Tumor Profiling at the Service of Cancer Therapy

Fernández–Rozadilla, Ceres; Simões, Ana Rita; Lleonart, Matilde E.; Carnero, Amancio; Carracedo, Ángel

doi:10.3389/fonc.2020.595613

Cited by 11 publications

(6 citation statements)

References 174 publications

(177 reference statements)

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“…Precision oncology utilizes molecular profiles to determine potential therapeutic targets (8,9). Next generation sequencing (NGS) has allowed for the routine integration of molecular markers such as identification of oncogenic mutations.…”

Section: Introductionmentioning

confidence: 99%

Brain Tumor Biobank Development for Precision Medicine: Role of the Neurosurgeon

et al. 2021

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Neuro-oncology biobanks are critical for the implementation of a precision medicine program. In this perspective, we review our first year experience of a brain tumor biobank with integrated next generation sequencing. From our experience, we describe the critical role of the neurosurgeon in diagnosis, research, and precision medicine efforts. In the first year of implementation of the biobank, 117 patients (Female: 62; Male: 55) had 125 brain tumor surgeries. 75% of patients had tumors biobanked, and 16% were of minority race/ethnicity. Tumors biobanked were as follows: diffuse gliomas (45%), brain metastases (29%), meningioma (21%), and other (5%). Among biobanked patients, 100% also had next generation sequencing. Eleven patients qualified for targeted therapy based on identification of actionable gene mutations. One patient with a hereditary cancer predisposition syndrome was also identified. An iterative quality improvement process was implemented to streamline the workflow between the operating room, pathology, and the research laboratory. Dedicated tumor bank personnel in the department of neurosurgery greatly improved standard operating procedure. Intraoperative selection and processing of tumor tissue by the neurosurgeon was integral to increasing success with cell culture assays. Currently, our institutional protocol integrates standard histopathological diagnosis, next generation sequencing, and functional assays on surgical specimens to develop precision medicine protocols for our patients. This perspective reviews the critical role of neurosurgeons in brain tumor biobank implementation and success as well as future directions for enhancing precision medicine efforts.

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Section: Introductionmentioning

confidence: 99%

Brain Tumor Biobank Development for Precision Medicine: Role of the Neurosurgeon

et al. 2021

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“…Beyond clinical categorization, BC subtypes can be further differentiated based on the variability in tumor growth, proliferation, and metastasis [130]. Moreover, tumor profiling provides the information on cancer severity and suitable therapeutic options [131]. In the context of tumor heterogeneity, the tumor proteomic profiling of induvial patient is necessary to target the molecular pathways and oncological features of heterogenous cancer cells.…”

Section: Proteomics-based Precision and Personalized Therapeutic Regi...mentioning

confidence: 99%

Realm of proteomics in breast cancer management and drug repurposing to alleviate intricacies of treatment

Behera,

Bisht,

Giri

et al. 2023

Proteomics Clinical Apps

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Breast cancer, a multi‐networking heterogeneous disease, has emerged as a serious impediment to progress in clinical oncology. Although technological advancements and emerging cancer research studies have mitigated breast cancer lethality, a precision cancer‐oriented solution has not been achieved. Thus, this review will persuade the acquiescence of proteomics‐based diagnostic and therapeutic options in breast cancer management. Recently, the evidence of breast cancer health surveillance through imaging proteomics, single‐cell proteomics, interactomics, and post‐translational modification (PTM) tracking, to construct proteome maps and proteotyping for stage‐specific and sample‐specific cancer subtyping have outperformed conventional ways of dealing with breast cancer by increasing diagnostic efficiency, prognostic value, and predictive response. Additionally, the paradigm shift in applied proteomics for designing a chemotherapy regimen to identify novel drug targets with minor adverse effects has been elaborated. Finally, the potential of proteomics in alleviating the occurrence of chemoresistance and enhancing reprofiled drugs' effectiveness to combat therapeutic obstacles has been discussed. Owing to the enormous potential of proteomics techniques, the clinical recognition of proteomics in breast cancer management can be achievable and therapeutic intricacies can be surmountable.

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“…Such complexity results in a heterogeneous disease characterized by subgroups with different genetic prognostic profiles. The previous gene expression-based subtyping efforts identified five breast cancer subtypes (Luminal A, Luminal B, Basal, HER2-positive, and Normal) [48] that have been associated with distinct genetic drivers and patterns of variation at multiple levels, and, most importantly, present significant differences in aggressiveness and survival [49] that influence treatment choice [7].…”

Section: Sponge Modules Predict Breast Cancer Subtypesmentioning

confidence: 99%

“…In addition to the traditional study of genome variation and gene expression, microRNAs (miRNAs) have been assessed as potential biomarkers, given their important roles in regulating gene expression both in physiological conditions and in cancer [5,6] and their stability in biological fluids [7]. Mature miRNAs are short non-coding RNAs with lengths of ∼20-23 nucleotides that play an important role in regulating gene product abundance [8].…”

Section: Introductionmentioning

confidence: 99%

spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape

Boniolo

Hoffmann

Roggendorf

et al. 2022

Preprint

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Cancer is one of the leading causes of death worldwide. Despite significant improvements in prevention and treatment, mortality remains high for many cancer types. Hence, innovative methods that use molecular data to stratify patients and identify biomarkers are needed. Promising biomarkers can also be inferred from competing endogenous RNA (ceRNA) networks that capture the gene-miRNA-gene regulatory landscape. Thus far, the role of these biomarkers could only be studied globally but not in a sample-specific manner. To mitigate this, we introduce spongEffects, a novel method that infers subnetworks (or modules) from ceRNA networks and calculates patient- or sample-specific scores related to their regulatory activity. Notably, these module scores can be inferred from gene expression data alone and can thus be applied to cohorts where miRNA expression information is lacking. We show how spongEffects can be used for downstream machine learning tasks such as tumor classification and for identifying subtype-specific regulatory interactions. In a concrete example of breast cancer subtype classification, we prioritize modules impacting the biology of the different subtypes. In summary, spongEffects can perform classification tasks and prioritize ceRNA modules as biomarkers, hence offering insights into the miRNA regulatory landscape from gene expression data alone.

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Tumor Profiling at the Service of Cancer Therapy

Cited by 11 publications

References 174 publications

Brain Tumor Biobank Development for Precision Medicine: Role of the Neurosurgeon

Brain Tumor Biobank Development for Precision Medicine: Role of the Neurosurgeon

Realm of proteomics in breast cancer management and drug repurposing to alleviate intricacies of treatment

spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape

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