Integrated analysis of circulating cell free nucleic acids for cancer genotyping and immune phenotyping of tumor microenvironment

Chaddha, Muskan; Rai, Hemlata; Gupta, Ritu; Thakral, Deepshi

doi:10.3389/fgene.2023.1138625

Cited by 4 publications

(2 citation statements)

References 109 publications

(120 reference statements)

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“…Using a targeted approach, we analyzed free circulating mRNA transcripts in serum samples of healthy individuals or SMA patients. Those circulating mRNA transcripts are often secreted into the blood circulation by healthy and affected cells via mechanisms such as apoptosis, necrosis, and active secretion, showing disease-related variations and serving as prospective biomarkers for different clinical conditions or as potential therapeutic targets [13][14][15].…”

Section: Discussionmentioning

confidence: 99%

Analysis of Free Circulating Messenger Ribonucleic Acids in Serum Samples from Late-Onset Spinal Muscular Atrophy Patients Using nCounter NanoString Technology

Leo,

Schmitt,

Mairinger

et al. 2023

Cells

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5q-related Spinal muscular atrophy (SMA) is a hereditary multi-systemic disorder leading to progressive muscle atrophy and weakness caused by the degeneration of spinal motor neurons (MNs) in the ventral horn of the spinal cord. Three SMN-enhancing drugs for SMA treatment are available. However, even if these drugs are highly effective when administrated early, several patients do not benefit sufficiently or remain non-responders, e.g., adults suffering from late-onset SMA and starting their therapy at advanced disease stages characterized by long-standing irreversible loss of MNs. Therefore, it is important to identify additional molecular targets to expand therapeutic strategies for SMA treatment and establish prognostic biomarkers related to the treatment response. Using high-throughput nCounter NanoString technology, we analyzed serum samples of late-onset SMA type 2 and type 3 patients before and six months under nusinersen treatment. Four genes (AMIGO1, CA2, CCL5, TLR2) were significantly altered in their transcript counts in the serum of patients, where differential expression patterns were dependent on SMA subtype and treatment response, assessed with outcome scales. No changes in gene expression were observed six months after nusinersen treatment, compared to healthy controls. These alterations in the transcription of four genes in SMA patients qualified those genes as potential SMN-independent therapeutic targets to complement current SMN-enhancing therapies.

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Section: Discussionmentioning

confidence: 99%

Analysis of Free Circulating Messenger Ribonucleic Acids in Serum Samples from Late-Onset Spinal Muscular Atrophy Patients Using nCounter NanoString Technology

Leo,

Schmitt,

Mairinger

et al. 2023

Cells

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show abstract

“…TAM control aerobic glycolysis and secrete various chemokines that propel metastatic transformation, invasive potential of tumors, promote epithelial-to-mesenchymal (EMT) transition, and intensify stemness [33]. Furthermore, TME is dotted with cluster of differentiation (CD)8 + T-cells, CD4 + T-cells, and FOXP3 + regulatory cells that circulate the microenvironment in variable percentages and are also observed in the peripheral blood in several cancers [34]. An interplay between CD8 + T-cells and CD4 + T-cells influences the clinical outcome.…”

Section: Immune Component-response and Dynamicsmentioning

confidence: 99%

Cancer Bioenergetics and Tumor Microenvironments—Enhancing Chemotherapeutics and Targeting Resistant Niches through Nanosystems

Farhana

Alsrhani

Khan

et al. 2023

Cancers

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Cancer is an impending bottleneck in the advanced scientific workflow to achieve diagnostic, prognostic, and therapeutic success. Most cancers are refractory to conventional diagnostic and chemotherapeutics due to their limited targetability, specificity, solubility, and side effects. The inherent ability of each cancer to evolve through various genetic and epigenetic transformations and metabolic reprogramming underlies therapeutic limitations. Though tumor microenvironments (TMEs) are quite well understood in some cancers, each microenvironment differs from the other in internal perturbations and metabolic skew thereby impeding the development of appropriate diagnostics, drugs, vaccines, and therapies. Cancer associated bioenergetics modulations regulate TME, angiogenesis, immune evasion, generation of resistant niches and tumor progression, and a thorough understanding is crucial to the development of metabolic therapies. However, this remains a missing element in cancer theranostics, necessitating the development of modalities that can be adapted for targetability, diagnostics and therapeutics. In this challenging scenario, nanomaterials are modular platforms for understanding TME and achieving successful theranostics. Several nanoscale particles have been successfully researched in animal models, quite a few have reached clinical trials, and some have achieved clinical success. Nanoparticles exhibit an intrinsic capability to interact with diverse biomolecules and modulate their functions. Furthermore, nanoparticles can be functionalized with receptors, modulators, and drugs to facilitate specific targeting with reduced toxicity. This review discusses the current understanding of different theranostic nanosystems, their synthesis, functionalization, and targetability for therapeutic modulation of bioenergetics, and metabolic reprogramming of the cancer microenvironment. We highlight the potential of nanosystems for enhanced chemotherapeutic success emphasizing the questions that remain unanswered.

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Liquid biopsy analysis of lipometabolic exosomes in pancreatic cancer

Guo

Ying

et al. 2023

Cytokine & Growth Factor Reviews

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Integrated analysis of circulating cell free nucleic acids for cancer genotyping and immune phenotyping of tumor microenvironment

Cited by 4 publications

References 109 publications

Analysis of Free Circulating Messenger Ribonucleic Acids in Serum Samples from Late-Onset Spinal Muscular Atrophy Patients Using nCounter NanoString Technology

Analysis of Free Circulating Messenger Ribonucleic Acids in Serum Samples from Late-Onset Spinal Muscular Atrophy Patients Using nCounter NanoString Technology

Cancer Bioenergetics and Tumor Microenvironments—Enhancing Chemotherapeutics and Targeting Resistant Niches through Nanosystems

Liquid biopsy analysis of lipometabolic exosomes in pancreatic cancer

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