Ecological and functional differences of abundant and rare sub-communities in wastewater treatment plants across China

The microbial community in activated sludge is composed of a small number of abundant sub-community with high abundance and a large number of rare sub-community with limited abundance. Our knowledge regarding the ecological properties of both abundant and rare sub-communities in activated sludge is limited. This article presented an analysis of functional prediction, assembly mechanisms, and biogeographic distribution characteristics of abundant and rare sub-communities in 211 activated sludge samples from 60 wastewater treatment plants across China. Moreover, this study investigated the dominant factors influencing the community structure of these two microbial groups. The results showed that the functions associated with carbon and nitrogen cycling were primarily detected in abundant sub-community, while rare sub-community were primarily involved in sulfur cycling. Both microbial groups were mainly influenced by dispersal limitation, which, to some extent, resulted in a distance-decay relationship in their biogeographic distribution. Moreover, a higher spatial turnover rate of rare sub-communities (0.0887) suggested that spatial differences in microbial community structure among different WWTPs may mainly result from rare sub-community. Moreover, SEM showed that geographic locations affected rare sub-communities greatly, which agreed with their higher dispersal limitation and turnover rate. In contrast, influent characteristics showed stronger correlations with abundant sub-communities, suggesting that abundant sub-community may contribute more to the removal of pollutants. This study enhanced our understanding of abundant and rare microorganisms in activated sludge especially the role of rare species and provided scientific evidence for precise regulation and control of wastewater treatment plants.

Q-TWiST analysis of survival benefits with brigatinib versus crizotinib in patients with anaplastic lymphoma kinase-positive non-small cell lung cancer based on results of the ALTA-1L trial

OBJECTIVES

The ALTA-1L phase 3 open-label trial demonstrated increased progression-free survival (PFS) with brigatinib versus crizotinib in patients with anaplastic lymphoma kinase-positive (ALK-positive) locally advanced or metastatic non-small cell lung cancer (NSCLC) previously untreated with ALK-targeted therapy. This post-hoc analysis of data from the ALTA-1L trial used the quality-adjusted (QA) time without symptoms of disease or toxicity (Q-TWiST) methodology to compare the QA survival benefit of brigatinib versus crizotinib in this patient population.

PATIENTS AND METHODS

The Q-TWiST analysis was performed using final (January 29, 2021) individual patient-level blinded independent review committee (BIRC)- and investigator-assessed survival data for brigatinib (n = 137) and crizotinib (n = 138) in adult patients (N = 275) with ALK-positive locally advanced or metastatic NSCLC previously untreated with ALK-targeted therapy. Q-TWiST was compared between the two treatments. Subgroup analyses were performed in patients stratified by various clinicopathological characteristics, including presence or absence of brain metastases at baseline.

RESULTS

Brigatinib was associated with significantly longer time without symptoms of disease or toxicity (P < 0.001) than crizotinib, with significantly greater Q-TWiST (mean [SE] months: BIRC-assessed, 28.2 [1.2] versus 25.1 [1.1], P = 0.045; investigator-assessed, 28.5 [1.2] versus 24.8 [1.1], P = 0.018). Relative gains in Q-TWiST with brigatinib compared to crizotinib were clinically meaningful (BIRC-assessed, 10.4%; investigator-assessed, 12.3%). Patients with brain metastases at baseline receiving brigatinib had significantly greater Q-TWiST (mean [SE] months: BIRC-assessed, 29.0 [1.9] versus 19.0 [1.9], P = 0.0001) than those receiving crizotinib.

CONCLUSION

First-line brigatinib treatment was associated with significant and clinically meaningful gains in Q-TWiST compared to crizotinib in patients with ALK-positive locally advanced or metastatic NSCLC, supporting the results of the ALTA-1L trial and brigatinib as a safe and effective first-line treatment for ALK-positive NSCLC.

[A clinical observational study on the preliminary effect of dupilumab in the treatment of severe asthma]

Objective: To investigate the effect and safety of dupilumab in the treatment of patients with severe asthma in a preliminary clinical observational study. Methods: This study retrospectively analyzed the clinical data of 20 patients with severe asthma who received dupilumab for 4-12 months between 2019 and 2022 at the First Hospital of Guangzhou Medical University, comparing pre-and post-treatment laboratory data, oral glucocorticoid dose (OCS), asthma control test (ACT) and adverse effects. The median age of the 20 patients was 48.5 (41.0-52.8) years, including 14 males and 6 females. The clinical data of 10 patients treated with other biologic agents were further analyzed to determine the reasons for switching to biologic drug treatment and the efficacy of dupilumab in these patients. Paired t-tests or Wilcoxon signed-rank tests were used for comparisons. Mann-Whitney analysis was used for inter-group comparison, and chi-square test or Fisher test was used for inter-group comparisons of count data. Results: A total of 20 patients were included in this study. All 20 severe asthma phenotypes were type 2 (T2)-high and completed at least the first 4 months of treatment, including 17 patients who completed 12 months of treatment. Among patients who completed 4 months of treatment, the asthma exacerbation score decreased from 1.0(0.3-1.0) episodes/4 months to 0.0(0.0-1.0) episodes/4 months, P<0.001, and FEV1/FVC increased from 58.4% (50.5%-69.0%) to 66.9% (59.6%-77.7%), P<0.01. The number of patients requiring OCS maintenance therapy decreased from 15 (75%) to 9 (45%), P<0.05. Among patients who completed 12 months of treatment, the asthma exacerbation score decreased from 1.0(0.5-1.0) episodes/4 months to 0.0 (0.0-0.0) episodes/4 months, P<0.01, and FEV1/FVC increased from 57.9% (49.6%-67.8%) to 72.7% (64.6%-78.7%), P<0.01. The number of patients requiring OCS maintenance therapy decreased from 13 (76%) to 6 (35%), P<0.01. In 10 patients with a history of previous biologic therapy, the most common reasons for switching to a biologic were a poor response to previous monoclonal antibodies (40%) and loss of control of asthma symptom control after discontinuation of monoclonal antibodies (30%). The remaining reasons were patients' uncontrolled symptoms of chronic rhinosinusitis (20%) and irregular or underdosed use of previous biologics (10%). After 4 months of switching to dupilumab, 10 patients experienced varying degrees of improvement in asthma control. Conclusions: The application of dupilumab for the treatment of T2-high severe asthma showed good efficacy and few adverse effects. Biologically targeted therapy is an important treatment approach to achieving better control of severe asthma.

[Anatomical classification of and laparoscopic surgery for left-sided colorectal cancer with persistent descending mesocolon]

Objective: To investigate anatomical morphology and classification of persistent descending mesocolon (PDM) in patients with left-sided colorectal cancer, as well as the safety of laparoscopic radical surgery for these patients. Methods: This is a descriptive study of case series. Relevant clinical data of 995 patients with left colon and rectal cancer who had undergone radical surgery in Fujian Medical University Union Hospital from July 2021 to September 2022 were extracted from the colorectal surgery database of our institution and retrospectively analyzed. Twenty-four (2.4%) were identified as PDM and their imaging data and intra-operative videos were reviewed. We determined the distribution and morphology of the descending colon and mesocolon, and evaluated the feasibility and complications of laparoscopic surgery. We classified PDM according to its anatomical characteristics as follows: Type 0: PDM combined with malrotation of the midgut or persistent ascending mesocolon; Type 1: unfixed mesocolon at the junction between transverse and descending colon; Type 2: PDM with descending colon shifted medially (Type 2A) or to the right side (Type 2B) of the abdominal aorta at the level of the origin of the inferior mesentery artery (IMA); and Type 3: the mesocolon of the descending-sigmoid junction unfixed and the descending colon shifted medially and caudally to the origin of IMA. Results: The diagnosis of PDM was determined based on preoperative imaging findings in 9 of the 24 patients (37.5%) with left-sided colorectal cancer, while the remaining diagnoses were made during intraoperative assessment. Among 24 patients, 22 were male and 2 were female. The mean age was (63±9) years. We classified PDM as follows: Type 0 accounted for 4.2% (1/24); Type 1 for 8.3% (2/24); Types 2A and 2B for 37.5% (9/24) and 25.0% (6/24), respectively; and Type 3 accounted for 25.0% (6/24). All patients with PDM had adhesions of the mesocolon that required adhesiolysis. Additionally, 20 (83.3%) of them had adhesions between the mesentery of the ileum and colon. Twelve patients (50.0%) required mobilization of the splenic flexure. The inferior mesenteric artery branches had a common trunk in 14 patients (58.3%). Twenty-four patients underwent D3 surgery without conversion to laparotomy; the origin of the IMA being preserved in 22 (91.7%) of them. Proximal colon ischemia occurred intraoperatively in two patients (8.3%) who had undergone high ligation at the origin of the IMA. One of these patients had a juxta-anal low rectal cancer and underwent intersphincteric abdominoperineal resection because of poor preoperative anal function. Laparoscopic subtotal colectomy was considered necessary for the other patient. The duration of surgery was (260±100) minutes and the median estimated blood loss was 50 (20-200) mL. The median number of No. 253 lymph nodes harvested was 3 (0-20), and one patient (4.2%) had No.253 nodal metastases. The median postoperative hospital stay was 8 (4-23) days, and the incidence of complications 16.7% (4/24). There were no instances of postoperative colon ischemia or necrosis observed. One patient (4.2%) with stage IIA rectal cancer developed Grade B (Clavien-Dindo III) anastomotic leak and underwent elective ileostomy. The other complications were Grade I-II. Conclusions: PDM is frequently associated with mesenteric adhesions. Our proposed classification can assist surgeons in identifying the descending colon and mesocolon during adhesion lysis in laparoscopic surgery. It is crucial to protect the colorectal blood supply at the resection margin to minimize the need for unplanned extended colectomy, the Hartmann procedure, or permanent stomas.

Kupffer cell pyroptosis mediated by METTL3 contributes to the progression of alcoholic steatohepatitis

Chronic alcohol consumption is a major risk factor for alcoholic steatohepatitis (ASH). Previous studies have shown that direct injury of hepatocytes is the key factor in its occurrence and development. However, our study shows that the role of Kupffer cells in ASH cannot be ignored. We isolated Kupffer cells from the livers of ASH mice and found that alcohol consumption induced Kupffer cell pyroptosis and increased the release of interleukin-1β (IL-1β). Furthermore, we screened the related m6A enzyme methyltransferase-like 3 (METTL3) from liver Kupffer cells, and found that silencing METTL3 alleviated inflammatory cytokine eruption by Kupffer cell pyroptosis in ASH mice. In vitro, we silenced METTL3 with lentivirus in BMDMs and RAW264.7 cells and confirmed that METTL3 could reduce pyroptosis by influencing the splicing of pri-miR-34A. Together, our results revealed a critical role of KC pyroptosis in ASH and highlighted the mechanism by which METLL3 relieves cell pyroptosis, which could be a promising therapeutic strategy for ASH.

Avapritinib versus Placebo in Indolent Systemic Mastocytosis

Avapritinib in Indolent Systemic MastocytosisIn a randomized trial, patients with indolent systemic mastocytosis were treated with avapritinib or placebo along with supportive care. The trial primary end point was the change in mean total symptom scores at 24 weeks. Avapritinib-treated patients had a decrease in mean total symptom score of 15.6 points compared with 9.2 points in the placebo group.

[Surgical treatment for perihilar cholangiocarcinoma:a single-center experience]

Objective: To investigate surgical strategies and the corresponding benefits for patients with perihilar cholangiocarcinoma(pCCA). Methods: A total of 81 patients with pCCA who underwent radical excision in the Department of Biliary and Pancreatic Surgery of Sun Yat-Sen Memorial Hospital between January 2014 and December 2021 were retrospectively collected.The cohort consisted of 50 male and 31 female patients,with an age of (62.5±11.5)years(range:26 to 83 years).Seventy-five cases were diagnosed with jaundice,60 of whom received preoperative biliary drainage,while 20 patients received portal vein embolization.Their serum bilirubin level within one week before the operation(M(IQR)) was 44.3 (41.9) μmol/L(range:8.0 to 344.2 μmol/L).Preoperative imaging examinations were performed to evaluate the Bismuth-Corlette type of pCCA,showing 3,6,21,27,and 24 cases of Bismuth-Corlette type Ⅰ,Ⅱ,Ⅲa,Ⅲb,and Ⅳ,respectively.The primary outcome was overall survival (OS),and the secondary outcomes were relapse-free survival (RFS),90-day postoperative morbidity and 90-day postoperative mortality.OS and RFS were estimated using the Kaplan-Meier method and compared by the Log-rank test.Significant prognostic factors were determined using univariate and multivariable Cox proportional hazard regression analyses. Results: In the cohort of 81 pCCA patients,67 cases(82.7%) underwent major hepatectomy while 3 cases received major hepatectomy combined with pancreaticoduodenectomy.Thirty-four patients underwent hepatectomy combined with vascular resection and reconstruction(18 cases of portal vein resection and reconstruction alone;9 cases of hepatic artery resection and reconstruction alone;7 cases of combination of portal vein and hepatic artery resection and reconstruction).Margin negative(R0 excision) were achieved in 53.1%(43/81) of these patients.The operation duration was (627±136)minutes(range:565 to 940 minutes),and the intraoperative blood loss was 400(455)ml(range:200 to 2 800 ml).The 90-day postoperative mortality was 3.7%(3/81).Grade 3-4 postoperative morbidity was 23.4% (19/81) according to the Clavien-Dindo classification of surgical complications.Up to the last follow-up at September 2022,the follow-up time was 34.0(24.2)months (range:0.4 to 103.6 months).Three patients who died within 90 days after surgery were excluded from the survival analysis.The median OS was 36.10 months (95%CI:18.23 to 42.97 months) and the 1-,3-and 5-year OS rates were 85.3%,46.8% and 27.3%,respectively.The median OS of 41 patients with negative margins was 47.83 months(95%CI:36.90 to 58.80 months) and that of 37 patients with positive margins was 20.47 months(95%CI:10.52 to 30.58 months).The median RFS of 70 patients with R0 and R1 resection was 24.50 months(95%CI:12.15 to 31.85 months)and the 1-,3-and 5-year RFS rates were 65.2%,45.7% and 29.9%,respectively.The median RFS of 41 patients with R0 resection was 38.57 months(95%CI:21.50 to 55.63 months) and that of 29 patients with R1 resection was 10.83 months(95%CI:2.82 to 19.86 months). Conclusions: The primary therapy for pCCA is radical surgical resection.A precise preoperative evaluation and sufficient preparation can reduce postoperative morbidity.Surgical treatment can achieve a better survival outcome by increasing the radical resection rate.

Mucus Hypersecretion and Ciliary Impairment in Conducting Airway Contribute to Alveolar Mucus Plugging in Idiopathic Pulmonary Fibrosis

Idiopathic pulmonary fibrosis (IPF) is a chronic lung disease attributed to the complex interplay of genetic and environmental risks. The muco-ciliary clearance (MCC) system plays a critical role in maintaining the conduit for air to and from the alveoli, but it remains poorly understood whether the MCC abnormalities in conducting airway are involved in IPF pathogenesis. In this study, we obtained the surgically resected bronchi and peripheral lung tissues from 31 IPF patients and 39 control subjects, and we sought to explore the morphologic characteristics of MCC in conducting airway by using immunostaining and scanning and transmission electron microscopy. In the submucosal regions of the bronchi, we found that the areas of mucus glands (MUC5B⁺) were significantly larger in IPF patients as compared with control subjects (p < 0.05). In the surface epithelium of three airway regions (bronchi, proximal bronchioles, and distal bronchioles), increased MUC5B and MUC5AC expression of secretory cells, decreased number of ciliated cells, and increased ciliary length were observed in IPF patients than control subjects (all p < 0.05). In addition, the mRNA expression levels of MUC5B were up-regulated in both the bronchi and peripheral lung of IPF patients than those of control subjects (p < 0.05), accompanied with 93.55% IPF subjects who had obvious MUC5B⁺ mucus plugs in alveolar regions. No MUC5B rs35705950 single-nucleotide polymorphism allele was detected in both IPF patients and control subjects. Our study shows that mucus hypersecretion and ciliary impairment in conducting airway are major causes of mucus plugs in alveolar regions and may be closely related to the alveolar injuries in IPF patients.

Investigation of the changes in lipid profiles induced by hydroxyl radicals in whiteleg shrimp (Litopenaeus vannamei) muscle using LC/MS-based lipidomics analysis

The oxidative effects of hydroxyl radical on the alterations of lipid profiles were investigated in shrimp muscle. Chemical results indicate peroxide value (PV) and thiobarbituric acid index (TBA-i) value in oxidation-treated shrimp significantly increased with oxidation time, and hydroxyl radical concentration increased, compared with those of in fresh samples. It was assumed that radical attack might induce lipid decomposition, backbone cleavage, and/or side-chain modifications. LC/MS-based lipidomics analysis revealed 835 lipids in shrimp assigned to 27 lipid classes, including 219 PCs and 98 CLs. In total, 86 and 34 differentially abundant lipids (DALs) accumulated at lower and higher levels, respectively, were identified in OS, compared with that in FS. This indicates hydroxyl radical attack altered the lipidomics profiles of shrimp muscle to a large extent. Furthermore, DALs, including CL 62:2, PC 38:3, and PE 34:9, could be considered as promising biomarkers to distinguish fresh and oxidation-treated shrimp products.

Safety and efficacy of avapritinib in advanced systemic mastocytosis: the phase 1 EXPLORER trial

Advanced systemic mastocytosis (AdvSM) is a rare hematologic neoplasm driven by the KIT D816V mutation and associated with poor survival. This phase 1 study (NCT02561988) evaluated avapritinib (BLU-285), a selective KIT D816V inhibitor, in patients with AdvSM. The primary endpoints were the maximum tolerated dose, recommended phase 2 dose and safety of avapritinib. Secondary endpoints included overall response rate and changes in measures of mast cell burden. Avapritinib was evaluated at doses of 30–400 mg once daily in 86 patients, 69 with centrally confirmed AdvSM. Maximum tolerated dose was not reached, and 200 mg and 300 mg daily were studied in dose-expansion cohorts. The most frequent adverse events observed were periorbital edema (69%), anemia (55%), diarrhea (45%), thrombocytopenia (44%) and nausea (44%). Intracranial bleeding occurred in 13% overall, but in only 1% of patients without severe thrombocytopenia (platelets <50 × 10⁹/l). In 53 response-evaluable patients, the overall response rate was 75%. The complete remission rate was 36%. Avapritinib elicited ≥50% reductions in marrow mast cells and serum tryptase in 92% and 99% of patients, respectively. Avapritinib induced deep and durable responses, including molecular remission of KIT D816V in patients with AdvSM, and was well tolerated at the recommended phase 2 dose of 200 mg daily.

In a phase 1 trial of patients with advanced systemic mastocytosis, avapritinib, a selective KIT inhibitor, was generally well tolerated, elicited durable clinical responses and led to reductions in mast cell disease burden.

EGFR testing patterns and detection of EGFR exon 20 insertions among patients with NSCLC in the US

Introduction/Objective

Epidermal growth factor receptor (EGFR) mutations are common in non-small cell lung cancer (NSCLC). EGFR exon 20 insertions (EGFRex20ins), a rare subset of EGFR mutations, are refractory to tyrosine kinase inhibitors. With the development of targeted therapies for EGFRex20ins, such as mobocertinib, molecular testing is required to optimize treatment. A better understanding of real-world EGFR detection patterns is needed to maximize patient outcomes.

Methods/Case Report

This retrospective study describes EGFR testing and EGFRex20ins detection patterns in patients with NSCLC in the United States. The Flatiron Health electronic health record database was used to identify patients ≥18 years, with advanced NSCLC, and with ≥2 clinic visits between 01/01/2011 and 12/31/2020. Baseline demographics, clinical characteristics, EGFR testing, and EGFRex20ins detection rates by sex, race, and smoking history were summarized.

Results (if a Case Study enter NA)

A total of 67,281 patients with NSCLC were identified. EGFR testing increased from 44% in 2011 to 77% in 2020. Of all patients, 44,926 (66.8%) were tested: 50.8% female; 3.3% Asian; 16.0% never-smokers. Of all patients, 22,355 (33.2%) were not tested: 41.4% female; 1.2% Asian; 7.5% never-smokers. Of those tested, 6,245 (13.9%) patients had EGFR mutations: 65.9% female; 11.8% Asian; 48.4% never-smokers.

EGFRex20ins detection rates changed from 0.6% in 2011 to 1.0% in 2019 and 0.7% in 2020. Of those tested, 304 patients had EGFRex20ins: 58.2% female; 8.2% Asian; 50.3% never-smokers. EGFR testing was higher in females (71.2%) than males (62.8%), never-smokers (84.5%) than those with a smoking history (64.6%), and Asian patients (84.2%) than White (66.6%), Black (65.4%), or other patients (69.5%). Of those tested, EGFRex20ins mutations were detected in 0.8% of females (males: 0.6%), 2.2% of never-smokers (with smoking history: 0.4%), and 1.7% of Asians (White: 0.6%, Black: 0.6%, other patients: 0.7%) had EGFRex20ins. A similar trend was observed for EGFR mutations with higher proportions of females, never-smokers, and Asian patients affected.

Conclusion

EGFR testing and EGFRex20ins detection rates have increased. However, not all patient subgroups were tested at the same rate and undertesting occurred in all subgroups. Further education of specialists diagnosing NSCLC is warranted to ensure all patients receive biomarker testing and benefit from emerging EGFRex20ins- targeted therapies.

Psychometric evaluation of the Indolent Systemic Mastocytosis Symptom Assessment Form (ISM-SAF) in a phase 2 clinical study

Background

Indolent systemic mastocytosis (ISM) is a rare, clonal mast cell neoplasm characterized by severe, unpredictable symptoms. The Indolent Systemic Mastocytosis Symptom Assessment Form (ISM-SAF) items compose a Total Symptom Score (TSS), Gastrointestinal Symptom Score (GSS), and Skin Symptom Score (SSS) to assess symptom severity. This study evaluated the psychometric performance of ISM-SAF among ISM patients.

Methods

In PIONEER, a Phase 2 trial evaluating safety and efficacy of selective kinase inhibitor avapritinib in patients with ISM, the 12-item ISM-SAF was administered daily. Psychometric evaluation of score reliability, validity, and clinical interpretation was conducted using the trial data.

Results

Thirty-eight patients contributed to analyses (78.9% female; mean age = 49). Baseline internal consistency reliability (α) for bi-weekly TSS, GSS, and SSS was 0.86, 0.83, and 0.82, respectively. Test–retest reliability among patients exhibiting no change in Patient Global Impression of Symptom Severity (PGIS) between Baseline and Day 15 exceeded 0.74 universally. Construct validity and known-groups analysis showed moderate to strong ISM-SAF score correlation (r = 0.382–0.881) to supportive patient-reported questionnaires (e.g., PGIS and Mastocytosis Quality of Life Questionnaire) symptom and skin scores, and ability to distinguish among clinically unique groups. Correlations of ISM-SAF and other assessment change scores reflect evidence of score sensitivity. Clinically important difference and response estimates were 7–10 and 19, respectively.

Discussion

ISM-SAF produced reliable, construct-valid, sensitive scores when administered in PIONEER to patients in the target population. Results of this study support the use of the ISM-SAF as a reliable and valid measure to evaluate disease symptomology in ISM patients.

Trial registration ClinicalTrials.gov, NCT03731260. Registered 10 October 2018, https://clinicaltrials.gov/ct2/show/study/NCT03731260.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13023-021-02037-3.

Abstract CT023: PATHFINDER: Interim analysis of avapritinib (ava) in patients (pts) with advanced systemic mastocytosis (AdvSM)

Introduction: Systemic mastocytosis is a clonal, hematologic neoplasm driven by KIT D816V mutation in &gt;90% of cases, with limited treatment options. In a phase I study, ava, a potent inhibitor of KIT D816V, induced durable responses which deepened over time in pts with AdvSM, regardless of prior therapy or AdvSM subtype. PATHFINDER (NCT03580655) is a pivotal open-label, single-arm phase II study of ava in pts with AdvSM. Methods: Pts were aged ≥18 years with centrally confirmed diagnosis of an AdvSM subtype. Primary endpoint was overall response rate (ORR) by modified International Working Group-Myeloproliferative Neoplasms Research and Treatment and European Competence Network on Mastocytosis criteria. This pre-specified interim analysis included 32 response-evaluable pts. Secondary endpoints included mean baseline change in AdvSM-Symptom Assessment Form Total Symptom Score (TSS) (Gotlib J et al. ASH 2018) and safety. Results: At June 23, 2020, 62 pts with AdvSM received ava primarily at 200 mg orally once daily (QD). Median age was 69 years (range 31-88), 31% had ECOG PS 2-3, and 68% had prior systemic treatment (55% with midostaurin). At 10.4 months median follow-up, 52/62 (84%) pts remained on treatment. ORR was 75% (95% CI 57-89; P=1.6×10-9) in 32 response-evaluable pts. Complete remission with full or partial hematologic recovery occurred in 19% of pts. Median time to response was 2 months; responses deepened over time. Median overall survival (OS) was not reached; estimated 12-month OS was 87%. There were ≥50% reductions from baseline serum tryptase (87%; n=54), marrow mast cell aggregates (71%; n=44), and KIT D816V allele fraction (53%; n=33). Mean TSS at baseline (n=56) was 18.3; fatigue, spots, itching, flushing, and abdominal pain were the most severe symptoms. Mean change in TSS was -7.7 (1-sided P&lt;0.001) after 6 months of treatment (n=36). Common (≥25%) adverse events (AEs; all grade, Grade ≥3) were peripheral (50%, 3%) and periorbital (35%, 3%) edema, thrombocytopenia (32%, 8%), and anemia (29%,16%). Overall, 5% of pts discontinued due to a treatment-related AE and 5% due to disease progression. There were 3 (5%) deaths, all unrelated to treatment. Seven (11%) pts had cognitive effect AEs (all Grade 1-2). One pt with pre-treatment severe thrombocytopenia (platelets &lt;50×109/L) had Grade 4 subdural hematoma. Subsequent pts with pre-treatment severe thrombocytopenia were excluded, platelet monitoring was intensified, and dose interruption for severe thrombocytopenia was recommended; no intracranial bleeding events occurred in 57 pts without pre-treatment severe thrombocytopenia. Conclusions: The pivotal PATHFINDER study showed that ava 200 mg QD induced rapid responses, which deepened over the course of treatment, and improved symptoms in pts with AdvSM. Ava was generally well tolerated with a manageable safety profile, including effective thrombocytopenia risk mitigation.

Citation Format: Daniel J. DeAngelo, Andreas Reiter, Deepti Radia, Michael W. Deininger, Tracy I. George, Jens Panse, Alessandro M. Vannucchi, Madlen Jentzsch, Iván Alvarez-Twose, Andrzej Mital, Olivier Hermine, Ingunn Dybedal, Elizabeth O. Hexner, Lisa K. Hicks, Lambert Span, Ruben Mesa, Prithviraj Bose, Kristen M. Pettit, Mark L. Heaney, Stephen Oh, Jayita Sen, Hui-Min Lin, Brenton G. Mar, Jason Gotlib. PATHFINDER: Interim analysis of avapritinib (ava) in patients (pts) with advanced systemic mastocytosis (AdvSM) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr CT023.

Psychometric evaluation of the Advanced Systemic Mastocytosis Symptom Assessment Form (AdvSM-SAF)

BACKGROUND

The Advanced Systemic Mastocytosis Symptom Assessment Form (AdvSM-SAF) was developed to evaluate symptoms of advanced systemic mastocytosis (AdvSM). This study aimed to psychometrically evaluate AdvSM-SAF scores and provide score interpretation guidelines.

METHODS

The 10-item AdvSM-SAF was administered daily (scored as a seven-day average) in EXPLORER, an open-label Phase 1 study in AdvSM. Score distribution, reliability, construct-related validity, sensitivity to change, and interpretation guidelines were evaluated for AdvSM-SAF items, gastrointestinal symptom score (GSS), skin symptom score (SSS), and total symptom score (TSS).

RESULTS

Thirty-one patients contributed to the analyses. At Baseline, the GSS, SSS, and TSS had adequate internal consistency (α > 0.7) and test-retest reliability (intraclass correlation coefficients >0.7). AdvSM-SAF scores were moderately to strongly correlated with variables as expected, and distinguished among clinically distinct groups. Observed relationships between change scores in the AdvSM-SAF and other assessments reflect evidence that AdvSM-SAF scores change in concert with other assessments designed to measure similar constructs. The magnitude of AdvSM-SAF weekly TSS mean change scores based on different anchor groupings was as expected (improvement > stable > worsening). Candidate clinically meaningful between-group difference estimates (GSS = 2-4, SSS = 2-3, and TSS = 4-7 points) and within-person change estimates (GSS = 6-9, SSS = 1-4, TSS = 9-14) for AdvSM-SAF weekly scores were generated.

CONCLUSION

The AdvSM-SAF produced reliable, construct-valid, and sensitive scores when administered in the target patient population. These results, along with its strong development history and evidence of content validity, indicate that the AdvSM-SAF is fit for the purpose of measuring treatment benefit in individuals with AdvSM.

Label-free proteomic analysis revealed the mechanisms of protein oxidation induced by hydroxyl radicals in whiteleg shrimp (Litopenaeus vannamei) muscle

The oxidative effects of hydroxyl radicals derived from a FeCl₃/ascorbic acid/H₂O₂ system on the stability of muscle proteins in peeled shrimp (Litopenaeus vannamei) were investigated. Physicochemical analysis indicated negative effects on the color (a* value), springiness, and pH of shrimp muscle, which appeared to be significantly exacerbated by higher concentrations of generated hydroxyl radicals when compared with the control. The microstructural results confirmed that a radical attack induced the incompact structure and disintegrated myofibers, thereby leading to weakened connective tissues and decreased stability of muscle proteins. Furthermore, label-free proteomic analysis revealed several differentially abundant proteins (DAPs) (i.e., ribosomal protein subunits, putative cytoskeleton proteins, and ion-binding proteins), which were detected and identified in oxidation-treated shrimp when compared with the control. The gene ontology (GO) and eukaryotic clusters of orthologous group (KOG) analyses further confirmed that the active hydroxyl radicals attacked vulnerable amino acids, modified peptide chains, and/or protein structures and/or conformations, which were responsible for a significant decrease in the muscle texture and stability of proteins in oxidation-treated shrimp. This study provides novel insight into the molecular mechanisms of muscle protein changes during oxidation development.

Exact simultaneous confidence intervals for logical selection of a biomarker cut-point

This article proposes four new principles for logical biomarker cut-point selection methods to adhere to: subgroup sensibility, sensitivity, specificity, and target monotonicity. At every cut-point value, our method gives confidence intervals not only for the efficacy at that cut-point value, but also efficacies in the marker-positive and marker-negative subgroups defined by that cut-point. These confidence intervals are given simultaneously for all possible cut-point values. Using Alzheimer's disease (AD) and type 2 diabetes (T2DM) as examples, we show our method achieves the four principles. Our method strongly controls familywise type I error rate (FWER) across both levels of multiplicity: the multiplicity of having marker-positive and marker-negative subgroups at each cut-point, and the multiplicity of searching through infinitely many cut-points. This is in contrast to other available methods. The confidence level of our simultaneous confidence intervals is in fact exact (not conservative). An application (app) is available, which implements the method we propose.

[Rectum-preserving surgery after consolidation neoadjuvant therapy or totally neoadjuvant therapy for low rectal cancer: a preliminary report]

Objective: To investigate the feasibility and safety of sphincter-preserving surgery after neoadjuvant chemoradiotherapy (nCRT) with consolidation chemotherapy in the interval period or total neoadjuvant therapy (TNT) for low rectal cancer. Methods: A descriptive case series study was carried out. Clinical data of patients with locally advanced low rectal cancer (LALRC) who achieved complete clinical response (cCR) or nearly cCR (near-cCR) after nCRT at the Department of Colorectal Surgery of Fujian Medical University Union Hospital from May 2015 to February 2019 were retrospectively analyzed. Case inclusion criteria: (1) Low rectal adenocarcinoma within 6 cm from the anal verge. (2) After nCRT, tumor presented markedly regression as mucosal nodule or abnormalities, superficial ulcer, scar or a mucosal erythema (< 2 cm); no regional lymph node metastasis or distant metastasis was found in rectal ultrasonography, pelvic MRI and PET-CT; MRI showed obvious fibrosis in the original tumor site; and post-treatment CEA was normal. (3) The patient and the family members adhered to receive the transanal full-thickness local excision with informed consent. (4) When the residual lesions were difficult to detect after nCRT, patients received the watch and wait (W&W) strategy. Exclusion criteria: (1) Before nCRT, pathological results showed poorly differentiated or signet-ring cell carcinoma; lateral lymph node metastasis was suspected. (2) When the residual lesion size was more than 3 cm after nCRT, it was difficult to perform local excision. The consolidation nCRT group received 3-4 cycles of CAPOX regimen (oxaliplatin and capecitabine) or six cycles of mFOLFOX6 (oxaliplatin, leucovorin, and 5-fluorouracil) combined with the long-course radiotherapy (intensity-modulated radiation therapy with a total dose of 50.4Gy). Patients with concurrent chemotherapy more than or equal to five cycles of CAPOX or eight cycles of mFOLFOX6 were defined as total neoadjuvant therapy (TNT) group. Local resection was recommended for patients who were near-cCR according to modified MSKCC criteria 8-33 weeks after the end of radiotherapy. Patients with a near-cCR, who were judged as ycN0 according to PET-CT and MRI and were ypT0 after local excision, could enter the W&W strategy. Patients with pathologic stage more advanced than ypT1, and those with positive resection margin, or lymphovascular invasion were recommended for salvage radical surgery after local excision. The ypT1 patients with a negative resection margin and without lymphovascular invasion might receive the W&W management carefully if they refused radicalsurgery to sacrifice the sphincter for low rectal cancer. Results: Of 32 patients, 14 were males and 18 were females with the average age of 59 years old. Twenty-three patients underwent consolidation nCRT, and 9 received TNT. The first evaluation after treatments showed 19 cases with cCR and 13 with near-cCR. Twenty-nine patients received local excision while 3 patients with undetectable lesions received W&W policy. Four cases (12.5%) underwent salvage radical surgery with abdominoperineal resection. After local excision, 3 cases underwent salvage radical surgery immediately, and the final pathologic result was ypT3N0, ypT2N0, and ypT2N0 respectively, of whom 2 cases were in the group of consolidation CRT and 1 was in the TNT group. Of these 3 cases, 1 case with an initial cT3 stage showed a pathologic stage of ypT1 and a negative circumferential resection margin after consolidation nCRT and local excision, however, the final pathologic stage was ypT3 with fragmented tumor deposits in the mesorectum after the salvage radical surgery. Meanwhile 1 patient in the TNT group receiving W&W suffered from intraluminal regrowth after 7.4 months follow-up and underwent salvage abdominoperineal resection. One patient in the consolidation nCRT group died of stroke 42.5 months after local resection. Another patient in the TNT group had cerebral metastasis 10 months after the W&W policy, but no local recurrence was found in the pelvic cavity, then received resection of the metastatic tumors. The average follow-up for all the patients was 23 (5-51) months. The cumulative local regrowth rate was 5.0%. The overall survival rate was 85.7%, and the sphincter-preservation rate was increased from 25.0% (28/32) in the original plan to 87.5% (28/32) actually. The 3-year disease-free survival rate was 89.7%. The 3-year organ-preserving survival rate was 85.7%, and the 3-year stoma-free survival rate was 82.5%. At present, 31 patients still survived. Conclusions: After nCRT with consolidation chemotherapy or TNT for low rectal cancer, patients with cCR, ycN0 according to PET-CT and MRI, and ypT0 after local excision, can consider the W&W strategy. Strict patient selection with a near-cCR for local resection and sphincter-preserving strategy can reduce the local regrowth of cancer, and the short-term outcomes are satisfactory.

[Identification of gene biomarkers to predict responses to neoadjuvant chemoradiotherapy in patients with rectal cancer and pathways enrichment analysis]

Objective: To screen out the potential gene biomarkers to predict responses to neoadjuvant chemoradiotherapy (CRT) in patients with rectal cancer and to explore the main downstream pathways of resistance. Methods: The gene expression profiles (GSE35452) of locally advanced rectal cancer undergoing neoadjuvant chemoradiotherapy from 46 specimens (24 responders, TRG 0/1, and 22 non-responders, TRG 2/3) were downloaded from the GEO database. The differentially expressed genes were identified to screen out the potential biomarkers by use of the GCBI platform. GO and KEGG pathways enrichment analysis were performed to integrate enrichment results of differentially expressed genes. Signal-signal interaction network was constructed and analyzed to screen out potential main downstream pathways. Results: A total of 1079 differentially expressed genes were screened, including 657 up-regulated and 422 down-regulated ones. Among these genes, REG4 had the maximum fold change value of -6.029 491. In GO term, these differentially expressed genes were mainly enriched in molecule metabolic process, cell cycle, DNA-dependent transcription, signal transduction and apoptotic process. The KEGG pathways enrichment analysis showed that the differentially expressed genes were enriched in 65 KEGG pathways, including metabolic pathways, cell cycle and metabolism pathways. Signal-signal interaction network analysis showed that MAPK signaling pathway and cell cycle pathway might play a determinant role in the development of neoadjuvant chemoradiotherapy resistance. Further analysis showed that CDKN1B, CDKN2A, RBL1, TFDP1, CCND2, CCNE2, CDC6 and CDK6 in cell cycle might induce chemoradiotherapy resistance by blocking G1/S phase cell cycle arrest, decreasing the apoptosis of tumor cells and increasing S phase ratio of chemoradiotherapy resistance. Conclusion: G1/S phase cell cycle arrest blocking plays an important role in the development of chemoradiotherapy resistance in patients with rectal cancer. Moreover, the key genes, such as REG4, may be useful in predicting responses to neoadjuvant chemoradiotherapy.

Reconstruction of Intratelencephalic Neurons in the Mouse Secondary Motor Cortex Reveals the Diverse Projection Patterns of Single Neurons

The secondary motor cortex (MOs) plays crucial roles in cognitive and executive processes and has reciprocal connections with numerous cortices in rodents. However, descriptions of the neuronal morphologies and projection patterns of the MOs at the level of a single neuron are lacking, severely hindering the comprehensive understanding of the wiring diagram of the MOs. Herein, we used a Cre-dependent adeno-associated virus (AAV) to fluorescently label ~80 pyramidal neurons nearby or in the MOs and acquired an uninterrupted whole-brain 3D dataset at a voxel resolution of 0.2 × 0.2 × 1 μm with a whole-brain fluorescence imaging system (fMOST). Based on our 3D dataset, we reconstructed the complete morphologies of 36 individual intratelencephalic (IT) neurons nearby or in the MOs and analyzed the projection patterns and projection strengths of these neurons at a single-neuron level based on several parameters, including the projection areas, the total number of branches, the fiber length, and the total number of terminal tips. We obtained a neuron with an axonal length of 318.43 mm, which is by far the longest reported axonal length. Our results show that all individual neurons in the MOs, regardless of whether they are located in layer 2/3 or layer 5, display diverse projection patterns and projection strengths, implying that these neurons might be involved in different brain circuits at different intensities. The results lay a solid foundation for exploring the relationship between neuronal morphologies and behavioral functions of the MOs at the level of a single neuron.

Air tamponade in retinal detachment surgery followed by ultra-widefield fundus imaging system

AIM

To report the surgical result of pars plana vitrectomy (PPV) with air tamponade for rhegmatogenous retinal detachment (RRD) by ultra-widefield fundus imaging system.

METHODS

Of 25 consecutive patients (25 eyes) with fresh primary RRD and causative retinal break and vitreous traction were presented. All the patients underwent PPV with air tamponade. Visual acuity (VA) was examined postoperatively and images were captured by ultra-widefield scanning laser ophthalmoscope system (Optos).

RESULTS

Initial reattachment was achieved in 25 cases (100%). The air volume was >60% on the postoperative day (POD) 1. The ultra-widefield images showed that the retina was reattached in all air-filled eyes postoperatively. The retinal break and laser burns in the superior were detected in 22 of 25 eyes (88%). A missed retinal hole was found under intravitreal air bubble in 1 case (4%). The air volume was range from 40% to 60% on POD 3. A double-layered image was seen in 25 of 25 eyes with intravitreal gas. Retinal breaks and laser burns around were seen in the intravitreal air. On POD 7, small bubble without effect was seen in 6 cases (24%) and bubble was completely disappeared in 4 cases (16%). Small oval bubble in the superior area was observed in 15 cases (60%). There were no missed and new retinal breaks and no retinal detachment in all cases on the POD 14 and 1mo and last follow-up. Air disappeared completely on a mean of 9.84d postoperatively. The mean final postoperative best-corrected visual acuity (BCVA) was 0.35 logMAR. Mean final postoperative BCVA improved significantly relative to mean preoperative (P<0.05). Final VA of 0.3 logMAR or better was seen in 13 eyes.

CONCLUSION

PPV with air tamponade is an effective management for fresh RRD with superior retinal breaks. The ultra-widefield fundus imaging can detect postoperative retinal breaks in air-filled eyes. It would be a useful facility for follow-up after PPV with air tamponade. Facedown position and acquired visual rehabilitation may be shorten.

Statistics for X-chromosome associations

In a genome-wide association study (GWAS), association between genotype and phenotype at autosomal loci is generally tested by regression models. However, X-chromosome data are often excluded from published analyses of autosomes because of the difference between males and females in number of X chromosomes. Failure to analyze X-chromosome data at all is obviously less than ideal, and can lead to missed discoveries. Even when X-chromosome data are included, they are often analyzed with suboptimal statistics. Several mathematically sensible statistics for X-chromosome association have been proposed. The optimality of these statistics, however, is based on very specific simple genetic models. In addition, while previous simulation studies of these statistics have been informative, they have focused on single-marker tests and have not considered the types of error that occur even under the null hypothesis when the entire X chromosome is scanned. In this study, we comprehensively tested several X-chromosome association statistics using simulation studies that include the entire chromosome. We also considered a wide range of trait models for sex differences and phenotypic effects of X inactivation. We found that models that do not incorporate a sex effect can have large type I error in some cases. We also found that many of the best statistics perform well even when there are modest deviations, such as trait variance differences between the sexes or small sex differences in allele frequencies, from assumptions.

Brentuximab vedotin or physician's choice in CD30-positive cutaneous T-cell lymphoma (ALCANZA): an international, open-label, randomised, phase 3, multicentre trial

BACKGROUND

Cutaneous T-cell lymphomas are rare, generally incurable, and associated with reduced quality of life. Present systemic therapies rarely provide reliable and durable responses. We aimed to assess efficacy and safety of brentuximab vedotin versus conventional therapy for previously treated patients with CD30-positive cutaneous T-cell lymphomas.

METHODS

In this international, open-label, randomised, phase 3, multicentre trial, we enrolled adult patients with CD30-positive mycosis fungoides or primary cutaneous anaplastic large-cell lymphoma who had been previously treated. Patients were enrolled across 52 centres in 13 countries. Patients were randomly assigned (1:1) centrally by an interactive voice and web response system to receive intravenous brentuximab vedotin 1·8 mg/kg once every 3 weeks, for up to 16 3-week cycles, or physician's choice (oral methotrexate 5-50 mg once per week or oral bexarotene 300 mg/m² once per day) for up to 48 weeks. The primary endpoint was the proportion of patients in the intention-to-treat population achieving an objective global response lasting at least 4 months per independent review facility. Safety analyses were done in all patients who received at least one dose of study drug. This trial was registered with ClinicalTrials.gov, number NCT01578499.

FINDINGS

Between Aug 13, 2012, and July 31, 2015, 131 patients were enrolled and randomly assigned to a group (66 to brentuximab vedotin and 65 to physician's choice), with 128 analysed in the intention-to-treat population (64 in each group). At a median follow-up of 22·9 months (95% CI 18·4-26·1), the proportion of patients achieving an objective global response lasting at least 4 months was 56·3% (36 of 64 patients) with brentuximab vedotin versus 12·5% (eight of 64) with physician's choice, resulting in a between-group difference of 43·8% (95% CI 29·1-58·4; p<0·0001). Grade 3-4 adverse events were reported in 27 (41%) of 66 patients in the brentuximab vedotin group and 29 (47%) of 62 patients in the physician's choice group. Peripheral neuropathy was seen in 44 (67%) of 66 patients in the brentuximab vedotin group (n=21 grade 2, n=6 grade 3) and four (6%) of 62 patients in the physician's choice group. One of the four on-treatment deaths was deemed by the investigator to be treatment-related in the brentuximab vedotin group; no on-treatment deaths were reported in the physician's choice group.

INTERPRETATION

Significant improvement in objective response lasting at least 4 months was seen with brentuximab vedotin versus physician's choice of methotrexate or bexarotene.

FUNDING

Millennium Pharmaceuticals Inc (a wholly owned subsidiary of Takeda Pharmaceutical Company Ltd), Seattle Genetics Inc.

Outcomes by CD30 expression in patients with CTCL receiving brentuximab vedotin (BV) vs physician's choice (PC) in the Phase 3 ALCANZA study

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Background: The Phase 3 ALCANZA study showed significant, durable responses with CD30-directed antibody-drug conjugate BV vs PC of methotrexate (MTX) or bexarotene (Bex) for CD30-positive (CD30+) cutaneous T cell lymphoma (CTCL). Uniform CD30 expression is characteristic of primary cutaneous anaplastic large cell lymphoma (pcALCL), but is variable among other subtypes including mycosis fungoides (MF). We examined activity of BV and MTX / Bex by CD30 expression in pts treated on the ALCANZA study. Methods: Adults with previously treated CD30+ MF or pcALCL were enrolled. MF pts had ≥2 skin biopsies from separate lesions, pcALCL had ≥1. Patients were scored CD30+ if ≥1 biopsy had ≥10% CD30+ lymphoid cells using an investigational Ventana diagnostic test, centrally assessed by one pathologist. We compared the proportion of MF subgroup pts (n=50 per treatment arm) with objective response lasting ≥4 months (ORR4; ALCANZA primary endpoint) and PFS in pts with all biopsies ≥10% CD30+ (CD30min ≥10%) vs ≥1 biopsy <10% CD30+ (CD30min <10%). Pts were randomized 1:1 to BV 1.8 mg/kg IV, Q3W, or PC for up to 16 three-week cycles. Results: 125/184 (68%) MF and 44/47 (94%) pcALCL pts were screened and scored CD30+. High inter-lesional variability in CD30 expression was seen in MF pts; 55/125 CD30+ MF pts (44%) had ≥1 biopsy with low (<10%) or undetectable CD30. 100/125 CD30+ MF pts were eligible and enrolled. In the BV arm, ORR4 was higher in MF pts with CD30min ≥10% vs <10%; median PFS with BV was higher in the CD30min <10% group (Table). ORR4 with BV was greater than PC over all CD30 expression ranges (CD30min <5%, 38% vs 13%; CD30 ≥5–≤20%, 35% vs 10%; CD30 >20%, 76% vs 7%, respectively). Conclusions: Notable inter-patient or inter-lesional variability in CD30 expression was seen in MF pts. Highly superior ORR4 and PFS endpoints were seen with BV over PC regardless of CD30min expression level. Clinical trial information: NCT01578499. [Table: see text]

Selecting stage ypT0-1N0 for locally advanced rectal cancer following preoperative chemoradiotherapy: implications for potential candidates of organ-sparing management

AIM

Local excision or a wait-and-see policy may offer the possibility of organ preservation for locally advanced rectal cancer (LARC) after preoperative chemoradiotherapy (CRT). Identifying associated factors of good responders (GR) with stage ypT0-1N0 would probably influence the selection of potential candidates who were theoretically eligible for organ-sparing management. This study was to establish a scoring system to select stage ypT0-1N0 for LARC following preoperative CRT.

METHOD

Between 2009 and 2014, 262 patients with middle and low LARC were treated with CRT and radical surgery. Clinicopathological data which were found to be significantly associated with GR were incorporated into a scoring system.

RESULTS

Fifty-seven (21.8%) patients were GR with stage ypT0-1N0 in the operative specimen. Multivariate analyses indicated that a low level of pretreatment carcinoembryonic antigen (CEA) and post-treatment CEA <2.55 ng/ml (P = 0.008 and P = 0.009 respectively) and long-axis diameter of residual tumours (P = 0.006) were independently associated with stage ypT0-1N0. The three factors were incorporated into a scoring system. Using receiver operating characteristic curve analysis, we determined a cutoff value of -0.3 for scores, at which the system's sensitivity was 71.9% and specificity 73.1%. When applied to testing samples, the sensitivity was 74.1% and specificity 76.2%.

CONCLUSION

We demonstrated that low levels of pretreatment and post-treatment CEA and the long-axis diameter of residual tumours were associated with stage ypT0-1N0 for LARC after CRT. Therefore, the three-factor scoring system may be used to select potential candidates for organ-sparing management.

Expression of PAM50 Genes in Lung Cancer: Evidence that Interactions between Hormone Receptors and HER2/HER3 Contribute to Poor Outcome

Non–small cell lung cancers (NSCLCs) frequently express estrogen receptor (ER) β, and estrogen signaling is active in many lung tumors. We investigated the ability of genes contained in the prediction analysis of microarray 50 (PAM50) breast cancer risk predictor gene signature to provide prognostic information in NSCLC. Supervised principal component analysis of mRNA expression data was used to evaluate the ability of the PAM50 panel to provide prognostic information in a stage I NSCLC cohort, in an all-stage NSCLC cohort, and in The Cancer Genome Atlas data. Immunohistochemistry was used to determine status of ERβ and other proteins in lung tumor tissue. Associations with prognosis were observed in the stage I cohort. Cross-validation identified seven genes that, when analyzed together, consistently showed survival associations. In pathway analysis, the seven-gene panel described one network containing the ER and progesterone receptor, as well as human epidermal growth factor receptor (HER)2/HER3 and neuregulin-1. NSCLC cases also showed a significant association between ERβ and HER2 protein expression. Cases positive for HER2 expression were more likely to express HER3, and ERβ-positive cases were less likely to be both HER2 and HER3 negative. Prognostic ability of genes in the PAM50 panel was verified in an ERβ-positive cohort representing all NSCLC stages. In The Cancer Genome Atlas data sets, the PAM50 gene set was prognostic in both adenocarcinoma and squamous cell carcinoma, whereas the seven-gene panel was prognostic only in squamous cell carcinoma. Genes in the PAM50 panel, including those linking ER and HER2, identify lung cancer patients at risk for poor outcome, especially among ERβ-positive cases and squamous cell carcinoma.

Expression profiles of immune-related genes are associated with neoadjuvant ipilimumab clinical benefit

Purpose: Patients with regionally advanced melanoma were treated with neoadjuvant ipilimumab in a previously reported study (PLOS One 2014). Gene expression profiles of tumors of treated patients were investigated for their association with immunotherapeutic benefit. Methods: Patients were treated with ipilimumab (10 mg/kg intravenously every 3 weeks × 2 doses) before and after surgery. Tumor specimens were obtained at baseline and at definitive surgery (weeks 6-8). Gene expression profiling was performed on the tumor biopsies of 27 patients. The primary endpoint was mRNA expression profiling using U133A 2.0 Affymetrix gene chips. Significance analysis of microarrays was performed to test the association of each gene with outcome. Pathway analysis was performed using Ingenuity Pathway Analysis software. The Benjamini and Hochberg method was used to adjust for multiple testing in the pathway analysis. Results: Pathway analysis identified biologically relevant pathways enriched with genes that are significantly associated with clinical outcome at baseline in relation to relapse-free survival (RFS) and disease non-progression (as assessed preoperatively at week 6) as well as early on-treatment (RFS and overall survival). The molecules and pathways that achieved differential expression of highest statistical significance were notably immune related. Association of the gene signature with clinical outcome overlapped between baseline and on-treatment specimens and across clinical endpoints tested. Conclusion: Gene expression profiling identified a signature reflecting an immune active and proinflammatory tumor microenvironment that derived clinical benefit from neoadjuvant ipilimumab at baseline and early on-treatment. These findings warrant further investigation in relation to ipilimumab and other immunotherapeutics.

Phenotypic and functional testing of circulating regulatory T cells in advanced melanoma patients treated with neoadjuvant ipilimumab

Background

We have previously investigated neoadjuvant ipilimumab (ipi) for patients with locally/regionally advanced melanoma. That initial assessment of peripheral blood mononuclear cells (PBMC) showed a significant increase in shared tumor associated antigen specific CD4⁺ and CD8⁺ T cell activation. We also observed a transient increase in circulating T regulatory cells (Treg) with a parallel increase in total CD4⁺ T cells, as well as a significant decrease in circulating myeloid derived suppressor cells (MDSC). The increase in circulating Treg frequency, as assessed at 6 weeks after initiation of ipilimumab, was significantly associated with improved progression free survival (PFS, p = 0.034; HR = 0.57) and returned to baseline levels by 12 weeks. To shed light on the unexpected positive correlation between increased Treg and PFS, we here investigated the suppressive activity of circulating Treg at baseline and 6 weeks.

Methods

Patients were treated with ipi (10 mg/kg intravenously every 3 weeks for 2 doses) bracketing definitive surgery. Treg (CD4⁺CD25⁺CD127^dim/-) were isolated from pre-ipi (baseline) and post-ipi (6 weeks) PBMC samples. Treg were co-cultured with autologous responder CD4⁺ T cells that were stimulated with OKT3/IL-2/CD28 and CFSE-labeled T cells. 1:1, 1:2, and 1:5 ratios were tested. Flow cytometery was used to evaluate the degree of Treg proliferation suppression.

Results

Thirty-five patients were enrolled in the study; 18 patients had adequate PBMC samples with sufficient Treg isolated for Treg functional analysis. At 6 weeks following ipi, a decrease in percent of maximal inhibition of Th by Treg compared to baseline was seen for some patients. Scatter plot analysis showed no association between Treg frequency and function at any ratio or between circulating Treg frequency and function at baseline and at 6 weeks post-ipi. An increase in Treg suppressive function was significantly associated with a decrease in PFS (p = 0.02).

Conclusions

We find that Treg frequency measures do not correlate with suppressive activity measured ex vivo. Treg suppressive activity increases correlate with poorer patient outcomes.

Electronic supplementary material

The online version of this article (doi:10.1186/s40425-016-0141-1) contains supplementary material, which is available to authorized users.

[Effects of neoadjuvant chemoradiotherapy on the rates of sphincter preserving surgery in lower rectal cancer and analysis of their prognostic factors]

Objectives: To identify independent factors of sphincter preserving surgery, and to evaluated whether preoperative chemoradiotherapy (CRT) improves the sphincter preservation rate for lower rectal cancers. Methods: A total of 541 consecutive patients who underwent curative surgery for locally advanced rectal cancer (cT3-4Nx or cTxN+ ) within 6 cm of the anal verge with or without neoadjuvant CRT in Department of Colorectal Surgery, Union Hospital, Fujian Medical University between September 2000 and September 2013 were reviewed. Of these, 333 patients underwent surgery alone (Non-CRT group) and 208 patients also received preoperative chemoradiotherapy (CRT group). Clinical data were retrospectively reviewed to determine the factors influencing sphincter preservation, and to evaluate sphincter preservation rate according to tumor height over 1-cm intervals. The categorical variables were compared using χ² test and Fisher exact test. Continuous variables were compared using t test. Logistic regression was used to identify factors influencing sphincter preservation. A receiver operating characteristic (ROC) curve was constructed, and Youden's index was calculated to evaluate the predictive abilities of factors. Results: Multivariate analysis indicated that the independent factors influencing sphincter preservation were tumor height (OR=5.867, 95% CI: 4.155 to 8.285, P=0.000), pathological T stage (OR=0.688, 95% CI: 0.462 to 1.025, P=0.066), CRT (OR=2.088, 95% CI: 0.971 to 4.492, P=0.060) and histopathological type (OR=0.288, 95% CI: 0.136 to 0.611, P=0.001). The results of ROC analysis showed that the cut-off points for factors affecting sphincter preservation were as follows: (1) tumor height prior to CRT higher than 4.5 cm, (2) not mucinous or signet ring adenocarcinoma, (3) pathological T stage higher than T3, (4) had received preoperative CRT. In an analysis according to tumor height, the sphincter preservation rate was higher in CRT group only when tumor was located in 3.0 to 3.9 cm and 4.0 to 4.9 cm from the annal verge (3.0 to 3.9 cm, 59.4% vs. 2.8%, χ²=26.138, P=0.000; 4.0 to 4.9 cm, 76.9% vs. 37.9%, χ²=10.563, P=0.001). Conclusions: There is a large increased rate of sphincter preservation when patients meet the following conditions: (1) tumor height prior to CRT higher than 4.5 cm, (2) not mucinous or signet ring adenocarcinoma, (3)pathological T stage higher than T3, (4) had received preoperative CRT. Only when tumors are between 3 and 5 cm from the anal verge, CRT could increase the rate of anal sphincter preservation.

[Prognostic factors of postoperative incisional surgical site infections for colorectal cancer]

Objective: To explore the prognostic factors of postoperative incisional surgical site infections (I-SSI) for colorectal cancer. Methods: Clinical data of 2 385 colorectal cancer patients undergoing resection by the same surgical team in Department of Colon and Rectum Surgery, Fujian Medical University Union Hospital from January 2000 to February 2014 was analyzed retrospectively. There were 1 421 male and 964 female patients, with a mean age of (59±13) years. Univariate analysis and multivariate Logistic regression analysis were performed for independent prognostic factors of I-SSI. Results: The I-SSI occurred in 77 patients (3.23%). The results of univariate analysis showed that there were statistical differences in body mass index (t=-3.356), operation time (t=-3.609), length of incision (t=-5.492), radical operation (χ²=8.963), laparoscopic surgery (χ²=25.884), combined evisceration (χ²=6.349) and intraoperative blood infusion (χ²=4.176) between two groups (all P<0.05) . The results of multivariate Logistic regression analysis showed that independent prognostic factors of I-SSI were identified to be body mass index (OR=1.087, 95%CI: 1.023 to 1.155, P=0.007), operation time (OR=1.007, 95%CI: 1.002 to 1.012, P=0.006), preoperative chemoradiotherapy (OR=2.434, 95%CI: 1.099 to 5.393, P=0.028) and combined evisceration (OR=2.596, 95%CI: 1.060 to 6.357, P=0.037). The independent protective prognostic factor of I-SSI was identified to be the laparoscopic surgery (OR=0.386, 95%CI: 0.170 to 0.877, P=0.023). Conclusions: Body mass index, operation time, preoperative chemoradiotherapy and combined evisceration are identified to be independent prognostic factors for I-SSI. High-risk patients should receive individualized perioperative intervention. Nevertheless, the laparoscopic surgery can decrease the incidence of I-SSI.

The effect of ferrous-chelating hairtail peptides on iron deficiency and intestinal flora in rats

BACKGROUND

Chelating agents, such as small peptides, can decrease free iron content and increase iron bioavailability. They may have promising therapeutic potential and may prevent the pro-oxidant effects of low molecular weight iron. Hairtail is a species of fish that is rich in easily digestible proteins. We extended this strategy for iron delivery by using an enzymatic hydrolysate of hairtail as the chelating agent and found that the ferrous-chelating hairtail peptides have anti-anaemic activity in Sprague-Dawley rats with anaemia.

RESULTS

The anti-anaemic activity of ferrous-chelating hairtail peptides prepared by enzymatic hydrolysis of the hairtail and ferrous chelation was studied in rat models of iron deficiency anaemia. After the end of the 35 d experiment, we noted significant differences in haemoglobin, mean corpuscular volume, haemoglobin distribution width, and ferritin concentrations between those animals supplemented with ferrous-chelating hairtail peptides and FeSO4 and healthy animals. There were no negative side effects on the animals' growth or behaviour. There was no obvious inflammation in the intestinal mucosa lamina propria and no unbalance of intestinal flora.

CONCLUSION

The novel ferrous-chelating hairtail peptides may be a suitable fortificant for improving iron-deficiency status. Our findings demonstrated that this multi-tracer technique has many applications in nutritional research. © 2015 Society of Chemical Industry.

Intratumor Heterogeneity Affects Gene Expression Profile Test Prognostic Risk Stratification in Early Breast Cancer

PURPOSE

To examine the effect of intratumor heterogeneity (ITH) on detection of genes within gene expression panels (GEPs) and the subsequent ability to predict prognostic risk.

EXPERIMENTAL DESIGN

Multiplexed barcoded RNA analysis was used to measure the expression of 141 genes from five GEPs (Oncotype Dx, MammaPrint, PAM50, EndoPredict, and Breast Cancer Index) in breast cancer tissue sections and tumor-rich cores from 71 estrogen receptor (ER)-positive node-negative tumors, on which clinical Oncotype Dx testing was previously performed. If the tumor had foci of high Ki67 (n = 26), low/negative progesterone receptor (PR; n = 13), or both (n = 5), additional cores were obtained. In total, 181 samples were processed. Oncotype Dx recurrence scores were calculated from NanoString nCounter gene expression data.

RESULTS

Hierarchical clustering using all GEP genes showed that majority (61 of 71) of tumor samples clustered by patient, indicating greater interpatient heterogeneity (IPH) than ITH. We found a strikingly high correlation between Oncotype Dx recurrence scores obtained from whole sections versus tumor-rich cores (r = 0.94). However, high Ki67 and low PR cores had slightly higher but not statistically significant recurrence scores. For 18 of 71 (25%) patients, scores were divergent between sections and cores and crossed the boundaries for low, intermediate, and high risk.

CONCLUSIONS

Our study indicates that in patients with highly heterogeneous tumors, GEP recurrence scores from a single core could under- or overestimate prognostic risk. Hence, it may be a useful strategy to assess multiple samples (both representative and atypical cores) to fully account for the ITH-driven variation in risk prediction. Clin Cancer Res; 22(21); 5362-9. ©2016 AACR.

Milk glucosidase activity enables suckled pup starch digestion

ᅟ

Starch requires six enzymes for digestion to free glucose: two amylases (salivary and pancreatic) and four mucosal maltase activities; sucrase-isomaltase and maltase-glucoamylase. All are deficient in suckling rodents.

Objective

The objective of this study is to test ¹³C-starch digestion before weaning by measuring enrichment of blood ¹³C-glucose in maltase-glucoamylase-null and wild-type mice.

Methods

Maltase-glucoamylase gene was ablated at the N-terminal. Dams were fed low ¹³C-diet and litters kept on low ¹³C-diet. Pups were weaned at 21 days. Digestion was tested at 13 and 25 days by intragastric feeding of amylase predigested ¹³C-α-limit dextrins. Blood ¹³C-glucose enrichment was measured by gas chromatography combustion isotope ratio mass spectrometry (GCRMS) using penta-acetate derivatives.

Results

Four hours after feeding, blood ¹³C-glucose was enriched by 26 × 10³ in null and 18 × 10³ in wild-type mice at 13 days and 0.3 × 10³ and 0.2 × 103 at 25 days (vs. fasting p = 0.045 and p = 0.045). By jejunal enzyme assay, immunohistochemistry, or Western blots, there was no maltase activity or brush border staining with maltase-glucoamylase antibodies at 13 days, but these were fully developed in the wild-type mice by 25 days. In 13-day null mice, luminal contents were stained by maltase-glucoamylase antibodies. Lactating the mammary gland revealed maltase-glucoamylase antibody staining of alveolar cells. Reverse transcription/polymerase chain reaction (RT/PCR) of lactating glands revealed a secreted form of maltase-glucoamylase.

Conclusions

(1) ¹³C-α-limit dextrins were rapidly digested to ¹³C-glucose in 13-day mice independent of maltase-glucoamylase genotype or mucosal maltase activity. (2) This experiment demonstrates that a soluble maltase activity is secreted in mouse mother’s milk which enables suckling pup starch digestion well before brush border enzyme development. (3) This experiment with ¹³C-α-limit dextrins needs to be repeated in human breast fed infants.

Abstract 4302: Long term monitoring of circulating regulatory T cells (Treg), myeloid derived suppressor cella (MDSC) and type I effector T cells in melanoma patients treated with neoadjuvant ipilimumab

Background: Patients with regionally advanced melanoma were treated with neoadjuvant ipilimumab in a previously reported study (Tarhini. PLOS One 2014) where significant changes in circulating Treg, MDSC and peptide specific type I CD4+ and CD8+ T cells were observed early on-treatment (6 weeks) that correlated with clinical outcome.

Methods: Patients were treated with ipilimumab (10 mg/kg IV every 3 weeks x 2 doses) bracketing surgery. Blood (serum / peripheral blood mononuclear cells) specimens were collected at baseline and during treatment for up to 9 months. We conducted longer term monitoring in patients with available specimens at 3 (n = 28), 6 (n = 22) and 9 (n = 13) months utilizing multicolor flow cytometry. We compared the frequencies of circulating suppressive Treg and MDSC on-study to baseline levels, as well as frequencies of CD4+ and CD8+ T cells specific to shared tumor-associated antigens (Gp-100, MART-1, NY-ESO-1) utilizing overlapping peptide libraries (15-mer peptides overlapping by 4). The prognostic value of cell frequencies in relation to the probability of the event of progression at 9 months was tested.

Results: Baseline levels of Treg (CD4+/CD25hi+/CD39+) were significantly associated with 9 months progression free survival (PFS) (p = 0.04). A significant increase in Treg (CD4+CD25hi+Foxp3+ and CD4+/CD25hi+/CD39+) frequencies reported previously at 6 weeks after initiation of ipilimumab appears to have reversed starting 3 months as no significant changes were seen at this or any of the later time points compared to baseline. However, in monitoring the time dependent change over time in circulating Treg there was a trend towards an association with PFS (p = 0.09). Unlike what we had observed and reported at 6 weeks, no significant decrease in MDSC levels was seen at 3 months or later time points compared to baseline. We detected evidence of spontaneous in vivo cross presentation resulting in type I (interferon-γ producing), fully activated (CD69+) CD4+ and CD8+ antigen-specific T-cell immunity against cancer-testis (NY-ESO-1) as well as melanocytic lineage (MART-1, gp100) antigens in the absence of therapeutic vaccination. These responses were significantly potentiated at 6 weeks and persisted at 3, 6 and 9 months following the initiation of ipilimumab.

Conclusions: Neoadjuvant ipilimumab significantly modulates the levels of cellular mediators of immune suppression (Treg and MDSC) early on-treatment with less significant changes seen on long term follow up. Significant potentiation of the type I effector T cell response is seen early and persists on long term monitoring. These biomarkers warrant further investigation in relation to the mechanism of action of ipilimumab and for their potential prognostic and therapeutic predictive value. (Supported by NIH award P50CA121973 and BMS)

Citation Format: Janet Retseck, Amanda Gillespie-Twardy, Alexis Nasr, Hui-Min Lin, Yan Lin, John Kirkwood, Lisa H. Butterfield, Haris Zahoor, Cindy Sander, Ahmad A. Tarhini. Long term monitoring of circulating regulatory T cells (Treg), myeloid derived suppressor cella (MDSC) and type I effector T cells in melanoma patients treated with neoadjuvant ipilimumab. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4302. doi:10.1158/1538-7445.AM2015-4302

Abstract 2911: Immune related melanoma gene expression profile predicts neoadjuvant ipilimumab clinical benefit

Background

Patients with regionally advanced melanoma were treated with neoadjuvant ipilimumab in a previously reported study (ASCO 2012). Gene expression profiles of tumors of treated patients were investigated for their therapeutic predictive value.

Methods

Patients were treated with ipilimumab (10mg/kg IV every 3weeks x2 doses) bracketing surgery. Tumor specimens were obtained at baseline and at definitive surgery (week 6-8). Gene expression profiling was performed on the tumor biopsies of 32 patients using U133A 2.0 Affymetrix gene chips. Significance Analysis of Microarrays (SAMR) was performed to test the association of each gene with outcome. Pathway analysis was performed using Ingenuity Pathway Analysis software. The Benjamini and Hochberg method was used to adjust for multiple testing in the pathway analysis.

Results

Pathway analysis identified biologically relevant pathways enriched with genes that are significantly associated with clinical outcome at baseline in relation to progression free survival (PFS) and disease non-progression (NP) as well as early on-treatment outcomes (PFS and overall survival, OS). These pathways and the top associated molecules were notably immune related and highly statistically significant. Pathways associated with clinical outcome overlapped between baseline and on-treatment specimens as well as across clinical endpoints tested. Table1 summarizes the top canonical pathways identified at baseline (PRE) and on-treatment (POST) and their association with PFS, NP and OS.

Conclusions

Gene expression profiling identified pathways and genes related to inflammation and autoimmunity that significantly predict clinical benefit from neoadjuvant ipilimumab at baseline and early on-treatment. These findings warrant further investigation in relation to ipilimumab and other immunotherapeutics. (Supported by NIH award P50CA121973 and BMS)

Table 1.Pathways identified at baseline and on-treatment and their association with PFS, NP and OSPathwaysPRE/PFS (Adjusted P)PRE/NP (Adj. p)POST/PFS (Adj. p)POST/OS (Adj. p)Antigen Presentation0.00024.2x10-050.0043.1x10-05Cytotoxic T Lymphocyte-mediated Apoptosis of Target Cells0.00043.9x10-070.0040.0009T Helper Cell Differentiation0.0010.00050.050.023B Cell Development7.0x10-121.1x10-132.3x10-064.3x10-07iCOS-iCOSL Signaling in T Helper Cells0.0064.2x10-070.110.11OX40 Signaling0.0071.3x10-050.0050.0002CD28 Signaling in T Helper Cells0.048.3x10-050.040.15IL-4 Signaling0.020.00080.060.002PKCθ Signaling in T Lymphocytes0.048.0x10-050.140.04Nur77 Signaling in T Lymphocytes0.030.00010.030.008SLE Signaling1.5x10-054.3x10-06Allograft Rejection Signaling0.00034.3x10-060.0040.0006Autoimmune Thyroid Signaling0.0044.5x10-050.0210.003

Citation Format: Ahmad A. Tarhini, Yan Lin, Hui-Min Lin, Cindy Sander, William A. La Framboise, John M. Kirkwood. Immune related melanoma gene expression profile predicts neoadjuvant ipilimumab clinical benefit. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 2911. doi:10.1158/1538-7445.AM2014-2911

Low intraoperative tidal volume ventilation with minimal PEEP is associated with increased mortality

Background

Anaesthetists have traditionally ventilated patients’ lungs with tidal volumes (TVs) between 10 and 15 ml kg⁻¹ of ideal body weight (IBW), without the use of PEEP. Over the past decade, influenced by the results of the Acute Respiratory Distress Syndrome Network trial, many anaesthetists have begun using lower TVs during surgery. It is unclear whether the benefits of low TV ventilation can be extended into the perioperative period.

Methods

We reviewed the records of 29 343 patients who underwent general anaesthesia with mechanical ventilation between January 1, 2008 and December 31, 2011. We calculated TV kg⁻¹ IBW, PEEP, peak inspiratory pressure (PIP), and dynamic compliance. Cox regression analysis with propensity score matching was performed to examine the association between TV and 30-day mortality.

Results

Median TV was 8.6 [7.7–9.6] ml kg⁻¹ IBW with minimal PEEP [4.0 (2.2–5.0) cm H₂O]. A significant reduction in TV occurred over the study period, from 9 ml kg⁻¹ IBW in 2008 to 8.3 ml kg⁻¹ IBW in 2011 (P=0.01). Low TV 6–8 ml kg⁻¹ IBW was associated with a significant increase in 30-day mortality vs TV 8–10 ml kg⁻¹ IBW: hazard ratio (HR) 1.6 [95% confidence interval (CI) [1.25–2.08], P=0.0002]. The association remained significant after matching: HR 1.63 [95% CI (1.22–2.18), P<0.001]. There was only a weak correlation between TV kg⁻¹ IBW and dynamic compliance (r=−0.006, P=0.31) and a weak-to-moderate correlation between TV kg⁻¹ IBW and PIP (r=0.32 P<0.0001).

Conclusions

Use of low intraoperative TV with minimal PEEP is associated with an increased risk of 30-day mortality.

Meta-analysis methods for combining multiple expression profiles: comparisons, statistical characterization and an application guideline

BACKGROUND

As high-throughput genomic technologies become accurate and affordable, an increasing number of data sets have been accumulated in the public domain and genomic information integration and meta-analysis have become routine in biomedical research. In this paper, we focus on microarray meta-analysis, where multiple microarray studies with relevant biological hypotheses are combined in order to improve candidate marker detection. Many methods have been developed and applied in the literature, but their performance and properties have only been minimally investigated. There is currently no clear conclusion or guideline as to the proper choice of a meta-analysis method given an application; the decision essentially requires both statistical and biological considerations.

RESULTS

We performed 12 microarray meta-analysis methods for combining multiple simulated expression profiles, and such methods can be categorized for different hypothesis setting purposes: (1) HS(A): DE genes with non-zero effect sizes in all studies, (2) HS(B): DE genes with non-zero effect sizes in one or more studies and (3) HS(r): DE gene with non-zero effect in "majority" of studies. We then performed a comprehensive comparative analysis through six large-scale real applications using four quantitative statistical evaluation criteria: detection capability, biological association, stability and robustness. We elucidated hypothesis settings behind the methods and further apply multi-dimensional scaling (MDS) and an entropy measure to characterize the meta-analysis methods and data structure, respectively.

CONCLUSIONS

The aggregated results from the simulation study categorized the 12 methods into three hypothesis settings (HS(A), HS(B), and HS(r)). Evaluation in real data and results from MDS and entropy analyses provided an insightful and practical guideline to the choice of the most suitable method in a given application. All source files for simulation and real data are available on the author's publication website.