. An unlimited supply of a commercially available methionine-free protein supplement was provided to minimize hunger and weight loss. The MRD extended from 2 weeks before initiation of RT, through 2 weeks beyond completion of RT. The primary endpoint for safety was the rate of grade 3 or higher acute and late toxicities per CTCAE, over 12 months follow-up. Feasibility was assessed with a biweekly quantitative plasma amino acid panel during the MRD. The target accrual was 15 subjects. Results: Over two years, 53 patients were offered enrollment, 9 subjects enrolled, 5 completed the MRD and RT, and 4 withdrew during the MRD. The table summarizes subjects’ characteristics and outcomes. There was no grade 3 or higher adverse events attributable to the MRD. Methionine plasma levels varied over the course of treatment, and while no subject achieved the target of 13 μM, two nadired at 14 μM. The trial was closed early due to slow accrual and subjects’ difficulty maintaining the diet. Clinical trial information: NCT03574194 .Conclusions: This study suggests a MRD is safe with thoracic or abdominopelvic RT, with toxicities comparable to those expected with RT alone. However, the diet was challenging, and unacceptable to most patients with cancer. [Table: see text]