Chemical screening by time-resolved X-ray scattering to discover allosteric probes

Drug discovery relies on efficient identification of small-molecule leads and their interactions with macromolecular targets. However, understanding how chemotypes impact mechanistically important conformational states often remains secondary among high-throughput discovery methods. Here, we present a conformational discovery pipeline integrating time-resolved, high-throughput small-angle X-ray scattering (TR-HT-SAXS) and classic fragment screening applied to allosteric states of the mitochondrial import oxidoreductase apoptosis-inducing factor (AIF). By monitoring oxidized and X-ray-reduced AIF states, TR-HT-SAXS leverages structure and kinetics to generate a multidimensional screening dataset that identifies fragment chemotypes allosterically stimulating AIF dimerization. Fragment-induced dimerization rates, quantified with time-resolved SAXS similarity analysis (kVR), capture structure-activity relationships (SAR) across the top-ranked 4-aminoquinoline chemotype. Crystallized AIF-aminoquinoline complexes validate TR-SAXS-guided SAR, supporting this conformational chemotype for optimization. AIF-aminoquinoline structures and mutational analysis reveal active site F482 as an underappreciated allosteric stabilizer of AIF dimerization. This conformational discovery pipeline illustrates TR-HT-SAXS as an effective technology for targeting chemical leads to important macromolecular states.

[Clinicopathologic characteristics and prognostic analysis of testicular diffuse large B-cell lymphoma]

Objective: To analyze the clinicopathologic characteristics and prognosis of testicular diffuse large B-cell lymphoma (DLBCL) . Methods: A retrospective analysis was performed on 68 patients with testicular DLBCL admitted to Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine from October 2001 to April 2020. The gene mutation profile was evaluated by targeted sequencing (55 lymphoma-related genes) , and prognostic factors were analyzed. Results: A total of 68 patients were included, of whom 45 (66.2% ) had primary testicular DLBCL and 23 (33.8% ) had secondary testicular DLBCL. The proportion of secondary testicular DLBCL patients with Ann Arbor stage Ⅲ-Ⅳ (P<0.001) , elevated LDH (P<0.001) , ECOG score ≥ 2 points (P=0.005) , and IPI score 3-5 points (P<0.001) is higher than that of primary testicular DLBCL patients. Sixty-two (91% ) patients received rituximab in combination with cyclophosphamide, adriamycin, vincristine, and prednisone (R-CHOP) -based first-line regimen, whereas 54 cases (79% ) underwent orchiectomy prior to chemotherapy. Patients with secondary testicular DLBCL had a lower estimated 5-year progression-free survival (PFS) rate (16.5% vs 68.1% , P<0.001) and 5-year overall survival (OS) rate (63.4% vs 74.9% , P=0.008) than those with primary testicular DLBCL, and their complete remission rate (57% vs 91% , P=0.003) was also lower than that of primary testicular DLBCL. The ECOG scores of ≥2 (PFS: P=0.018; OS: P<0.001) , Ann Arbor stages Ⅲ-Ⅳ (PFS: P<0.001; OS: P=0.018) , increased LDH levels (PFS: P=0.015; OS: P=0.006) , and multiple extra-nodal involvements (PFS: P<0.001; OS: P=0.013) were poor prognostic factors in testicular DLBCL. Targeted sequencing data in 20 patients with testicular DLBCL showed that the mutation frequencies of ≥20% were PIM1 (12 cases, 60% ) , MYD88 (11 cases, 55% ) , CD79B (9 cases, 45% ) , CREBBP (5 cases, 25% ) , KMT2D (5 cases, 25% ) , ATM (4 cases, 20% ) , and BTG2 (4 cases, 20% ) . The frequency of mutations in KMT2D in patients with secondary testicular DLBCL was higher than that in patients with primary testicular DLBCL (66.7% vs 7.1% , P=0.014) and was associated with a lower 5-year PFS rate in patients with testicular DLBCL (P=0.019) . Conclusion: Patients with secondary testicular DLBCL had worse PFS and OS than those with primary testicular DLBCL. The ECOG scores of ≥2, Ann Arbor stages Ⅲ-Ⅳ, increased LDH levels, and multiple extra-nodal involvements were poor prognostic factors in testicular DLBCL. PIM1, MYD88, CD79B, CREBBP, KMT2D, ATM, and BTG2 were commonly mutated genes in testicular DLBCL, and the prognosis of patients with KMT2D mutations was poor.

Nonfood Probiotic, Prebiotic, and Synbiotic Use Reduces All-Cause and Cardiovascular Mortality Risk in Older Adults: A Population-Based Cohort Study

OBJECTIVES

Pro-, pre-, and synbiotic supplements improve cardiovascular risk factors. However, the association between nonfood pro-, pre-, and synbiotics (NPPS) and long-term all-cause and cardiovascular mortality has not been studied. Thus, our objective was to determine the impact of nonfood pro-, pre-, and synbiotics on all-cause and cardiovascular mortality.

DESIGN, SETTING, AND PARTICIPANTS

This was a retrospective, cohort study of 4837 nationally representative American participants aged 65 years or older with a median follow-up duration of 77 months.

MEASUREMENTS

All-cause and cardiovascular mortality were measured.

RESULTS

A total of 1556 participants died during the median 77-month follow-up, and 517 died from cardiovascular disease. Compared with participants without NPPS use, participants who used NPPS experienced a reduced risk of all-cause mortality by nearly 41% (hazard ratio 0.59, 95% CI 0.43 to 0.79) and cardiovascular mortality by 52% (HR 0.48, 95% CI 0.30 to 0.76). Such an effect persisted in most subgroup analyses and complete-case analyses.

CONCLUSION AND RELEVANCE

In this study, we found a protective effect of NPPS against all-cause and cardiovascular mortality in Americans aged 65 years or older. Nonfood pro-, pre-, and synbiotics can be a novel, inexpensive, low-risk treatment addition for all-cause and cardiovascular mortality for older individuals.

Applying HT-SAXS to chemical ligand screening

Chemical probes are invaluable tools for investigating essential biological processes. Understanding how small-molecule probes engage biomolecular conformations is critical to developing their functional selectivity. High-throughput solution X-ray scattering is well-positioned to profile target-ligand complexes during probe development, bringing conformational insight and selection to traditional ligand binding assays. Access to high-quality synchrotron SAXS datasets and high-throughput data analysis now allows routine academic users to incorporate conformational information into small-molecule development pipelines. Here we describe a general approach for benchmarking and preparing HT-SAXS chemical screens from small fragment libraries. Using the allosteric oxidoreductase Apoptosis-Inducing Factor (AIF) as an exemplary system, we illustrate how HT-SAXS efficiently identifies an allosteric candidate among hits of a microscale thermophoresis ligand screen. We discuss considerations for pursuing HT-SAXS chemical screening with other systems of interest and reflect on advances to extend screening throughput and sensitivity.

Effects of dezocine combined with dexmedetomidine on adverse reactions and inflammatory factors in patients undergoing HIPEC after intestinal surgery and its protective effect on the heart in the perioperative period

OBJECTIVE

The aim of this study was to explore the effects of dezocine combined with dexmedetomidine on adverse reactions and inflammatory factors in patients undergoing hyperthermic intraperitoneal chemotherapy (HIPEC) after intestinal surgery and its protective effect on the heart in the perioperative period.

PATIENTS AND METHODS

A total of 80 patients treated with HIPEC after intestinal surgery in our hospital from September 2018 to December 2019 were enrolled as research subjects. All patients were evenly divided into two groups using a random number table. As to analgesia and sedation during treatment, dezocine was injected intramuscularly at 30 min before treatment in the control group. Meanwhile, dezocine combined with dexmedetomidine was given in the same way in the observation group. Adverse reactions and changes in numeric rating scale (NRS) pain score during intervention were compared between the two groups. The changes in the levels of inflammatory and myocardial injury-related factors, and vascular endothelial function and regeneration ability among cardiovascular indicators at 12 h after intervention were compared as well. Additionally, the correlations of left ventricular mass index (LVMI) with the changes in the levels of inflammatory factor high-sensitivity C-reactive protein (hs-CRP), myocardial injury-related factor lactic dehydrogenase (LDH), vascular endothelial function indicator endothelin-1 (ET-1) and cardiovascular regeneration ability index vascular endothelial growth factor (VEGF) were analyzed.

RESULTS

Compared with control group, the total prevalence rate of severe pain, respiratory depression, nausea and vomiting, diarrhea, and muscle rigidity during intervention was significantly reduced in the observation group (p<0.05). NRS pain score at 1, 4, 8 and 12 h after intervention decreased remarkably in the observation group compared with the control group (p<0.05). Meanwhile, the levels of inflammatory factors tumor necrosis factor-α (TNF-α) and hs-CRP, and myocardial injury-related factors LDH and creatine kinase MB (CKMB) as well as ET-1 at 12 h after intervention declined remarkably in observation group compared with control group (p<0.05). However, the levels of nitric oxide (NO), VEGF and basic fibroblast growth factor (bFGF) rose significantly in the observation group (p<0.05). Besides, LVMI was positively correlated with hs-CRP and LDH, whereas was negatively associated with ET-1 and VEGF (p<0.05).

CONCLUSIONS

In HIPEC, dezocine combined with dexmedetomidine used for sedation and analgesia is able to effectively reduce adverse reactions and relieve inflammatory responses in vivo, exerting a cardio-protective effect.

Potential biomarkers and lncRNA-mRNA regulatory networks in invasive growth hormone-secreting pituitary adenomas

PURPOSE

Growth hormone-secreting pituitary adenomas (GH-PAs) are common subtypes of functional PAs. Invasive GH-PAs play a key role in restricting poor outcomes. The transcriptional changes in GH-PAs were evaluated.

METHODS

In this study, the transcriptome analysis of six different GH-PA samples was performed. The functional roles, co-regulatory network, and chromosome location of differentially expressed (DE) genes in invasive GH-PAs were explored.

RESULTS

Bioinformatic analysis revealed 101 DE mRNAs and 70 DE long non-coding RNAs (lncRNAs) between invasive and non-invasive GH-PAs. Functional enrichment analysis showed that epithelial cell differentiation and development pathways were suppressed in invasive GH-PAs, whereas the pathways of olfactory transduction, retinol metabolism, drug metabolism-cytochrome P450, and metabolism of xenobiotics by cytochrome P450 had an active trend. In the protein-protein interaction network, 11 main communities were characterized by cell- adhesion, -motility, and -cycle; transport process; phosphorus and hormone metabolic processes. The SGK1 gene was suggested to play a role in the invasiveness of GH-PAs. Furthermore, the up-regulated genes OR51B6, OR52E4, OR52E8, OR52E6, OR52N2, MAGEA6, MAGEC1, ST8SIA6-AS1, and the down-regulated genes GAD1-AS1 and SPINT1-AS1 were identified in the competing endogenous RNA network. The RT-qPCR results further supported the aberrant expression of those genes. Finally, the enrichment of DE genes in chromosome 11p15 and 12p13 regions were detected.

CONCLUSION

Our findings provide a new perspective for studies evaluating the underlying mechanism of invasive GH-PAs.

[Comparisons of clinical characteristics and prognosis between patients with primary and secondary thyroid lymphoma]

Objective: To compare clinical characteristics and prognosis between patients with primary (PTL) and secondary thyroid lymphoma (STL) . Methods: A retrospective analysis was performed on 46 patients with thyroid lymphoma (PTL 19, STL 27) from January 2002 to October 2018. Results: ①PTL group included 4 males and 15 females, with a median age of 57 years. The STL group included 10 males and 17 females, with a median age of 61 years. Diffuse large B-cell lymphoma (DLBCL) was the main pathological subtype in both PTL and STL groups, with 14 cases (73.7%) and 20 cases (74.1%) respectively. In terms of clinical manifestations, goiter was the most common symptom in PTL patients 100.0% (19/19) , while 29.6% (8/27) STL had goiter (P<0.001) . The incidences of increased thyroglobulin antibody (TRAb) /thyroid peroxidase antibody (TPO) were 81.3% (13/16) in PTL group and 43.8% (7/16) in STL group (P=0.028) respectively. Concerning the clinical features of patients, only two PTL patients (10.5%) with advanced Ann Arbor stage (Ⅲ/Ⅳ) , while 21 (77.8%) STL experienced advanced Ann Arbor stage (P<0.001) . Elevated serum β(2)-MG were appeared in 1 (7.1%) PTL and 9 (47.4%) STL patients (P=0.013) , and advanced IPI score (3-5) was more common in STL than PTL (59.3% vs 5.3%, P<0.001) . ②Among the 17 PTL patients who received treatments, 15 (88.2%) achieved remission; as for STL patients received treatments, 23/25 (92.0%) were in remission. The 5-year overall survival (OS) rates of PTL (n=17) and STL groups (n=25) were (87.4±8.4) % and (70.0±13.1) % (P=0.433) respectively. ③The 5-year OS rate in 41 patients with B-cell thyroid lymphoma was (81.1±7.5) %. Univariate analysis showed that IPI score of 3-5 (P=0.040) and high level of serum IL-8 (P=0.022) were significantly associated with poor outcome. Conclusion: DLBCL was the most common subtype in both PTL and STL, and goiter was the major symptom in PTL. IPI score of 3-5 and high level of serum IL-8 were unfavorable prognostic factors for patients with B-cell thyroid lymphoma.

Identification of the CD200R1 promoter and the association of its polymorphisms with the risk of Parkinson's disease

BACKGROUND AND PURPOSE

Neuroinflammation is known to be involved in the pathogenesis of Parkinson's disease (PD). Abnormal activation of microglia plays a key role in this pathological process. CD200R1 is a membrane glycoprotein that is expressed primarily on myeloid cells including microglia and is involved in the maintenance of microglia in a stationary state. Our previous study reported that the regulation of CD200R1 expression is altered in PD patients. Such alteration will lead to neuroinflammation and is related to the pathogenesis of PD. The possible role of promoter polymorphisms for abnormal CD200R1 expression in PD was examined in this study.

METHOD

The UCSC database and dual-luciferase assays were used to confirm the promoter region of CD200R1. The promoter of CD200R1 was sequenced in 457 PD patients and 520 matched healthy controls from the Chinese Han population. Dual-luciferase assays were conducted to examine the promoter activity of CD200R1.

RESULTS

It was confirmed that the promoter of CD200R1 is located in the region 876-146 bp upstream of the coding DNA sequence. The frequencies of rs144721913 (P = 0.001) and rs72952157 (P = 0.022) in the promoter were significantly different between the PD group and control group. rs144721913 increases the risk of PD by approximately 14-fold and rs72952157 by 2.6-fold. The dual-luciferase assay indicated that the rs144721913 T allele and the rs72952157 G allele reduced the transcriptional activity of the CD200R1 promoter.

CONCLUSIONS

For the first time the promoter region of CD200R1 has been defined and two potential risk polymorphisms (rs144721913 and rs72952157) in the region for PD in Chinese Han populations have been reported.

Ultra-deep next-generation sequencing of plasma cell-free DNA in patients with advanced lung cancers: results from the Actionable Genome Consortium

BACKGROUND

Noninvasive genotyping using plasma cell-free DNA (cfDNA) has the potential to obviate the need for some invasive biopsies in cancer patients while also elucidating disease heterogeneity. We sought to develop an ultra-deep plasma next-generation sequencing (NGS) assay for patients with non-small-cell lung cancers (NSCLC) that could detect targetable oncogenic drivers and resistance mutations in patients where tissue biopsy failed to identify an actionable alteration.

PATIENTS AND METHODS

Plasma was prospectively collected from patients with advanced, progressive NSCLC. We carried out ultra-deep NGS using cfDNA extracted from plasma and matched white blood cells using a hybrid capture panel covering 37 lung cancer-related genes sequenced to 50 000× raw target coverage filtering somatic mutations attributable to clonal hematopoiesis. Clinical sensitivity and specificity for plasma detection of known oncogenic drivers were calculated and compared with tissue genotyping results. Orthogonal ddPCR validation was carried out in a subset of cases.

RESULTS

In 127 assessable patients, plasma NGS detected driver mutations with variant allele fractions ranging from 0.14% to 52%. Plasma ddPCR for EGFR or KRAS mutations revealed findings nearly identical to those of plasma NGS in 21 of 22 patients, with high concordance of variant allele fraction (r = 0.98). Blinded to tissue genotype, plasma NGS sensitivity for de novo plasma detection of known oncogenic drivers was 75% (68/91). Specificity of plasma NGS in those who were driver-negative by tissue NGS was 100% (19/19). In 17 patients with tumor tissue deemed insufficient for genotyping, plasma NGS identified four KRAS mutations. In 23 EGFR mutant cases with acquired resistance to targeted therapy, plasma NGS detected potential resistance mechanisms, including EGFR T790M and C797S mutations and ERBB2 amplification.

CONCLUSIONS

Ultra-deep plasma NGS with clonal hematopoiesis filtering resulted in de novo detection of targetable oncogenic drivers and resistance mechanisms in patients with NSCLC, including when tissue biopsy was inadequate for genotyping.

Magnetic resonance spectroscopy may serve as a presurgical predictor of somatostatin analog therapy response in patients with growth hormone-secreting pituitary macroadenomas

PURPOSE

Somatostatin analogs (SSAs) are considered one of the most effective medical treatments for patients with growth hormone-secreting pituitary adenomas (GH-PAs). The postoperative electron microscopy (EM) pathological subtype and SSTR2 expression in the tumor are the most established predictors of patient response to SSA therapy. The aim of this study was to evaluate how will magnetic resonance spectroscopy (MRS) measurements before surgery predict the EM pathological subtypes and SSTR2 expression of tumors, and thereby serve as an indicator for the therapeutic sensitivity to SSAs of patients with GH-PAs.

METHODS

Eighteen patients with GH pituitary macroadenomas who underwent transsphenoidal surgery were included in this retrospective study. The preoperative MRS data and T2 signal intensity were obtained from patients by 1.5 T MR spectroscopy of the sellar mass. The EM pathological subtypes of tumors were determined after surgery through examination of cell granulations. The expressions of somatostatin receptor 2 (SSTR2), SSTR5, P21, P27, and Ki-67 were evaluated by immunohistochemistry.

RESULTS

The MRS parameters that were found to significantly predict the EM pathological subtypes of tumors, as calculated by the receiver operating characteristic curve, were the choline (Ch) value at 3140.5 MR units (sensitivity 69.2%, specificity 100%) and the choline/creatine (Ch/Cr) ratio at 1.27 (sensitivity 92.3%, specificity 100%). Further, the Ch/Cr ratio, but not other MRS data, was shown to negatively correlate with the expression of SSTR2 (P = 0.02). The Ch/Cr ratio was also found to positively correlate with the Ki-67 value (P < 0.05) and T2 signal (P < 0.05), but not with other factors that were examined in this study. Moreover, the Ch/Cr ratio could predict the EM pathological subtypes of tumors with an accuracy of 83.3% (5/6) for patients with an isointense T2 signal.

CONCLUSION

The Ch/Cr ratio by MRS could effectively predict the tumor subtype and was significantly correlated with the expression of SSTR2, which was consistent with other predictors. It was also able to distinguish the patients with isointense T2 signals. Our results provide a potentially new and non-invasive method to predict the response to SSAs in patients with GH pituitary macroadenomas.

Quantum Oscillations of the Positive Longitudinal Magnetoconductivity: A Fingerprint for Identifying Weyl Semimetals

Weyl semimetals (WSMs) host charged Weyl fermions as emergent quasiparticles. We develop a unified analytical theory for the anomalous positive longitudinal magnetoconductivity (LMC) in a WSM, which bridges the gap between the classical and ultraquantum approaches. More interestingly, the LMC is found to exhibit periodic-in-1/B quantum oscillations, originating from the oscillations of the nonequilibrium chiral chemical potential. The quantum oscillations, superposed on the positive LMC, are a remarkable fingerprint of a WSM phase with a chiral anomaly, whose observation is a valid criteria for identifying a WSM material. In fact, such quantum oscillations were already observed by several experiments.

Time-reversal invariant resonant backscattering on a topological insulator surface driven by a time-periodic gate voltage

We study the scattering of the Dirac electrons by a point-like nonmagnetic impurity on the surface of a topological insulator, driven by a time-periodic gate voltage. It is found that, due to the doublet degenerate crossing points of different Floquet sidebands, resonant backscattering can happen for the surface electrons, even without breaking the time-reversal (TR) symmetry of the topological surface states (TSSs). The energy spectrum is reshuffled in a way quite different from that for the circularly polarized light, so that new features are exhibited in the Friedel oscillations of the local charge and spin density of states. Although the electron scattering is dramatically modified by the driving voltage, the 1/ρ scale law of the spin precession persists for the TSSs. The TR invariant backscattering provides a possible way to engineer the Dirac electronic spectrum of the TSSs, without destroying the unique property of spin-momentum interlocking of the TSSs.

Targeted methylation sequencing of plasma cell-free DNA for cancer detection and classification

Background

Targeted methylation sequencing of plasma cell-free DNA (cfDNA) has a potential to expand liquid biopsies to patients with tumors without detectable oncogenic alterations, which can be potentially useful in early diagnosis.

Patients and methods

We developed a comprehensive methylation sequencing assay targeting 9223 CpG sites consistently hypermethylated according to The Cancer Genome Atlas. Next, we carried out a clinical validation of our method using plasma cfDNA samples from 78 patients with advanced colorectal cancer, non-small-cell lung cancer (NSCLC), breast cancer or melanoma and compared results with patients' outcomes.

Results

Median methylation scores in plasma cfDNA samples from patients on therapy were lower than from patients off therapy (4.74 versus 85.29; P = 0.001). Of 68 plasma samples from patients off therapy, methylation scores detected the presence of cancer in 57 (83.8%), and methylation-based signatures accurately classified the underlying cancer type in 45 (78.9%) of these. Methylation scores were most accurate in detecting colorectal cancer (96.3%), followed by breast cancer (91.7%), melanoma (81.8%) and NSCLC (61.1%), and most accurate in classifying the underlying cancer type in colorectal cancer (88.5%), followed by NSCLC (81.8%), breast cancer (72.7%) and melanoma (55.6%). Low methylation scores versus high were associated with longer survival (10.4 versus 4.4 months, P < 0.001) and longer time-to-treatment failure (2.8 versus 1.6 months, P = 0.016).

Conclusions

Comprehensive targeted methylation sequencing of 9223 CpG sites in plasma cfDNA from patients with common advanced cancers detects the presence of cancer and underlying cancer type with high accuracy. Methylation scores in plasma cfDNA correspond with treatment outcomes.

Cystathionine γ-Lyase Is Involved in the Renoprotective Effect of Brief and Repeated Ischemic Postconditioning After Renal Ischemia/Reperfusion Injury in Diabetes Mellitus

BACKGROUND

The aim of this study was to determine whether the protective effects of brief and repeated ischemic postconditioning (IPoC) are associated with the modulation of cystathionine γ-lyase (CSE) expression after renal ischemia/reperfusion (I/R) injury in diabetes mellitus (DM).

METHODS

We subjected diabetic rats to 45 minutes of ischemia followed by reperfusion at 24 hours. Before reperfusion, diabetic rats were treated with 3 cycles of 6 seconds of reperfusion, followed by 6 seconds of ischemia. DL-Propargylglycine (PAG, a CSE inhibitor) was administered to the diabetic rats to investigate its effects on the severity of renal I/R injury in diabetes mellitus (DM). Blood samples and left kidneys were collected for the measurement of blood urea nitrogen (BUN) and serum creatinine (SCr) levels and renal pathologic changes. Western blot and immunochemistry techniques were also performed for the localization of CSE. Levels of superoxidase dismutase (SOD), malonyldialdehyde (MDA), tumor necrosis-alpha (TNF-α), and hydrogen sulfide (H₂S) were quantified using commercially available kits.

RESULTS

The results showed that BUN and SCr levels increased on renal ischemia/reperfusion injury (RI/RI) in the DM group. Diabetic rats treated with IPoC exhibited significantly less renal damage on I/R. Kit measurements showed that IPoC could markedly inhibit the levels of MDA and TNF-α and also improve SOD and H₂S levels. Western blot and immunochemistry showed that expression of CSE was downregulated on I/R in the DM group and IPoC upregulated CSE expression, whereas PAG treatment resulted in opposite effects.

CONCLUSION

Our findings show that brief and repeated IPoC increased the expression of CSE after I/R in DM, and the modulation of CSE may underlie the renoprotective effect of IPoC.

Abstract PD1-15: The landscape of somatic genetic alterations in breast cancers from ATM germline mutation carriers

Introduction:Pathogenic and/or founder germline variants in the ataxia-telangiectasia mutated (ATM) gene confer an increased breast cancer (BC) risk. The protein kinase ATM plays a central role inDNA double-strand break-repair and in the activation of downstream targets such as p53 and BRCA1. We sought to define the repertoire of somatic genetic alterations of BCs from patients with pathogenic germline ATM mutations and whether somatic loss of heterozygosity (LOH) of ATM would be present in these cancers.

Methods: 21 BCs from ATM germline mutation carriers were microdissected. Tumor and normal DNA samples were subjected to whole-exome sequencing (WES, n=12) or massively parallel sequencing targeting all coding regions and selected intronic and regulatory regions of 410 key cancer genes (n=9). Somatic mutations, copy number alterations, cancer cell fractions, large-scale state transitions (LSTs) and mutational signatures were defined using state-of-the-art bioinformatics algorithms. ABSOLUTE and FACETS were employed to assess LOH of the wild-type allele of ATM.

Results: Of the patients included in this study, 71%, 24% and 5% of cases harbored ATM missense (all but one p.V2424G), frame-shift and nonsense germline mutations, respectively. All tumors were ER-positive and four (19%) were HER2-positive. The median age of the patients was 46 years (32–79 years). Our analyses revealed biallelic inactivation of ATM through LOH of the wild-type allele in 16 of 21 cases (76%), and second somatic ATM mutations were not found. The median number of non-synonymous somatic mutations was 38 (range 15-113) and 2 (range 0-8)in tumors subjected to WES and targeted sequencing, respectively. The repertoire of somatic genetic alterations of ATM-associated BCs was found to be heterogeneous, including clonal PIK3CA mutations (24%), GATA3 mutations (19%), FANCI amplifications (19%) and CCND1 amplifications (14%). Importantly, however, no somatic mutations affecting TP53 were found. Analysis of the WES data revealed that 5 (42%) ATM-associated BCs displayed high LST scores, all of which harbored bi-allelic ATM inactivation. In contrast to BRCA1- and BRCA2-associated BCs, which frequently display the mutational signature 3 associated with defective homologous recombination DNA repair, the ATM-associated BCs studied displayed the ageing mutational signature (i.e. signature 1). Comparison of the mutational profiles of the ATM--associated BCs subjected to WES (n=12) with those of BRCA1- (n=11) and BRCA2-associated (n=10) BCs from The Cancer Genome Atlas revealed that TP53 was more frequently mutated in BCs from BRCA1 germline mutation carriers (0% vs 72%, P&lt;0.001), while no differences with BRCA2-associated BCs were found.

Conclusion: ATM-associated BCs frequently display bi-allelic ATM inactivation through LOH of the wild-type allele and a subset of these cases displayed high levels of LSTs. These findings suggest that at least in a subset of ATM-associated BCs, biallelic inactivation of ATM rather than a dominant negative effect of the germline mutation may be the mechanism of inactivation of this tumor suppressor gene. The repertoire of somatic genetic alterations of ATM-associated BCs is heterogeneous, with a noticeable lack of TP53 somatic mutations.

Citation Format: Weigelt B, Bi R, Kumar R, James PA, Thorne H, Couch FJ, Eccles DM, Blows F, Geyer FC, Li A, Selenica P, Lim RS, Blecua P, Shen R, Wen H, Robson ME, Reis-Filho JS, Chenevix-Trench G. The landscape of somatic genetic alterations in breast cancers from ATM germline mutation carriers [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr PD1-15.

Abstract PD8-09: Bi-allelic alterations in homologous recombination (HR) DNA repair-related genes as the basis for HR defects in human cancers: A pan-cancer genomics and functional analysis

Background: BRCA1 and BRCA2 are involved in homologous recombination (HR) DNA repair and are germ-line cancer pre-disposition genes that result in the hereditary breast and ovarian cancer (HBOC) syndrome. Whether germ-line or somatic alterations in these genes or other members of the HR pathway and if mono- or bi-allelic alterations of HR-related genes have a phenotypic impact in breast and other cancers remains to be fully elucidated. Here we took a combined genomic and functional approach to identify the role of mutations in HR-related genes and their impact on HR DNA repair.

Methods: Whole-exome sequencing and Affymetrix SNP6 array data from 8,178 tumors, comprising 24 different cancer types including breast cancer, were retrieved from The Cancer Genome Atlas (TCGA). We identified the prevalence of missense and pathogenic (frame-shift, nonsense, start/stop codon and splice site variants) somatic and germline mutations in 102 HR-related genes curated from the literature. For each mutation, we determined if the alterations were bi-allelic. We evaluated genomic signatures of HR-deficiency in each tumor using large-scale state transitions (LSTs) and a mutational signature of HR-deficiency (signature 3). An independent set of 24 fresh sporadic breast cancer tissue specimens from our institution was subjected to i) an ex-vivo assay that assesses the ability of cancer cells to form RAD51 foci in response to ex-vivo irradiation (IR), and ii) whole exome-sequencing to define whether RAD51 deficient tumors would display LSTs, signature 3 and bi-allelic inactivation of HR-related genes.

Results: 13% and 5% of all TCGA cases displayed pathogenic mono- and bi-allelic alterations of HR-related genes, respectively. Of the biallelic alterations, only 45% occurred in traditional BRCA1/2 associated hereditary cancers (HBOCs, namely breast, ovarian and prostate cancer). Bi-allelic, but not mono-allelic, pathogenic genetic alterations in HR-related genes were significantly associated with genomic evidence of HR deficiency across cancer types, in HBOCs and within breast cancer. In HBOCs, bi-allelic alterations in HR-related genes were mutually exclusive (p=0.02). In breast cancer, bi-allelic inactivation of HR DNA repair-related genes was observed in 9.8%, of which 7.8% involved a germline pathogenic mutation and 2.0% were solely somatic. In breast cancer, in addition to BRCA1 and BRCA2, bi-allelic inactivation of PALB2 (0.2%), ATM (1.1%) and POLQ (0.3%) were found to be associated with genomic features of HR deficiency. In the 24 additional breast cancers, 9 were classified by the functional ex-vivo RAD51 assay as HR-deficient, 8 of which displayed bi-allelic inactivation of one HR-related gene, whereas only 1 of the 15 HR-proficient breast cancers harbored bi-allelic inactivation of HR-related genes (p&lt;0.001).

Conclusion: Bi-allelic germline and somatic alterations of HR-related genes in addition to BRCA1 and BRCA2 are present in breast and other cancer types. Irrespective of the gene, these bi-allelic alterations are associated with HR deficiency as defined by genomic methods and functional assays, expanding the potential opportunities for therapies targeting HR DNA repair defects.

Citation Format: Riaz N, Blecua P, Lim RS, Shen R, Higginson DS, Weinhold N, Norton L, Weigelt B, Powell SN, Reis-Filho JS. Bi-allelic alterations in homologous recombination (HR) DNA repair-related genes as the basis for HR defects in human cancers: A pan-cancer genomics and functional analysis [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr PD8-09.

Analytical theory and possible detection of the ac quantum spin Hall effect

We develop an analytical theory of the low-frequency ac quantum spin Hall (QSH) effect based upon the scattering matrix formalism. It is shown that the ac QSH effect can be interpreted as a bulk quantum pumping effect. When the electron spin is conserved, the integer-quantized ac spin Hall conductivity can be linked to the winding numbers of the reflection matrices in the electrodes, which also equal to the bulk spin Chern numbers of the QSH material. Furthermore, a possible experimental scheme by using ferromagnetic metals as electrodes is proposed to detect the topological ac spin current by electrical means.

Theory of Inverse Edelstein Effect of The Surface States of A Topological Insulator

The surface states of three-dimensional topological insulators possess the unique property of spin-momentum interlocking. This property gives rise to the interesting inverse Edelstein effect (IEE), in which an applied spin bias μ is converted to a measurable charge voltage difference V. We develop a semiclassical theory for the IEE of the surface states of Bi2Se3 thin films, which is applicable from the ballistic regime to diffusive regime. We find that the efficiency of the spin-charge conversion, defined as γ = V/μ, exhibits a universal dependence on the ratio between sample size and electron mean free path. The efficiency increases from γ = π/4 in the ballistic limit to γ = π in the diffusive limit, suggesting that sufficient strength of impurity scattering is favorable for the IEE.

What hides behind the MASC: clinical response and acquired resistance to entrectinib after ETV6-NTRK3 identification in a mammary analogue secretory carcinoma (MASC)

Here, we describe the dramatic response of a patient with an ETV6-NTRK3-driven mammary analogue secretory carcinoma to treatment with a pan-Trk inhibitor, and the development of acquired resistance linked to a novel NTRK3 mutation that interferes with drug binding. This case emphasizes how molecular profiling can identify therapies for rare diseases and dissect mechanisms of drug resistance.

Background

Mammary analogue secretory carcinoma (MASC) is a recently described pathologic entity. We report the case of a patient with an initial diagnosis of salivary acinic cell carcinoma later reclassified as MASC after next-generation sequencing revealed an ETV6-NTRK3 fusion.

Patients and methods

This alteration was targeted with the pan-Trk inhibitor entrectinib (Ignyta), which possesses potent in vitro activity against cell lines containing various NTRK1/2/3 fusions.

Results

A dramatic and durable response was achieved with entrectinib in this patient, followed by acquired resistance that correlated with the appearance of a novel NTRK3 G623R mutation. Structural modeling predicts that this alteration sterically interferes with drug binding, correlating to decreased sensitivity to drug inhibition observed in cell-based assays.

Conclusions

This first report of clinical activity with TrkC inhibition and the development of acquired resistance in an NTRK3-rearranged cancer emphasize the utility of comprehensive molecular profiling and targeted therapy for rare malignancies (NCT02097810).

Entanglement, subsystem particle numbers and topology in free fermion systems

We study the relationship between bipartite entanglement, subsystem particle number and topology in a half-filled free fermion system. It is proposed that the spin-projected particle numbers can distinguish the quantum spin Hall state from other states, and can be used to establish a new topological index for the system. Furthermore, we apply the new topological invariant to a disordered system and show that a topological phase transition occurs when the disorder strength is increased beyond a critical value. It is also shown that the subsystem particle number fluctuation displays behavior very similar to that of the entanglement entropy. This provides a lower-bound estimation for the entanglement entropy, which can be utilized to obtain an estimate of the entanglement entropy experimentally.

Phase I study of weekly nab-paclitaxel + weekly cetuximab + intensity-modulated radiation therapy (IMRT) in patients with stage III-IVB head and neck squamous cell carcinoma (HNSCC)

BACKGROUND

There is a clinical need to improve the efficacy of standard cetuximab + concurrent intensity-modulated radiation therapy (IMRT) for patients with locally and/or regionally advanced HNSCC. Taxanes have radiosensitizing activity against HNSCC, and nab-paclitaxel may offer therapeutic advantage in comparison with other taxanes.

PATIENTS AND METHODS

This was a single-institution phase I study with a modified 3 + 3 design. Four dose levels (DLs) of weekly nab-paclitaxel were explored (30, 45, 60, and 80 mg/m(2)), given with standard weekly cetuximab (450 mg/m(2) loading dose followed by 250 mg/m(2) weekly) and concurrent IMRT (total dose, 70 Gy).

RESULTS

Twenty-five eligible patients (20 M, 5 F) enrolled, with median age 58 years (range, 46-84 years). Primary tumor sites were oropharynx, 19 (10 human papillomavirus [HPV] pos, 8 HPV neg, 1 not done); neck node with unknown primary, 2; larynx 2; and oral cavity and maxillary sinus, 1 each. Seven patients had received prior induction chemotherapy. Maximum tolerated dose (MTD) was exceeded at DL4 (nab-paclitaxel, 80 mg/m(2)) with three dose-limiting toxicities (DLTs) (grade 3 neuropathy, grade 3 dehydration, with grade 3 mucositis grade 3 anemia) among five assessable patients. There was only one DLT (grade 3 supraventricular tachycardia) among six patients at DL3 (nab-paclitaxel, 60 mg/m(2)), and this was deemed the MTD. Among 23 assessable patients, the most common ≥ g3 AEs were lymphopenia 100%, functional mucositis 65%, and pain in throat/oral cavity 52%. At a median follow-up of 33 months, 2-year failure-free survival (FFS) is 65% [95% confidence interval (CI) 42% to 81%] and 2-year overall survival (OS) is 91% (95% CI 69-97).

CONCLUSION

The recommended phase II dose for nab-paclitaxel is 60 mg/m(2) weekly when given standard weekly cetuximab and concurrent IMRT. This regimen merits further study as a nonplatinum alternative to IMRT + cetuximab alone.

CLINICALTRIALSGOV ID

NCT00736619.

Stabilization of the quantum spin Hall effect by designed removal of time-reversal symmetry of edge states

The quantum spin Hall (QSH) effect is known to be unstable to perturbations violating time-reversal symmetry. We show that creating a narrow ferromagnetic region near the edge of a QSH sample can push one of the counterpropagating edge states to the inner boundary of the ferromagnetic region and leave the other at the outer boundary, without changing their spin polarizations and propagation directions. Since the two edge states are spatially separated into different "lanes," the QSH effect becomes robust against symmetry-breaking perturbations.

Kosterlitz-Thouless transition in disordered two-dimensional topological insulators

The disorder-driven metal-insulator transition in the quantum spin Hall systems is studied by scaling analysis of the Thouless conductance g. Below a critical disorder strength, the conductance is independent of the sample size M, an indication of critically delocalized electron states. The calculated beta function β = d ln g/d ln M indicates that the metal-insulator transition is of Kosterlitz-Thouless (KT) type, which is characterized by binding and unbinding of vortex-antivortex pairs of the local currents. The KT-like metal-insulator transition is a basic characteristic of the quantum spin Hall state, being independent of the time-reversal symmetry.

Transdifferentiation of cultured human prostate cancer cells to a neuroendocrine cell phenotype in a hormone-depleted medium

Neuroendocrine (NE) cells are enigmatically found in association with human prostate cancers and their numbers are reported to increase in advanced and hormoneresistant tumors. The origin of this cell type and the reason for their appearance in prostate tumors remains unresolved. Previously, Bang et al. (Proc Natl Acad Sci USA 1994;91:5330) reported that dibutyryl adenosine 3',5'-cyclic phosphate (db-cAMP), an agent that upregulates intracellular cAMP, was able to induce a NE cell-like phenotype of cultured human prostate cancer cells, including the androgen-sensitive LNCaP line. Here we report that chronic incubation of LNCaP cells in a medium containing 10% charcoal-stripped fetal bovine serum (CSFBS) likewise induces NE differentiation of these cells. Within 5 days of switching low density cultures of LNCaP cells to this modified medium, the cells growth arrest and acquire an altered morphology with numerous cytoplasmic secretory granules and elongated processes that resemble cultured neurons. This morphology predominates at 10 days with complete transformation seen by 20 days of culture. Electron microscopic analysis of sections of CS-FBS maintained cells showed the presence of abundant dense core secretory granules characteristic of NE cells. Immunohistochemical staining identified the upregulation of the expression of NE markers bombesin, neuron-specific enolase, and S-100 in this modified culture medium. Once established, the NE cell-like phenotype was found to be reversible upon replacement with a medium containing unmodified fetal bovine serum, but not by direct supplementation of CS-FBS medium with dihydrotestosterone (DHT) (I nM). DHT supplementation did, however, suppress the development of the NE cell-like phenotype when it was present at the initiation of exposure to CS-FBS medium. In contrast to db-cAMP treatment, which did not affect prostate specific antigen (PSA) or androgen receptor (AR) expression of LNCaP cells, NE-differentiated LNCaP cells derived in this hormone-deficient medium showed marked downregulation of PSA and AR expression. These in vitro results further support the concept that prostate cancer cells can tranform in vivo to cells with a NE phenotype and suggest that this transformation might be accelerated in patients by certain therapies for prostate cancer.

p14ARF repression induced by promoter methylation associated with metastasis in esophageal squamous cell carcinoma

The objective of this study is to evaluate the promoter methylation status of the p14ARF in esophageal squamous cell carcinoma (ESCC). Cell lines were treated with the demethylation agent 5-aza-2'-deoxycytidine, and p14ARF messenger RNA (mRNA) expression was detected by reverse transcription-polymerase chain reaction. We analyzed the methylation status of p14ARF promoter by methylation-specific polymerase chain reaction in 50 ESCC and their noncarcinoma tissues. Then demethylation caused by 5-aza-2'-deoxycytidine increased the p14ARF mRNA expression level in esophagus cancer cell lines. p14ARF methylation was found in 48% (24 of 50) of ESCC patients but only in 18% (9 of 50) corresponding noncarcinoma tissues (P = 0.001). There was a statistically significant correlation between the presence of methylation and tumor metastasis (P < 0.001). The p14ARF mRNA was lower in ESCC tissues than nontumor tissues (mean ± standard deviation, 0.47 ± 0.32 vs. 1.40 ± 0.58; P = 0.002). Meanwhile, a signification association was found between the methylation status of p14ARF promoter and p14ARF mRNA expression in tissues (P < 0.05). The aberrant promoter methylation of p14ARF is a common phenomenon in ESCC, which may be an important mechanism of downregulating p14ARF mRNA expression.

Tumor suppressor menin mediates peripheral nerve injury-induced neuropathic pain through potentiating synaptic plasticity

Synaptic plasticity is a crucial step in the development of central sensitization in the pathogenesis of neuropathic hyperalgesia. Menin, the product of the multiple endocrine neoplasia type 1 (MEN1) gene, possesses the property of synaptogenesis which plays an essential role in neuronal activity. We tested the contributing role of spinal menin in peripheral nerve injury-induced neuropathic hypersensitivity through modulating neuronal synaptic plasticity. After approval by the Institutional Animal Care and Use Committee, nociceptive responses were detected with von Frey filaments and thermal plate after spared nerve injury in C57BL/6 mice who were treated with either intrathecal antisense oligonucleotide of MEN1 (ASO) or vehicle. Extracellular spontaneous discharge frequency, field excitatory postsynaptic potential (fEPSP), and monosynaptic excitatory postsynaptic currents (EPSCs) were measured electrophysiologically. Intrathecal ASO alleviated nerve injury-induced mechanical and thermal hypersensitivity. Upregulated spinal menin after nerve injury colocalized with NeuN in the superficial laminae; genetic knockdown of spinal menin reduced nerve injury induced in vivo spontaneous activity and instantaneous frequency and in vitro field potentials; ASO decreased the frequency and amplitude of monosynaptic EPSCs, and reduced synaptic strength and total charge. Collectively, these findings highlight the role of upregulated neuronal menin in the spinal cord in potentiating spinal synaptic plasticity in peripheral nerve injury-induced neuropathic hypersensitivity.

Electron entanglement detected by quantum spin Hall systems

We propose a promising electron entanglement detector consisting of two quantum spin Hall systems weakly coupled to a superconductor. The detection of electron spins along various polarization directions, which is a prerequisite for testing Bell's inequality on solid state spins, can be achieved in an all-electrical-controlled manner utilizing the helical edge states. It is found that the violation of Bell's inequality exists in a large range of the tunneling parameters, which can be realized in mercury telluride quantum wells.