Gene expression profiling of CD34(+) cells from patients with myeloproliferative neoplasms

Myeloproliferative neoplasms (MPN) are clonal disorders characterized by the increased proliferation of hematopoietic stem cell precursors and mature blood cells. Mutations of Janus kinase 2 (JAK2), Calreticulin (CALR) and MPL (myeloproliferative leukemia virus) are key driver mutations in MPN. However, the molecular profile of triple negative MPN has been a subject of ambiguity over the past few years. Mutations of, methylcytosine dioxygenase TET2, polycomb group protein ASXL1 and histone-lysine N-methyltransferase EZH2 genes have accounted for certain subsets of triple negative MPNs but the driving cause for majority of cases is still unexplored. The present study performed a microarray-based transcriptomic profile analysis of bone marrow-derived CD34(+) cells from seven MPN samples. A total of 21,448 gene signatures were obtained, which were further filtered into 472 upregulated and 202 downregulated genes. Gene ontology and protein-protein interaction (PPI) network analysis highlighted an upregulation of genes involved in cell cycle and chromatin modification in JAK2V617F negative vs. positive MPN samples. Out of the upregulated genes, seven were associated with the hematopoietic stem cell signature, while forty-seven were associated with the embryonic stem cell signature. The majority of the genes identified were under the control of NANOG and E2F4 transcription factors. The PPI network indicated a strong interaction between chromatin modifiers and cell cycle genes, such as histone-lysine N-methyltransferase SUV39H1, SWI/SNF complex subunit SMARCC2, SMARCE2, chromatin remodeling complex subunit SS18, tubulin β (TUBB) and cyclin dependent kinase CDK1. Among the upregulated epigenetic markers, there was a ~10-fold increase in MYB expression in JAK2V617F negative samples. A significant increase in total CD34 counts in JAK2V617F negative vs. positive samples (P<0.05) was also observed. Overall, the present data showed a distinct pattern of expression in JAK2V617F negative vs. positive samples with upregulated genes involved in epigenetic modification.

RhoC regulates radioresistance via crosstalk of ROCK2 with the DNA repair machinery in cervical cancer

Background

Radioresistance remains a challenge to the successful treatment of various tumors. Intrinsic factors like alterations in signaling pathways regulate response to radiation. RhoC, which has been shown to modulate several tumor phenotypes has been investigated in this report for its role in radioresistance. In vitro and clinical sample-based studies have been performed to understand its contribution to radiation response in cervical cancer and this is the first report to establish the role of RhoC and its effector ROCK2 in cervical cancer radiation response.

Methods

Biochemical, transcriptomic and immunological approaches including flow cytometry and immunofluorescence were used to understand the role of RhoC and ROCK2. RhoC variants, siRNA and chemical inhibitors were used to alter the function of RhoC and ROCK2. Transcriptomic profiling was performed to understand the gene expression pattern of the cells. Live sorting using an intracellular antigen has been developed to isolate the cells for transcriptomic studies.

Results

Enhanced expression of RhoC conferred radioprotection on the tumor cells while inhibition of RhoC resulted in sensitization of cells to radiation. The RhoC overexpressing cells had a better DNA repair machinery as observed using transcriptomic analysis. Similarly, overexpression of ROCK2, protected tumor cells against radiation while its inhibition increased radiosensitivity in vitro. Further investigations revealed that ROCK2 inhibition abolished the radioresistance phenotype, conferred by RhoC on SiHa cells, confirming that it is a downstream effector of RhoC in this context. Additionally, transcriptional analysis of the live sorted ROCK2 high and ROCK2 low expressing SiHa cells revealed an upregulation of the DNA repair pathway proteins. Consequently, inhibition of ROCK2 resulted in reduced expression of pH2Ax and MRN complex proteins, critical to repair of double strand breaks. Clinical sample-based studies also demonstrated that ROCK2 inhibition sensitizes tumor cells to irradiation.

Conclusions

Our data primarily indicates that RhoC and ROCK2 signaling is important for the radioresistance phenotype in cervical cancer tumor cells and is regulated via association of ROCK2 with the proteins of DNA repair pathway involving pH2Ax, MRE11 and RAD50 proteins, partly offering insights into the mechanism of radioresistance in tumor cells. These findings highlight RhoC-ROCK2 signaling involvement in DNA repair and urge the need for development of these molecules as targets to alleviate the non-responsiveness of cervical cancer tumor cells to irradiation treatment.

Electronic supplementary material

The online version of this article (10.1186/s13046-019-1385-7) contains supplementary material, which is available to authorized users.

A Next-Generation Sequencing-Based Molecular Approach to Characterize a Tick Vector in Lyme Disease

Next-generation sequencing approaches have revolutionized genomic medicine and enabled rapid diagnosis for several diseases. These approaches are widely used for pathogen detection in several infectious diseases. Lyme disease is a tick-borne infectious disease, which affects multiple organs. The causative organism is a spirochete, Borrelia burgdorferi, which is transmitted by ticks. Lyme disease can be treated easily if detected early, but its diagnosis is often delayed or is incorrect leading to a chronic debilitating condition. Current confirmatory diagnostic tests for Lyme disease rely on detection of antigens derived from B. burgdorferi, which are prone to both false positives and false negatives. Instead of focusing only on the human host for the diagnosis of Lyme disease, one could also attempt to identify the vector (tick) and the causative organism carried by the tick. Since all ticks do not transmit Lyme disease, it can be informative to accurately identify the tick from the site of bite, which is often observed by the patient and discarded. However, identifying ticks based on morphology alone requires a trained operator and can still be incorrect. Thus, we decided to take a molecular approach by sequencing DNA and RNA from a tick collected from an individual bitten by the tick. Using next-generation sequencing, we confirmed the identity of the tick as a dog tick, Dermacentor variabilis, and did not identify any pathogenic bacterial sequences, including Borrelia species. Despite the limited availability of nucleotide sequences for many types of ticks, our approach correctly identified the tick species. This proof-of-principle study demonstrates the potential of next-generation sequencing in the diagnosis of tick-borne infections, which can also be extended to other zoonotic diseases.