Lemon-shaped halo archaeal virus His1 with uniform tail but variable capsid structure

Lemon-shaped viruses are common in nature but so far have been observed to infect only archaea. Due to their unusual shape, the structures of these viruses are challenging to study and therefore poorly characterized. Here, we have studied haloarchaeal virus His1 using cryo-electron tomography as well as biochemical dissociation. The virions have different sizes, but prove to be extremely stable under various biochemical treatments. Subtomogram averaging of the computationally extracted virions resolved a tail-like structure with a central tail hub density and six tail spikes. Inside the tail there are two cavities and a plug density that separates the tail hub from the interior genome. His1 most likely uses the tail spikes to anchor to host cells and the tail hub to eject the genome, analogous to classic tailed bacteriophages. Upon biochemical treatment that releases the genome, the lemon-shaped virion transforms into an empty tube. Such a dramatic transformation demonstrates that the capsid proteins are capable of undergoing substantial quaternary structural changes, which may occur at different stages of the virus life cycle.There seems to be only a limited number of different virus particle architectures (virion-based structural lineages) due to the limited protein-fold space (1–3). Examples of the uncommon architectures are spindle-, bottle-, and droplet-shaped virions, so far found only in archaeal viruses (4). Archaea, organisms forming the third domain of cellular life, are known to thrive in both moderate and extreme environments (5–7). Interestingly, archaeal viruses are morphologically diverse, resembling eukaryotic viruses in this respect (4). Of these morphotypes, the spindle-shaped (also known as lemon-shaped) viruses are the most common ones in archaea-dominated habitats (8–15). It appears that this architecture is unique. However, deeper structural and biochemical analyses are needed to confirm this claim.Lemon-shaped virions are wider in the middle and narrow toward the ends. Three types of such viruses have been described based on the virion appearance: (i) those with one very short tail, (ii) those with one long tail, and (iii) those having two long tails (16–18). However, based on the comparison of the structural proteins, it was recently proposed that all known lemon-shaped viruses could be classified into two evolutionary lineages or viral families: Fuselloviridae, containing type i viruses, and Bicaudaviridae, containing type ii and iii viruses (19). Most of the isolated lemon-shaped viruses belong to the family Fuselloviridae, whose type species is the Sulfolobus spindle-shaped virus 1 (SSV1). Fuselloviruses infect hyperthermophilic crenarchaea and have one short tail with tail fibers (4, 20). The physical properties of the studied spindle-shaped viruses have recently been summarized (21). However, 3D structural understanding of lemon-shaped viruses remains limited.His1 is the only high-salinity lemon-shaped virus isolate, and it infects an extremely halophilic euryarchaeon, Haloarcula hispanica, and morphologically resembles fuselloviruses (22). However, unlike fuselloviruses, which have a circular double-stranded DNA (dsDNA) genome, His1 has a linear dsDNA genome encoding a putative type-B DNA polymerase; consequently, His1 has been classified in the floating genus Salterprovirus (20, 23). The 14,462-bp genome of His1 is predicted to have 35 ORFs, and 4 of these have been shown to encode structural proteins of the virion (21, 23). His1 virion contains one major capsid protein (MCP), VP21. In addition, a few minor ones have been detected: VP11, VP26, and VP27. Interestingly, VP21 exists in two forms. One form is lipid modified, although there is no detectable lipid bilayer in the His1 virion (21). The His1 MCP is 47% similar to the MCP of SSV1, indicating that His1 and fuselloviruses may share a common ancestor, and it has been proposed that His1 could be classified into the family Fuselloviridae (19, 21). In addition to the DNA polymerase, the His1 genome is predicted to encode an ATPase and a glycosyltransferase (21, 23). His1, like the other lemon-shaped viruses, is nonlytic, and many of them also encode an integrase (16, 17, 21, 24–26). Despite its typically hypersaline environment, His1 tolerates a variety of salinities, from 50 mM up to 4 M NaCl (21).Few attempts have been made to determine the structures of nonicosahedral viruses, mainly due to the fact that their pleomorphic nature introduces great challenges in particle structure classification and averaging. Recent advances in image-processing methods in cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET) have been demonstrated to be a useful tool in the structural studies of nonicosahedral viruses, such as Tula hantavirus (27) and the immature capsid in HIV-1 virus (28), and some archaeal viruses, such as pleomorphic, two-tailed spindle-shaped, and linear viruses (17, 21, 29) and bottle-shaped and filamentous archaeal viruses (30–32). Recent structural studies of the spindle-shaped virus SSV1 revealed its 3D structure with a spindle body and a short tail at one end (33).Here, we used cryo-ET and symmetry-free and model-free subtomogram averaging to reveal the previously unrecognized tail organization of the lemon-shaped virus His1, with a central tail hub and six surrounding tail spikes. Further analysis of a larger population of subtomograms showed variable dimensions of the lemon particles but a constant structure of the tail. Biochemical analysis of the virion under different chemical conditions revealed unexpected biochemical properties of the His1 virion, which may be relevant to the life cycle of this virus.     

CD14-expressing cancer cells establish the inflammatory and proliferative tumor microenvironment in bladder cancer

Nonresolving chronic inflammation at the neoplastic site is consistently associated with promoting tumor progression and poor patient outcomes. However, many aspects behind the mechanisms that establish this tumor-promoting inflammatory microenvironment remain undefined. Using bladder cancer (BC) as a model, we found that CD14-high cancer cells express higher levels of numerous inflammation mediators and form larger tumors compared with CD14-low cells. CD14 antigen is a glycosyl-phosphatidylinositol (GPI)-linked glycoprotein and has been shown to be critically important in the signaling pathways of Toll-like receptor (TLR). CD14 expression in this BC subpopulation of cancer cells is required for increased cytokine production and increased tumor growth. Furthermore, tumors formed by CD14-high cells are more highly vascularized with higher myeloid cell infiltration. Inflammatory factors produced by CD14-high BC cells recruit and polarize monocytes and macrophages to acquire immune-suppressive characteristics. In contrast, CD14-low BC cells have a higher baseline cell division rate than CD14-high cells. Importantly, CD14-high cells produce factors that further increase the proliferation of CD14-low cells. Collectively, we demonstrate that CD14-high BC cells may orchestrate tumor-promoting inflammation and drive tumor cell proliferation to promote tumor growth.Solid tumors represent a complex mass of tissue composed of multiple distinct cell types (1, 2). Cells within the tumor produce a range of soluble factors to create a complex of signaling networks within the tumor microenvironment (3–7). One of the outcomes of this crosstalk is tumor-promoting inflammation (TPI) (8, 9). TPI can modulate the functions of tumor-infiltrating myeloid lineage cells including macrophages (10–12). Tumor-associated macrophages (TAMs) consistently display an alternatively activated phenotype (M2) commonly found in sites of wound healing (13–18). These macrophages promote tumor growth while suppressing the host immune response locally (19–22). Polarization and subversion of tumor-infiltrating macrophages is accomplished via immune mediators in the tumor microenvironment (23, 24). Adding to the complexity of solid tumors is the heterogeneity of the cancer cells (2). Tumor cells of varying differentiation states and different characteristics coexist within a tumor (25–29). However, the different roles of each tumor cell subset during cancer progression remain undefined.Bladder cancer (BC) represents a growing number of solid tumors characterized by the infiltration of a significant number of myeloid cells in the neoplastic lesion (30, 31). We have previously determined that keratin 14 (KRT14) expression marks the most primitive differentiation state in BC cells (32). KRT14 expression is significantly associated with poor overall patient survival. However, the mechanisms used by KRT14-expressing cells to promote tumor growth remain unclear. In the current study, we found that KRT14+ basal BC cells also express higher levels of CD14. Here, we investigate the strategies used by KRT14+ CD14-high BC cells to promote tumor growth.     

Targeting CXCL12/CXCR4 signaling with oncolytic virotherapy disrupts tumor vasculature and inhibits breast cancer metastases

Oncolytic viruses hold promise for the treatment of cancer, but their interaction with the tumor microenvironment needs to be elucidated for optimal tumor cell killing. Because the CXCR4 receptor for the stromal cell-derived factor-1 (SDF-1/CXCL12) chemokine is one of the key stimuli involved in signaling interactions between tumor cells and their stromal microenvironment, we used oncolytic virotherapy with a CXCR4 antagonist to target the CXCL12/CXCR4 signaling axis in a triple-negative 4T1 breast carcinoma in syngeneic mice. We show here that CXCR4 antagonist expression from an oncolytic vaccinia virus delivered intravenously to mice with orthotopic tumors attains higher intratumoral concentration than its soluble counterpart and exhibits increased efficacy over that mediated by oncolysis alone. A systemic delivery of the armed virus after resection of the primary tumor was efficacious in inhibiting the development of spontaneous metastasis and increased overall tumor-free survival. Inhibition of tumor growth with the armed virus was associated with destruction of tumor vasculature, reductions in expression of CXCL12 and VEGF, and decrease in intratumoral numbers of bone marrow-derived endothelial and myeloid cells. These changes led to induction of antitumor antibody responses and resistance to tumor rechallenge. Engineering an oncolytic virus armed with a CXCR4 antagonist represents an innovative strategy that targets multiple elements within the tumor microenvironment. As such, this approach could have a significant therapeutic impact against primary and metastatic breast cancer.The chemokine receptor CXCR4 and its cognate ligand CXCL12 form a pivotal axis for enabling metastasis by many solid tumor types, including breast carcinomas (1). Overexpression of CXCR4 in primary breast tumors is related to an aggressive phenotype and lymph-node metastases (2–4). Similarly, elevated CXCR4 expression in estrogen (ER) and progestin receptor (PR)-negative breast cancers, as well as ER2⁻/PR2⁻/HER-2⁻ triple-negative breast cancers, is closely associated with lymph-node metastasis and poor prognosis (5, 6). Binding of CXCL12 to CXCR4 promotes tumor progression by several mechanisms associated with the activation of a number of signaling pathways required for biological responses, including chemotaxis (7). First, CXCR4 is essential for metastatic spread to organs where CXCL12 is expressed (8, 9). Second, CXCL12 can stimulate survival and growth of neoplastic cells in a paracrine fashion (10–12), and promotes tumor angiogenesis by recruiting circulating endothelial progenitor cells (CEPs) to the tumor stroma (10, 13). CXCL12 also attracts protumor Gr1⁺CD11b⁺ myeloid cells and regulatory T cells (CD4⁺ subtype) into the tumor (14, 15), which impede innate and adaptive immune mechanisms of tumor destruction.In contrast to normal breast tissue, breast cancer cells typically express high levels of CXCR4 that can direct chemotaxis and invasive responses (1, 4). Therefore, modulation of the CXCL12/CXCR4 signaling pathway in breast cancer could impact multiple aspects of tumor progression. Several CXCR4 antagonists have shown antitumor activity in preclinical models and have been evaluated in clinical trials (8, 16, 17). However, given the abundant expression of CXCR4 by many cell types, including those of the central nervous, gastrointestinal, and immune systems (18), the side-effects of these antagonists need to be considered. Moreover, the impact of soluble CXCR4 antagonists on the mobilization of CXCR4-expressing hematopoietic stem and progenitor cells represents an additional concern, particularly when combined with chemotherapeutic agents, because of the potential for increased toxicity to the normal process of hematopoiesis (8, 19).To overcome some of these concerns related to the systemic delivery of soluble CXCR4 antagonists, we designed a tumor cell-targeted therapy that delivered the CXCR4 antagonist via an oncolytic vaccinia virus (OVV). To that end, a new antagonist was cloned into the genome of OVV, whose selective replication in cancer cells is associated with cellular EGFR/Ras signaling, thymidine kinase (TK) elevation, and type-I IFN resistance (20, 21). We have chosen an OVV as the delivery vector because the virus has evolved mechanisms for intravenous stability and spread to distant tissues, including resistance to antibody- and complement-mediated neutralization in the blood (22, 23). In addition, the highly destructive nature of a poxvirus infection results in the release of several cellular and viral danger signals, leading to generation of potent inflammatory responses that ultimately overcome tumor-mediated immune suppression to clear the virus (24, 25). Furthermore, complete tumor responses in preclinical models with vaccinia viruses containing deletions of the B18R secreted inhibitor of type-I IFN (26) and TK genes were accompanied by immune-mediated protection against tumor rechallenge (27). Oncolytic poxvirus therapy may therefore be considered as a method to achieve vaccination in situ, with the adaptive immune response being able to clear minimal residual disease and provide long-term protection against tumor relapse.As a template for the virally delivered CXCR4 antagonist, we used the CTCE-9908 dimer corresponding to the N-terminal region of CXCL12 chemokine (KGVSLSYR-K-RYSLSVGK). This CXCR4 antagonist, the safety of which has been demonstrated in a phase I/II trial in cancer patients (17), is capable of blocking the CXCL12/CXCR4 interaction (28) and delaying the development of metastasis in breast cancer mouse models (29, 30). In the virally delivered construct, the first eight amino acids of CTCE-9908 were expressed in the context of murine (mFc) or human (hFc) fragment of IgG with disulfide bonds in a hinge region for preservation of its dimeric structure (Fig. S1 A–C). Using a highly metastatic 4T1 tumor model, which emulates stage IV breast cancer in humans (31), we demonstrated that the virally delivered CXCR4-A-mFc antagonist was predominantly retained in the tumor and inhibited the growth of both primary and metastatic lesions. A systemic delivery of the armed virus after resection of the primary tumor further reduced the development of spontaneous metastasis and resulted in increased tumor-free survival. The OVV-CXCR4-A-mFc antitumor efficacy was associated with destruction of intratumoral microvessels, lower accumulation of CEPs and neutrophils/granulocytic-myeloid derived suppressor cells (G-MDSCs), as well as enhancement of the vaccinia-mediated activation of antitumor antibody responses.     

Application of desorption electrospray ionization mass spectrometry imaging in breast cancer margin analysis

Distinguishing tumor from normal glandular breast tissue is an important step in breast-conserving surgery. Because this distinction can be challenging in the operative setting, up to 40% of patients require an additional operation when traditional approaches are used. Here, we present a proof-of-concept study to determine the feasibility of using desorption electrospray ionization mass spectrometry imaging (DESI-MSI) for identifying and differentiating tumor from normal breast tissue. We show that tumor margins can be identified using the spatial distributions and varying intensities of different lipids. Several fatty acids, including oleic acid, were more abundant in the cancerous tissue than in normal tissues. The cancer margins delineated by the molecular images from DESI-MSI were consistent with those margins obtained from histological staining. Our findings prove the feasibility of classifying cancerous and normal breast tissues using ambient ionization MSI. The results suggest that an MS-based method could be developed for the rapid intraoperative detection of residual cancer tissue during breast-conserving surgery.Breast cancer is the most commonly diagnosed carcinoma in women in the United States and Western countries. Breast conservation surgery (BCS) has become the preferred treatment option for many women with early-stage breast cancer (1). BCS entails resection of the tumor, with a clean margin of normal tissue around it. Surgery is usually followed by radiation therapy. Results from seven large randomized prospective studies, with the largest two having over 20 y of follow-up, have shown equal survival when comparing BCS coupled with whole-breast radiation and mastectomy (2, 3).Normally, breast surgeons aim to remove a patient’s tumor, along with a rim of normal tissue that is free of cancer. Preoperative mammography, ultrasonography, or MRI may be used by the surgeon to guide adequate resection (4–6). Despite numerous improvements in imaging and surgical technique, the need for reexcision to achieve complete tumor resection in the United States typically ranges from 20–40% (7–15), and has been reported as being as high as 60% (16). The importance of reexcision is underscored by numerous studies, which have shown that incomplete resection of tumor and positive margins are associated with increased locoregional recurrence compared with negative margins (12, 17–20). Furthermore, the landmark meta-analysis performed by the Early Breast Cancer Trialists’ Collaborative Group (18, 21) directly linked local recurrence to survival, placing great emphasis on the surgeon’s role in minimizing local recurrence by obtaining adequate margins.Breast tumor reexcisions are accompanied by a number of undesirable problems: The completion of therapy is delayed, infection rates are increased, cost is increased, there can be a negative psychological impact on the patient, and there can be diminished aesthetic outcomes (22–24). The development of an intraoperative technique that allows the fast and accurate identification of residual tumor at surgical resection margins could decrease the reexcision rate, and therefore improve the care delivered to patients with cancer who are receiving BCS.To this end, multiple intraoperative methods have been explored, with various benefits as well as limitations. These methods include touch frozen section analysis (25), touch preparation cytology (26), specimen radiography (27, 28), rf spectroscopy (29, 30), Raman spectroscopy (31), radioguided occult lesion localization (32), near-IR fluorescence (33, 34), and high-frequency ultrasound (35–37). The intraoperative application of MRI, which has been successfully applied in brain surgery (38–42), is limited in its application in BCS. These limitations include MRI interpretation in the presence of acute surgical changes; lack of real-time imaging, requiring the interruption of surgery; and accurate localization of tumor based on images requiring development of fiducials (43–46).Mass spectrometry imaging (MSI) has been applied to investigate the molecular distribution of proteins, lipids, and metabolites without the use of labels (47, 48). In particular, the newly developed ambient ionization technique of desorption electrospray ionization (DESI) allows direct tissue analysis with little to no sample preparation (49, 50). Therefore, with the advantage of easy use, DESI-MSI has great potential in the application of intraoperative tumor assessment. The development of DESI-MSI enables the correlation of lipid distribution in two or three dimensions with tissue morphology (47, 51) and the distinction of cancerous from noncancerous tissues based on lipidomic information (52–54). Distinctive lipid profiles associated with different human cancers have been investigated by DESI-MSI (55–58). Moreover, the grades and subtypes of human brain tumors have been discriminated using this technique. Additionally, tumor margins have been delineated using DESI-MSI, and the results have been correlated with histopathological examination (59, 60).It has been reported that breast cancer demonstrates metabolic profiles that are distinct from those metabolic profiles found in normal breast tissue. This finding suggests a potential for using metabolite information for breast cancer diagnosis and tumor margin identification (61, 62). Here, we demonstrate an MS-based methodology for using lipidomic information to distinguish cancerous from noncancerous tissue and to delineate tumor boundaries.     

A common solution to group 2 influenza virus neutralization

The discovery and characterization of broadly neutralizing antibodies (bnAbs) against influenza viruses have raised hopes for the development of monoclonal antibody (mAb)-based immunotherapy and the design of universal influenza vaccines. Only one human bnAb (CR8020) specifically recognizing group 2 influenza A viruses has been previously characterized that binds to a highly conserved epitope at the base of the hemagglutinin (HA) stem and has neutralizing activity against H3, H7, and H10 viruses. Here, we report a second group 2 bnAb, CR8043, which was derived from a different germ-line gene encoding a highly divergent amino acid sequence. CR8043 has in vitro neutralizing activity against H3 and H10 viruses and protects mice against challenge with a lethal dose of H3N2 and H7N7 viruses. The crystal structure and EM reconstructions of the CR8043-H3 HA complex revealed that CR8043 binds to a site similar to the CR8020 epitope but uses an alternative angle of approach and a distinct set of interactions. The identification of another antibody against the group 2 stem epitope suggests that this conserved site of vulnerability has great potential for design of therapeutics and vaccines.Influenza viruses are a significant and persistent threat to human health worldwide. Annual epidemics cause 3–5 million cases of severe illness and up to 0.5 million deaths (1), and periodic influenza pandemics have the potential to kill millions (2). Inhibitors against the viral surface glycoprotein neuraminidase are widely used for the treatment of influenza infections, but their efficacy is being compromised by the emergence of drug-resistant viral strains (3). Vaccination remains the most effective strategy to prevent influenza virus infection. However, protective efficacy is suboptimal in the highest risk groups: infants, the elderly, and the immunocompromised (1). Furthermore, because immunity after vaccination is typically strain-specific and influenza viruses evolve rapidly, vaccines must be updated almost annually. The antigenic composition of the vaccine is based on a prediction of strains likely to circulate in the coming year, therefore, mismatches between vaccine strains and circulating strains occur that can render the vaccine less effective (4). Consequently, there is an urgent need for new prophylactic and therapeutic interventions that provide broad protection against influenza.Immunity against influenza viruses is largely mediated by neutralizing antibodies that target the major surface glycoprotein hemagglutinin (HA) (5, 6). Identification of antigenic sites on HA indicates that influenza antibodies are primarily directed against the immunodominant HA head region (7), which mediates endosomal uptake of the virus into host cells by binding to sialic acid receptors (8). Because of high mutation rates in the HA head region and its tolerance for antigenic changes, antibodies that target the HA head are typically only effective against strains closely related to the strain(s) by which they were elicited, although several receptor binding site-targeting antibodies with greater breadth have been structurally characterized (9–15). In contrast, antibodies that bind to the membrane-proximal HA stem region tend to exhibit much broader neutralizing activity and can target strains within entire subtypes and groups (16–25) as well as across influenza types (24). These stem-directed antibodies inhibit major structural rearrangements in HA that are required for the fusion of viral and host endosomal membranes and thus, prevent the release of viral contents into the cell (8). The stem region is less permissive for mutations than the head and relatively well-conserved across divergent influenza subtypes.Anti-stem antibodies are elicited in some, but not all, individuals during influenza infection or vaccination (20, 26) and thus, hold great promise as potential broad spectrum prophylactic or therapeutic agents and for the development of a universal influenza vaccine (27–29). The majority of the known heterosubtypic stem binding antibodies neutralize influenza A virus subtypes belonging to group 1 (17–20, 23, 25). Furthermore, two antibodies that target a similar epitope in the HA stem, like most heterosubtypic group 1 antibodies, are able to more broadly recognize both group 1 and 2 influenza A viruses (22) or influenza A and B viruses (24). Strikingly, group 2-specific broadly neutralizing Abs (bnAbs) seem to be rare, because only one has been reported to date (21). CR8020 uniquely targets a distinct epitope in the stem in close proximity to the viral membrane at the HA base and binds lower down the stem than any other influenza HA antibody (21).In the discovery process that led to the isolation of bnAb CR8020, we recovered additional group 2-specific bnAbs. Here, we describe one such bnAb, CR8043, which recognizes a similar but nonidentical footprint on the HA as CR8020 and approaches the HA from a different angle. Furthermore, these two bnAbs are derived from different germ-line genes and, consequently, use distinct sets of interactions for HA recognition. Thus, the human immune system is able to recognize this highly conserved epitope in different ways using different germ-line genes. Hence, this valuable information can be used for the design of therapeutics and vaccines targeting this site of vulnerability in group 2 influenza A viruses that include the pandemic H3N2 subtype.     

Mitigation of acute kidney injury by cell-cycle inhibitors that suppress both CDK4/6 and OCT2 functions

Acute kidney injury (AKI) is a potentially fatal syndrome characterized by a rapid decline in kidney function caused by ischemic or toxic injury to renal tubular cells. The widely used chemotherapy drug cisplatin accumulates preferentially in the renal tubular cells and is a frequent cause of drug-induced AKI. During the development of AKI the quiescent tubular cells reenter the cell cycle. Strategies that block cell-cycle progression ameliorate kidney injury, possibly by averting cell division in the presence of extensive DNA damage. However, the early signaling events that lead to cell-cycle activation during AKI are not known. In the current study, using mouse models of cisplatin nephrotoxicity, we show that the G1/S-regulating cyclin-dependent kinase 4/6 (CDK4/6) pathway is activated in parallel with renal cell-cycle entry but before the development of AKI. Targeted inhibition of CDK4/6 pathway by small-molecule inhibitors palbociclib (PD-0332991) and ribociclib (LEE011) resulted in inhibition of cell-cycle progression, amelioration of kidney injury, and improved overall survival. Of additional significance, these compounds were found to be potent inhibitors of organic cation transporter 2 (OCT2), which contributes to the cellular accumulation of cisplatin and subsequent kidney injury. The unique cell-cycle and OCT2-targeting activities of palbociclib and LEE011, combined with their potential for clinical translation, support their further exploration as therapeutic candidates for prevention of AKI.Cell division is a fundamental biological process that is tightly regulated by evolutionarily conserved signaling pathways (1, 2). The initial decision to start cell division, the fidelity of subsequent DNA replication, and the final formation of daughter cells is monitored and regulated by these essential pathways (2–6). The cyclin-dependent kinases (CDKs) are the central players that orchestrate this orderly progression through the cell cycle (1, 2, 6, 7). The enzymatic activity of CDKs is regulated by complex mechanisms that include posttranslational modifications and expression of activating and inhibitory proteins (1, 2, 6, 7). The spatial and temporal changes in the activity of these CDK complexes are thought to generate the distinct substrate specificities that lead to sequential and unidirectional progression of the cell cycle (1, 8, 9).Cell-cycle deregulation is a universal feature of human cancer and a long-sought-after target for anticancer therapy (1, 10–13). Frequent genetic or epigenetic changes in mitogenic pathways, CDKs, cyclins, or CDK inhibitors are observed in various human cancers (1, 4, 11). In particular, the G1/S-regulating CDK4/6–cyclin D–inhibitors of CDK4 (INK4)–retinoblastoma (Rb) protein pathway frequently is disrupted in cancer cells (11, 14). These observations provided an impetus to develop CDK inhibitors as anticancer drugs. However, the earlier class of CDK inhibitors had limited specificity, inadequate clinical activity, poor pharmacokinetic properties, and unacceptable toxicity profiles (10, 11, 14, 15). These disappointing initial efforts now have been followed by the development of the specific CDK4/6 inhibitors palbociclib (PD0332991), ribociclib (LEE011), and abemaciclib (LY2835219), which have demonstrated manageable toxicities, improved pharmacokinetic properties, and impressive antitumor activity, especially in certain forms of breast cancer (14, 16). Successful early clinical trials with these three CDK4/6 inhibitors have generated cautious enthusiasm that these drugs may emerge as a new class of anticancer agents (14, 17). Palbociclib recently was approved by Food and Drug Administration for the treatment of metastatic breast cancer and became the first CDK4/6 inhibitor approved for anticancer therapy (18).In addition to its potential as an anticancer strategy, CDK4/6 inhibition in normal tissues could be exploited therapeutically for wide-ranging clinical conditions. For example, radiation-induced myelosuppression, caused by cell death of proliferating hematopoietic stem/progenitor cells, can be rescued by palbociclib (19, 20). Furthermore, cytotoxic anticancer agents cause significant toxicities to normal proliferating cells, which possibly could be mitigated by the concomitant use of CDK4/6 inhibitors (20, 21). More broadly, cell-cycle inhibition could have beneficial effects in disorders in which maladaptive proliferation of normal cells contributes to the disease pathology, as observed in vascular proliferative diseases, hyperproliferative skin diseases, and autoimmune disorders (22, 23). In support of this possibility, palbociclib treatment recently was reported to ameliorate disease progression in animal models of rheumatoid arthritis through cell-cycle inhibition of synovial fibroblasts (24).Abnormal cellular proliferation also is a hallmark of various kidney diseases (25), and cell-cycle inhibition has been shown to ameliorate significantly the pathogenesis of polycystic kidney disease (26), nephritis (27), and acute kidney injury (AKI) (28). Remarkably, during AKI, the normally quiescent renal tubular cells reenter the cell cycle (29–34), and blocking cell-cycle progression can reduce renal injury (28). Here, we provide evidence that the CDK4/6 pathway is activated early during AKI and demonstrate significant protective effects of CDK4/6 inhibitors in animal models of cisplatin-induced AKI. In addition, we found that the CDK4/6 inhibitors palbociclib and LEE011 are potent inhibitors of organic cation transporter 2 (OCT2), a cisplatin uptake transporter highly expressed in renal tubular cells (35–37). Our findings provide a rationale for the clinical development of palbociclib and LEE011 for the prevention and treatment of AKI.     

Trichomonas vaginalis homolog of macrophage migration inhibitory factor induces prostate cell growth,invasiveness, and inflammatory responses

The human-infective parasite Trichomonas vaginalis causes the most prevalent nonviral sexually transmitted infection worldwide. Infections in men may result in colonization of the prostate and are correlated with increased risk of aggressive prostate cancer. We have found that T. vaginalis secretes a protein, T. vaginalis macrophage migration inhibitory factor (TvMIF), that is 47% similar to human macrophage migration inhibitory factor (HuMIF), a proinflammatory cytokine. Because HuMIF is reported to be elevated in prostate cancer and inflammation plays an important role in the initiation and progression of cancers, we have explored a role for TvMIF in prostate cancer. Here, we show that TvMIF has tautomerase activity, inhibits macrophage migration, and is proinflammatory. We also demonstrate that TvMIF binds the human CD74 MIF receptor with high affinity, comparable to that of HuMIF, which triggers activation of ERK, Akt, and Bcl-2–associated death promoter phosphorylation at a physiologically relevant concentration (1 ng/mL, 80 pM). TvMIF increases the in vitro growth and invasion through Matrigel of benign and prostate cancer cells. Sera from patients infected with T. vaginalis are reactive to TvMIF, especially in males. The presence of anti-TvMIF antibodies indicates that TvMIF is released by the parasite and elicits host immune responses during infection. Together, these data indicate that chronic T. vaginalis infections may result in TvMIF-driven inflammation and cell proliferation, thus triggering pathways that contribute to the promotion and progression of prostate cancer.Prostate cancer is the most common noncutaneous cancer of men in the United States, affecting one in six men (1). Although the causes of prostate cancer are poorly understood, inflammation has been implicated in both initiation and progression of the disease (2, 3). The origin of inflammation in prostate cancer is unclear, although chronic infections are believed to promote and establish a tumor-enhancing proinflammatory environment.Trichomonas vaginalis is the causative agent of the most common nonviral sexually transmitted infection, infecting ∼275 million people worldwide (4). T. vaginalis is a flagellated, protozoan parasite that infects the prostate epithelium (5, 6). Over 75% of men harboring T. vaginalis are asymptomatic and may not seek treatment, resulting in chronic inflammation (5). Several studies have positively associated T. vaginalis infection with increased incidence and severity of prostate cancer, as well as benign prostate hyperplasia (2, 6–9). The magnitude of the association between T. vaginalis seropositivity and overall prostate cancer risk is between 1.23 and 1.43 based on two large, nested case–control studies (7, 8). Additionally there is a statistically significant increase in risk of extraprostatic cancer [odds ratio (OR) = 2.17] or cancer-specific death (OR = 2.69) with T. vaginalis seropositive status (7).Our research focuses on the potential contribution of a proinflammatory protein, T. vaginalis macrophage migration inhibitory factor (TvMIF), to prostate cancer, because the human homolog has a role in the growth and invasion of prostate cancer (10, 11). Human macrophage migration inhibitory factor (HuMIF) has been implicated in a broad array of conditions associated with inflammation, including autoimmunity, cell proliferation, angiogenesis, and tumorigenesis (12–15). Increased expression of HuMIF has been reported in several cancers, including prostate cancer (16–18). Studies show high expressers of HuMIF have a heightened risk of prostate cancer, as well as a significant increase in prostate cancer progression and drug resistance (17–23). Several clinical studies have shown HuMIF production correlates with both tumor aggressiveness and metastatic potential (23, 24). Additionally, the expression of the HuMIF receptor CD74 is increased in prostate cancer (10, 25).HuMIF induces ERK1/2, MAPK, and Akt activation via binding with the extracellular domain of the MIF receptor CD74 (26). HuMIF has multiple functions with regard to regulating the immune system, including protecting monocytes and macrophages from activation-induced apoptosis, which results in sustained inflammation (27, 28). Consequently, HuMIF is implicated in the pathogenesis of several inflammatory and autoimmune diseases in addition to cancer (29, 30).Recent studies have shown that several parasitic eukaryotes encode MIF-like proteins with considerable structural and biological similarity to their mammalian hosts (31–34). These parasite MIF proteins have been shown to modulate host immune responses and regulate pathways to promote parasite survival. Here, we characterize TvMIF and show that it can act as a molecular mimic of HuMIF. We find that TvMIF binding to the human CD74 receptor activates extracellular signal-regulated kinases (ERK)1/2 and Akt protein kinase/proapoptotic Bcl-2–associated death promoter (BAD) pathways as well as secretion of proinflammatory IL-8 from monocytes, reduces monocyte migration, and increases growth and invasiveness of benign prostate hyperplasia (BPH-1) and prostate cancer (PC3) cells. This research is, to our knowledge, the first to identify a human inflammatory cytokine mimic in T. vaginalis and to begin to explore the link between this sexually transmitted infection and prostate cancer.     

The NMR–Rosetta capsid model of M13 bacteriophage reveals a quadrupled hydrophobic packing epitope

Filamentous phage are elongated semiflexible ssDNA viruses that infect bacteria. The M13 phage, belonging to the family inoviridae, has a length of ∼1 μm and a diameter of ∼7 nm. Here we present a structural model for the capsid of intact M13 bacteriophage using Rosetta model building guided by structure restraints obtained from magic-angle spinning solid-state NMR experimental data. The C5 subunit symmetry observed in fiber diffraction studies was enforced during model building. The structure consists of stacked pentamers with largely alpha helical subunits containing an N-terminal type II β-turn; there is a rise of 16.6–16.7 Å and a tilt of 36.1–36.6° between consecutive pentamers. The packing of the subunits is stabilized by a repeating hydrophobic stacking pocket; each subunit participates in four pockets by contributing different hydrophobic residues, which are spread along the subunit sequence. Our study provides, to our knowledge, the first magic-angle spinning NMR structure of an intact filamentous virus capsid and further demonstrates the strength of this technique as a method of choice to study noncrystalline, high-molecular-weight molecular assemblies.Filamentous bacteriophage are long, thin, and semiflexible rod viruses that infect bacteria (1, 2). These large assemblies (∼15–35 MDa) contain a circular single-stranded (ss) DNA genome encapsulated in a protein shell. All filamentous phage have a similar life cycle and virion structure despite the relatively high number of strains, with DNA sequence homology varying from almost complete to very little. The unique phage properties make them ideal for a large range of applications such as phage display (3), DNA cloning and sequencing (4, 5), nanomaterial fabrication (6–8), and as drug-carrying nanomachines (9). In addition, filamentous viruses form a variety of liquid crystals driving the development of both theory and practice of soft-matter physics (10, 11). Filamentous viruses are also associated with various diseases, e.g., CTXϕ phage in cholera toxin (12) and Pf4 phage in cystic fibrosis (13).Phage belonging to the Ff family (M13, fd, f1) are F-pilus–specific viruses that share almost identical genomes and very similar structures. M13 is a 16-MDa virus having a diameter of ∼7 nm and a length of ∼1 μm. The capsid is composed of several thousand identical copies of a major coat protein subunit arranged in a helical array surrounding a core of a circular ssDNA. The major coat proteins constitute ∼85% of the total virion mass, the ssDNA ∼12%, and all other minor proteins (gp3, gp6, gp7, gp9) that are specific for infection and assembly constitute about 3% of the total virion mass (1, 14).Previous structural models for a small number of phages have been obtained by means of X-ray fiber diffraction (15–19), static solid-state NMR (20, 21), and cryo-EM (22). Structural models for the Ff family have been proposed based on the three methods; however, satisfactory resolution was only obtained for the Y21M mutant of the fd phage (17, 18, 21) (wt fd is related to M13 by one additional mutation, N12D). The only reported model for M13 (23) (no coordinates available) and models of fd-Y21M from different methods differ in detail (24) and lack accuracy in some structural details such as the N-terminus orientation, the nature of DNA–protein interactions, and sidechain interactions, which are the dominant packing elements of the capsid. The most recent model was built using a combination of static NMR and fiber diffraction (17).According to fiber diffraction, the symmetry of the Ff capsid is C₅S₂, also referred to as class I symmetry. That is, a fivefold rotation of the major coat protein subunit around the virion axis (pentamers) and an approximate 36° rotation relating two successive pentamers [in fd-Y21M a precise 36° rotation was reported; for fd, values of −33.23° (18) and −34.62° (22) were reported]. All studies report that the coat protein is mostly right-handed, curved, α-helical, with a flexible or disordered N terminus.Magic-angle spinning (MAS) solid-state NMR has become a popular tool for studying the structure and dynamics of biological molecules (25–27). The method can be implemented on a variety of systems from small peptides to macromolecular biological assemblies. Integrated approaches can be used to resolve structures of large assemblies (28, 29) and recently, the combination of MAS NMR data, cryo-EM, and Rosetta modeling resulted in a detailed atomic structure of the recombinant type III secretion system needle (30, 31). We have previously performed MAS NMR studies on both wt fd and M13 in a precipitated form (32–34). Their chemical shifts pointed to a single homogeneous capsid subunit that is mostly helical and curved with a mobile N terminus. NMR studies of the interactions between the capsid and the DNA reported on the subunit orientation with respect to the viral axis, and indicated that the C terminus undergoes electrostatic interactions with the DNA.In this study, we use homonuclear 2D ¹³C–¹³C correlation experiments on sparsely labeled M13 samples together with our prior backbone and sidechain resonance assignments of the M13 phage to acquire MAS NMR structure restraints. Using the CS-Rosetta fold-and-dock protocol (35) we derive an atomic detailed well-converged quaternary structural model of the intact M13 phage viral capsid. The specific bacteriophage symmetry produces four identical, repeating hydrophobic pockets for each subunit, resulting in tight subunit packing that stabilizes the phage assembly.     

Evolution of the H9N2 influenza genotype that facilitated the genesis of the novel H7N9 virus

The emergence of human infection with a novel H7N9 influenza virus in China raises a pandemic concern. Chicken H9N2 viruses provided all six of the novel reassortant’s internal genes. However, it is not fully understood how the prevalence and evolution of these H9N2 chicken viruses facilitated the genesis of the novel H7N9 viruses. Here we show that over more than 10 y of cocirculation of multiple H9N2 genotypes, a genotype (G57) emerged that had changed antigenicity and improved adaptability in chickens. It became predominant in vaccinated farm chickens in China, caused widespread outbreaks in 2010–2013 before the H7N9 viruses emerged in humans, and finally provided all of their internal genes to the novel H7N9 viruses. The prevalence and variation of H9N2 influenza virus in farmed poultry could provide an important early warning of the emergence of novel reassortants with pandemic potential.Human infection with a novel avian-origin H7N9 influenza A virus causing severe respiratory symptoms and mortality was first reported in eastern China in March 2013 (1). To date, the novel virus has caused two outbreaks of human infection, including 375 known cases and 115 deaths as of 11 March 2014 (2). Phylogenetic analysis suggests that the virus is a triple reassortant of H7, N9, and H9N2 avian influenza viruses (3, 4). The H7 and N9 genes may have been transferred from migratory birds to domestic ducks and then to chickens in the live poultry markets (3–5), after which reassortment with enzootic H9N2 viruses formed the H7N9 viruses identified in humans (3–5).H9N2 influenza virus has low pathogenicity for avians, replicating mainly in the upper respiratory tract and causing mild or no overt signs of illness in specific pathogen-free (SPF) chickens (6). In 1994, the H9N2 subtype was first identified in chicken farms in the Guangdong province of south China (7); it has since become widespread in chickens and has caused great economic loss from reduced egg production and highly lethal coinfections (8–11). To reduce the impact of H9N2 infection in chickens, the flocks have been vaccinated since 1998 with commercial inactivated vaccines, such as A/chicken/Guangdong/SS/1994 (Ck/GD/SS/94), A/chicken/Shandong/6/1996 (Ck/SD/6/96), and A/chicken/Shanghai/F/1998 (Ck/SH/F/98) (8, 12, 13). These H9N2 vaccines initially limited the outbreaks and virus spread. However, despite multiple doses, the H9N2 vaccines became less effective, especially after 2007, and H9N2 influenza virus continues to circulate in vaccinated chicken flocks and has caused sporadic disease outbreaks (8, 10, 12–20). However, the recent prevalence and molecular evolution of the H9N2 viruses in chickens especially in the flocks receiving large-scale vaccination, and their role in the emergence of human H7N9 virus, are not fully understood. In this study, we systematically investigated the prevalence and evolution of H9N2 viruses mainly focusing on farm chickens and their role in the genesis of the novel H7N9 viruses.     

Targeting RPL39 and MLF2 reduces tumor initiation and metastasis in breast cancer by inhibiting nitric oxide synthase signaling

We previously described a gene signature for breast cancer stem cells (BCSCs) derived from patient biopsies. Selective shRNA knockdown identified ribosomal protein L39 (RPL39) and myeloid leukemia factor 2 (MLF2) as the top candidates that affect BCSC self-renewal. Knockdown of RPL39 and MLF2 by specific siRNA nanoparticles in patient-derived and human cancer xenografts reduced tumor volume and lung metastases with a concomitant decrease in BCSCs. RNA deep sequencing identified damaging mutations in both genes. These mutations were confirmed in patient lung metastases (n = 53) and were statistically associated with shorter median time to pulmonary metastasis. Both genes affect the nitric oxide synthase pathway and are altered by hypoxia. These findings support that extensive tumor heterogeneity exists within primary cancers; distinct subpopulations associated with stem-like properties have increased metastatic potential.Large-scale sequencing analyses of solid cancers have identified extensive tumor heterogeneity within individual primary cancers (1). Recent studies indicate that such tumoral heterogeneity is associated with heterogeneous protein function, which fosters tumor adaptation, treatment resistance, and failure through Darwinian selection (2–4). Cancer stem cells are a subpopulation of cells within the primary tumor responsible for tumor initiation and metastases (5–9). Three groups have recently independently provided functional evidence for the presence of cancer stem cells by lineage-tracing experiments (10–12). These observations suggest that these subpopulations of cancer stem cells (CSCs) within the bulk primary tumor are resistant to conventional therapies through different adaptive mechanisms with the potential for self-renewal and metastases (7, 13, 14). However, few studies have determined the genetic profile of the cells that escape the primary cancer and evolve in distant metastatic sites (1). Additionally, no large-scale sequencing studies of metastases have been conducted because the majority of patients are treated with systemic therapies and not surgery.Tumor clonal heterogeneity within a primary tumor may in part be explained by hypoxic regions within the bulk tumor that have been correlated with invasiveness, therapeutic resistance, and metastasis (15–18). Cancer stem cells have been found to reside near hypoxic regions in some solid cancers (19–21). We have previously published a 477-gene tumorigenic signature by isolating breast cancer stem cells (BCSCs) derived from patient biopsies (22). Here, we have identified two previously unidentified cancer genes, ribosomal protein L39 (RPL39) and myeloid leukemia factor 2 (MLF2), by selective shRNA knockdown of genes from this tumorigenic signature, that impact breast cancer stem cell self-renewal and lung metastases. Analysis of 53 patient lung metastases confirmed damaging mutations in RPL39 and MLF2 in a significant number of samples, which conferred a gain-of-function phenotype. These mutations were statistically associated with shorter median time to distant relapse. We further describe a common mechanism of action through nitric oxide synthase signaling that is regulated by hypoxia.     

Dynamic ubiquitination drives herpesvirus neuroinvasion

Neuroinvasive herpesviruses display a remarkable propensity to enter the nervous system of healthy individuals in the absence of obvious trauma at the site of inoculation. We document a repurposing of cellular ubiquitin during infection to switch the virus between two invasive states. The states act sequentially to defeat consecutive host barriers of the peripheral nervous system and together promote the potent neuroinvasive phenotype. The first state directs virus access to nerve endings in peripheral tissue, whereas the second delivers virus particles within nerve fibers to the neural ganglia. Mutant viruses locked in either state remain competent to overcome the corresponding barrier but fail to invade the nervous system. The herpesvirus “ubiquitin switch” may explain the unusual ability of these viruses to routinely enter the nervous system and, as a consequence, their prevalence in human and veterinary hosts.Herpesviruses such as herpes simplex virus type 1 (HSV-1) and pseudorabies virus (PRV) routinely enter the peripheral nervous system following casual contact between infected and uninfected individuals. Recent findings have provided insights into this complex phenotype, but the molecular mechanisms directing nervous system invasion are poorly understood (1–5). A critical effector of this process is a conserved herpesvirus deubiquitinase (DUB) (a cysteine protease that removes ubiquitin from target posttranslationally modified proteins) (6–8). The DUB is housed in the amino terminus of the pUL36 protein (protein encoded by the 36th open reading frame in the unique-long segment of the viral genome), amounting to less than 10% of the total mass of this large (>250 kDa) structural component of the virion (9). pUL36 is attached directly to the icosahedral capsid shell of these enveloped viruses (10–12) and, due to its location between the capsid and envelope, is referred to as a herpesvirus tegument protein. Upon virus entry into a cell, pUL36 becomes exposed to the cytosol (4, 13, 14) and directs delivery of the capsid and its DNA content to the nucleus (2, 15–19). Following replication, pUL36 is also essential for viral assembly and egress (20–22).The presence of the pUL36 DUB on the exposed surface of the intracellular viral particle suggests that removal of ubiquitin from cellular cytosolic proteins, or from the virus particle itself, is instrumental for these viruses to transmit between peripheral tissues and the neurons that innervate them (8). This necessarily implicates the prior addition of ubiquitin as a factor in disease progression, either as part of the virus neuroinvasive program or as a cellular defense mechanism that is overcome by the DUB. Although several substrates of the DUB have been identified, how this enzyme promotes the potent neuroinvasive property of these viruses is unknown (23–30). To elucidate the role of the DUB, we set out to examine the role of ubiquitination during neuroinvasive herpesvirus infection. We report that ubiquitin addition and removal from a conserved lysine residue in pUL36 switches PRV between two invasive states that act successively to promote virus dissemination into the peripheral nervous system. Supporting evidence that the “ubiquitin switch” is conserved in HSV-1, and possibly all neuroinvasive alphaherpesviruses, is provided.     

Cellular heterogeneity profiling by hyaluronan probes reveals an invasive but slow-growing breast tumor subset

Tumor heterogeneity confounds cancer diagnosis and the outcome of therapy, necessitating analysis of tumor cell subsets within the tumor mass. Elevated expression of hyaluronan (HA) and HA receptors, receptor for HA-mediated motility (RHAMM)/HA-mediated motility receptor and cluster designation 44 (CD44), in breast tumors correlates with poor outcome. We hypothesized that a probe for detecting HA–HA receptor interactions may reveal breast cancer (BCa) cell heterogeneity relevant to tumor progression. A fluorescent HA (F-HA) probe containing a mixture of polymer sizes typical of tumor microenvironments (10–480 kDa), multiplexed profiling, and flow cytometry were used to monitor HA binding to BCa cell lines of different molecular subtypes. Formulae were developed to quantify binding heterogeneity and to measure invasion in vivo. Two subsets exhibiting differential binding (HA^−/low vs. HA^high) were isolated and characterized for morphology, growth, and invasion in culture and as xenografts in vivo. F-HA–binding amounts and degree of heterogeneity varied with BCa subtype, were highest in the malignant basal-like cell lines, and decreased upon reversion to a nonmalignant phenotype. Binding amounts correlated with CD44 and RHAMM displayed but binding heterogeneity appeared to arise from a differential ability of HA receptor-positive subpopulations to interact with F-HA. HA^high subpopulations exhibited significantly higher local invasion and lung micrometastases but, unexpectedly, lower proliferation than either unsorted parental cells or the HA^−/low subpopulation. Querying F-HA binding to aggressive tumor cells reveals a previously undetected form of heterogeneity that predicts invasive/metastatic behavior and that may aid both early identification of cancer patients susceptible to metastasis, and detection/therapy of invasive BCa subpopulations.Breast tumors display substantial heterogeneity driven by genetic and epigenetic mechanisms (1–3). These processes select and support tumor cell subpopulations with distinct phenotypes in proliferation, metastatic/invasive proclivity, and treatment susceptibility that contribute to clinical outcomes. Currently, there is a paucity of biomarkers to identify these subpopulations (3–12). Although detection of genetic heterogeneity may itself be a breast cancer (BCa) prognostic marker (3, 13–15), the phenotypes manifested from this diversity are context-dependent. Therefore, phenotypic markers provide additional powerful tools for biological information required to design diagnostics and therapeutics. Glycomic approaches have enormous potential for revealing tumor cell phenotypic heterogeneity because glycans are themselves highly heterogeneous and their complexity reflects the nutritional, microenvironmental, and genetic dynamics of the tumors (16–18).We used hyaluronan (HA) as a model carbohydrate ligand for probing heterogeneity in glycosaminoglycan–BCa cell receptor interactions. We reasoned this approach would reveal previously undetected cellular and functional heterogeneity linked to malignant progression because the diversity of cell glycosylation patterns, which can occur as covalent and noncovalent modifications of proteins and lipids as well as different sizes of such polysaccharides as HA, is unrivaled (16, 17, 19). In particular, tumor and wound microenvironments contain different sizes of HA polymers that bind differentially to cell receptors to activate signaling pathways regulating cell migration, invasion, survival, and proliferation (19–22).More than other related glycosaminoglycans, HA accumulation within BCa tumor cells and peritumor stroma is a predictor of poor outcome (23) and of the conversion of the preinvasive form of BCa, ductal carcinoma in situ, to an early invasive form of BCa (24). HA is a nonantigenic and large, relatively simple, unbranched polymer, but the manner in which it is metabolized is highly complex (19, 25). There are literally thousands of different HA sizes in remodeling microenvironments, including tumors. HA polymers bind to cells via at least six known receptors (16, 19, 20, 26–32). Two of these, cluster designation 44 (CD44) and receptor for HA-mediated motility/HA-mediated motility receptor (RHAMM/HMMR), form multivalent complexes with different ranges of HA sizes (19, 29, 33), and both receptors are implicated in BCa progression (19–21, 23, 29, 30, 33–36). Elevated CD44 expression in the peritumor stroma is associated with increased relapse (37), and in primary BCa cell subsets may contribute to tumor initiation and progression (38–40). Elevated RHAMM expression in BCa tumor subsets is a prognostic indicator of poor outcome and increased metastasis (22, 33, 41). RHAMM polymorphisms may also be a factor in BCa susceptibility (42, 43).We postulated that multivalent interactions resulting from mixture of a polydisperse population of fluorescent HA (F-HA) sizes, typical of those found in remodeling microenvironments of wounds and tumors (19, 20, 29), with cellular HA receptors would uncover a heterogeneous binding pattern useful for sorting tumor cells into distinct subsets. We interrogated the binding of F-HA to BCa lines of different molecular subtypes, and related binding/uptake patterns to CD44 and RHAMM display, and to tumor cell growth, invasion, and metastasis.     

Modeling putative therapeutic implications of exosome exchange between tumor and immune cells

Development of effective strategies to mobilize the immune system as a therapeutic modality in cancer necessitates a better understanding of the contribution of the tumor microenvironment to the complex interplay between cancer cells and the immune response. Recently, effort has been directed at unraveling the functional role of exosomes and their cargo of messengers in this interplay. Exosomes are small vesicles (30–200 nm) that mediate local and long-range communication through the horizontal transfer of information, such as combinations of proteins, mRNAs and microRNAs. Here, we develop a tractable theoretical framework to study the putative role of exosome-mediated cell–cell communication in the cancer–immunity interplay. We reduce the complex interplay into a generic model whose three components are cancer cells, dendritic cells (consisting of precursor, immature, and mature types), and killer cells (consisting of cytotoxic T cells, helper T cells, effector B cells, and natural killer cells). The framework also incorporates the effects of exosome exchange on enhancement/reduction of cell maturation, proliferation, apoptosis, immune recognition, and activation/inhibition. We reveal tristability—possible existence of three cancer states: a low cancer load with intermediate immune level state, an intermediate cancer load with high immune level state, and a high cancer load with low immune-level state, and establish the corresponding effective landscape for the cancer–immunity network. We illustrate how the framework can contribute to the design and assessments of combination therapies.Immunotherapeutic approaches have recently emerged as effective therapeutic modalities (1) exemplified by immune checkpoint blockade with anti–CTLA-4 to activate T-cells and induce tumor cell killing, which has been shown to be effective for some cancers but not others (2). A better understanding of the intricate interplay between cancer and the immune system, and of mechanisms of immune evasion and of hijacking of the host response by cancer cells, is relevant to the development of effective immunotherapeutic approaches (3–6).The immune-based suppression of tumor development and progression is mediated through nonspecific innate immunity and antigen-specific adaptive immunity (7). However, cancer cells can inhibit the immune response, thus evading suppression in multiple ways (8) (see below for details), and additionally hijack the immune system to their advantage (3, 4). The challenge to understand the tumor–immune interplay stems from the dynamic nature, and complexity and heterogeneity of both the cancer cells and the immune system and their interactions through the tumor microenvironment (9).Here we consider immune cells as consisting of macrophages (10), natural killer cells (11), cytotoxic T cells (12), helper T cells (13), and regulatory T cells (3). These various immune cells are produced, activated, and perform their functions separated by space and time, which contributes to additional complexity (14). Among the immune cells, dendritic cells (DCs) are the most efficient antigen-presenting cells to bridge innate immunity with adaptive immunity (15). DCs also secrete cytokines that promote the antitumor functions of both natural killer cells and macrophages (16, 17). We consider the tumor microenvironment as comprised of a heterogeneous population of cancer cells (18), stromal cells (19), and tumor-infiltrating immune cells (20). The interactions among these cell types contribute to tumor development and progression. Tumor-associated macrophages and cancer-associated fibroblasts regulate tumor metabolism and engender an immune-suppressive environment by secreting TGF-β and other cytokines (21). Fluctuations in energy sources and oxygen within a tumor contribute to malignant progression and cell phenotypic diversity (22, 23).Though secreted factors play critical roles in cell–cell communications, here we focus on the additional role of cell–cell communication mediated by the exchange of special extracellular lipid vesicles called exosomes (24). These nanovesicles of ∼30–200 nm are formed in the multivesicular bodies and then released from the cell into the extracellular space (25). The exosomes carry a broad range of cargo, including proteins, microRNAs, mRNAs, and DNA fragments, to specific target cells at a remote location (26). Membrane markers assign the exosomes to specific targeted cells. Notably, upon entering the target cell, the exosomes induce modulation of cell function and even identity switch (phenotypic, epigenetic, and even genetic) (27). Exosomes have recently emerged as playing an important role in the immune system interaction with tumors (28, 29). Tumor-derived exosomes can promote metastatic niche formation by influencing bone marrow-derived cells toward a prometastatic phenotype through upregulation of c-Met (29). DCs have been shown to induce tumor cell killing through release of exosomes that contain potent tumor-suppressive factors such as TNF and through activation of natural killer cells, cytotoxic T cells, and helper T cells (24, 30–32). However, tumor-derived exosomes (Tex) can directly inhibit the differentiation of DCs in bone marrow (33), which strongly inhibits the dendritic cell-mediated immune response to the tumor. In addition, Tex can also directly inhibit natural killer cells (34).Mathematical models have been devised to study the complex interactions of cancer and immune system, including those that consider spatial heterogeneity (as reviewed in ref. 35) and those that consider spatially homogeneous populations (as reviewed in ref. 36). Cancer–immunity models have been constructed to investigate the effects of therapy (37–39), cancer dormancy (40), and interactions with time delay (41). Other types of modeling methods have also been applied. For example, tumor growth has also been fitted to experimental data by artificial neural networks (42); a detailed network of cancer immune system has been modeled by multiple subset models (43).In this study, we have developed an exosome exchange-based cancer–immunity interplay (ECI) model, to incorporate the special role of DCs and exosome-mediated communications. Distinct from the previous approaches, our modeling strategy is adapted from methodology used in studies of gene regulatory circuits, allowing us to check the multistability features of the system (44). We find that, by including exosome exchange, the cancer–immunity interplay can give rise to three quasi-stable cancer states, which may be associated with the elimination/equilibrium/escape phases proposed in the immunoediting theory (45). The ECI model is also capable of explaining tumorigenesis by considering the time evolution of immune responses. Guided by the treatment simulations, we assess the effectiveness of various therapeutic protocols with and without time delay and noise.