Insights into the structural perturbations of spliced variants of CD44: a modeling and simulation approach

Atomic-Resolution Experimental Structural Biology and Molecular Dynamics Simulations of Hyaluronan and Its Complexes

This review summarizes the atomic-resolution structural biology of hyaluronan and its complexes available in the Protein Data Bank, as well as published studies of atomic-resolution explicit-solvent molecular dynamics simulations on these and other hyaluronan and hyaluronan-containing systems. Advances in accurate molecular mechanics force fields, simulation methods and software, and computer hardware have supported a recent flourish in such simulations, such that the simulation publications now outnumber the structural biology publications by an order of magnitude. In addition to supplementing the experimental structural biology with computed dynamic and thermodynamic information, the molecular dynamics studies provide a wealth of atomic-resolution information on hyaluronan-containing systems for which there is no atomic-resolution structural biology either available or possible. Examples of these summarized in this review include hyaluronan pairing with other hyaluronan molecules and glycosaminoglycans, with ions, with proteins and peptides, with lipids, and with drugs and drug-like molecules. Despite limitations imposed by present-day computing resources on system size and simulation timescale, atomic-resolution explicit-solvent molecular dynamics simulations have been able to contribute significant insight into hyaluronan's flexibility and capacity for intra- and intermolecular non-covalent interactions.

Structural Characterization of the CD44 Stem Region for Standard and Cancer-Associated Isoforms

CD44 is widely expressed in most vertebrate cells, whereas the expression of CD44v6 is restricted to only a few tissues and has been considered to be associated with tumor progression and metastasis. Thus, CD44v6 has been recognized as a promising prognostic biomarker and therapeutic target for various cancers for more than a decade. However, despite many experimental studies, the structural dynamics and differences between CD44s and CD44v6, particularly in their stem region, still remain elusive. Here, a computational study was conducted to address these problems. We found that the stem of CD44s adopted predominantly two conformations, one featuring antiparallel β-sheets and the other featuring parallel β-sheets, whereas the stem of CD44v6 adopted mainly one conformation with relatively highly suppressed β-sheet contents. Moreover, Phe215 was found to be essential in the β-sheets of both CD44s and CD44v6. We finally found intramolecular Phe215-Trp224 hydrogen-bonding interactions and hydrophobic interactions with Phe215 that cooperatively drove conformational differences upon the addition of the v6 region to CD44. Our study elucidated the structural differences between the stem regions of CD44s and CD44v6 and thus can offer useful structural information for drug design to specifically target CD44v6 in promising clinical applications.

hnRNPK promotes gastric tumorigenesis through regulating CD44E alternative splicing

Background

The high prevalence of alternative splicing among genes implies the importance of genomic complexity in regulating normal physiological processes and diseases such as gastric cancer (GC). The standard form of stem cell marker CD44 (CD44S) and its alternatives with additional exons are reported to play important roles in multiple types of tumors, but the regulation mechanism of CD44 alternative splicing is not fully understood.

Methods

Here the expression of hnRNPK was analyzed among the Cancer Genome Atlas (TCGA) cohort of GC. The function of hnRNPK in GC cells was analyzed and its downstream targeted gene was identified by chromatin immunoprecipitation and dual luciferase report assay. Finally, effect of hnRNPK and its downstream splicing regulator on CD44 alternative splicing was investigated.

Results

The expression of hnRNPK was significantly increased in GC and its upregulation was associated with tumor stage and metastasis. Loss-of-function studies found that hnRNPK could promote GC cell proliferation, migration, and invasion. The upregulation of hnRNPK activates the expression of the splicing regulator SRSF1 by binding to the first motif upstream the start codon (- 65 to - 77 site), thereby increasing splicing activity and expression of an oncogenic CD44 isoform, CD44E (has additional variant exons 8 to 10, CD44v8-v10).

Conclusion

These findings revealed the importance of the hnRNPK-SRSF1-CD44E axis in promoting gastric tumorigenesis.

Evaluation of KI-67, Apoptosis, and Hyaluronic Acid in Grading Retinoblastoma

Hyaluronic acid (HA) is a glycosaminoglycan with a straight-chain polymer arrangement defined as the extracellular matrix constituent. High molecular weight HA has normal physicochemical, biological, and physiological properties whereas low molecular weight has the property of angiogenesis, inflammation, and suppresses apoptosis. This study occupied the samples of 35 paraffin block from poorly and well differentiated retinoblastoma tissue and 8 normal retinal block which have been collected for 4 years from 2010-2013 at Dr. Soetomo Hospital, Surabaya, Indonesia. Afterwards, the paraffin blocks were immunohistochemically examined for HA staining, expression of cell proliferation (Ki-67), and cell apoptosis to determine intratumoral aggressiveness of retinoblastoma. HA on poorly differentiated retinoblastoma stain with a high immunostaining of 76.2%, while well differentiated retinoblastoma on the highest HA staining was revealed to be at moderate level of 64.3%, and not appear in normal retina. In poorly differentiated retinoblastoma, the location of most HA stain is in the cell cytoplasm (87.5%). In the well differentiated retinoblastoma, the HA immunostaning mainly occurred in the cell membrane (73.7%). Histopathological retinoblastoma grading showed a significant correlation (p <0.01) towards several variables of HA immunostaining, Ki-67, and cell apoptosis. In addition, the histopathological retinoblastoma grading also revealed a significant correlation (p <0.01) towards the location of HA staining (cell membrane and cytoplasm). Both stainings are also play role in retinoblastoma differentiation. The malignancy of retinoblastoma can be proven by the increased HA staining at cytoplasm in poorly differentiated and associated with increased of cell proliferation along with decreased apoptosis.

Circulating tumor stem like cells in oral squamous cell carcinoma: An unresolved paradox

OBJECTIVE

Circulating tumor cells (CTCs) are increasingly gaining importance due to their immense potential in enhancing diagnosis, prognosis and response to therapy in solid malignancies. Therefore, we aimed to comprehend the molecular diversity and critical role of this disseminated tumor population in OSCC.

METHODOLOGY

CD44+ subpopulation was isolated using immuno-magnetic cell separation and their purity was validated using flow cytometry. Characterisation of self renewal potential and resistance to chemotherapy was assessed using tumor sphere forming and cytotoxicity assay. Gene expression profile of pertinent CSC (CD44s, CD44v3, CD44v6) and stemness markers (Bmi1 and Nanog) was carried out in CD44+ cells using Real Time PCR. Predominantly expressed markers and their association with clinico-pathological conditions were substantiated in 30 OSCC patients.

RESULT

Flow cytometry analysis depicted a predominant population of CD44+CD24-CD45- cells suggesting that circulating tumor cells had a subpopulation of CSC like cells in the circulation. These cells demonstrated increased sphere forming capability and intrinsic chemo-resistance compared to non-CSC, thus indicating the CSC features of self-renewal and chemo-resistance. Additionally, CD44+ cells showed significantly increased expression levels of CD44v6 and Nanog compared to CD44- cells. Clinically, expression pattern of CD44v6 and Nanog correlated with different anatomical subsites, loco-regional aggressiveness of the disease and recurrence, thus opening newer avenues that can be explored for better prognostic and therapeutic implications.

CONCLUSION

This study explored the inevitable role of CD44v6 and Nanog as circulating stem like cell markers in assessment of loco-regional aggressiveness, detection of relapse and therapeutic response and resistance.