An 11-Gene Signature Based on Treatment Responsiveness Predicts Radiation Therapy Survival Benefit Among Breast Cancer Patients

PurposeWe developed a strategy of building prognosis gene signature based on clinical treatment responsiveness to predict radiotherapy survival benefit in breast cancer patients.Methods and MaterialsAnalyzed data came from the public database. PFS was used as an indicator of clinical treatment responsiveness. WGCNA was used to identify the most relevant modules to radiotherapy response. Based on the module genes, Cox regression model was used to build survival prognosis signature to distinguish the benefit group of radiotherapy. An external validation was also performed.ResultsIn the developed dataset, MEbrown module with 534 genes was identified by WGCNA, which was most correlated to the radiotherapy response of patients. A number of 11 hub genes were selected to build the survival prognosis signature. Patients that were divided into radio-sensitivity group and radio-resistant group based on the signature risk score had varied survival benefit. In developed dataset, the 3-, 5-, and 10-year AUC of the signature were 0.814 (CI95%: 0.742–0.905), 0.781 (CI95%: 0.682–0.880), and 0.762 (CI95%: 0.626–0.897), respectively. In validation dataset, the 3- and 5-year AUC of the signature were 0.706 (CI95%: 0.523–0.889) and 0.743 (CI95%: 0.595–0.891). The signature had higher predictive power than clinical factors alone and had more clinical prognosis efficiency. Functional enrichment analysis revealed that the identified genes were mainly enriched in immune-related processes. Further immune estimated analysis showed the difference in distribution of immune micro-environment between radio-sensitivity group and radio-resistant group.ConclusionsThe 11-gene signature may reflect differences in tumor immune micro-environment that underlie the differential response to radiation therapy and could guide clinical-decision making related to radiation in breast cancer patients.

Ex Vivo Chemosensitivity Profiling of Acute Myeloid Leukemia and Its Correlation With Clinical Response and Outcome to Chemotherapy

We evaluated the predictive value of the ex-vivo PharmaFlow PM platform in measuring the pharmacological activity of drug combinations consisting of 20 different chemotherapy regimens (20 Tx) administered in 104 acute myeloid leukemia (AML) patients. The predicted sensitivities of alternative treatments for each patient were ranked in five 20% categories, from resistant to sensitive (Groups 1–5). The complete remission (CR) rates of the five groups were 0%, 12.5%, 38.5%, 50.0%, and 81.3%, respectively. The heat map showed a good relationship between drug sensitivity with CR (Group 4 + 5 vs. Group 1 + 2+3: 77.5% vs. 27.3%, p = 0.002) and the European Leukemia Net risk group (22.6% vs. 63.6%, p = 0.015). The predicted coincidence rate was 90.9% in Group 1 + 2 and 81.3% in Group 5. According to the recommendations of the PharmaFlow PM platform, the CR rate would have increased by about 16.3% in one cycle. The overall survival (OS) was shorter in patients predicted to be resistant (Group 1 + 2 vs. Group 3 + 4+5, p = 0.086). In multivariable analysis, CR after one cycle was an independent prognostic factor for OS [p = 0.001; 95% CI 0.202 (0.080–0.511)], and ex-vivo chemosensitivity was a potential predictive factor for OS [p = 0.078; 95% CI 0.696 (0.465–1.041)]. To conclude, the PharmaFlow PM platform is a rapid and valuable tool for predicting clinical response and outcomes in AML patients.

Nystagmus Parameters of Supine Roll Test Correlates With Prognosis After Repositioning Maneuver in Horizontal Semicircular Canal Benign Paroxysmal Positional Vertigo

Background: Positional nystagmus induced by supine roll test is characteristic for diagnosing horizontal semicircular canal benign paroxysmal positional vertigo (HC-BPPV). In this study, we aimed to explore the value of nystagmus parameters in by supine roll test (SRT) as prognostic factors in HC-BPPV.Methods: We retrospectively analyzed the nystagmus parameters of 813 patients diagnosed with HC-BPPV by the SRT model in the SRM-IV system through video nystagmography. Then we used the computer-controlled canalith repositioning procedure (CCRP) mode for treatment. Based on the outcomes, patients were divided into either the cured group or the resistant group. The 1:1 propensity score matching (PSM) was applied to minimize potential selection bias. Then univariable and multivariable analyses were performed to identify the association of nystagmus parameters and the efficacy of CCRP.Results: Among the 813 patients, 99 (12.2%) were classified in the resistant group. The right side of HC-BPPV patients was twice the number of the left side patients (537 vs. 276). PSM is used to pair resistant patients to the cured patients, in which 99 pairs were successfully matched. Results of univariate and multivariate analyses showed that patients in the resistant group have longer latency in the affected side [odds ratio (OR) = 1.231 (1.110–1.366); P < 0.001] and slower slow phase velocity (SPV) in the healthy side [OR = 0.957 (0.917–0.999); P = 0.045].Conclusion: Nystagmus parameters may represent the characteristics of canalith. HC-BPPV patients with a longer latency in the affected side and slower SPV on the healthy side during SRT have a higher risk of HC-BPPV persisting after a single CCRP.

Retention in Care, Mortality, Loss-to-Follow-Up, and Viral Suppression among Antiretroviral Treatment-Naïve and Experienced Persons Participating in a Nationally Representative HIV Pre-Treatment Drug Resistance Survey in Mexico

We describe associations of pretreatment drug resistance (PDR) with clinical outcomes such as remaining in care, loss to follow-up (LTFU), viral suppression, and death in Mexico, in real-life clinical settings. We analyzed clinical outcomes after a two-year follow up period in participants of a large 2017–2018 nationally representative PDR survey cross-referenced with information of the national ministry of health HIV database. Participants were stratified according to prior ART exposure and presence of efavirenz/nevirapine PDR. Using a Fine-Gray model, we evaluated virological suppression among resistant patients, in a context of competing risk with lost to follow-up and death. A total of 1823 participants were followed-up by a median of 1.88 years (Interquartile Range (IQR): 1.59–2.02): 20 (1%) were classified as experienced + resistant; 165 (9%) naïve + resistant; 211 (11%) experienced + non-resistant; and 1427 (78%) as naïve + non-resistant. Being ART-experienced was associated with a lower probability of remaining in care (adjusted Hazard Ratio(aHR) = 0.68, 0.53–0.86, for the non-resistant group and aHR = 0.37, 0.17–0.84, for the resistant group, compared to the naïve + non-resistant group). Heterosexual cisgender women compared to men who have sex with men [MSM], had a lower viral suppression (aHR = 0.84, 0.70–1.01, p = 0.06) ART-experienced persons with NNRTI-PDR showed the worst clinical outcomes. This group was enriched with women and persons with lower education and unemployed, which suggests higher levels of social vulnerability.

Optimal subsequent treatments for patients with hepatocellular carcinoma resistant to anti-PD-1 treatment

Aim: The subsequent treatments for patients with hepatocellular carcinoma (HCC) resistant to immunotherapy remain unclear. This study aimed to identify optimal treatments for HCC patients with progression after anti-PD-1 therapy. Methods: The authors retrospectively analyzed 197 HCC patients with progressive disease after anti-PD-1 treatment. These patients were classified into initial resistant and secondary resistant groups. Results: In the initial resistant group, subsequent treatment with PD-1 antibody plus locoregional therapy prolonged post-progression survival and overall survival (p = 0.025 and 0.029, respectively). In the secondary resistant group, subsequent treatment did not improve the prognosis of patients. Conclusion: Subsequent PD-1 antibody plus locoregional therapy could achieve survival benefits in HCC patients initially resistant to anti-PD-1 immunotherapy.

Phosphoproteomic Analysis of Primary Myeloma Patient Samples Identifies Distinct Phosphorylation Signatures Correlating with Chemo-Sensitivity Profiles in an Ex Vivo Drug Sensitivity Testing Platform

Introduction: Multiple myeloma (MM) is characterized by the clonal expansion of plasma cells in the bone marrow resulting in end-organ damage. Despite an extensive increase in the five-year survival rate in recent years, MM is still considered an incurable disease as patients will repeatedly relapse and develop resistance to current chemotherapies. A key focus for the personalization of myeloma therapy is understanding the biological mechanisms of drug resistance and identifying clinically useful biomarkers of therapeutic response. Highly efficient techniques for the enrichment of phosphorylated peptides followed by high resolution mass spectrometry facilitates the quantitation of thousands of site-specific phosphorylation events. Here, we have performed a phosphoproteomic analysis on MM cell lysates stratified based on their ex vivo drug response profiles to advance our understanding of drug resistance mechanisms. Materials and Methods: CD138 + plasma cells were isolated from 20 adult MM patient bone marrow aspirates at diagnosis (n=7) or relapse (n=13). Samples were grouped based on ex vivo drug sensitivity and resistance testing (DSRT) as follows: highly sensitive (Group I), sensitive (Group II), resistant (Group III), highly resistant (Group IV) [1]. For the phosphoproteomic analysis, peptides were generated and purified using the filter aided sample preparation (FASP) protocol. Peptide tandem mass tag (TMT) labelling, Fe 3+ immobilized metal ion affinity chromatography (IMAC), synchronous precursor selection (SPS), and triple stage tandem mass spectrometry (MS3) was performed. Nonenriched peptides were used for proteomic analysis. Resulting data was analysed using MaxQuant, followed by normalization of phosphosite intensities using the internal reference scale (IRS) method, and statistical analysis using Perseus. Functional enrichment and kinase enrichment analyses were performed on significant phosphoproteins using g:profiler and KEA2, respectively. Results: Our quantitative MS-based phosphoproteomic analysis identified 2,945 phosphorylation sites on 2,232 phosphopeptides from 690 phosphoproteins. Of these phosphorylation sites, 176 were significantly changed between all four DSRT groups and 267 were significantly changed between Group I and Group IV (False Discovery Rate (FDR) < 0.05). Hierarchical clustering was performed to highlight the distinct phosphoproteomic profiles associated with each DSRT group, of which the very sensitive (Group I) and very resistant (Group IV) subgroups demonstrated a well-defined separation (Fig. 1A, 1B). KEGG pathway analysis and gene ontology (GO) analysis of significantly increased phosphorylated proteins in Group IV compared to Group I MM patients demonstrated an increased phosphorylation of proteins associated with tight junctions, the Rap1 signalling pathway and the phosphatidylinositol signalling system; indicating an upregulation of cell adhesion associated processes in drug resistant MM. Phosphoproteins increased in abundance in Group I compared to Group IV MM patients revealed an increased phosphorylation of proteins involved in translation and RNA processing including the spliceosome, RNA transport and RNA binding pathways (Fig. 1C). We identified filamin A serine 2152, RAS guanyl-releasing protein 2 serine 576 and proto-oncogene tyrosine-protein kinase Src serine 17 as increased in Group IV MM, and nuclease-sensitive element-binding protein 1 (YBX1) serine 165, CD44 serine 697 and Bcl2-associated agonist of cell death (BAD) serine 99 as increased in Group I MM. KEA of the upregulated phosphoproteome in Group IV revealed an enrichment of cyclin dependent kinase 1 (CDK1) and ribosomal s6 kinases (RPS6K) whereas casein kinase 2 (CK2) and the glycolysis-associated kinases were enriched in Group I (Fig. 1D). Conclusion: Our study has generated a phosphoproteomic dataset demonstrating distinct phosphorylation signatures associated with drug sensitivity in clinical MM plasma cells. The identification of phosphorylation events associated with drug resistance provides a basis for further exploration of these events and associated signalling pathways to further understand drug resistance mechanisms in MM and identify potential biomarkers of therapeutic response and targets for drug re-sensitization in MM. References: [1] M. M. Majumder et al., Oncotarget 8(34), 56338 (2017) Figure 1 Figure 1. Disclosures Heckman: Novartis: Research Funding; Orion Pharma: Research Funding; Celgene/BMS: Research Funding; Oncopeptides: Consultancy, Research Funding; Kronos Bio, Inc.: Research Funding.

Clinical Significance of Screening Differential Metabolites in Ovarian Cancer Tissue and Ascites by LC/MS

Tumor cells not only show a vigorous metabolic state, but also reflect the disease progression and prognosis from their metabolites. To judge the progress and prognosis of ovarian cancer is generally based on the formation of ascites, or whether there is ascites recurrence during chemotherapy after ovarian cancer surgery. To explore the relationship between the production of ascites and ovarian cancer tissue, metabolomics was used to screen differential metabolites in this study. The significant markers leading to ascites formation and chemoresistance were screened by analyzing their correlation with the formation of ascites in ovarian cancer and the clinical indicators of patients, and then provided a theoretical basis. The results revealed that nine differential metabolites were screened out from 37 ovarian cancer tissues and their ascites, among which seven differential metabolites were screened from 22 self-paired samples. Sebacic acid and 20-COOH-leukotriene E4 were negatively correlated with the high expression of serum CA125. Carnosine was positively correlated with the high expression of serum uric acid. Hexadecanoic acid was negatively correlated with the high expression of serum γ-GGT and HBDH. 20a,22b-Dihydroxycholesterol was positively correlated with serum alkaline phosphatase and γ-GGT. In the chemotherapy-sensitive and chemotherapy-resistant ovarian cancer tissues, the differential metabolite dihydrothymine was significantly reduced in the chemotherapy-resistant group. In the ascites supernatant of the drug-resistant group, the differential metabolites, 1,25-dihydroxyvitamins D3-26, 23-lactonel and hexadecanoic acid were also significantly reduced. The results indicated that the nine differential metabolites could reflect the prognosis and the extent of liver and kidney damage in patients with ovarian cancer. Three differential metabolites with low expression in the drug-resistant group were proposed as new markers of chemotherapy efficacy in ovarian cancer patients with ascites.

Criblage de variétés de tomate pour de la résistance au flétrissement bactérien causé par Ralstonia solanacearum au Togo

Objectifs : Dans le cadre de la recherche de mesures de lutte efficace et durable contre le flétrissement bactérien causé par Ralstonia solanacearum (Rs), la présente étude s’est proposé d’évaluer les variétés de tomate pour leur résistance à la maladie. Méthodologie et Résultats : Six variétés de tomate cultivées aux Togo ont été inoculées par une suspension de la souche de Rs isolée du site de CECO de la prefecture de Sotouboua (Togo). Les résultats ont montré de fortes incidences et sévérités du flétrissement bactérien sur les variétés testées. Cependant, des différences de comportement vis-à-vis de cette maladie ont été observées entre les variétés. En considérant l’indice de maladie après inoculation et l’analyse des closters, deux groupes de variétés ont été identifiés parmi les six testées : un groupe “Résistant” constitué de la seule variété Cobra et un groupe “Sensible” constitué des variétés Petomech, Tropimech, Padma, Roma et Platinum. Conclusions et application des résultats : Cette étude a permis d’obtenir des données sur l’incidence et la sévérité du flétrissement bactérien cause par Rs et le comportement des variétés de tomate vis-à-vis de cette pathologie, et a permis aussi d’identifier les variétés Cobra, Roma et Platinum comme résistantes au flétrissement bactérien en conditions contrôlées. Ces résultats constituent une base de données importante pour des investigations futures en conditions de champs dans diverses zones agroécologiques du pays. Ces expérimentations permettront d’identifier des variétés résistantes pouvant être recommandées aux producteurs pour une gestion durable du flétrissement bactérien. Mots clés : R. solancearum, flétrissement bactérien de la tomate, criblage, résistance. Banito et al., J. Appl. Biosci. Vol : 166 2021 Criblage de variétés de tomate pour de la résistance au flétrissement bactérien causé par Ralstonia solanacearum au Togo 17213 ABSTRACT Objectives: In order to develop a control strategy against bacterial wilt caused by Ralstonia solanacearum (Rs), one of the most destructive diseases of tomato worldwide, the present study aimed to evaluate tomato varieties for resistance to Rs. Methodology and Results: Six tomato varieties cultivated in Togo were inoculated with Rs strain isolated from CECO site in the Prefecture of Sotouboua (Togo).The results revealed high incidence and severity occurring on these varieties. However, differences were observed among the tested varieties. The discrimination analysis based on the disease index after inoculation and the clusters analysis identified two groups of varieties: the resistant group composed of the varieties Cobra, Roma and Platinum and the susceptible group including the varieties Petomech, Tropimech, Padma. Conclusions and application of findings: The results provided useful information in terms of incidence and severity of Rs wilt on tomato and the behaviour of varieties against the disease. The results allowed identifying three tomato varieties, Cobra, Roma and Platinum as resistant to bacterial wilt under controlled conditions. These results are useful for further experiments under field conditions in different agroecological zones to find out resistant tomato varieties for sustainable management of bacterial wilt caused by Rs. Keywords: R. solancearum, bacterial wilt of tomato, screening, resistance.

Prediction of repeated intravenous immunoglobulin resistance in children with Kawasaki disease

Background Repeated intravenous immunoglobulin (IVIG) resistance prediction is one of the pivotal topics in Kawasaki disease (KD). Those non-responders of repeated IVIG treatment might be improved by an early-intensified therapy to reduce coronary artery lesion and medical costs. This study investigated predictors of resistance to repeated IVIG treatment in KD. Methods A total of 94 children with IVIG-resistant KD treated at our hospital between January 2016 and August 2020 were retrospectively analyzed. According to the therapeutic effect of a second dose IVIG treatment, the children were divided into repeated IVIG-responsive group and repeated IVIG-resistant group, and the clinical and laboratory data were compared. Predictors of repeated IVIG resistance and the optimal cut-off value were determined by multiple logistic regression analysis and receiver operating characteristic (ROC) curve analysis. Results The Pre-IVIG laboratory data showed the percentage of neutrophils (N%) and levels of serum procalcitonin (PCT), N-terminal pro-brain natriuretic peptide (NT-proBNP) were significantly higher in repeated IVIG-resistant group compared with repeated IVIG-responsive group, while levels of serum sodium and albumin (ALB) were significantly lower (P < 0.05). The post-IVIG laboratory values of N% and C-reactive protein (CRP) were significantly higher in the repeated IVIG-resistant group compared with repeated IVIG-responsive group, while hemoglobin and ALB were lower (P < 0.05). Pre-IVIG PCT and post-IVIG CRP exhibited AUC of 0.751 and 0.778 respectively in predicting repeated IVIG resistance in KD. Pre-IVIG PCT > 1.81ng/ml (OR 4.1, 95 % CI 1.4 ~ 12.0, P < 0.05) and post-IVIG CRP > 45 mg/L (OR 4.6, 95 % CI 1.3 ~ 16.2, P < 0.05) were independent predictors of repeated IVIG resistance in KD. Conclusions Our study illustrates the serum PCT level before initial IVIG treatment and CRP after initial IVIG could be used to predict repeated IVIG resistance in KD.

Mineral profiling of resistant and susceptible tomato varieties against Alternaria solani causing early blight

The current research was conducted to investigate the alterations in the mineral status in the leaves of tomato plants against early blight (EB) caused by Alternaria solani. Six tomato varieties; viz. Riograndae, Roma and Basket (resistant) and T-88572, BHN-961 and BHN-1021(susceptible) were inoculated with a blend of five isolates of Alternaria solani, collected from different regions of Faisalabad District. These six varieties for mineral profiling were selected after two years screening from twenty-five varieties of tomatoes under field conditions. These varieties were sown in pots and artificial inoculation was performed to develop disease in inoculated type of tomato plants while distilled water was applied on un-inoculated type of plants. Newly infected leaves from upper, middle and lower parts of tomato plants from resistant and susceptible groups were used to prepare sample for mineral analysis at p ≤ 0.05 and variation in mineral profiling of resistant and susceptible groups of tomato plants was determined through Nested Structured Design. Significant variation was observed in inoculated (3.12, 0.48 %, 1.17, 0.14, 0.42, 0.21, 0.69 and 1.49 ppm and un-inoculated type (8.67, 1.61%, 10.45, 0.22, 1.75, 1.98, 3.09 and 3.39 ppm) while resistant group expressed 6.59, 1.19%, 8.13, 1.973, 1.69, 1.26, 1.36, 2.43 and 2.87ppm and susceptible group exhibited 5.19, 0.91%, 5.69, 1.693, 1.24, 0.91,0.83, 1.35 and 2.22 ppm with respect to NPK, Ca, Mg, Na, Zn, Iron and copper. Resistant variety, Riograndae expressed maximum amount while T-88572 exhibited minimum amount of all mineral contents. Alterations in the mineral profiling in leaves of tomato plants can be used by researchers as biochemical markers for identification and development of resistant source against early blight of tomato and for the development of ecofriendly management strategy towards A. solani.