Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions

Selected reaction monitoring (SRM) is a targeted mass spectrometry technique that is emerging in the field of proteomics as a complement to untargeted shotgun methods. SRM is particularly useful when predetermined sets of proteins, such as those constituting cellular networks or sets of candidate biomarkers, need to be measured across multiple samples in a consistent, reproducible and quantitatively precise manner. Here we describe how SRM is applied in proteomics, review recent advances, present selected applications and provide a perspective on the future of this powerful technology.     

Veterinary vaccines

Vaccination of animals for the prevention of infectious diseases has been practised for a number of years with little change in product composition. Recent advances in molecular biology, pathogenesis and immunology have laid the groundwork for the development of a new generation of veterinary vaccines based on pure subunits as well as live vectored bacteria and viruses. Along with novel methods of antigen preparation, the use of new adjuvants and delivery systems will permit targeting of the appropriate immune response as well as offering flexibility in terms of vaccination protocols. These new technologies are also being applied to the development of vaccines to enhance animal productivity and to control reproduction.     

Blastocystis: past pitfalls and future perspectives

Blastocystis is a genetically heterogeneous protist found in the intestinal tract (IT) of many vertebrates, and although it is implicated in a variety of human intestinal disorders, data regarding the clinical relevance of Blastocystis is at best speculative. Several research issues, including a lack of standardization across studies, the potential for intrasubtype variation in pathogenicity, and difficulties associated with diagnostics for many idiopathic disorders of the human IT have led to conflicting reports in support of a role for Blastocystis pathogenicity. Here, several research areas and methodologies are reviewed that if integrated appropriately into a prospective study may prove useful and facilitate a better understanding of the role of Blastocystis in human health and disease.     

Aromatase inhibitors: future directions

Estrogen and its cognate estrogen receptor are key players in the etiology and progression of breast cancer. Aromatase inhibitors, suppressing tumor and plasma estrogen levels by blocking testosterone conversion to estrogen, have been proven to provide the most effective endocrine therapy for postmenopausal breast cancer patients. Aromatase inhibitors are now the first choice endocrine therapy in the metastatic setting for postmenopausal women. These endocrine agents also seem likely to soon become the standard adjuvant therapy, either alone or in sequence with tamoxifen, though their long-term toxicity and the optimum duration of therapy still remain to be defined. Advanced experimental studies and some clinical observations reveal the importance of blocking both the genomic and non-genomic activities of the estrogen receptor, as well as its crosstalk with growth factor and other cellular signaling, for greatest effectiveness of endocrine therapy. Consequently, these studies provide a mechanistic explanation for the superb performance of aromatase inhibitors, and also suggest how inhibiting selected growth factor receptors might delay or prevent the onset of resistance to aromatase inhibitors and other endocrine therapies.     

Amphibian declines: future directions

Abstract. The amphibian decline problem is complex, and there is no easy solution. I highlight four major areas of future research that should increase our ability to detect declines, elucidate their underlying mechanisms, and advance our capacity to manage and conserve amphibian populations. First, a statistically sensitive monitoring approach is necessary to determine the distribution and abundance of amphibian populations, to assess whether they are declining, and to quantify the extent of declines. Most amphibian populations characteristically fluctuate, detection probabilities may be low for many species and populations tend to decline in numbers between years more often than they increase. These traits make establishing monitoring programmes difficult and distinguishing declines from natural fluctuations challenging. It is thus necessary to determine the best monitoring techniques based on their statistical power and to use appropriate statistical methods for detecting population trends. Secondly, although amphibian population studies occur most commonly at single or few breeding sites, research should occur often at the landscape level, and conservation efforts should focus on suitable habitat (whether or not it is occupied) and dispersal capabilities of species. Metapopulation dynamics are probably important for many species, but we must be cautious how we define metapopulations. That is, the term ‘metapopulation’ is currently used to define a wide range of demographic situations in amphibian populations, each with different management implications. Thirdly, recent advances in molecular genetic techniques make it possible to infer demographic events such as effects of recent fragmentation, bottlenecks or hybridization. Molecular techniques can be used in conjunction with census surveys to bolster knowledge about demographic processes such as declines. Alternatively, in the absence of long‐term census data, molecular data can be used to infer population trends. New genomic approaches may make estimating adaptive genetic variation more feasible. Fourthly, multi‐factorial studies are needed to disentangle the complexity of the several putative causes that probably interact to cause amphibian declines. Recent studies demonstrate the value of a multi‐factorial approach, and more work is needed to elucidate the synergistic effects of multiple environmental factors affecting amphibian populations simultaneously worldwide.     

Habitat complexity: approaches and future directions

Habitat complexity is one of the most important factors structuring biotic assemblages, yet we still lack basic understanding of the underlying mechanisms. Although it is one of the primary targets in conservation management, no methods are available for comparing complexity across ecosystems, and system-specific qualitative assessment predominates. Despite its overwhelming importance for faunal diversity and abundance, there has been surprisingly little interest in examining its effects on other community and ecosystem attributes. We discuss possibilities of such effects, outlining potentially fruitful areas for future research, and argue that complexity may be implicated in community persistence and ecosystem stability by acting as a decoupling mechanism in predator–prey interactions. We provide a brief overview of methods used to quantify complexity in different ecosystems, highlighting contributions of the current issue of Hydrobiologia, and discuss potential application of these approaches for cross-ecosystem comparisons. Better understanding of the role of habitat complexity resulting from such comparisons is critically important for preservation of biodiversity and ecosystem function in an era of unprecedented habitat loss.     

Catumaxomab: Clinical development and future directions

Catumaxomab, a monoclonal bispecific trifunctional antibody, was approved in the european Union in April 2009 for the intraperitoneal treatment of patients with malignant ascites. The marketing authorization holder Fresenius Biotech GmbH developed catumaxomab (Removab^®) together with its partner TRiOn Pharma GmbH, Germany. it is the first substance worldwide with a regulatory label for the treatment of malignant ascites due to epithelial carcinomas. Since the peritoneum is of mesothelial origin and therefore lacks epCAM expression, the intraperitoneal administration of catumaxomab is an attractive targeted immunotherapeutic approach. Catumaxomab is able to destroy epCAM positive tumor cells in the peritoneal cavity known as the main cause of malignant ascites. in addition, catumaxomab is a potential therapeutic option for several primary tumors since the epCAM molecule is expressed on the majority of epithelial carcinomas. This review focuses on the clinical development of catumaxomab and indicates future directions.Key words: catumaxomab, Removab^®, monoclonal antibody, trifunctional, EpCAM, malignant ascites, peritoneal carcinomatosis, immunotherapy     

DNA vaccines: designing strategies against parasitic infections

The complexity of parasitic infections requires novel approaches to vaccine design. The versatility of DNA vaccination provides new perspectives. This review discusses the use of prime-boost immunizations, genetic adjuvants, multivalent vaccines and codon optimization for optimal DNA vaccine design against parasites.     

Bio-ontologies: current trends and future directions

In recent years, as a knowledge-based discipline, bioinformatics has been made more computationally amenable. After its beginnings as a technology advocated by computer scientists to overcome problems of heterogeneity, ontology has been taken up by biologists themselves as a means to consistently annotate features from genotype to phenotype. In medical informatics, artifacts called ontologies have been used for a longer period of time to produce controlled lexicons for coding schemes. In this article, we review the current position in ontologies and how they have become institutionalized within biomedicine. As the field has matured, the much older philosophical aspects of ontology have come into play. With this and the institutionalization of ontology has come greater formality. We review this trend and what benefits it might bring to ontologies and their use within biomedicine.     

Anti-idiotype cancer vaccines: past and future

 Anti-idiotypic antibodies (Ab2) binding to the antigen-combining site of antitumor antibodies (Ab1) can induce anti-anti-idiotypic antibodies (Ab3) that specifically bind to the tumor antigen recognized by Ab1. Furthermore, Ab2, mimicking tumor antigens, have been shown to induce anti-anti-idiotypic proliferative T lymphocytes of the helper and suppressor type, as well as cytotoxic lymphocytes. The immunomodulatory activities of Ab2 have been demonstrated both in animals and in patients. The demonstration of tumor growth inhibition by anti-idiotypes in preclinical and phase I clinical studies emphasizes that randomized control trials should be performed to demonstrate clinical efficacy of Ab2 vaccines. Received: 25 July 1996 / Accepted: 22 August 1996     

PARP inhibitors and metastatic castration-resistant prostate cancer: uture directions and pitfalls

PARP inhibitors (PARPi) gained major interest among prostate cancer researchers in the last few years, thanks to the outstanding results coming from the PROfound an TRITON2 studies. Following that, PARPi gained approval also in metastatic, castration-resistant prostate cancer (mCRPC) with mutations in homologous repair (HR) – related genes. Nevertheless, some questions still remain unanswered concerning the management of drug resistance and PARPi-sensitivity in patients harboring alterations in various DNA damage response (DDR) related genes, not only BRCA1 and BRCA2.In this perspective article we focus on the key issues concerning PARPi in mCRPC, specifically those related to drug sensitivity and resistance mechanisms, exploring the possible role of combination therapeutic approaches and trying to depict potential future addresses in translational oncology research.

Perspective Article (max: 1200 words)The DNA damage repair (DDR) pathway gained major interest between cancer researchers since 2005, when emerging studies demonstrated that the simultaneous inhibition of both Poly(ADP-ribose) polymerase 1 (PARP1) and tumor suppressors Breast Related Cancer Antigens 1 and 2 (BRCA1 and BRCA2) generates excessive DNA instability and, ultimately, leads to cellular death. This process, called synthetic lethal theory, constituted the rationale for the development of drugs targeting PARP1 in BRCA1/2 deficient clones, the PARP inhibitors (PARPi) [1, 2].In normal conditions, PARP1 plays a key role as regulator of multiple cellular processes, including DDR. When a DNA damage occurs, the activation of PARP1 results in the recruitment of several DNA repair factors, including BRCA1 and BRCA2, leading to the restoration of single-strand (SSBs) and double-strand DNA breaks (DSBs) [1,2]^. Particularly, BRCA1 and BRCA2 act downstream the PARP1 cascade in one of the two major pathways for DSBs repair, largely error free: the homologous repair (HR). Another crucial mechanism, which sees the synergic contribution of PARP1, BRCA1 and BRCA 2, is the stabilization of replication fork during the S phase of the cell cycle [2]. As a consequence of that, heterozygous germline mutations in DDR genes, especially BRCA1 and BRCA2, dramatically increase the risk of developing multiple neoplasms (e.g. breast, ovarian, prostate and pancreatic cancers )². In addition, somatic and germline mutations in one of these genes confer a strong sensitivity to DNA-damaging agents (e.g. platinum salts): these fundamental observations led researchers to successfully study and test pharmacological inhibition of the DDR pathway, using PARPi [2].Of note, it has been calculated that approximately 12% of metastatic, castration-resistant prostate cancer (mCRPC) patients harbor germline DDR mutations, while 20–25% harbor somatic DDR mutations. Overall, it is estimated that in almost 22.7% of mCRPC patients could be identified mutations in DDR-related genes, making them a considerable number of people who could take an advantage from PARPi administration [3].In 2014, the U.S. Food and Drug Administration (FDA) granted approval to Olaparib as the first PARPi viable for women suffering from BRCA 1–2 mutated metastatic ovarian cancer both for cases previously treated with three or more lines of chemotherapy, and also as maintenance therapy following platinum-based chemotherapy [2]. Since that, following the consistent results described by subsequent clinical trials, Olaparib and other PARPi (e.g. Rucaparib, Niraparib) gained approval for different clinical settings in ovarian cancer and for BRCA-mutated breast, pancreatic and prostate cancer [2].In 2020, thanks to the outstanding results of the PROFound trial, the FDA approved the administration of Olaparib in patients with metastatic castration-resistant prostate cancer (mCRPC) progressing after therapy with enzalutamide or abiraterone and harboring mutations in HR-related genes [4]. Later the same year, the European Medicines Agency (EMA) recommended Olaparib in the same setting, with a slight but substantial difference: the main requirement was the identification of a BRCA 1 and BRCA 2 mutation (somatic or germline) in prostate cancer patients who have progressed to a prior therapy that included a new hormonal agent [5].Similarly, Rucaparib received the FDA accelerated approval after the publication of the TRITON2 study, that showed consistent overall response rate (ORR) and Prostate Specific Antigen (PSA) response rate values in patients with BRCA 1 and BRCA2 alterations [6].Nevertheless, it is well known that DDR mechanisms, including homologous repair (HR), are characterized by the interplay of a huge number of enzymes, co-factors, and molecules, not only BRCA1 and BRCA2 [2,5]. Specifically, HR requires the intervention of co-factors as PALB2 (Partner And Localizer Of BRCA2) and RAD51 (RAD51 Recombinase) to perform an accurate repair of double strand DNA breaks. In addition, BRCA1 and BRCA2 exhibit a crucial role during the S phase of the cell cycle, as protectors of the replication fork from the degradation activity carried out by nucleases. This is why, although PARPi seem to be more effective against BRCA1 and 2 mutations, data extrapolated from clinical trials suggest a benefit also for people harboring alterations in others genes, such as PALB2, RAD51 and ATM (Ataxia-Telangectasia Mutated) [2]. The PROFound trial, considered as a milestone, enlightened this aspect and its possible implications in prostate cancer: administering Olaparib to the whole cohort of HR-deficient patients could extend the survival benefit to a significant number of people, albeit the subgroup of BRCA1 and BRCA2 mutated cohort might have generated an overestimation of this effect in that trial [7]. Further studies need to be carried out in order to perform a correct prognostic and predictive gene-signature based stratification of patients.One of major concerns related to anti-cancer drugs, particularly targeted therapies, is drug-resistance. Even PARPi, although frequently characterized by initial good responses, ultimately loose their effectiveness, leading to disease relapse [2]. The reason is that cancerous cells learn how to escape from the pharmacological attack of PARPi via several mechanisms: upregulation of drug efflux pumps; mutations of the drug target; recovery of BRCA1 and BRCA2 function; re-establishment of replication fork stability [2,8]. The deep knowledge of these mechanisms could lead to overcome drug resistance: the most appealing hypothesis to get through this barrier appears to combine PARPi with agents affecting HR from other sides, such as Vascular Endothelial Growth Factor (VEGF) inhibitors, for which some encouraging data have been published in a cohort of ovarian cancer patients [2]. An interesting observation is also that HR deficient cancers might exhibit a high tumor mutational burden, often associated with an improved sensitivity to immunotherapy. Thus, clinical trials are now investigating the combination of PARPi and immune check-point inhibitors (ICIs) in mCRPC [9].Furthermore, several trials are ongoing to evaluate the efficacy of the combination of PARPi and new hormone agents (i.e. Abiraterone acetate, Enzalutamide) for metastatic prostate cancer, both in the hormone-sensitive and castration-resistant phases.Unfortunately, most of data concerning combination therapies were extrapolated from preliminary analyses of clinical trials, with many open issues still remaining. Firstly, drug safety: as previously stated in a phase I/II clinical trial, the addition of ICIs to PARPi seems to be well tolerated with no significant increase of severe adverse effects; at the same time, the administration of PARPi plus Abiraterone in mCRPC patients was investigated in a randomized, double-blind, placebo controlled phase II clinical trial, obtaining promising results in term of safety and also efficacy [2,10]. Another major concern regards the need to identify reliable biomarkers predictive of drug response, and this must be one of the addresses of future researches [1,2]. The last issue involves health care costs of such combinations therapies, again emphasizing the importance to perform a thorough stratification of mCRPC patients. [2]. These might be some branches for future researches, to explore where and when to combine PARPi with other agents, and in which patients subgroup [1,2,9].We have now several weapons in our hands, ready to be used, the most important represented by genomic analyses techniques [2]. In addition, following that principle of synthetic lethality, we need to hit cellular DNA repairing system from many sides, employing old and new drugs. The only way to cope with this huge amount of data is to team up with different professional figures (e.g. biotechnologists, pharmacologists, biostatisticians), constructing a cooperative network system. Only by doing this we will make it up to the mountain.

Palate morphogenesis: Current understanding and future directions

In the past, most scientists conducted their inquiries of nature via inductivism, the patient accumulation of “pieces of information” in the pious hope that the sum of the parts would clarify the whole. Increasingly, modern biology employs the tools of bioinformatics and systems biology in attempts to reveal the “big picture.” Most successful laboratories engaged in the pursuit of the secrets of embryonic development, particularly those whose research focus is craniofacial development, pursue a middle road where research efforts embrace, rather than abandon, what some have called the “pedestrian” qualities of inductivism, while increasingly employing modern data mining technologies. The secondary palate has provided an excellent paradigm that has enabled examination of a wide variety of developmental processes. Examination of cellular signal transduction, as it directs embryogenesis, has proven exceptionally revealing with regard to clarification of the “facts” of palatal ontogeny—at least the facts as we currently understand them. Herein, we review the most basic fundamentals of orofacial embryology and discuss how functioning of TGFβ, BMP, Shh, and Wnt signal transduction pathways contributes to palatal morphogenesis. Our current understanding of palate medial edge epithelial differentiation is also examined. We conclude with a discussion of how the rapidly expanding field of epigenetics, particularly regulation of gene expression by miRNAs and DNA methylation, is critical to control of cell and tissue differentiation, and how examination of these epigenetic processes has already begun to provide a better understanding of, and greater appreciation for, the complexities of palatal morphogenesis. Birth Defects Research (Part C) 90:133–154, 2010. © 2010 Wiley‐Liss, Inc.     

Ecological traps: current evidence and future directions

Ecological traps, which occur when animals mistakenly prefer habitats where their fitness is lower than in other available habitats following rapid environmental change, have important conservation and management implications. Empirical research has focused largely on assessing the behavioural effects of traps, by studying a small number of geographically close habitat patches. Traps, however, have also been defined in terms of their population-level effects (i.e. as preferred habitats of sufficiently low quality to cause population declines), and this is the scale most relevant for management. We systematically review the ecological traps literature to (i) describe the geographical and taxonomic distribution of efforts to study traps, (ii) examine how different traps vary in the strength of their effects on preference and fitness, (iii) evaluate the robustness of methods being used to identify traps, and (iv) determine whether the information required to assess the population-level consequences of traps has been considered. We use our results to discuss key knowledge gaps, propose improved methods to study traps, and highlight fruitful avenues for future research.     

Cancer metabolism: current perspectives and future directions

Cellular metabolism influences life and death decisions. An emerging theme in cancer biology is that metabolic regulation is intricately linked to cancer progression. In part, this is due to the fact that proliferation is tightly regulated by availability of nutrients. Mitogenic signals promote nutrient uptake and synthesis of DNA, RNA, proteins and lipids. Therefore, it seems straight-forward that oncogenes, that often promote proliferation, also promote metabolic changes. In this review we summarize our current understanding of how ‘metabolic transformation'' is linked to oncogenic transformation, and why inhibition of metabolism may prove a cancer′s ‘Achilles'' heel''. On one hand, mutation of metabolic enzymes and metabolic stress sensors confers synthetic lethality with inhibitors of metabolism. On the other hand, hyperactivation of oncogenic pathways makes tumors more susceptible to metabolic inhibition. Conversely, an adequate nutrient supply and active metabolism regulates Bcl-2 family proteins and inhibits susceptibility to apoptosis. Here, we provide an overview of the metabolic pathways that represent anti-cancer targets and the cell death pathways engaged by metabolic inhibitors. Additionally, we will detail the similarities between metabolism of cancer cells and metabolism of proliferating cells.     

Kabat Database and its applications: future directions

The Kabat Database was initially started in 1970 to determine the combining site of antibodies based on the available amino acid sequences. The precise delineation of complementarity determining regions (CDR) of both light and heavy chains provides the first example of how properly aligned sequences can be used to derive structural and functional information of biological macromolecules. This knowledge has subsequently been applied to the construction of artificial antibodies with prescribed specificities, and to many other studies. The Kabat database now includes nucleotide sequences, sequences of T cell receptors for antigens (TCR), major histocompatibility complex (MHC) class I and II molecules, and other proteins of immunological interest. While new sequences are continually added into this database, we have undertaken the task of developing more analytical methods to study the information content of this collection of aligned sequences. New examples of analysis will be illustrated on a yearly basis. The Kabat Database and its applications are freely available at http://immuno.bme.nwu.edu.