Multimodal analysis of methylomics and fragmentomics in plasma cell-free DNA for multi-cancer early detection and localization

Despite their promise, circulating tumor DNA (ctDNA)-based assays for multi-cancer early detection face challenges in test performance, due mostly to the limited abundance of ctDNA and its inherent variability. To address these challenges, published assays to date demanded a very high-depth sequencing, resulting in an elevated price of test. Herein, we developed a multimodal assay called SPOT-MAS (screening for the presence of tumor by methylation and size) to simultaneously profile methylomics, fragmentomics, copy number, and end motifs in a single workflow using targeted and shallow genome-wide sequencing (~0.55×) of cell-free DNA. We applied SPOT-MAS to 738 non-metastatic patients with breast, colorectal, gastric, lung, and liver cancer, and 1550 healthy controls. We then employed machine learning to extract multiple cancer and tissue-specific signatures for detecting and locating cancer. SPOT-MAS successfully detected the five cancer types with a sensitivity of 72.4% at 97.0% specificity. The sensitivities for detecting early-stage cancers were 73.9% and 62.3% for stages I and II, respectively, increasing to 88.3% for non-metastatic stage IIIA. For tumor-of-origin, our assay achieved an accuracy of 0.7. Our study demonstrates comparable performance to other ctDNA-based assays while requiring significantly lower sequencing depth, making it economically feasible for population-wide screening.

Pebbles and sand on asteroid (162173) Ryugu: In situ observation and particles returned to Earth

The Hayabusa2 spacecraft investigated the C-type (carbonaceous) asteroid (162173) Ryugu. The mission performed two landing operations to collect samples of surface and subsurface material, the latter exposed by an artificial impact. We present images of the second touchdown site, finding that ejecta from the impact crater was present at the sample location. Surface pebbles at both landing sites show morphological variations ranging from rugged to smooth, similar to Ryugu's boulders, and shapes from quasi-spherical to flattened. The samples were returned to Earth on 6 December 2020. We describe the morphology of >5 grams of returned pebbles and sand. Their diverse color, shape, and structure are consistent with the observed materials of Ryugu; we conclude that they are a representative sample of the asteroid.

Characteristics of severe malaria in hospitalized children in Ho Chi Minh City from 2012 to 2019

In Vietnam, severe malaria is currently rare but is a life-threatening disease. It may be misdiagnosed with other common diseases. This descriptive study aimed to characterize severe malaria and its clinical aspects, as well as outcomes of infected pediatric patients to improve case management. The case-series study was carried out based on medical records of children aged between one month and 15 years with malaria diagnosed by blood smear or rapid diagnostic test. Chi-squared test with the p values less than 0.05 were considered statistically significant. There were 47 cases enrolled in the study. The prevalence of severe malaria was 29.8% (57.1% in children under five). The morbidity was 71.4% in male and 28.6% in female. Common clinical signs of severe malaria were fever (100%), severe anemia (21.4%), hepatomegaly (85.7%), and splenomegaly (71.4%). Common biological abnormalities in severe malaria were anemia, thrombocytopenia, increased liver enzymes, and high CRP level. The severe malaria was mainly caused by P. falciparum (100%). The age range for those infected with P. falciparum was 6.5 ± 4.5 years (min 0.3; max 14.9). The successful rate of treatment was 92.9% with artesunate. Antimalarial treatment time was 9.0 (6 - 12) days for severe malaria, which was twice as many as that for non-severe malaria (p = 0.067). The current clinical and biological findings of severe malaria are different from those in previous times, which make it easy to be overlooked. Therefore, it's important to perform malaria diagnostic tests when there're clinical suggestions of severe malaria, including fever, hepatomegaly or splenomegaly.

Inhibition of p38alpha MAPK enhances proteasome inhibitor-induced apoptosis of myeloma cells by modulating Hsp27, Bcl-X(L), Mcl-1 and p53 levels in vitro and inhibits tumor growth in vivo

Inhibition of p38 kinase blocks the production of tumor-promoting factors in the multiple myeloma (MM) bone marrow microenvironment. Proteasome inhibitors MG132 and bortezomib have been shown to have direct cytotoxic effects on MM cells. We show that a selective inhibitor of p38alpha, SCIO-469, enhances the ability of MG132 and bortezomib to induce the apoptosis of MM cells. Previously, we showed that p38 inhibition with SCIO-469 enhances MM cytotoxicity of bortezomib by inhibiting the transient expression and phosphorylation of Hsp27, a downstream target of p38. Here we show that continued treatment of MM cells with bortezomib leads to a SCIO-469-enhanced downregulation of Hsp27 and to increased MM apoptosis. Furthermore, we show that p38 inhibition enhances the bortezomib-induced MM apoptosis by upregulation of p53 and downregulation of Bcl-X(L) and Mcl-1. In a mouse xenograft plasmacytoma model of MM, we found that inhibiting p38 augments the effects of bortezomib in decreasing MM tumor growth in vivo. Thus, in addition to its role in suppressing an activated MM microenvironment, co-treatment with a p38 inhibitor, such as SCIO-469, may enhance the cytotoxicity of bortezomib by modulating pro-apoptotic and anti-apoptotic factors in MM cells, suggesting great potential for co-therapy.

Dysregulative lymphoma theory revisited; what can we learn from cytokines, CD classes and genes?

Based largely on animal experiments, a dysregulative lymphoma theory was designed some 15 years ago as a basis for computer simulation studies. The basic concept of this theory was that lymphomas arise when persistent immunostimulation coincides with some kind of immune deficiency. The present article reviews exemplary data from human lymphoma cases in an attempt to further support or to reject the hypothesis. T- and B-cell lymphomas according to the REAL classification were reviewed with regard to the functional effects of their CD markers and their ligands, interleukin activities and cytogenetic changes. The results are summarized and further discussed. Essentially in all cases, a combination of enhanced stimulation of lymphoid cells and functional deficiency is identified, thus supporting the general pathogenetic hypothesis of malignant lymphomas. Despite using the most modem lymphoma classification, however, lymphoma entities and theirfunctional changes are so heterogeneous that cases need to be studied individually when it comes to pathogenetic considerations.

A java-based application for differential diagnosis of hematopoietic neoplasms using immunophenotyping by flow cytometry

We describe the implementation of a Java-based application for differential diagnosis of hematopoietic neoplasms using immunophenotyping by flow cytometry. The current version of this Java applet includes the knowledge-base for 33 hematopoietic neoplasms and 43 diagnostic immunophenotyping markers. Java, a new object-oriented computing language, helps facilitate development of this applet, a platform-independent module that can be implemented on the World Wide Web. As the Web rapidly becomes more accessible to users around the world, Web-based software may eventually form the core of decision-support systems in clinical settings. Java-based applications, such as the one described in this paper, are expected to contribute significantly in this area.

Multistep phosphorelay proteins transmit oxidative stress signals to the fission yeast stress-activated protein kinase

In response to oxidative stress, eukaryotic cells induce transcription of genes required for detoxification of oxidants. Here we present evidence that oxidative stress stimuli are transmitted by a multistep phosphorelay system to the Spc1/Sty1 stress-activated protein kinase in the fission yeast Schizosaccharomyces pombe. The fission yeast mpr1(+) gene encodes a novel protein with a histidine-containing phosphotransfer domain homologous to the budding yeast Ypd1. Spc1 activation upon oxidative stress is severely impaired in the Deltampr1 mutant as well as in the mpr1HQ strain, in which the putative phosphorylation site Mpr1-His221 is substituted with glutamine. In response to oxidative stress, Mpr1 binds to the Mcs4 response regulator that functions upstream of the Spc1 cascade, suggesting that Mcs4 is a cognate response regulator for Mpr1. Unexpectedly, when exposed to hydrogen peroxide, Deltampr1 cells can induce the catalase gene ctt1(+), one of the transcriptional targets of the Spc1 pathway, and survive oxidative stress in the absence of significant Spc1 activation. We have found that Pap1, a bZIP transcription factor homologous to human c-Jun, can mediate induction of ctt1(+) expression upon oxidative stress independently of the Spc1 stress-activated protein kinase. These studies show that oxidative stress stimuli are transmitted by multiple pathways to induce specific gene expression.

A web-based teaching program for laboratory diagnosis of coagulation disorders

OBJECTIVE

To implement an interactive program for teaching coagulation disorders on the World Wide Web.

DESIGN AND RESULTS

The core materials in this program were derived from a personal computer software program previously designed by the authors. Three modules were developed in this program: (1) a coagulation profile to display typical results of coagulation screening tests for each disorder; (2) a differential diagnosis module to generate a list of diagnoses that fit the test results in a given case; and (3) a synopsis of coagulopathy and therapy to provide essential information on disorders and therapeutic options. A total of 41 coagulation disorders were included in the knowledge base.

CONCLUSIONS

Since the World Wide Web is increasingly more accessible to computer users, it has become an ideal medium for teaching purposes. Our experience with this program in teaching medical students and pathology residents at our institution has been very encouraging.

A relational database for diagnosis of hematopoietic neoplasms using immunophenotyping by flow cytometry

A relational database was developed to facilitate the diagnosis of hematopoietic neoplasms using results of immunophenotyping by flow cytometry. This database runs on personal computers and uses backward-chaining search to arrive at conclusions. Results of immunologic marker studies are processed by the database to obtain a set of differential diagnoses. The current version of this database includes diagnostic immunophenotyping pattern for 33 hematopoietic neoplasms. We tested this database using 92 clinical cases from 2 tertiary care medical centers. The database ranked the actual diagnosis as 1 of the top 5 differential diagnoses in 93% of the cases tested. The user can modify the database contents to suit individual needs. This database has been posted on the World Wide Web for direct access. We propose that this user-friendly database is a potential tool for computer-assisted diagnosis of hematopoietic neoplasms.

Heat-shock-induced activation of stress MAP kinase is regulated by threonine- and tyrosine-specific phosphatases

In eukaryotic species from yeast to human, stress-activated protein kinases (SAPKs), members of a MAP kinase (MAPK) subfamily, regulate the transcriptional response to various environmental stress. It is poorly understood how diverse forms of stress are sensed and transmitted to SAPKs. Here, we report the heat shock regulation of the fission yeast Spc1 SAPK, a homolog of human p38 and budding yeast Hog1p. Although osmostress and oxidative stress induce strong activation of the Wis1 MAPK kinase (MEK), which activates Spc1 through Thr-171/Tyr-173 phosphorylation, activation of Wis1 upon heat shock is relatively weak and transient. However, in heat-shocked cells, Pyp1, the major tyrosine phosphatase that dephosphorylates and inactivates Spc1, is inhibited for its interaction with Spc1, which leads to strong activation of Spc1. Subsequently, Spc1 activity is rapidly attenuated by Thr-171 dephosphorylation, whereas Tyr-173 remains phosphorylated. Thr-171 dephosphorylation is compromised in a strain lacking functional type 2C serine/threonine phosphatases (PP2C), Ptc1 and Ptc3. Moreover, Ptc1 and Ptc3 can dephosphorylate Thr-171 of Spc1 both in vivo and in vitro. These observations strongly suggest that PP2C enzymes play an important role in the attenuation of Spc1 activity in heat-shocked cells. Thus, transient activation of Spc1 upon heat shock is ensured by differential regulation of threonine and tyrosine phosphorylation.

Regulation of mammalian Shaker-related K+ channels: evidence for non-conducting closed and non-conducting inactivated states

1. Using the whole-cell recording mode we have characterized two non-conducting states in mammalian Shaker-related voltage-gated K+ channels induced by the removal of extracellular potassium, K+o. 2. In the absence of K+o, current through Kv1.4 was almost completely abolished due to the presence of a charged lysine residue at position 533 at the entrance to the pore. Removal of K+o had a similar effect on current through Kv1.3 when the histidine at the homologous position (H404) was protonated (pH 6.0). Channels containing uncharged residues at the corresponding position (Kv1.1: Y; Kv1.2: V) did not exhibit this behaviour. 3. To characterize the nature of the interaction between Kv1.3 and K+o concentration ([K+]o), we replaced H404 with amino acids of different character, size and charge. Substitution of hydrophobic residues (A, V and L) either in all four subunits or in only two subunits in the tetramer made the channel insensitive to the removal of K+o, possibly by stabilizing the channel complex. Replacement of H404 with the charged residue arginine, or the polar residue asparagine, enhanced the sensitivity of the channel to 0 mM K+o, possibly by making the channel unstable in the absence of K+o. Mutation at a neighbouring position (400) had a similar effect. 4. The effect of removing K+o on current amplitude does not seem to be correlated with the rate of C-type inactivation since the slowly inactivating G380F mutant channel exhibited a similar [K+]o dependence as the wild-type Kv1.3 channel. 5. CP-339,818, a drug that recognizes only the inactivated conformation of Kv1.3, could not block current in the absence of K+o unless the channels were inactivated through depolarizing pulses. 6. We conclude that removal of K+o induces the Kv1.3 channel to transition to a non-conducting 'closed' state which can switch into a non-conducting 'inactivated' state upon depolarization.

A rule-based expert system for laboratory diagnosis of hemoglobin disorders

OBJECTIVE

To illustrate the utility of a rule-based expert system in diagnosing hemoglobin disorders.

DESIGN

A rule-based expert system was developed for diagnosing hemoglobin disorders. This expert system runs on IBM-compatible personal computers and uses a backward-chaining search strategy to draw conclusions. Laboratory data (ie, results of hemoglobin electrophoresis, quantitative measurements of hemoglobin F and hemoglobin A2 levels, and result of a sickle cell screen) are processed by the system using defined rules to obtain a set of differential diagnoses. Additional data, such as hematologic parameters, ethnicity of the patient, and the presence or absence of certain clinical signs and symptoms, aid in making a final diagnosis. The rules in the current version of this expert system include diagnostic criteria for 71 hemoglobin disorders.

SETTING

Regional academic medical center.

PATIENTS

We tested the system by using 58 survey sample cases offered by the College of American Pathologists during the period of January 1989 through December 1994.

MAIN OUTCOME MEASURE

The established diagnosis for a given case must be included in the list of differential diagnoses suggested by the expert system.

RESULTS

The expert system included the actual diagnosis as one of the top four differential diagnoses in 90% of the cases, whereas all the laboratories participating in the survey included it in 84% (mean) of the cases.

CONCLUSION

We propose that this user-friendly expert system is a potential tool for computer-assisted diagnosis of hemoglobin disorders.

The P-region and S6 of Kv3.1 contribute to the formation of the ion conduction pathway

The loop between transmembrane regions S5 and S6 (P-region) of voltage-gated K+ channels has been proposed to form the ion-conducting pore, and the internal part of this segment is reported to be responsible for ion permeation and internal tetraethylammonium (TEA) binding. The two T-cell K+ channels, Kv3.1 and Kv1.3, with widely divergent pore properties, differ by a single residue in this internal P-region, leucine 401 in Kv3.1 corresponding to valine 398 in Kv1.3. The L401V mutation in Kv3.1 was created with the anticipation that the mutant channel would exhibit Kv1.3-like deep-pore properties. Surprisingly, this mutation did not alter single channel conductance and only moderately enhanced internal TEA sensitivity, indicating that residues outside the P-region influence these properties. Our search for additional residues was guided by the model of Durell and Guy, which predicted that the C-terminal end of S6 formed part of the K+ conduction pathway. In this segment, the two channels diverge at only one position, Kv3.1 containing M430 in place of leucine in Kv1.3. The M430L mutant of Kv3.1 exhibited permeant ion- and voltage-dependent flickery outward single channel currents, with no obvious changes in other pore properties. Modification of one or more ion-binding sites located in the electric field and possibly within the channel pore could give rise to this type of channel flicker.

Pharmacological characterization of five cloned voltage-gated K+ channels, types Kv1.1, 1.2, 1.3, 1.5, and 3.1, stably expressed in mammalian cell lines

We have analyzed the biophysical and pharmacological properties of five cloned K+ (Kv) channels (Kv1.1, Kv1.2, Kv1.3, Kv1.5, and Kv3.1) stably expressed in mammalian cell lines. Kv1.1 is biophysically similar to a K+ channel in C6 glioma cells and astrocytes, Kv1.3 and Kv3.1 have electrophysiological properties identical to those of the types n and l K+ channels in T cells, respectively, and Kv1.5 closely resembles a rapidly activating delayed rectifier in the heart. Each of these native channels may be formed from the homomultimeric association of the corresponding Kv subunits, and pharmacological compounds that selectively modulate them may be useful for the treatment of neurological, immune, and cardiac disorders. The cell lines described in this report could be used to identify such drugs and we have therefore embarked on a pharmacological characterization of the five cloned channels. The compounds tested in this study include 4-aminopyridine, capsaicin, charybdotoxin, cromakalim, dendrotoxin, diltiazem, D-sotalol, flecainide, kaliotoxin, mast cell degranulating peptide, nifedipine, noxiustoxin, resiniferatoxin, and tetraethylammonium.

Calcium-activated potassium channels in resting and activated human T lymphocytes. Expression levels, calcium dependence, ion selectivity, and pharmacology

Ca(2+)-activated K+[K(Ca)] channels in resting and activated human peripheral blood T lymphocytes were characterized using simultaneous patch-clamp recording and fura-2 monitoring of cytosolic Ca2+ concentration, [Ca2+]i. Whole-cell experiments, using EGTA-buffered pipette solutions to raise [Ca2+]i to 1 microM, revealed a 25-fold increase in the number of conducting K(Ca) channels per cell, from an average of 20 in resting T cells to > 500 channels per cell in T cell blasts after mitogenic activation. The opening of K(Ca) channels in both whole-cell and inside-out patch experiments was highly sensitive to [Ca2+]i (Hill coefficient of 4, with a midpoint of approximately 300 nM). At optimal [Ca2+]i, the open probability of a K(Ca) channel was 0.3-0.5. K(Ca) channels showed little or no voltage dependence from -100 to 0 mV. Single-channel I-V curves were linear with a unitary conductance of 11 pS in normal Ringer and exhibited modest inward rectification with a unitary conductance of approximately 35 pS in symmetrical 160 mM K+. Permeability ratios, relative to K+, determined from reversal potential measurements were: K+ (1.0) > Rb+ (0.96) > NH4+ (0.17) > Cs+ (0.07). Slope conductance ratios were: NH4+ (1.2) > K+ (1.0) > Rb+ (0.6) > Cs+ (0.10). Extracellular Cs+ or Ba2+ each induced voltage-dependent block of K(Ca) channels, with block increasing at hyperpolarizing potentials in a manner suggesting a site of block 75% across the membrane field from the outside. K(Ca) channels were blocked by tetraethylammonium (TEA) applied externally (Kd = 40 mM), but were unaffected by 10 mM TEA applied inside by pipette perfusion. K(Ca) channels were blocked by charybdotoxin (CTX) with a half-blocking dose of 3-4 nM, but were resistant to block by noxiustoxin (NTX) at 1-100 nM. Unlike K(Ca) channels in Jurkat T cells, the K(Ca) channels of normal resting or activated T cells were not blocked by apamin. We conclude that while K(Ca) and voltage-gated K+ channels in the same cells share similarities in ion permeation, Cs+ and Ba2+ block, and sensitivity to CTX, the underlying proteins differ in structural characteristics that determine channel gating and block by NTX and TEA.