Neoadjuvant chemotherapy is associated with suppression of the B cell-centered immune landscape in pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is typically diagnosed at advanced stages and associated with early distant metastasis and poor survival. Besides clinical factors, the tumor microenvironment (TME) emerged as a crucial determinant of patient survival and therapy response in many tumors, including PDAC. Thus, the presence of tumor-infiltrating lymphocytes and the formation of tertiary lymphoid structures (TLS) is associated with longer survival in PDAC. Although neoadjuvant therapy (NeoTx) has improved the management of locally advanced tumors, detailed insight into its effect on various TME components is limited. While a remodeling towards a proinflammatory state was reported for PDAC-infiltrating T cells, the effect of NeoTx on B cell subsets, including plasma cells, and TLS formation is widely unclear. We thus investigated the frequency, composition, and spatial distribution of PDAC-infiltrating B cells in primary resected (PR) versus neoadjuvant-treated patients using a novel multiplex immunohistochemistry panel. The NeoTx group displayed significantly lower frequencies of pan B cells, GC B cells, plasmablasts, and plasma cells, accompanied by a reduced abundance of TLS. This finding was supported by bulk RNA-sequencing analysis of an independent fresh frozen tissue cohort, which revealed that major B cell pathways were downregulated in the NeoTx group. We further observed that plasma cells frequently formed aggregates that localized close to TLS and that TLS+ patients displayed significantly higher plasma cell frequencies compared to TLS- patients in the PR group. Additionally, high densities of CD20+ intratumoral B cells were significantly associated with longer overall survival in the PR group. While CD20+ B cells held no prognostic value for NeoTx patients, an increased frequency of proliferating CD20+Ki67+ B cells emerged as an independent prognostic factor for longer survival in the NeoTx group. These results indicate that NeoTx differentially affects PDAC-infiltrating immune cells and may have detrimental effects on the existing B cell landscape and the formation of TLS. Gaining further insight into the underlying molecular mechanisms is crucial to overcome the intrinsic immunotherapy resistance of PDAC and develop novel strategies to improve the long-term outcome of PDAC patients.

Phenotype screens of murine pancreatic cancer identify a Tgf-α-Ccl2-paxillin axis driving human-like neural invasion

Solid cancers like pancreatic ductal adenocarcinoma (PDAC), a type of pancreatic cancer, frequently exploit nerves for rapid dissemination. This neural invasion (NI) is an independent prognostic factor in PDAC, but insufficiently modeled in genetically engineered mouse models (GEMM) of PDAC. Here, we systematically screened for human-like NI in Europe's largest repository of GEMM of PDAC, comprising 295 different genotypes. This phenotype screen uncovered 2 GEMMs of PDAC with human-like NI, which are both characterized by pancreas-specific overexpression of transforming growth factor α (TGF-α) and conditional depletion of p53. Mechanistically, cancer-cell-derived TGF-α upregulated CCL2 secretion from sensory neurons, which induced hyperphosphorylation of the cytoskeletal protein paxillin via CCR4 on cancer cells. This activated the cancer migration machinery and filopodia formation toward neurons. Disrupting CCR4 or paxillin activity limited NI and dampened tumor size and tumor innervation. In human PDAC, phospho-paxillin and TGF-α-expression constituted strong prognostic factors. Therefore, we believe that the TGF-α-CCL2-CCR4-p-paxillin axis is a clinically actionable target for constraining NI and tumor progression in PDAC.

Carcinoid syndrome caused by a pulmonary carcinoid mimics intestinal manifestations of ulcerative colitis: A case report

BACKGROUND

Pulmonary carcinoids are rare, low-grade malignant tumors characterized by neuroendocrine differentiation and relatively indolent clinical behavior. Most cases present as a slow-growing polypoidal mass in the major bronchi leading to hemoptysis and pulmonary infection due to blockage of the distal bronchi. Carcinoid syndrome is a paraneoplastic syndrome caused by the systemic release of vasoactive substances that presents in 5% of patients with neuroendocrine tumors. Due to such nonspecific presentation, most patients are misdiagnosed or diagnosed late and may receive several courses of antibiotics to treat recurrent pneumonia before the tumor is diagnosed.

CASE SUMMARY

We report the case of a 48-year-old male who presented with cough, dyspnea, a history of recurrent pneumonitis, and therapy-refractory ulcerative colitis that completely subsided after the resection of a pulmonary carcinoid.

CONCLUSION

We report and emphasize pulmonary carcinoid as a differential diagnosis in patients with nonresponding inflammatory bowel diseases and recurrent pneumonia.

Abstract 2254: Immunotopography characterization after neoadjuvant therapy in the pancreatic cancer microenvironment

Pancreatic cancer is one of the most common cancers worldwide and its incidence is increasing globally. Treatment consists of surgical resection followed by adjuvant or neoadjuvant therapy. Neoadjuvant therapy (neoTx) has dramatically improved the prognosis of patients with locally advanced and borderline resectable pancreatic cancer. NeoTX has been shown to reverse the immunosuppression exerted by malignant cells and selectively deplete regulatory T cells and myeloid-derived suppressor cells in the peritumoral niche. In addition, neoTx mediates a significant decrease in the severity of neural invasion and stroma activation. However, the effect of neoTx on the topographical interactions between the different populations of tumor-infiltrating immune cells, the degree of intratumoral immune infiltration and distance to tumor cells as well as their spatial interactions with other key features of the tumor microenvironment (TME) remained unknown. In this study, we employed a multiplex immunofluorescence approach on the COMET™ platform from Lunaphore. COMET™ performs full-automated sequential immunofluorescence (seqIF™) assays, which consist of cycles of staining, imaging, and elution. We developed a customized 12-plex panel on COMET™ to characterize the TME of paraffin-embedded sections of pancreatic cancer samples. COMET™ outputs are OME.TIFF files that were analyzed and quantified with QuPath and CellProfiler for cell segmentation and cell phenotyping respectively. The optimized panel was used to analyze the immune architecture of neoadjuvant-treated pancreatic cancer patients compared to primary resected ones who underwent surgical resection with curative intention. We detected the following immune phenotypes: cytotoxic T cells (CD8+, CD3+), helper T cells (CD4+, CD3+), B cells (CD20+, CD3-), regulatory T cells (FoxP3+, CD4+), macrophages (CD68+), neutrophils (CD163+, CD11b+), and myeloid-derived suppressor cells (CD163, CD11b+, CD66b+). We also quantified the presence of both immune checkpoints (PD1+) cells and their apoptotic rate (Caspase-3), and how those correlate with the immunotopography after neoadjuvant therapy. Our optimized 12-plex panel was successfully transferred to an initial cohort of 10 patients. Our preliminary analysis shows interesting results on the effect of neoTx treatment on the immune microenvironment, such as decreased immune cell density, induction of apoptosis in lymphoid cells, and increased PD1 expression in T-killer cells compared to samples from primary resected patients. Our approach demonstrates the importance of a deep topographic characterization to understand the TME composition of pancreatic cancers, with or without neoTx treatment. Our preliminary findings highlight new differential cell identities in neoTx-treated patients, confirming their suitability for application in future clinical immunotherapy trials.

Citation Format: Carmen Mota Reyes, Maximilian Kiessler, Pino Bordignon, Samuel Aubert, Pamela Pulimeno, Helmut Friess, Rouzanna Istvanffy, Ihsan Ekin Demir. Immunotopography characterization after neoadjuvant therapy in the pancreatic cancer microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2254.

Evidence for phosphorylation-dependent, dynamic, regulation of mGlu5 and Homer2 in expression of cocaine aversion in mice

Cocaine-induced changes in the expression of the glutamate-related scaffolding protein Homer2 influence this drug's psychostimulant and rewarding properties. In response to neuronal activity, Homer2 is phosphorylated on S117/S216 by calcium-calmodulin kinase IIα (CaMKIIα), which induces a rapid dissociation of mGlu5-Homer2 scaffolds. Herein, we examined the requirement for Homer2 phosphorylation in cocaine-induced changes in mGlu5-Homer2 coupling, to include behavioral sensitivity to cocaine. For this, mice with alanine point mutations at (S117/216)-Homer2 (Homer2^AA/AA ) were generated and we determined their affective, cognitive and sensorimotor phenotypes, as well as cocaine-induced changes in conditioned reward and motor hyperactivity. The Homer2^AA/AA mutation prevented activity-dependent phosphorylation of S216 Homer2 in cortical neurons, but Homer2^AA/AA mice did not differ from wild-type controls with respect to Morris maze performance, acoustic startle, spontaneous or cocaine-induced locomotion. Homer2^AA/AA mice exhibited signs of hypo-anxiety similar to the phenotype of transgenic mice with a deficit in signal-regulated mGluR5 phosphorylation (Grm5^AA/AA ). However, opposite of Grm5^AA/AA mice, Homer2^AA/AA mice were less sensitive to the aversive properties of high-dose cocaine under both place- and taste-conditioning procedures. Acute injection with cocaine caused dissociation of mGluR5 and Homer2 in striatal lysates from WT, but not Homer2^AA/AA mice, suggesting a molecular basis for the deficit in cocaine aversion. These findings indicate that CaMKIIα-dependent phosphorylation of Homer2 gates the negative motivational valence of high-dose cocaine via regulation of mGlu5 binding, furthering an important role for dynamic changes in mGlu5-Homer interactions in addiction vulnerability.Significance statementGlobally, psychostimulant use has again risen to reach epidemic proportions, particularly in the United States. Yet, we continue to face a knowledge gap regarding the biological bases of psychostimulant addiction vulnerability to inform disease prognosis and treatment-based recovery. Herein, we show that the psychomotor stimulant cocaine induces the uncoupling of the mGlu5 glutamate receptor from its scaffolding protein Homer2 in brain. Using a transgenic mouse model with deficits cocaine-induced uncoupling of mGlu5-Homer2, we demonstrate an important role for Homer2 scaffolding of mGlu5 in regulating cocaine's aversive properties, without influencing cocaine reward. Findings suggest that environmental factors, to include cocaine exposure, that affect mGlu5-Homer2 scaffolding dynamics may contribute to an individual's subjective response to cocaine to influence addiction vulnerability.

Molecular Profiling in Pancreatic Cancer: Current Role and Its Impact on Primary Surgery

Background

The advent of next-generation sequencing technologies has enabled the identification of molecular subtypes of pancreatic ductal adenocarcinoma (PDAC) with different biological traits and clinically targetable features.

Summary

Although current chemotherapy trials are currently exploiting this knowledge, these molecular subtypes have not yet sufficiently caught the attention of surgeons. In fact, integration of these molecular subtypes into the timing of surgery can in theory improve patient outcome. Here, we present the molecular subtypes of PDAC from the surgeon's perspective and a clinically applicable algorithm that integrates the molecular subtyping of PDAC preoperatively into the decision of primary surgery versus neoadjuvant therapy. Furthermore, we point out the potential of "tailored" (in addition to conventional) neoadjuvant treatment for exploiting the molecular subtypes of PDAC.

Key Messages

We believe that for surgeons, the preoperative knowledge on the subtype of PDAC can properly guide in deciding between upfront surgery versus neoadjuvant treatment for improving patient outcome.

Innervated mouse pancreas organoids as an ex vivo model to study pancreatic neuropathy in pancreatic cancer

Pancreatic cancer is characterized by bi-directional interactions between pancreatic cancer cells and stromal cells including neural cells. The absence of neural cells in pancreatic organoids limits the investigation of cell- cell interaction and tumor innervation. This protocol describes how to generate innervated wild type (WT) and Kras^+/LSLG12D Trp53^{fl/f l}p48^+/Cre (KPC) murine pancreatic organoids. To specifically investigate neurogenesis, organoids are co-cultured with iPSCs-derived neural crest cells, while co-culture with dorsal root ganglia explants is used for comparing organoids with mature neurons.

For complete details on the use and execution of this protocol, please refer to Huch et al. (2013), Boj et al. (2015), and Demir et al. (2014).

•

Protocol for the generation of “innervated” pancreas organoids

•

Generation of innervated wildtype (WT) and cancer (KPC) murine pancreas organoids

•

Innervation enables investigation of neuron – cancer cell interactions in PDAC

•

NCCs-pancreas organoid co-cultures are also useful for studying neurogenesis in pancreas development

Future directions in preclinical and translational cancer neuroscience research

Recent advances in cancer neuroscience necessitate the systematic analysis of neural influences in cancer as potential therapeutic targets in oncology. Here, we outline recommendations for future preclinical and translational research in this field.

Future directions of neoadjuvant therapy in pancreatic cancer

Neoadjuvant therapy with conventional chemotherapies have visibly improved the prognosis of locally advanced pancreatic cancer (PCa). However, molecular targeted therapies that have provided durable responses in other tumor entities, have not yet found access into neoadjuvant therapy of PCa. In fact, due to the presence of the tumor burden serving as an antigen source for T cell priming, neoadjuvant chemotherapy may unleash a more potent antitumoral immune response than adjuvant or palliative chemotherapy.

Neoadjuvant therapy in pancreatic cancer: what is the true oncological benefit?

BACKGROUND

Neoadjuvant therapies (neoTx) have revolutionized the treatment of borderline resectable (BR) and locally advanced (LA) pancreatic cancer (PCa) by significantly increasing the rate of R0 resections, which remains the only curative strategy for these patients. However, there is still room for improvement of neoTx in PCa.

PURPOSE

Here, we aimed to critically analyze the benefits of neoTx in LA and BR PCa and its potential use on patients with resectable PCa. We also explored the feasibility of arterial resection (AR) to increase surgical radicality and the incorporation of immunotherapy to optimize neoadjuvant approaches in PCa.

CONCLUSION

For early stage, i.e., resectable, PCa, there is not enough scientific evidence for routinely recommending neoTx. For LA and BR PCa, optimization of neoadjuvant therapy necessitates more sophisticated complex surgical resections, machine learning and radiomic approaches, integration of immunotherapy due to the high antigen load, standardized histopathological assessment, and improved multidisciplinary communication.

Clinically Actionable Strategies for Studying Neural Influences in Cancer

Neuro-glial activation is a recently identified hallmark of growing cancers. Targeting tumor hyperinnervation in preclinical and small clinical trials has yielded promising antitumor effects, highlighting the need of systematic analysis of neural influences in cancer (NIC). Here, we outline the strategies translating these findings from bench to the clinic.

Neoadjuvant Therapy Remodels the Pancreatic Cancer Microenvironment via Depletion of Protumorigenic Immune Cells

PURPOSE

Neoadjuvant therapy (neoTx) has dramatically improved the prognosis of patients with locally advanced and borderline resectable pancreatic ductal adenocarcinoma, yet its mechanisms of action on tumor cells and the tumor microenvironment are still unknown. Here, we aimed to characterize the multiple facets of neoTx-induced alterations in the pancreatic cancer microenvironment.

EXPERIMENTAL DESIGN

We performed the currently most comprehensive histopathologic analysis of desmoplasia, angiogenesis, neural invasion, and immune cell infiltration at the tumor-host interface of pancreatic cancer after neoTx (n = 37) versus after primary resection (n = 37) through quantitative IHC and double immunofluorescence using automated and software-based quantification algorithms.

RESULTS

We demonstrate that, independently of the applied pretreatment, neoadjuvant regimes are able to reverse the immunosuppressive behavior of malignant cells on pancreatic cancer microenvironment. Here, neoTx-driven selective depletion of regulatory T cells and myeloid-derived suppressor cells was associated with enrichment of antitumor immune cells in the peritumoral niche, decreased stromal activation, and less neural invasion. Importantly, the degree of this antitumor immune remodeling correlates to the degree of histopathologic response to neoTx. Survival analysis revealed that the tumor proliferation rate together with the activation of the stroma and the intratumoral infiltration with CD4⁺ T cells and natural killer cells constitute as independent prognostic factors for neoadjuvantly treated pancreatic cancer.

CONCLUSIONS

NeoTx is not only cytotoxic but has pleiotropic, beneficial effects on all cellular and noncellular components of pancreatic cancer. Combinational approaches including immunotherapy may unleash long-term and more effective antitumor responses and improve prognosis of pancreatic cancer.

Targeting nNOS ameliorates the severe neuropathic pain due to chronic pancreatitis

BACKGROUND

Pain due to pancreatic cancer/PCa or chronic pancreatitis/CP, is notoriously resistant to the strongest pain medications. Here, we aimed at deciphering the specific molecular mediators of pain at surgical-stage pancreatic disease and to discover novel translational targets.

METHODS

We performed a systematic, quantitative analysis of the neurotransmitter/neuroenzmye profile within intrapancreatic nerves of CP and PCa patients. Ex vivo neuronal cultures treated with human pancreatic extracts, conditional genetically engineered knockout mouse models of PCa and CP, and the cerulein-induced CP model were employed to explore the therapeutic potential of the identified targets.

FINDINGS

We identified a unique enrichment of neuronal nitric-oxide-synthase (nNOS) in the pancreatic nerves of CP patients with increasing pain severity. Employment of ex vivo neuronal cultures treated with pancreatic tissue extracts of CP patients, and brain-derived-neurotrophic-factor-deficient (BDNF^+/-) mice revealed neuronal enrichment of nNOS to be a consequence of BDNF loss in the progressively destroyed pancreatic tissue. Mechanistically, nNOS upregulation in sensory neurons was induced by tryptase secreted from perineural mast cells. In a head-to-head comparison of several genetically induced, painless mouse models of PCa (KPC, KC mice) or CP (Ptf1a-Cre;Atg5^fl/fl) against the hypersecretion/cerulein-induced, painful CP mouse model, we show that a similar nNOS enrichment is present in the painful cerulein-CP model, but absent in painless genetic models. Consequently, mice afflicted with painful cerulein-induced CP could be significantly relieved upon treatment with the specific nNOS inhibitor NPLA.

INTERPRETATION

We propose nNOS inhibition as a novel strategy to treat the unbearable pain in CP. FUND: Deutsche Forschungsgemeinschaft/DFG (DE2428/3-1 and 3-2).

The impact of neoadjuvant therapy on the histopathological features of pancreatic ductal adenocarcinoma - A systematic review and meta-analysis

BACKGROUND

Due to increased rates of curative tumor resections exceeding 60% after FOLFIRINOX-treatment, neoadjuvant therapy/NTx is increasingly recognized as an effective therapy option for downstaging borderline or locally advanced pancreatic ductal adenocarcinoma/PDAC. Yet, the effects of NTx on the common histopathological features of PDAC have not been systematically analysed. Therefore, the aim of the current study was to assess the impact of NTx on relevant histopathological features of PDAC.

PATIENTS AND METHODS

Biomedical databases were systematically screened for predefined searching terms related to NTx and PDAC. The Preferred-Reporting-Items-for-Systematic-review-and-Meta-Analysis/PRISMA-guidelines were used to perform a systematic review and meta-analysis. Articles meeting the predefined criteria were analysed on relevance, and a meta-analysis was performed.

RESULTS

A total of 9031 studies could be identified that analysed the effect of NTx on PDAC. Only 35 studies presented comparative data on the histological features of neoadjuvantly treated vs. upfront resected PDAC patients. In meta-analyses, the beneficial effect of NTx was reflected by reduced tumor size (T1/2: RR 2.87, 95%-CI: 1.52-5.42, P=0.001, T3/4: RR 0.78, 95%-CI: 0.69-0.89, P=0.0002), lower N-Stage (N0: RR 2.14, 95%-CI: 1.85-2.46, P<0.00001, N1: RR 0.59, 95%-CI: 0.53-0.65, P<0.00001), higher R0-rates (R0: RR 1.13, 95%-CI: 1.08-1.18, P<0.00001, R1: RR 0.66, 95%-CI: 0.58-0.76, P<0.00001), less perineural invasion (Pn1: RR 0.78, 95%-CI: 0.73-0.83, P<0.00001), less lymphatic vessel invasion (RR: 0.50, 95%-CI: 0.36-0.70, P<0.0001) and fewer G3-tumors (RR 0.82, 95%-CI: 0.71-0.94, P=0.005).

CONCLUSIONS

NTx in PDAC seems to exert its beneficial effect in borderline or locally advanced PDAC over genuine tumor downstaging. Thus, although at least 40% of all NTx treated patients remain unresectable even with modern NTx regimes, neoadjuvantly treated PDAC showed not only increasing resectability rates especially after FOLFIRINOX, but even reach a lower tumor stage than primarily resected PDAC.

The influence of neural invasion on survival and tumor recurrence in pancreatic ductal adenocarcinoma - A systematic review and meta-analysis

OBJECTIVES

To assess the impact of neural invasion/NI on overall survival/OS and tumor recurrence in pancreatic ductal adenocarcinoma/PDAC.

SUMMARY BACKGROUND DATA

NI is a histopathological hallmark of PDAC. Although some studies suggested an important role for NI on OS, disease-free/DFS and progression-free survival/PFS in PDAC, there is still no consensus on the actual role of NI on survival and local recurrence in PDAC.

METHODS

Pubmed, Cochrane library, Ovid and Google Scholar were screened for the terms "pancreatic ductal adenocarcinoma", "pancreatic cancer", "survival", "tumor recurrence" and "perineural invasion". The Preferred-Reporting-Items-for-Systematic-review-and-Meta-Analysis/PRISMA-guidelines were used for systematic review and meta-analysis. Articles meeting predefined criteria were critically analysed on relevance, and meta-analyses were performed by pooling univariate and multivariate hazard ratios/HR.

RESULTS

A total number of 25 studies on the influence of NI on tumor recurrence, and 121 studies analysing the influence of NI on survival were identified by systematic review. The HR of the univariate (HR 1.88; 95%-CI 1.71-2.07; p < 0.00001) and multivariate meta-analysis (HR 1.68; 95%-CI 1.47-1.92; p < 0.00001) showed a major impact of NI on OS. Likewise, NI was associated with decreased DFS (HR 2.53; 95%-CI: 1.67-3.83; p = 0.0001) and PFS (HR 2.41; 95%-CI: 1.73-3.37: p < 0.00001) multivariate meta-analysis.

CONCLUSIONS

Although the power of this study is limited by missing pathological procedures to assess the true incidence of NI, NI appears to be an independent prognostic factor for OS, DFS and PFS in PDAC. Therefore, NI should be increasingly considered in patient stratification and in the development of novel therapeutic algorithms.

Modelling the cost-effectiveness of sentinel lymph node mapping and adjuvant interferon treatment for stage II melanoma

Clinical studies have demonstrated that high dose adjuvant interferon therapy improves disease-free and overall survival among high risk (stage IIb and III) melanoma patients. Sentinel lymph node mapping (SLM) has been shown to accurately detect micrometastasis and may be used to identify higher risk stage II patients, who might benefit most from adjuvant interferon therapy. We modelled the cost-effectiveness of first testing with SLM and then treating with adjuvant interferon (IFN) therapy for stage II melanoma. We used a decision analytical model to compare four strategies for stage II patients after surgical excision of their melanoma: (1) treat all with low dose IFN; (2) test first with SLM and then treat only those with positive micrometastasis with high dose IFN; (3) test first with SLM and treat positives with high dose IFN and negatives with low dose IFN (test and treat appropriately); and (4) surgery only. Treatment, toxicity, follow-up and relapse costs were included over a 5 year time period. The primary outcome was cost per quality-adjusted relapse-free life year saved. Our analysis shows that, compared with the current surgery-only strategy, all three treatment strategies provide incremental benefits. The test and treat appropriately strategy is the most effective, with an incremental improvement of 0.64 quality-adjusted life-years (QALY). The cost-effectiveness of test and treat some with high dose IFN compared with the surgery-only strategy is $18,700/QALY. The test and treat appropriately strategy is also cost-effective compared with test and treat some at $31,100/QALY. In conclusion appropriate dosing of IFN therapy based on the results of SLM is a cost-effective strategy for stage II melanoma patients.

Molecular dynamics and binding specificity analysis of the bovine immunodeficiency virus BIV Tat-TAR complex

We have performed molecular dynamics (MD) simulations, with particle-mesh Ewald, explicit waters, and counterions, and binding specificity analyses using combined molecular mechanics and continuum solvent (MM-PBSA) on the bovine immunodeficiency virus (BIV) Tat peptide-TAR RNA complex. The solution structure for the complex was solved independently by Patel and co-workers and Puglisi and co-workers. We investigated the differences in both structures and trajectories, particularly in the formation of the U-A-U base triple, the dynamic flexibility of the Tat peptide, and the interactions at the binding interface. We observed a decrease in RMSD in comparing the final average RNA structures and initial RNA structures of both trajectories, which suggests the convergence of the RNA structures to a MD equilibrated RNA structure. We also calculated the relative binding of different Tat peptide mutants to TAR RNA and found qualitative agreement with experimental studies.

Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions

Computer modeling has been developed and widely applied in studying molecules of biological interest. The force field is the cornerstone of computer simulations, and many force fields have been developed and successfully applied in these simulations. Two interesting areas are (a) studying enzyme catalytic mechanisms using a combination of quantum mechanics and molecular mechanics, and (b) studying macromolecular dynamics and interactions using molecular dynamics (MD) and free energy (FE) calculation methods. Enzyme catalysis involves forming and breaking of covalent bonds and requires the use of quantum mechanics. Noncovalent interactions appear ubiquitously in biology, but here we confine ourselves to review only noncovalent interactions between protein and protein, protein and ligand, and protein and nucleic acids.

Molecular dynamics studies of the HIV-1 TAR and its complex with argininamide

The dynamic behavior of HIV-1 TAR and its complex with argininamide is investigated by means of molecular dynamics simulations starting from NMR structures, with explicit inclusion of water and periodic boundary conditions particle mesh Ewald representation of the electrostatic energy. During simulations of free and argininamide-bound TAR, local structural patterns, as determined by NMR experiments, were reproduced. An interdomain motion was observed in the simulations of free TAR, which is absent in the case of bound TAR, leading to the conclusion that the free conformation of TAR is intrinsically more flexible than the bound conformation. In particular, in the bound conformation the TAR-argininamide interface is very well ordered, as a result of the formation of a U.A.U base triple, which imposes structural constraints on the global conformation of the molecule. Free energy analysis, which includes solvation contributions, was used to evaluate the influence of van der Waals and electrostatic terms on formation of the complex and on the conformational rearrangement from free to bound TAR.

Structure and thermodynamics of RNA-protein binding: using molecular dynamics and free energy analyses to calculate the free energies of binding and conformational change

An adaptive binding mechanism, requiring large conformational rearrangements, occurs commonly with many RNA-protein associations. To explore this process of reorganization, we have investigated the conformational change upon spliceosomal U1A-RNA binding with molecular dynamics (MD) simulations and free energy analyses. We computed the energetic cost of conformational change in U1A-hairpin and U1A-internal loop binding using a hybrid of molecular mechanics and continuum solvent methods. Encouragingly, in all four free energy comparisons (two slightly different proteins, two different RNAs), the free macromolecule was more stable than the bound form by the physically reasonable value of approximately 10 kcal/mol. We calculated the absolute binding free energies for both complexes to be in the same range as that found experimentally.

Investigating the binding specificity of U1A-RNA by computational mutagenesis

The mammalian spliceosomal protein U1A binds a hairpin RNA with picomolar affinity. To examine the origin of this binding specificity, we carried out computational mutagenesis on protein and RNA residues in the U1A-RNA binding interface. Our computational mutagenesis methods calculate the relative binding affinity between mutant and wild-type as the sum of molecular mechanical energies and solvation free energies estimated with a continuum solvent model. We obtained good agreement with experimental studies and we verified mutations that abolish and improve binding. Therefore, we offer these methods as computationally inexpensive tools for investigating and predicting the effects of site-specific mutagenesis.

Molecular dynamics studies of U1A-RNA complexes

The U1A protein binds to a hairpin RNA and an internal-loop RNA with picomolar affinities. To probe the molecular basis of U1A binding, we performed state-of-the-art nanosecond molecular dynamics simulations on both complexes. The good agreement with experimental structures supports the protocols used in the simulations. We compare the dynamics, hydrogen-bonding occupancies, and interfacial flexibility of both complexes and also describe a rigid-body motion in the U1A-internal loop complex that is not observed in the U1A-hairpin simulation. We relate these observations to experimental mutational studies and highlight their significance in U1A binding affinity and specificity.

Seroepidemiology of hepatitis B virus in the Philippines

Hepatitis B virus markers were studied in 2,842 Philippine rural subjects from four villages in 1979-1982. The prevalence of hepatitis B surface antigen (HBsAg) and all markers for hepatitis B virus averaged 12% and 58%, respectively, in these rural populations. It is estimated that five million Filipinos are HBsAg positive. The rural age-specific HBsAg prevalence shows an "early peak" (in persons 3-4-years-old) in two communities and a "late peak" (in persons 30-40-years-old) in the other two communities. Family studies suggest that the prevalence of HBsAg and hepatitis B e antigen (HBeAg) among parents of the young children in an "early peak" and a "late peak" village cannot fully account for the difference in the patterns of prevalence of all markers, or the HBsAg marker. Horizontal intrafamilial and extrafamilial transmission may also be significant. Further research is needed on risk factors for hepatitis B virus infection.