bims-ectoca 2022-12-18 papers

bims-ectoca

Biomed News

on Epigenetic control of tolerance in cancer

Issue of 2022‒12‒18
six papers selected by
Ankita Daiya, Birla Institute of Technology and Science

A network medicine approach for identifying diagnostic and prognostic biomarkers and exploring drug repurposing in human cancer.
Single-Cell Transcriptome Analysis Reveals Paraspeckles Expression in Osteosarcoma Tissues.
Potential target identification for osteosarcoma treatment: Gene expression re-analysis and drug repurposing.
Computational Analysis Reveals the Temporal Acquisition of Pathway Alterations during the Evolution of Cancer.
Do Tumor Mechanical Stresses Promote Cancer Immune Escape?
Role of YAP as a Mechanosensing Molecule in Stem Cells and Stem Cell-Derived Hematopoietic Cells.

Comput Struct Biotechnol J. 2023 ;21 34-45

A network medicine approach for identifying diagnostic and prognostic biomarkers and exploring drug repurposing in human cancer.

Le Zhang, Shiwei Fan, Julio Vera, Xin Lai.

  Cancer is a heterogeneous disease mainly driven by abnormal gene perturbations in regulatory networks. Therefore, it is appealing to identify the common and specific perturbed genes from multiple cancer networks. We developed an integrative network medicine approach to identify novel biomarkers and investigate drug repurposing across cancer types. We used a network-based method to prioritize genes in cancer-specific networks reconstructed using human transcriptome and interactome data. The prioritized genes show extensive perturbation and strong regulatory interaction with other highly perturbed genes, suggesting their vital contribution to tumorigenesis and tumor progression, and are therefore regarded as cancer genes. The cancer genes detected show remarkable performances in discriminating tumors from normal tissues and predicting survival times of cancer patients. Finally, we developed a network proximity approach to systematically screen drugs and identified dozens of candidates with repurposable potential in several cancer types. Taken together, we demonstrated the power of the network medicine approach to identify novel biomarkers and repurposable drugs in multiple cancer types. We have also made the data and code freely accessible to ensure reproducibility and reusability of the developed computational workflow.

Keywords:  Drug repositioning; Gene prioritization; Machine learning; Network oncology; Pan-cancer diagnosis and prognosis; Systems medicine

DOI:  https://doi.org/10.1016/j.csbj.2022.11.037
Cancer Inform. 2022 ;21 11769351221140101

Single-Cell Transcriptome Analysis Reveals Paraspeckles Expression in Osteosarcoma Tissues.

Emel Rothzerg, Wenyu Feng, Dezhi Song, Hengyuan Li, Qingjun Wei, Archa Fox, David Wood, Jiake Xu, Yun Liu.

  Nuclear paraspeckles are subnuclear bodies contracted by nuclear-enriched abundant transcript 1 (NEAT1) long non-coding RNA, localised in the interchromatin space of mammalian cell nuclei. Paraspeckles have been critically involved in tumour progression, metastasis and chemoresistance. To this date, there are limited findings to suggest that paraspeckles, NEAT1 and heterogeneous nuclear ribonucleoproteins (hnRNPs) directly or indirectly play roles in osteosarcoma progression. Herein, we analysed NEAT1, paraspeckle proteins (SFPQ, PSPC1 and NONO) and hnRNP members (HNRNPK, HNRNPM, HNRNPR and HNRNPD) gene expression in 6 osteosarcoma tumour tissues using the single-cell RNA-sequencing method. The normalised data highlighted that the paraspeckles transcripts were highly abundant in osteoblastic OS cells, except NEAT1, which was highly expressed in myeloid cell 1 and 2 subpopulations.

Keywords:  NEAT1; Osteosarcoma; hnRNP; lncRNA; paraspeckles; single cell RNA sequencing; tumour microenvironment

DOI:  https://doi.org/10.1177/11769351221140101
Gene. 2022 Dec 10. pii: S0378-1119(22)00926-X. [Epub ahead of print] 147106

Potential target identification for osteosarcoma treatment: Gene expression re-analysis and drug repurposing.

Rawikant Kamolphiwong, Kanyanatt Kanokwiroon, Weerinrada Wongrin, Parunya Chaiyawat, Jeerawan Klangjorhor, Jongkolnee Settakorn, Pimpisa Teeyakasem, Apiwat Sangphukieo, Dumnoensun Pruksakorn.

  Survival rate of osteosarcoma has remained plateaued for the past three decades. New treatment is needed to improve survival rate. Drug repurposing, a method to identify new indications of previous drugs, which save time and cost compared to the de novo drug discovery. Data mining from gene expression profile was carried out and new potential targets were identified by using drug repurposing strategy. Selected data were newly categorized as pathophysiology and metastasis groups. Data were normalized and calculated the differential gene expression. Genes with log fold change ≥ 2 and adjusted p-value ≤ 0.05 were selected as primary candidate genes (PCGs). PCGs were further enriched to determine the secondary candidate genes (SCGs) by protein interaction analysis, upstream transcription factor and related-protein kinase identification. PCGs and SCGs were further matched with gene targeted of corresponding drugs from the Drug Repurposing Hub. A total of 778 targets were identified (360 from PCGs, and 418 from SCGs). This newly identified KLHL13 as a new candidate target based on its molecular function. KLHL13 was upregulated in clinical samples. We found 256 drugs from matching processes (50anti-cancerand206non-anticancerdrugs). Clinical trial of anti-cancer drugs from 5 targets (CDK4, BCL-2, JUN, SRC, PIK3CA) are being performed for osteosarcoma treatment. Niclosamide and synthetic PPARɣ ligands are candidates for repurposing due to the possibility based on their mechanism and pharmacology properties. Re-analysis of gene expression profile could identify new potential targets, confirm a current implication, and expand the chance of repurposing drugs for osteosarcoma treatment.

Keywords:  Drug repurposing; Gene expression; KLHL13; Metastasis; Osteosarcoma

DOI:  https://doi.org/10.1016/j.gene.2022.147106
Cancers (Basel). 2022 Nov 25. pii: 5817. [Epub ahead of print]14(23):

Computational Analysis Reveals the Temporal Acquisition of Pathway Alterations during the Evolution of Cancer.

Johanne Ahrenfeldt, Ditte S Christensen, Mateo Sokač, Judit Kisistók, Nicholas McGranahan, Nicolai J Birkbak.

  Cancer metastasis is the lethal developmental step in cancer, responsible for the majority of cancer deaths. To metastasise, cancer cells must acquire the ability to disseminate systemically and to escape an activated immune response. Here, we endeavoured to investigate if metastatic dissemination reflects acquisition of genomic traits that are selected for. We acquired mutation and copy number data from 8332 tumours representing 19 cancer types acquired from The Cancer Genome Atlas and the Hartwig Medical Foundation. A total of 827,344 non-synonymous mutations across 8332 tumour samples representing 19 cancer types were timed as early or late relative to copy number alterations, and potential driver events were annotated. We found that metastatic cancers had a significantly higher proportion of clonal mutations and a general enrichment of early mutations in p53 and RTK/KRAS pathways. However, while individual pathways demonstrated a clear time-separated preference for specific events, the relative timing did not vary between primary and metastatic cancers. These results indicate that the selective pressure that drives cancer development does not change dramatically between primary and metastatic cancer on a genomic level, and is mainly focused on alterations that increase proliferation.

Keywords:  bioinformatics; cancer biology; cancer evolution; cancer genomics; metastasis

DOI:  https://doi.org/10.3390/cancers14235817
Cells. 2022 Nov 30. pii: 3840. [Epub ahead of print]11(23):

Do Tumor Mechanical Stresses Promote Cancer Immune Escape?

Killian Onwudiwe, Julian Najera, Saeed Siri, Meenal Datta.

  Immune evasion-a well-established cancer hallmark-is a major barrier to immunotherapy efficacy. While the molecular mechanisms and biological consequences underpinning immune evasion are largely known, the role of tissue mechanical stresses in these processes warrants further investigation. The tumor microenvironment (TME) features physical abnormalities (notably, increased fluid and solid pressures applied both inside and outside the TME) that drive cancer mechanopathologies. Strikingly, in response to these mechanical stresses, cancer cells upregulate canonical immune evasion mechanisms, including epithelial-mesenchymal transition (EMT) and autophagy. Consideration and characterization of the origins and consequences of tumor mechanical stresses in the TME may yield novel strategies to combat immunotherapy resistance. In this Perspective, we posit that tumor mechanical stresses-namely fluid shear and solid stresses-induce immune evasion by upregulating EMT and autophagy. In addition to exploring the basis for our hypothesis, we also identify explicit gaps in the field that need to be addressed in order to directly demonstrate the existence and importance of this biophysical relationship. Finally, we propose that reducing or neutralizing fluid shear stress and solid stress-induced cancer immune escape may improve immunotherapy outcomes.

Keywords:  autophagy; epithelial–mesenchymal transition; fluid shear stress; immune evasion; immunotherapy; interstitial fluid pressure; solid stress; solid tumors

DOI:  https://doi.org/10.3390/cells11233840
Int J Mol Sci. 2022 Nov 23. pii: 14634. [Epub ahead of print]23(23):

Role of YAP as a Mechanosensing Molecule in Stem Cells and Stem Cell-Derived Hematopoietic Cells.

Nattaya Damkham, Surapol Issaragrisil, Chanchao Lorthongpanich.

  Yes-associated protein (YAP) and WW domain-containing transcription regulator protein 1 (WWTR1, also known as TAZ) are transcriptional coactivators in the Hippo signaling pathway. Both are well-known regulators of cell proliferation and organ size control, and they have significant roles in promoting cell proliferation and differentiation. The roles of YAP and TAZ in stem cell pluripotency and differentiation have been extensively studied. However, the upstream mediators of YAP and TAZ are not well understood. Recently, a novel role of YAP in mechanosensing and mechanotransduction has been reported. The present review updates information on the regulation of YAP by mechanical cues such as extracellular matrix stiffness, fluid shear stress, and actin cytoskeleton tension in stem cell behaviors and differentiation. The review explores mesenchymal stem cell fate decisions, pluripotent stem cells (PSCs), self-renewal, pluripotency, and differentiation to blood products. Understanding how cells sense their microenvironment or niche and mimic those microenvironments in vitro could improve the efficiency of producing stem cell products and the efficacy of the products.

Keywords:  YAP; differentiation; hematopoietic stem cells; mechanical forces; mechanosensing; stem cells

DOI:  https://doi.org/10.3390/ijms232314634