Orthologs at the Base of the Olfactores Clade.

Tunicate orthologs in the human genome comprise just 84 genes of the 19,872 protein-coding genes and 23 of the 16,528 non-coding genes, yet they stand at the base of the Olfactores clade, which radiated to generate thousands of tunicate and vertebrate species. What were the powerful drivers among these genes that enabled this process? Many of these orthologs are present in gene families. We discuss the biological role of each family and the orthologs' quantitative contribution to the family. Most important was the evolution of a second type of cadherin. This, a Type II cadherin, had the property of detaching the cell containing that cadherin from cells that expressed the Type I class. The set of such Type II cadherins could now detach and move away from their Type I neighbours, a process which would eventually evolve into the formation of the neural crest, "the fourth germ layer", providing a wide range of possibilities for further evolutionary invention. A second important contribution were key additions to the broad development of the muscle and nerve protein and visual perception toolkits. These developments in mobility and vision provided the basis for the development of the efficient predatory capabilities of the Vertebrata.

Temperature Dependence of Relativistic Valence Band Splitting Induced by an Altermagnetic Phase Transition.

Altermagnetic (AM) materials exhibit non-relativistic, momentum-dependent spin-split states, ushering in new opportunities for spin electronic devices. While the characteristics of spin-splitting are documented within the framework of the non-relativistic spin group symmetry, there is limited exploration of the inclusion of relativistic symmetry and its impact on the emergence of a novel spin-splitting in the band structure. This study delves into the intricate relativistic electronic structure of an AM material, α-MnTe. Employing temperature-dependent angle-resolved photoelectron spectroscopy across the AM phase transition, the emergence of a relativistic valence band splitting concurrent with the establishment of magnetic order is elucidated. This discovery is validated through disordered local moment calculations, modeling the influence of magnetic order on the electronic structure and confirming the magnetic origin of the observed splitting. The temperature-dependent splitting is ascribed to the advent of relativistic spin-splitting resulting from the strengthening of AM order in α-MnTe as the temperature decreases. This sheds light on a previously unexplored facet of this intriguing material.

Assessing the effectiveness of a DASH diet in hypertensive patients attending the Ngaoundere Regional Hospital - Cameroon: a case-control study.

Hypertension remains a public health issue in Cameroon, though lifestyle and dietetic measures are the main approaches for the prevention and management of hypertension. The present study aimed at evaluating the impact of a Dietary Approaches to Stop Hypertension (DASH) diet using local foodstuffs on the status of hypertensive patients at the Ngaoundere Regional Hospital. A case-control study was carried out with 160 hypertensive patients divided into two groups, a test and a control group. A food questionnaire was used to evaluate the food habits of patients and design the sheet of the DASH diet to provide a maximum of 2000 kcal/d. The DASH diet was administered to the test group (eighty-eight patients), while the control group (seventy-two patients) consumed their normal diet. Both groups were followed up for 8 weeks. The systolic and diastolic blood pressures (SBP, DBP), body mass index (BMI), triglycerides, HDL-c, LDL-c and total-cholesterol levels of patients of the two groups were measured before and after the intervention. The results indicate that the DASH diet improves all the markers of hypertension in the test group with significant decreases in BMI, SBP, DBP, LDL-c and total-cholesterol. Patients of the control group had fourteen and seven times more risk of having increased systolic and diastolic pressures, respectively, and are thus exposed to hypertension complications. The DASH diet established in this study is therefore effective for the management of hypertension.

Ancient lineages of the keratin-associated protein (KRTAP) genes and their co-option in the evolution of the hair follicle.

BLAST searches against the human genome showed that of the 93 keratin-associated proteins (KRTAPs) of Homo sapiens, 53 can be linked by sequence similarity to an H. sapiens metallothionein and 16 others can be linked similarly to occludin, while the remaining KRTAPs can themselves be linked to one or other of those 69 directly-linked proteins. The metallothionein-linked KRTAPs comprise the high-sulphur and ultrahigh-sulphur KRTAPs and are larger than the occludin-linked set, which includes the tyrosine- and glycine-containing KRTAPs. KRTAPs linked to metallothionein appeared in increasing numbers as evolution advanced from the deuterostomia, where KRTAP-like proteins with strong sequence similarity to their mammalian congeners were found in a sea anemone and a starfish. Those linked to occludins arose only with the later-evolved mollusca, where a KRTAP homologous with its mammalian congener was found in snails. The presence of antecedents of the mammalian KRTAPs in a starfish, a sea anemone, snails, fish, amphibia, reptiles and birds, all of them animals that lack hair, suggests that some KRTAPs may have a physiological role beyond that of determining the characteristics of hair fibres. We suggest that homologues of these KRTAPs found in non-hairy animals were co-opted by placodes, formed by the ectodysplasin pathway, to produce the first hair-producing cells, the trichocytes of the hair follicles.

During evolution from the earliest tetrapoda, newly-recruited genes are increasingly paralogues of existing genes and distribute non-randomly among the chromosomes.

BACKGROUND: The present availability of full genome sequences of a broad range of animal species across the whole range of evolutionary history enables one to ask questions as to the distribution of genes across the chromosomes. Do newly recruited genes, as new clades emerge, distribute at random or at non-random locations? RESULTS: We extracted values for the ages of the human genes and for their current chromosome locations, from published sources. A quantitative analysis showed that the distribution of newly-added genes among and within the chromosomes appears to be increasingly non-random if one observes animals along the evolutionary series from the precursors of the tetrapoda through to the great apes, whereas the oldest genes are randomly distributed. CONCLUSIONS: Randomization will result from chromosome evolution, but less and less time is available for this process as evolution proceeds. Much of the bunching of recently-added genes arises from new gene formation as paralogues in gene families, near the location of genes that were recruited in the preceding phylostratum. As examples we cite the KRTAP, ZNF, OR and some minor gene families. We show that bunching can also result from the evolution of the chromosomes themselves when, as for the KRTAP genes, blocks of genes that had previously been on disparate chromosomes become linked together.

Histopathological Evaluation and Analysis of Immunohistochemical Expression of Bcl-2 Oncoprotein in Colorectal Carcinoma.

BACKGROUND & OBJECTIVE: Colorectal cancer is the third most prevalent malignancy with high mortality rate, necessitating markers that predict survival and guide the treatment. Previous studies have examined the immunohistochemical expression of Bcl-2, an apoptotic marker, in colorectal carcinoma, but results have been contradictory. To evaluate the histopathological features of colorectal carcinoma, immunohistochemical expression of Bcl-2 must be analyzed to find out statistical association of Bcl-2 expression with certain prognostic factors histopathologic type, grade and TNM staging. METHODS: This prospective study was conducted on the colectomy specimens of colorectal carcinoma, over a period of two years. The tumor morphology and Bcl-2 status were evaluated by immunohistochemistry in each case. RESULTS: The study included 58 cases, with mean patient age of 47.07 years and male: female ratio of 1.89:1. Bcl-2 positivity was seen in 32.7% of the cases. Weak, moderate, and strong expression of Bcl-2 was seen in 12.1%, 12.1%, and 8.5% of cases respectively. Even though early stages of colorectal carcinoma showed greater frequency of Bcl-2 expression than advanced stages (36.3% versus 28%), however this association was not statistically significant. CONCLUSION: Lack of statistically significant correlation between Bcl-2 immuno-histochemical expression and prognostic parameters like tumor grade and stage, suggests that Bcl-2 immunoexpression may not be a significant prognostic marker in colorectal carcinoma.

Adjuvant and neoadjuvant cancer therapies: A historical review and a rational approach to understand outcomes.

Drug development in oncology usually establishes efficacy in metastatic disease before advancing a therapy to the adjuvant or neoadjuvant settings. Unfortunately, too often use in adjuvant or neoadjuvant settings fails to improve overall survival. Reasons for the modest benefits include the fact that in many cases surgery cures a majority of patients making it difficult to demonstrate gains. We begin by looking at the history of adjuvant and neoadjuvant therapies and the principles guiding their development. We summarize accepted adjuvant and neoadjuvant therapies in several cancers and tabulate their outcomes. Then, extending our work on the growth and regression rate constants of tumors and the fraction of cells killed we demonstrate that therapies developed in the metastatic setting primarily delay tumor growth rather than kill more cells and argue this is a likely explanation for poor outcomes in adjuvant or neoadjuvant settings. We suggest a rational approach for enhancing success.

The ages of the cancer-associated genes.

In the accompanying manuscript (Litman and Stein, 2018) we list the ages of all the protein-coding genes and of many of the noncoding genes of the human genome. The present manuscript uses those results to derive the ages of the genes on the COSMIC list of somatic mutations in cancer. The lymphoma-associated genes in the COSMIC list are younger than the sarcoma-associated or the carcinoma-associated genes, or the genes shared by lymphomas and carcinomas. Genes that accreted to the evolving genome with the appearance of the fish are major contributors to the sarcoma-, lymphoma-, or carcinoma-associated gene sets, but it is genes accreted during the development of multicellularity that contribute most to the genes common to the classes. Genes arising with the evolution of the fish are also dominant in a list of noncoding genes associated with cancer. A list is provided of the COSMIC genes which have not yet been reported as drug targets.

Obtaining estimates for the ages of all the protein-coding genes and most of the ontology-identified noncoding genes of the human genome, assigned to 19 phylostrata.

Following Liebeskind et al [1], we have attempted to find consensus ages for the protein-coding and the noncoding genes of the human genome, using publicly-available ortholog databases. For each database separately, we determined its age estimate for the genes it listed, determining this by identifying the earliest ortholog for the gene in question. We assigned these ages to 1 of the 19 major phylostrata defined by Domazet-Loso and Tautz [2], 2 of which were further subdivided. From these various estimates, we found the modal value if 1 was present, defining this as the consensus age for the gene. For the genes where no consensus value could be found, we recorded the median value of the age estimates across the databases interrogated. We present a resource that lists the age, as so defined, of every one of the 19,660 protein-coding genes and of 5,981 of the 16,528 non-protein-coding genes of the human genome, the age being the time when the gene was accreted to the evolving human genome. We calculate the number of genes that accreted to the genome, epoch by epoch, and consider the rate at which they accreted.

Iron is a substrate of the Plasmodium falciparum chloroquine resistance transporter PfCRT in Xenopus oocytes.

The chloroquine resistance transporter of the human malaria parasite Plasmodium falciparum, PfCRT, is an important determinant of resistance to several quinoline and quinoline-like antimalarial drugs. PfCRT also plays an essential role in the physiology of the parasite during development inside erythrocytes. However, the function of this transporter besides its role in drug resistance is still unclear. Using electrophysiological and flux experiments conducted on PfCRT-expressing Xenopus laevis oocytes, we show here that both wild-type PfCRT and a PfCRT variant associated with chloroquine resistance transport both ferrous and ferric iron, albeit with different kinetics. In particular, we found that the ability to transport ferrous iron is reduced by the specific polymorphisms acquired by the PfCRT variant as a result of chloroquine selection. We further show that iron and chloroquine transport via PfCRT is electrogenic. If these findings in the Xenopus model extend to P. falciparum in vivo, our data suggest that PfCRT might play a role in iron homeostasis, which is essential for the parasite's development in erythrocytes.

Estimation of tumour regression and growth rates during treatment in patients with advanced prostate cancer: a retrospective analysis.

BACKGROUND: We applied mathematical models to clinical trial data available at Project Data Sphere LLC (Cary, NC, USA), a non-profit universal access data-sharing warehouse. Our aim was to assess the rates of cancer growth and regression using the comparator groups of eight randomised clinical trials that enrolled patients with metastatic castration-resistant prostate cancer. METHODS: In this retrospective analysis, we used data from eight randomised clinical trials with metastatic castration-resistant prostate cancer to estimate the growth (g) and regression (d) rates of disease burden over time. Rates were obtained by applying mathematical models to prostate-specific antigen levels as the representation of tumour quantity. Rates were compared between study interventions (prednisone, mitoxantrone, and docetaxel) and off-treatment data when on-study treatment had been discontinued to understand disease behaviour during treatment and after discontinuation. Growth (g) was examined for association with a traditional endpoint (overall survival) and for its potential use as an endpoint to reduce sample size in clinical trials. FINDINGS: Estimates for g, d, or both were obtained in 2353 (88%) of 2678 patients with data available for analysis; g differentiated docetaxel (a US Food and Drug Administration-approved therapy) from prednisone and mitoxantrone and was predictive of overall survival in a landmark analysis at 8 months. A simulated sample size analysis, in which g was used as the endpoint, compared docetaxel data with mitoxantrone data and showed that small sample sizes were sufficient to achieve 80% power (16, 47, and 25 patients, respectively, in the three docetaxel comparator groups). Similar results were found when the mitoxantrone data were compared with the prednisone data (41, 39, and 41 patients in the three mitoxantrone comparator groups). Finally, after discontinuation of docetaxel therapy, median tumour growth (g) increased by nearly five times. INTERPRETATION: The application of mathematical models to existing clinical data allowed estimation of rates of growth and regression that provided new insights in metastatic castration-resistant prostate cancer. The availability of clinical data through initiatives such as Project Data Sphere, when combined with innovative modelling techniques, could greatly enhance our understanding of how cancer responds to treatment, and accelerate the productivity of clinical development programmes. FUNDING: None.

Mitogen-activated protein kinase signaling causes malignant melanoma cells to differentially alter extracellular matrix biosynthesis to promote cell survival.

BACKGROUND: Intrinsic and acquired resistance to drug therapies remains a challenge for malignant melanoma patients. Intratumoral heterogeneities within the tumor microenvironment contribute additional complexity to the determinants of drug efficacy and acquired resistance. METHODS: We use 3D biomimetic platforms to understand dynamics in extracellular matrix (ECM) biogenesis following pharmaceutical intervention against mitogen-activated protein kinases (MAPK) signaling. We further determined temporal evolution of secreted ECM components by isogenic melanoma cell clones. RESULTS: We found that the cell clones differentially secrete and assemble a myriad of ECM molecules into dense fibrillar and globular networks. We show that cells can modulate their ECM biosynthesis in response to external insults. Fibronectin (FN) is one of the key architectural components, modulating the efficacy of a broad spectrum of drug therapies. Stable cell lines engineered to secrete minimal levels of FN showed a concomitant increase in secretion of Tenascin-C and became sensitive to BRAF(V600E) and ERK inhibition as clonally- derived 3D tumor aggregates. These cells failed to assemble exogenous FN despite maintaining the integrin machinery to facilitate cell- ECM cross-talk. We determined that only clones that increased FN production via p38 MAPK and ß1 integrin survived drug treatment. CONCLUSIONS: These data suggest that tumor cells engineer drug resistance by altering their ECM biosynthesis. Therefore, drug treatment may induce ECM biosynthesis, contributing to de novo resistance.

NUAK2 Amplification Coupled with PTEN Deficiency Promotes Melanoma Development via CDK Activation.

The AMPK-related kinase NUAK2 has been implicated in melanoma growth and survival outcomes, but its therapeutic utility has yet to be confirmed. In this study, we show how its genetic amplification in PTEN-deficient melanomas may rationalize the use of CDK2 inhibitors as a therapeutic strategy. Analysis of array-CGH data revealed that PTEN deficiency is coupled tightly with genomic amplification encompassing the NUAK2 locus, a finding strengthened by immunohistochemical evidence that phospho-Akt overexpression was correlated with NUAK2 expression in clinical specimens of acral melanoma. Functional studies in melanoma cells showed that inactivation of the PI3K pathway upregulated p21 expression and reduced the number of cells in S phase. NUAK2 silencing and inactivation of the PI3K pathway efficiently controlled CDK2 expression, whereas CDK2 inactivation specifically abrogated the growth of NUAK2-amplified and PTEN-deficient melanoma cells. Immunohistochemical analyses confirmed an association of CDK2 expression with NUAK2 amplification and p-Akt expression in melanomas. Finally, pharmacologic inhibition of CDK2 was sufficient to suppress the growth of NUAK2-amplified and PTEN-deficient melanoma cells in vitro and in vivo. Overall, our results show how CDK2 blockade may offer a promising therapy for genetically defined melanomas, where NUAK2 is amplified and PTEN is deleted.

Multiple drugs compete for transport via the Plasmodium falciparum chloroquine resistance transporter at distinct but interdependent sites.

Mutations in the "chloroquine resistance transporter" (PfCRT) are a major determinant of drug resistance in the malaria parasite Plasmodium falciparum. We have previously shown that mutant PfCRT transports the antimalarial drug chloroquine away from its target, whereas the wild-type form of PfCRT does not. However, little is understood about the transport of other drugs via PfCRT or the mechanism by which PfCRT recognizes different substrates. Here we show that mutant PfCRT also transports quinine, quinidine, and verapamil, indicating that the protein behaves as a multidrug resistance carrier. Detailed kinetic analyses revealed that chloroquine and quinine compete for transport via PfCRT in a manner that is consistent with mixed-type inhibition. Moreover, our analyses suggest that PfCRT accepts chloroquine and quinine at distinct but antagonistically interacting sites. We also found verapamil to be a partial mixed-type inhibitor of chloroquine transport via PfCRT, further supporting the idea that PfCRT possesses multiple substrate-binding sites. Our findings provide new mechanistic insights into the workings of PfCRT, which could be exploited to design potent inhibitors of this key mediator of drug resistance.

Therapies with diverse mechanisms of action kill cells by a similar exponential process in advanced cancers.

Successful cancer treatments are generally defined as those that decrease tumor quantity. In many cases, this decrease occurs exponentially, with deviations from a strict exponential being attributed to a growing fraction of drug-resistant cells. Deviations from an exponential decrease in tumor quantity can also be expected if drugs have a nonuniform spatial distribution inside the tumor, for example, because of interstitial pressure inside the tumor. Here, we examine theoretically different models of cell killing and analyze data from clinical trials based on these models. We show that the best description of clinical outcomes is by first-order kinetics with exponential decrease of tumor quantity. We analyzed the total tumor quantity in a diverse group of clinical trials with various cancers during the administration of different classes of anticancer agents and in all cases observed that the models that best fit the data describe the decrease of the sensitive tumor fraction exponentially. The exponential decrease suggests that all drug-sensitive cancer cells have a single rate-limiting step on the path to cell death. If there are intermediate steps in the path to cell death, they are not rate limiting in the observational time scale utilized in clinical trials--tumor restaging at 6- to 8-week intervals. On shorter time scales, there might be intermediate steps, but the rate-limiting step is the same. Our analysis, thus, points to a common pathway to cell death for cancer cells in patients. See all articles in this Cancer Research section, "Physics in Cancer Research."

A HECT ubiquitin-protein ligase as a novel candidate gene for altered quinine and quinidine responses in Plasmodium falciparum.

The emerging resistance to quinine jeopardizes the efficacy of a drug that has been used in the treatment of malaria for several centuries. To identify factors contributing to differential quinine responses in the human malaria parasite Plasmodium falciparum, we have conducted comparative quantitative trait locus analyses on the susceptibility to quinine and also its stereoisomer quinidine, and on the initial and steady-state intracellular drug accumulation levels in the F1 progeny of a genetic cross. These data, together with genetic screens of field isolates and laboratory strains associated differential quinine and quinidine responses with mutated pfcrt, a segment on chromosome 13, and a novel candidate gene, termed MAL7P1.19 (encoding a HECT ubiquitin ligase). Despite a strong likelihood of association, episomal transfections demonstrated a role for the HECT ubiquitin-protein ligase in quinine and quinidine sensitivity in only a subset of genetic backgrounds, and here the changes in IC50 values were moderate (approximately 2-fold). These data show that quinine responsiveness is a complex genetic trait with multiple alleles playing a role and that more experiments are needed to unravel the role of the contributing factors.

Diverse mutational pathways converge on saturable chloroquine transport via the malaria parasite's chloroquine resistance transporter.

Mutations in the chloroquine resistance transporter (PfCRT) are the primary determinant of chloroquine (CQ) resistance in the malaria parasite Plasmodium falciparum. A number of distinct PfCRT haplotypes, containing between 4 and 10 mutations, have given rise to CQ resistance in different parts of the world. Here we present a detailed molecular analysis of the number of mutations (and the order of addition) required to confer CQ transport activity upon the PfCRT as well as a kinetic characterization of diverse forms of PfCRT. We measured the ability of more than 100 variants of PfCRT to transport CQ when expressed at the surface of Xenopus laevis oocytes. Multiple mutational pathways led to saturable CQ transport via PfCRT, but these could be separated into two main lineages. Moreover, the attainment of full activity followed a rigid process in which mutations had to be added in a specific order to avoid reductions in CQ transport activity. A minimum of two mutations sufficed for (low) CQ transport activity, and as few as four conferred full activity. The finding that diverse PfCRT variants are all limited in their capacity to transport CQ suggests that resistance could be overcome by reoptimizing the CQ dosage.

Appendiceal Carcinoma with Krukenberg's Tumour Mimicking Primary Ovarian Cancer.

Appendiceal adenocarcinoma (AACa) is a rare tumour which represents 0.5% of all gastrointestinal malignancies. The prognosis is poor, because it is usually found at an advanced stage, that in turn, is partly due to a low threshold of suspicion and difficulties in diagnosis prior to surgery. It may occasionally demonstrate ovarian metastases that are large and which dominate the clinical and radiological presentations, leading to a misdiagnosis of an ovarian primary malignancy. We are reporting a case of an occult AACa which manifested clinically as a primary ovarian cancer which was at an advanced stage. Staging laparatomy revealed large bilateral ovarian tumours of clinical FIGO Stage III, with presumed appendiceal implants. Histological examination revealed a mucinous adenocarcinoma with a signet ring component, which involved bilateral ovaries and the appendix transmurally. Immunophenotypic analysis revealed a positive expression of CK 20 and CDX 2 and absence of CK 7 staining, which was compatible with appendiceal primary and ovarian metastases. The diagnosis was subsequently revised to AACa with Krukenberg's metastasis, Stage IV. Although AACas are uncommon, they should be considered in the differential diagnosis of intraabdominal masses and the distinction between ovarian and appendiceal primary malignancies is critical, as the treatment modalities vary.

Sunitinib does not accelerate tumor growth in patients with metastatic renal cell carcinoma.

Preclinical studies have suggested that sunitinib accelerates metastases in animals, ascribing this to inhibition of the vascular endothelial growth factor receptor or the tumor's adaptation. To address whether sunitinib accelerates tumors in humans, we analyzed data from the pivotal randomized phase III trial comparing sunitinib and interferon alfa in patients with metastatic renal cell carcinoma. The evidence clearly shows that sunitinib was not harmful, did not accelerate tumor growth, and did not shorten survival. Specifically, neither longer sunitinib treatment nor a greater effect of sunitinib on tumors reduced survival. Sunitinib did reduce the tumor's growth rate while administered, thereby improving survival, without appearing to alter tumor biology after discontinuation. Concerns arising from animal models do not apply to patients receiving sunitinib and likely will not apply to similar agents.

Analyzing the pivotal trial that compared sunitinib and IFN-α in renal cell carcinoma, using a method that assesses tumor regression and growth.

PURPOSE: We applied a method that analyzes tumor response, quantifying the rates of tumor growth (g) and regression (d), using tumor measurements obtained while patients receive therapy. We used data from the phase III trial comparing sunitinib and IFN-α in metastatic renal cell carcinoma (mRCC) patients. METHODS: The analysis used an equation that extracts d and g. RESULTS: For sunitinib, overall survival (OS) was strongly correlated with log g (Rsq = 0.44, P < 0.0001); much less with log d (Rsq = 0.04; P = 0.0002). The median g of tumors in these patients (0.00082 per days; log g = -3.09) was about half that (P < 0.001) of tumors in patients receiving IFN-α (0.0015 per day; log g = -2.81). With IFN-α, the OS/log g correlation (Rsq = 0.14) was weaker. Values of g from measurements obtained by study investigators or central review were highly correlated (Rsq = 0.80). No advantage resulted in including data from central review in regressions. Furthermore, g can be estimated accurately four months before treatment discontinuation. Extrapolating g in a model that incorporates survival generates the hypothesis that g increased after discontinuation of sunitinib but did not accelerate. CONCLUSIONS: In patients with mRCC, sunitinib reduced tumor growth rate, g, more than did IFN-α. Correlating g with OS confirms earlier analyses suggesting g may be an important clinical trial endpoint, to be explored prospectively and in individual patients.