O-235 ACLY entry into the nucleus to bind with EP300 and regulate the genomic DNA and ribosomal DNA transcription during early embryonic development

Study question

ATP citrate lyase (ACLY) is one of the key enzymes to produce acetyl coenzyme A. What is its role in early embryonic development?

Summary answer

ACLY affected by activation of T447, S451 and S455 sites into nucleus and band with EP300 to affect genomic DNA and ribosomal DNA transcription.

What is known already

ACLY is one of the key enzymes to produce acetyl coenzyme A, which participates in fatty acid metabolism and regulates acetylation. Studies have found that ACLY knockout cells can survive, while the cell proliferation capacity will be weakened. ACLY is highly expressed in the cytoplasm of Hela cells colon cancer cells and other somatic cells. When AKT phosphorylates S455 site, ACLY enters the nucleus and participates in DNA damage repair. Its localization and role in embryos have not been studied. The only thing we know is homozygous mice could not be detected at E8.5 days after implantation.

Study design, size, duration

Twenty-four human day 6 developmentally arrested embryos were used to detect ACLY localization. Dozens of ACLY heterozygous female mice were used to test the time points of ACLY homozygous lethality after mating with heterozygous male mice. After zygotes were taken from wild-type C57BL6 mice, microinjection technology was used to explore the effects of knocking down ACLY, changing ACLY location or mutating ACLY. HeLa cells were used to explore at the molecular level.

Participants/materials, setting, methods

In this experiment, we used human abandoned or donated embryos, gene knockout mice, wild-type C57BL6 mice and Hela cell.

The experimental techniques used include in vitro embryo culture, EU staining, plasmid transfection, immunoprecipitation, western blot analysis, in vitro transcription, microinjection, immunofluorescence, RT-PCR and RNA-seq.

Main results and the role of chance

Firstly, our study found its special nuclear localization in early embryos for the first time and proved that its localization was related to embryonic development potential.

Secondly, the specific period of ACLY homozygous death was identified by ACLY heterozygous mice. And by knocking down ACLY or adding inhibitor SB204990, It was found that ACLY played an important role in cell proliferation, blastocyst formation and lineage differentiation of early embryo development.

Thirdly, we proved that ACLY nucleation played an important role in the development of early embryos. and the activated form of T447, S451 and S455 three sites led to ACLY nucleation.

Finally, we found that ACLY affected the level of histone acetylation and UBF acetylation. And then genomic DNA and ribosomal DNA transcription level were decreased. We further explored how the acetyl group produced by ACLY regulated transcription. The interaction between ACLY and EP300 was confirmed by immunofluorescence and COIP experiments. After knocking down EP300 in embryos or inhibiting its function with inhibitor c646, the results are consistent with knocking down ACLY. The above experimental data prove that ACLY affects histone acetylation level and regulates gene opening through the interaction with EP300.

Limitations, reasons for caution

We need to further explore the factors that promote ACLY into the nucleus, so as to add it to in vitro culture to enhance the embryonic development potential.

Wider implications of the findings

The study provides a new mechanism for insulin or lysophosphatidic acid to promote embryo development, and helps to improve the quality of embryo development in the process of embryo culture in vitro.

Trial registration number

not applicable

[Rethinking the marketing strategy of anti-tumor drugs by single-arm trials supported]

Single-arm trial refers to a clinical trial design that does not set up parallel control group, adopts open design, and does not involve randomization and blind method. These features, on the one hand, speed up the process of clinical trials, significantly shorten the time to market and meet the needs of patients with advanced malignancies, but also lead to the uncertainty of single-arm clinical trials themselves. Recently, the US Food and Drug Administration held a meeting of the oncologic drug advisory committee to discuss six tumor indications that have been accelerated approved, which once again triggered the discussion of single-arm trials. The basis of accelerated approval by single-arm trial is actually a compromise on the level of evidence-based medical evidence requirements after assessing the benefit risk. Therefore, the sponsor should strictly grasp the applicable conditions of single-arm trial in anti-tumor drugs and conduct single-arm trial scientifically. Post-marketing clinical trial should be implement as early as possible to ensure the benefit of patients. Based on the characteristics of single-arm trial, combined with two guidance relevant to single-arm trial issued by National Medical Products Administration recently, this article is supposed to propose and summarize the strategy of single-arm trial supporting the marketing of anti-tumor drugs.

Study of the doubly charmed tetraquark [Formula: see text]

Quantum chromodynamics, the theory of the strong force, describes interactions of coloured quarks and gluons and the formation of hadronic matter. Conventional hadronic matter consists of baryons and mesons made of three quarks and quark-antiquark pairs, respectively. Particles with an alternative quark content are known as exotic states. Here a study is reported of an exotic narrow state in the D0D0π+ mass spectrum just below the D*+D0 mass threshold produced in proton-proton collisions collected with the LHCb detector at the Large Hadron Collider. The state is consistent with the ground isoscalar [Formula: see text] tetraquark with a quark content of [Formula: see text] and spin-parity quantum numbers JP = 1+. Study of the DD mass spectra disfavours interpretation of the resonance as the isovector state. The decay structure via intermediate off-shell D*+ mesons is consistent with the observed D0π+ mass distribution. To analyse the mass of the resonance and its coupling to the D*D system, a dedicated model is developed under the assumption of an isoscalar axial-vector [Formula: see text] state decaying to the D*D channel. Using this model, resonance parameters including the pole position, scattering length, effective range and compositeness are determined to reveal important information about the nature of the [Formula: see text] state. In addition, an unexpected dependence of the production rate on track multiplicity is observed.

Angular Analysis of D^{0}→π^{+}π^{-}μ^{+}μ^{-} and D^{0}→K^{+}K^{-}μ^{+}μ^{-} Decays and Search for CP Violation

The first full angular analysis and an updated measurement of the decay-rate CP asymmetry of the D^{0}→π^{+}π^{-}μ^{+}μ^{-} and D^{0}→K^{+}K^{-}μ^{+}μ^{-} decays are reported. The analysis uses proton-proton collision data collected with the LHCb detector at center-of-mass energies of 7, 8, and 13 TeV. The dataset corresponds to an integrated luminosity of 9  fb^{-1}. The full set of CP -averaged angular observables and their CP asymmetries are measured as a function of the dimuon invariant mass. The results are consistent with expectations from the standard model and with CP symmetry.

Tests of Lepton Universality Using B^{0}→K_{S}^{0}ℓ^{+}ℓ^{-} and B^{+}→K^{*+}ℓ^{+}ℓ^{-} Decays

Tests of lepton universality in B^{0}→K_{S}^{0}ℓ^{+}ℓ^{-} and B^{+}→K^{*+}ℓ^{+}ℓ^{-} decays where ℓ is either an electron or a muon are presented. The differential branching fractions of B^{0}→K_{S}^{0}e^{+}e^{-} and B^{+}→K^{*+}e^{+}e^{-} decays are measured in intervals of the dilepton invariant mass squared. The measurements are performed using proton-proton collision data recorded by the LHCb experiment, corresponding to an integrated luminosity of 9  fb^{-1} . The results are consistent with the standard model and previous tests of lepton universality in related decay modes. The first observation of B^{0}→K_{S}^{0}e^{+}e^{-} and B^{+}→K^{*+}e^{+}e^{-} decays is reported.

Observation of the Decay Λ_{b}^{0}→Λ_{c}^{+}τ^{-}ν[over ¯]_{τ}

The first observation of the semileptonic b-baryon decay Λ_{b}^{0}→Λ_{c}^{+}τ^{-}ν[over ¯]_{τ}, with a significance of 6.1σ, is reported using a data sample corresponding to 3  fb^{-1} of integrated luminosity, collected by the LHCb experiment at center-of-mass energies of 7 and 8 TeV at the LHC. The τ^{-} lepton is reconstructed in the hadronic decay to three charged pions. The ratio K=B(Λ_{b}^{0}→Λ_{c}^{+}τ^{-}ν[over ¯]_{τ})/B(Λ_{b}^{0}→Λ_{c}^{+}π^{-}π^{+}π^{-}) is measured to be 2.46±0.27±0.40, where the first uncertainty is statistical and the second systematic. The branching fraction B(Λ_{b}^{0}→Λ_{c}^{+}τ^{-}ν[over ¯]_{τ})=(1.50±0.16±0.25±0.23)% is obtained, where the third uncertainty is from the external branching fraction of the normalization channel Λ_{b}^{0}→Λ_{c}^{+}π^{-}π^{+}π^{-}. The ratio of semileptonic branching fractions R(Λ_{c}^{+})≡B(Λ_{b}^{0}→Λ_{c}^{+}τ^{-}ν[over ¯]_{τ})/B(Λ_{b}^{0}→Λ_{c}^{+}μ^{-}ν[over ¯]_{μ}) is derived to be 0.242±0.026±0.040±0.059, where the external branching fraction uncertainty from the channel Λ_{b}^{0}→Λ_{c}^{+}μ^{-}ν[over ¯]_{μ} contributes to the last term. This result is in agreement with the standard model prediction.

A Blueprint of Microstructures and Stage-Specific Transcriptome Dynamics of Cuticle Formation in Bombyx mori

Insect cuticle is critical for the environmental adaptability and insecticide resistance of insects. However, there is no clear understanding of the structure and protein components of the cuticle during each developmental stage of holometabolous insects, and knowledge about the protein components within each layer is vague. We conducted serial sectioning, cuticular structure analysis, and transcriptome sequencing of the larval, pupal, and adult cuticles of Bombyx mori. The deposition processes of epicuticle, exocuticle, and endocuticle during larval, pupal, and adult cuticle formation were similar. Transcriptome analysis showed that these cuticle formations share 74% of the expressed cuticular protein (CP) genes and 20 other structural protein genes, such as larval serum protein and prisilkin. There are seven, six, and eleven stage-specific expressed CP genes in larval, pupal, and adult cuticles, respectively. The types and levels of CP genes may be the key determinants of the properties of each cuticular layer. For example, the CPs of the RR-2 protein family with high contents of histidine (His) are more essential for the exocuticle. Functional analysis suggested that BmorCPAP1-H is involved in cuticle formation. This study not only offers an in-depth understanding of cuticle morphology and protein components but also facilitates the elucidation of molecular mechanisms underlying cuticle formation in future studies.

Observation of Two New Excited Ξ_{b}^{0} States Decaying to Λ_{b}^{0}K^{-}π^{+}

Two narrow resonant states are observed in the Λ_{b}^{0}K^{-}π^{+} mass spectrum using a data sample of proton-proton collisions at a center-of-mass energy of 13 TeV, collected by the LHCb experiment and corresponding to an integrated luminosity of 6  fb^{-1}. The minimal quark content of the Λ_{b}^{0}K^{-}π^{+} system indicates that these are excited Ξ_{b}^{0} baryons. The masses of the Ξ_{b}(6327)^{0} and Ξ_{b}(6333)^{0} states are m[Ξ_{b}(6327)^{0}]=6327.28_{-0.21}^{+0.23}±0.12±0.24 and m[Ξ_{b}(6333)^{0}]=6332.69_{-0.18}^{+0.17}±0.03±0.22  MeV, respectively, with a mass splitting of Δm=5.41_{-0.27}^{+0.26}±0.12  MeV, where the uncertainties are statistical, systematic, and due to the Λ_{b}^{0} mass measurement. The measured natural widths of these states are consistent with zero, with upper limits of Γ[Ξ_{b}(6327)^{0}]<2.20(2.56) and Γ[Ξ_{b}(6333)^{0}]<1.60(1.92)  MeV at a 90% (95%) credibility level. The significance of the two-peak hypothesis is larger than nine (five) Gaussian standard deviations compared to the no-peak (one-peak) hypothesis. The masses, widths, and resonant structure of the new states are in good agreement with the expectations for a doublet of 1D Ξ_{b}^{0} resonances.

Study of Z Bosons Produced in Association with Charm in the Forward Region

Events containing a Z boson and a charm jet are studied for the first time in the forward region of proton-proton collisions. The data sample used corresponds to an integrated luminosity of 6  fb^{-1} collected at a center-of-mass energy of 13 TeV with the LHCb detector. In events with a Z boson and a jet, the fraction of charm jets is determined in intervals of Z-boson rapidity in the range 2.0<y(Z)<4.5. A sizable enhancement is observed in the forwardmost y(Z) interval, which could be indicative of a valencelike intrinsic-charm component in the proton wave function.

Evidence for a New Structure in the J/ψp and J/ψp[over ¯] Systems in B_{s}^{0}→J/ψpp[over ¯] Decays

An amplitude analysis of flavor-untagged B_{s}^{0}→J/ψpp[over ¯] decays is performed using a sample of 797±31 decays reconstructed with the LHCb detector. The data, collected in proton-proton collisions between 2011 and 2018, correspond to an integrated luminosity of 9  fb^{-1}. Evidence for a new structure in the J/ψp and J/ψp[over ¯] systems with a mass of 4337_{-4}^{+7} _{-2}^{+2}  MeV and a width of 29_{-12}^{+26} _{-14}^{+14}  MeV is found, where the first uncertainty is statistical and the second systematic, with a significance in the range of 3.1 to 3.7σ, depending on the assigned J^{P} hypothesis.

[Effects of unsafe sexual behavior and sexual orientation on previous HIV testing and HIV testing willingness among college students in Harbin]

Objective: To analyze the effects of unsafe sexual behavior and sexual orientation on previous HIV testing and HIV testing willingness among college students in Harbin, to provide a theoretical basis for promoting and promoting HIV testing among them. Methods: A cross-sectional survey design was used to place the automatic vending machine of HIV urine test kit in 9 universities in Harbin from December 2017 to January 2018. The questionnaire star was used to design and recruit college students to carry out an anonymous online survey. The estimated sample size was 6 659. A multivariate logistic regression model was used to analyze the effects of unsafe sexual behavior and sexual orientation on previous HIV testing and HIV testing willingness among college students. WPS 2016 was used to sort out the database, and SPSS 21.0 software was used for statistical analysis. Results: A total of 60 849 valid questionnaires were collected. 19.1% (11 189/58 605) of college students reported having sex. College students who used condoms correctly every time, occasionally or never during sex in the past six months 58.5% (6 206/10 603), 25.2%(2 669/10 603)and 16.3% (1 728/10 603), respectively. Heterosexuality, homosexuality and bisexuality accounted for 94.1% (54 393/57 823), 2.4% (1 369/57 823) and 3.5% (2 061/57 823), respectively. The HIV testing willingness of college students was 73.3% (44 572/60 849). The proportion of previous HIV testing was 10.3% (951/9 241). Results of the multivariate logistic analysis showed that compared with the college students who used condoms correctly whenever they had sex in the past six months, there was no significant difference in the proportion of previous HIV testing among college students who sometimes/occasionally used or never used condoms (OR=0.94,95%CI:0.69-1.29; OR=1.11,95%CI:0.73-1.67), but their willingness to HIV testing was lower (OR=0.79, 95%CI:0.71-0.89; OR=0.48, 95%CI:0.42-0.55); Compared with heterosexual college students, homosexual or bisexual college students have a higher proportion of previous HIV testing (OR=2.62, 95%CI:1.62-4.24; OR=2.04, 95%CI:1.25-3.32), but have lower HIV testing willingness (OR=0.76, 95%CI: 0.62-0.93; OR=0.64, 95%CI: 0.53-0.77). Conclusions: Unsafe sexual behavior existed among college students in Harbin, and college students with weak awareness of HIV prevention also have weak awareness of testing. Behavioral intervention should be strengthened and HIV testing promoted. Compared with heterosexuals, homosexual or bisexual college students had a higher proportion of previous HIV testing, but their willingness to test was lower. The HIV detection mode with better concealment, accuracy, and convenience should be promoted on the college's campus.

The Hox gene Antennapedia is essential for wing development in insects

A long-standing view in the field of evo-devo is that insect forewings develop without any Hox gene input. The Hox gene Antennapedia (Antp), despite being expressed in the thoracic segments of insects, has no effect on wing development. This view has been obtained from studies in two main model species: Drosophila and Tribolium. Here, we show that partial loss of function of Antp resulted in reduced and malformed adult wings in Bombyx, Drosophila and Tribolium. Antp mediates wing growth in Bombyx by directly regulating the ecdysteriod biosynthesis enzyme gene (shade) in the wing tissue, which leads to local production of the growth hormone 20-hydroxyecdysone. Additional targets of Antp are wing cuticular protein genes CPG24, CPH28 and CPG9, which are essential for wing development. We propose, therefore, that insect wing development occurs in an Antp-dependent manner. This article has an associated 'The people behind the papers' interview.

Crystalline tetra-aniline with chloride interactions towards a biocompatible supercapacitor

Recent advances in wearable and implantable electronics have increased the demand for biocompatible integrated energy storage systems. Conducting polymers, such as polyaniline (PANi), have been suggested as promising electrode materials for flexible biocompatible energy storage systems, based on their intrinsic structural flexibility and potential polymer chain compatibility with biological interfaces. However, due to structural disorder triggering insufficient electronic conductivity and moderate electrochemical stability, PANi still cannot fully satisfy the requirements for flexible and biocompatible energy storage systems. Herein, we report a biocompatible physiological electrolyte activated flexible supercapacitor encompassing crystalline tetra-aniline (c-TANi) as the active electrode material, which significantly enhances the specific capacitance and electrochemical cycling stability with chloride electrochemical interactions. The crystallization of TANi endows it with sufficient electronic conductivity (8.37 S cm^-1) and a unique Cl^- dominated redox charge storage mechanism. Notably, a fully self-healable and biocompatible supercapacitor has been assembled by incorporating polyethylene glycol (PEG) with c-TANi as a self-healable electrode and a ferric-ion cross-linked sodium polyacrylate (Fe³⁺-PANa)/0.9 wt% NaCl as a gel electrolyte. The as-prepared device exhibits a remarkable capacitance retention even after multiple cut/healing cycles. With these attractive features, the c-TANi electrode presents a promising approach to meeting the power requirements for wearable or implantable electronics.

[Diagnosis and treatment status of perioperative anemia in patients with gastrointestinal neoplasms: a multi-center study in Hubei Province]

Objective: To investigate the incidence and treatment of perioperative anemia in patients with gastrointestinal neoplasms in Hubei Province. Methods: The clinicopathological data of 7 474 patients with gastrointestinal neoplasms in 62 hospitals in 15 cities (state) of Hubei Province in 2019 were collected in the form of network database. There were 4 749 males and 2 725 females. The median age of the patients was 62 years (range: 17 to 96 years). The hemoglobin value of the first time in hospital and the first day after operation was used as the criterion of preoperative anemia and postoperative anemia. Anemia was defined as male hemoglobin <120 g/L and female hemoglobin <110.0 g/L, mild anemia as 90 to normal, moderate anemia as 60 to <90 g/L, severe anemia as <60 g/L. The t test and χ² test were used for inter-group comparison. Results: The overall incidence of preoperative anemia was 38.60%(2 885/7 474), and the incidences of mild anemia, moderate anemia and severe anemia were 25.09%(1 875/7 474), 11.37%(850/7 474) and 2.14%(160/7 474), respectively. The overall incidence of postoperative anemia was 61.40%(4 589/7 474). The incidence of mild anemia, moderate anemia and severe anemia were 48.73%(3 642/7 474), 12.20%(912/7 474) and 0.47%(35/7 474), respectively. The proportion of preoperative anemia patients receiving treatment was 26.86% (775/2 885), and the proportion of postoperative anemia patients receiving treatment was 14.93% (685/4 589). The proportions of preoperative anemia patients in grade ⅢA, grade ⅢB, and grade ⅡA hospitals receiving treatment were 26.12% (649/2 485), 32.32% (85/263), and 29.93% (41/137), and the proportions of postoperative anemia patients receiving treatment were 14.61% (592/4 052), 22.05% (73/331), and 9.71% (20/206). The proportion of intraoperative blood transfusion (16.74% (483/2 885) vs. 3.05% (140/4 589), χ²=434.555, P<0.01) and the incidence of postoperative complications (17.78% (513/2 885) vs. 14.08% (646/4 589), χ²=18.553, P<0.01) in the preoperative anemia group were higher than those in the non-anemia group, and the postoperative hospital stay in the preoperative anemia group was longer than that in the non-anemia group ((14.1±7.3) days vs. (13.3±6.2) days, t=5.202, P<0.01). Conclusions: The incidence of perioperative anemia in patients with gastrointestinal neoplasms is high. Preoperative anemia can increase the demand for intraoperative blood transfusion and affect the short-term prognosis of patients. At present, the concept of standardized treatment of perioperative anemia among gastrointestinal surgeons in Hubei Province needs to be improved.

Genomic signatures define three subtypes of EGFR-mutant stage II-III non-small-cell lung cancer with distinct adjuvant therapy outcomes

The ADJUVANT study reported the comparative superiority of adjuvant gefitinib over chemotherapy in disease-free survival of resected EGFR-mutant stage II–IIIA non-small cell lung cancer (NSCLC). However, not all patients experienced favorable clinical outcomes with tyrosine kinase inhibitors (TKI), raising the necessity for further biomarker assessment. In this work, by comprehensive genomic profiling of 171 tumor tissues from the ADJUVANT trial, five predictive biomarkers are identified (TP53 exon4/5 mutations, RB1 alterations, and copy number gains of NKX2-1, CDK4, and MYC). Then we integrate them into the Multiple-gene INdex to Evaluate the Relative benefit of Various Adjuvant therapies (MINERVA) score, which categorizes patients into three subgroups with relative disease-free survival and overall survival benefits from either adjuvant gefitinib or chemotherapy (Highly TKI-Preferable, TKI-Preferable, and Chemotherapy-Preferable groups). This study demonstrates that predictive genomic signatures could potentially stratify resected EGFR-mutant NSCLC patients and provide precise guidance towards future personalized adjuvant therapy.

Adjuvant gefitinib improves outcomes in non-small cell lung cancer (NSCLC) patients compared to chemotherapy, but not in all cases. Here, the authors find genomic biomarkers of response to gefitinib in NSCLC patients from the ADJUVANT trial, and propose a score to stratify them by potential benefit from the treatment.

Genomic Profiling Reveals the Molecular Landscape of Gastrointestinal Tract Cancers in Chinese Patients

Gastrointestinal tract cancers have high incidence and mortality in China, but their molecular characteristics have not been fully investigated. We sequenced 432 tumor samples from the colorectum, stomach, pancreas, gallbladder, and biliary tract to investigate cancer-related mutations and detail the landscape of microsatellite instability (MSI), tumor mutation burden (TMB), and chromosomal instability (CIN). We observed the highest TMB in colorectal and gastric cancers and the lowest TMB in gastrointestinal stromal tumors (GISTs). Twenty-four hyper-mutated tumors were identified only in colorectal and gastric cancers, with a significant enrichment of mutations in the polymerase genes (POLE, POLD1, and POLH) and mismatch repair (MMR) genes. Additionally, CIN preferentially occurred in colorectal and gastric cancers, while pancreatic, gallbladder, and biliary duct cancers had a much lower CIN. High CIN was correlated with a higher prevalence of malfunctions in chromosome segregation and cell cycle genes, including the copy number loss of WRN, NAT1, NF2, and BUB1B, and the copy number gain of MYC, ERBB2, EGFR, and CDK6. In addition, TP53 mutations were more abundant in high-CIN tumors, while PIK3CA mutations were more frequent in low-CIN tumors. In colorectal and gastric cancers, tumors with MSI demonstrated much fewer copy number changes than microsatellite stable (MSS) tumors. In colorectal and gastric cancers, the molecular characteristics of tumors revealed the mutational diversity between the different anatomical origins of tumors. This study provides novel insights into the molecular landscape of Chinese gastrointestinal cancers and the genetic differences between tumor locations, which could be useful for future clinical patient stratification and targeted interventions.

The Landscapes of Full-Length Transcripts and Splice Isoforms as Well as Transposons Exonization in the Lepidopteran Model System, Bombyx mori

The domesticated silkworm, Bombyx mori, is an important model system for the order Lepidoptera. Currently, based on third-generation sequencing, the chromosome-level genome of Bombyx mori has been released. However, its transcripts were mainly assembled by using short reads of second-generation sequencing and expressed sequence tags which cannot explain the transcript profile accurately. Here, we used PacBio Iso-Seq technology to investigate the transcripts from 45 developmental stages of Bombyx mori. We obtained 25,970 non-redundant high-quality consensus isoforms capturing ∼60% of previous reported RNAs, 15,431 (∼47%) novel transcripts, and identified 7,253 long non-coding RNA (lncRNA) with a large proportion of novel lncRNA (∼56%). In addition, we found that transposable elements (TEs) exonization account for 11,671 (∼45%) transcripts including 5,980 protein-coding transcripts (∼32%) and 5,691 lncRNAs (∼79%). Overall, our results expand the silkworm transcripts and have general implications to understand the interaction between TEs and their host genes. These transcripts resource will promote functional studies of genes and lncRNAs as well as TEs in the silkworm.

Genetic Profiling of Cell-Free DNA From Pleural Effusion in Advanced Lung Cancer as a Surrogate for Tumor Tissue and Revealed Additional Clinical Actionable Targets

BACKGROUND

Pleural effusion (PE) has been one of the promising sources of liquid biopsy in advanced lung cancer patients. However, its clinical utility is not widely accepted due to the lack of full estimation of its potential versus routine clinical samples.

METHOD

A total of 164 advanced lung cancer patients were enrolled with 164 matched tumor tissue and PE-cfDNA, 153 accompanied plasma and 63 ¹PE-sDNA.

RESULT

PE-cfDNA displayed significantly higher median mutant allele frequency and an overall mutation concordance rate of 65% to tissue, which was higher than PE-sDNA (43%) and plasma-cfDNA (43%). The discrepancies between PE-cfDNA and tumor tissue were high in several genes, including SMARCA4, PIK3CA, ERBB2, KM T2A, ALK and NF1. For clinically actionable mutations, the concordance rate between PE-cfDNA and tumor tissue is 87%. Eleven patients were identified with actionable mutations in PE-cfDNA and four patients benefited from PE-cfDNA-guided targeted. Meanwhile, PE-cfDNA recapitulated mutations of diverse tissue origins and provided more mutational information under the circumstance that tumor tissue or tumor tissue of different origins were unavailable. The combination of tumor tissue and PE-cfDNA profiling increased positive detection rates of patients compared to tumor tissue alone. Our finding highlighted the importance of PE-cfDNA in the optimal selection of patients for targeted therapy.

CONCLUSION

The PE-cfDNA-based liquid biopsy displays better performance in the characterization of gene alterations than PE-sDNA and plasma-cfDNA. PE-cfDNA together with tumor tissue profiling optimizes comprehensively genomic profiling of lung cancer patients, which might be important for selecting patients for better treatment management.

Comparison of Sericins from Different Sources as Natural Therapeutics against Ulcerative Colitis

Sericin has become a promising natural anti-inflammatory protein. However, the biological functions of sericins largely depend on their origins; no study has yet been carried out to comparatively investigate the therapeutic effects of sericins from different sources against inflammatory diseases. Herein, we extracted and purified three kinds of sericins, namely silkworm sericin (SS), tussah sericin (TS), and castor silk sericin (CSS). These sericins showed negligible cytotoxicities against colitis-associated cells (colon epitheliums and activated macrophages). Further investigations displayed that these sericins could remarkably downregulate the secreted amounts of TNF-α, promote the recovery of the damaged colonic epithelial barrier, and eliminate endogenous reactive oxygen species in Raw 264.7 macrophages and Caenorhabditis elegans. In vivo experiments demonstrated that chitosan/alginate hydrogel-encapsulating SS could achieve efficient accumulation of SS in the colitis tissues and thereby play a more effective role in relieving ulcerative colitis (UC) than TS and CSS. Our findings collectively demonstrate that SS can be extracted, formulated, and used as a robust therapeutic agent for the oral treatment of UC.

Comparative Transcriptome Analysis Reveals bmo-miR-6497-3p Regulate Circadian Clock Genes during the Embryonic Diapause Induction Process in Bivoltine Silkworm

Diapause is one of the survival strategies of insects for confronting adverse environmental conditions. Bombyx mori displays typical embryonic diapause, and offspring diapause depends on the incubation environment of the maternal embryo in the bivoltine strains of the silkworm. However, the molecular mechanisms of the diapause induction process are still poorly understood. In this study, we compared the differentially expressed miRNAs (DEmiRs) in bivoltine silkworm embryos incubated at diapause- (25 °C) and non-diapause (15 °C)-inducing temperatures during the blastokinesis (BK) and head pigmentation (HP) phases using transcriptome sequencing. There were 411 known miRNAs and 71 novel miRNAs identified during the two phases. Among those miRNAs, there were 108 and 74 DEmiRs in the BK and HP groups, respectively. By the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the predicted target genes of the DEmiRs, we found that aside from metabolism, the targets were also enriched in phototransduction-fly and insect hormone biosynthesis in the BK group and the HP group, respectively. Dual luciferase reporter assay illustrated that bmo-miR-6497-3p directly regulated Bmcycle and subsequently regulated the expression of circadian genes. These results imply that microRNAs, as vitally important regulators, respond to different temperatures and participate in the diapause induction process across species.

[Discussion of grading method of small opacity profusion of pneumoconiosis on CT scans and the corresponding reference images]

Objective: To explore the CT grading method of small opacity profusion of pneumoconiosis, and draw up the corresponding CT reference film. Methods: In December 2019, Three hundred thirty-seven cases of pneumoconosis and suspected pneumoconiosis were examined by chest radiography and Computed Tomography (CT) in the same period. According to Diagnosis of Occupational Pneumoconiosis (GBZ 70-2015) , small opacity profusion of pneumoconiosis in each zone of lung was divided. On CT scans, it was divided into 5 grades of 0, 0+, 1, 2 and 3. Grade 0 corresponded to Sub-grade 0/- and Sub-grade 0/0 of Grade 0 in chest radiograph. Grade 0+ was equivalent to Sub-grade 0/1 of Grade 0. Grade 1, 2, 3 were equivalent to Grade 1, 2 and 3, respectively (including each sub-grade) . The CT image quality of each zone of lung was divided into 1 to 4 levels. Results of level 4 were not included in statistical analyses.Based on the results of small opacity profusion in each zone of lung, consistency analysis was performed between chest radiograph and CT. The selection method of reference films was developed. Based on the types and grades of small opacity, the final reference films were determined. Results: There were 1877 zones of lung with CT image quality from level 1 to 3, including 335 in upper right, 319 in middle right, 284 in lower right, 334 in upper left, 320 in middle left and 286 in lower left. The Kappa values of small opacity profusion in upper right zone, upper left zone, left middle zone, and lower left zone were all between 0.4-0.75. In middle right zone and lower right zone, they were all above 0.75.Among all 6 zones of lung, the diagnostic concordance rates between CT and chest radiograph were all above 80%.The corresponding CT reference films were proposed, including type p and q in Grade 2 and 3, type r in Grade 2, type s and t in Grade 0+ to 3. Conclusion: The CT grading method for small opacity profusion of pneumoconiosis is feasible, and the application value of its reference films needs to be further verified.

Characterization of the public transit air microbiome and resistome reveals geographical specificity

BACKGROUND

The public transit is a built environment with high occupant density across the globe, and identifying factors shaping public transit air microbiomes will help design strategies to minimize the transmission of pathogens. However, the majority of microbiome works dedicated to the public transit air are limited to amplicon sequencing, and our knowledge regarding the functional potentials and the repertoire of resistance genes (i.e. resistome) is limited. Furthermore, current air microbiome investigations on public transit systems are focused on single cities, and a multi-city assessment of the public transit air microbiome will allow a greater understanding of whether and how broad environmental, building, and anthropogenic factors shape the public transit air microbiome in an international scale. Therefore, in this study, the public transit air microbiomes and resistomes of six cities across three continents (Denver, Hong Kong, London, New York City, Oslo, Stockholm) were characterized.

RESULTS

City was the sole factor associated with public transit air microbiome differences, with diverse taxa identified as drivers for geography-associated functional potentials, concomitant with geographical differences in species- and strain-level inferred growth profiles. Related bacterial strains differed among cities in genes encoding resistance, transposase, and other functions. Sourcetracking estimated that human skin, soil, and wastewater were major presumptive resistome sources of public transit air, and adjacent public transit surfaces may also be considered presumptive sources. Large proportions of detected resistance genes were co-located with mobile genetic elements including plasmids. Biosynthetic gene clusters and city-unique coding sequences were found in the metagenome-assembled genomes.

CONCLUSIONS

Overall, geographical specificity transcends multiple aspects of the public transit air microbiome, and future efforts on a global scale are warranted to increase our understanding of factors shaping the microbiome of this unique built environment.

The evolution and genetics of lepidopteran egg and caterpillar coloration

Insect colors and color patterns have fascinated biologists for centuries. While extensive research has focused on the adult colors of Drosophila and butterflies, our understanding of how colors are generated and diversified in embryonic and larval stages remains limited, especially, the genetics behind the protective coloration of the immobile embryonic and larval stages. Lepidoptera, one of the most widespread and species-rich insect orders, are extremely helpful uncovering those mechanisms due to their remarkable diverse colors in eggs and caterpillars within or among species, and these colors usually are variable in different developmental stages or in response to different environments. Here we review the recent progress on coloration of lepidopteran eggs and caterpillars, focusing on the genetic basis, developmental mechanisms, ecology, and evolution underlying the remarkable color diversity.

Assembly of Nanofluidic MXene Fibers with Enhanced Ionic Transport and Capacitive Charge Storage by Flake Orientation

MXenes are an emerging class of highly conductive two-dimensional (2D) materials with electrochemical storage features. Oriented macroscopic Ti₃C₂T_x fibers can be fabricated from a colloidal 2D nematic phase dispersion. The layered conductive Ti₃C₂T_x fibers are ideal candidates for constructing high-speed ionic transport channels to enhance the electrochemical capacitive charge storage performance. In this work, we assemble Ti₃C₂T_x fibers with a high degree of flake orientation by a wet spinning process with controlled spinning speeds and morphology of the spinneret. In addition to the effects of cross-linking of magnesium ions between Ti₃C₂T_x flakes, the electronic conductivity and mechanical strength of the as-prepared fibers have been improved to 7200 S cm^-1 and 118 MPa, respectively. The oriented Ti₃C₂T_x fibers present a volumetric capacitive charge storage capability of up to 1360 F cm^-3 even in a Mg-ion based neutral electrolyte, with contributions from both nanofluidic ion transport and Mg-ion intercalation pseudocapacitance. The oriented 2D Ti₃C₂T_x driven nanofluidic channels with great electronic conductivity and mechanical strength endows the MXene fibers with attributes for serving as conductive ionic cables and active materials for fiber-type capacitive electrochemical energy storage, biosensors, and potentially biocompatible fibrillar tissues.

Lepidopteran wing scales contain abundant cross-linked film-forming histidine-rich cuticular proteins

Scales are symbolic characteristic of Lepidoptera; however, nothing is known about the contribution of cuticular proteins (CPs) to the complex patterning of lepidopteran scales. This is because scales are resistant to solubilization, thus hindering molecular studies. Here we succeeded in dissolving developing wing scales from Bombyx mori, allowing analysis of their protein composition. We identified a distinctive class of histidine rich (His-rich) CPs (6%-45%) from developing lepidopteran scales by LC-MS/MS. Functional studies using RNAi revealed CPs with different histidine content play distinct and critical roles in constructing the microstructure of the scale surface. Moreover, we successfully synthesized films in vitro by crosslinking a 45% His-rich CP (BmorCPR152) with laccase2 using N-acetyl- dopamine or N-β-alanyl-dopamine as the substrate. This molecular study of scales provides fundamental information about how such a fine microstructure is constructed and insights into the potential application of CPs as new biomaterials.

The genomic landscape of young and old lung cancer patients highlights age-dependent mutation frequencies and clinical actionability in young patients

The aim of the study was to investigate age-dependent tendency of genomic alterations in lung cancer, and also to examine mutational profiles and its association with clinical treatment outcomes in young adenocarcinoma patients. By studying 7858 lung cancer samples using targeted-gene sequencing, we investigated genomic differences and clinical on-treatment time (OTT) to different therapies between young (≤ 45 years) and old (> 45 years) patients. The age-dependent trend test for genomic alterations in all patients revealed steady increases in tumor mutation burden and alterations in a number of genes with age, including KRAS, MET, CDKN2A, PIK3CA and MDM2, while the frequencies of ALK, ROS1 and RET fusions and ERBB2 mutations were decreasing. The highest rate of EGFR alterations was observed in the 45 ~ 50 years age group. Comparisons of young and old adenocarcinoma patients found that young patients were characterized by a higher prevalence of ALK, ROS1 and RET fusions, and ERBB2 exon-20 insertions and EGFR exon-19 deletions. Actionable mutations were highly prevalent in young adenocarcinoma patients, with 88% of patients harboring at least one actionable genetic alteration. First-line therapies in EGFR-positive patients (n = 979) by EGFR tyrosine kinase inhibitors or chemotherapy resulted in similar OTT between young and old patients. Somatic interaction analyses implied that young EGFR-positive patients were more likely to also have PIK3CA, MET, TP53 and RB1 mutations than old patients. Lung cancer in young patients, and especially those with adenocarcinoma, exhibited different clinical features and genomic attributes compared to old patients, which should be considered for therapeutic decision-making purposes.

Gene mapping reveals the association between tyrosine protein kinase Abl1 and the silk yield of Bombyx mori

The Z chromosome of the silkworm contains a major gene that influences silk yield. This major locus on chromosome Z accounts for 35.10% of the phenotypic variance. The location and identification of the gene have been a focus of silkworm genetics research. Unfortunately, identification of this gene has been difficult. We used extreme phenotype subpopulations and selected from a backcross population, BC₁ M, which was obtained using the high-yield strain 872B and the low-yield strain IS-Dazao as parents, for mapping the gene on the chromosome Z. The candidate region was narrowed down to 134 kb at the tip of the chromosome. BmAbl1 in this region correlated with silk gland development by spatiotemporal expression analysis. This gene was differentially expressed in the posterior silk glands of the high- and low-yield strains. In BmAbl1, an insertion-deletion (indel) within the 10th exonic region and an SNP within the 6th intronic region were detected and shown to be associated with cocoon shell weight in 84 Bombyx mori strains with different yields. Nucleotide diversity analysis of BmAbl1 and its 50 kb flanking regions indicated that BmAbl1 has experienced strong artificial selection during silkworm domestication. This study is the first to identify the genes controlling silk yield in the major QTL of the Z chromosome using forward genetics.

DIA-based proteome reveals the involvement of cuticular proteins and lipids in the wing structure construction in the silkworm

Wing discs of Bombyx mori (B. mori) are transformed into wings during metamorphosis via dramatic morphological and structural changes. Mutations in genes related to the wings cause the adults to have altered wing shapes or abnormal wing colour. At present, there are more than 20 wing mutants recorded in the silkworm. However, the key factors that influence B. mori wing development are still unclear. Here, we used the strains +^Wes/+^Wes and Wes/+^Wes that are typical for the normal wing and shriveled wing phenotypes, respectively, to identify differentially expressed proteins by label-free data-independent acquisition (DIA). Ten enriched GO terms and 9 KEGG pathways were identified based on the 3993 proteins in the wings. Among the identified and quantified proteins, 370 differentially expressed proteins (DEPs) were detected (P-value <0.01, |log2FC| > 0.58). Mapping of the DEPs to the reference canonical pathways in KEGG showed that the top 20% of the pathways were related to fatty acid, cutin, suberin and wax biosynthesis, protein processing in endoplasmic reticulum, protein export, etc. Of the 370 DEPs, 238 were down-regulated, and 132 were up-regulated of Wes/+^Wes compared with +^Wes/+^Wes. Numerous cuticular proteins were down-regulated, and fatty metabolism enzymes were up-regulated, in Wes/+^Wes compared with +^Wes/+^Wes. SIGNIFICANCE: The comparative analysis of proteomes suggested that cuticular proteins and fatty metabolism enzymes are the main abnormally expressed proteins in the pupal wings of Wes/+^Wes, leading to curly and shrunken wings after moth transformation. Our results also identify the substances affecting the development of silkworm wings from the perspective of proteins. The information from this study is important for further research on the molecular mechanisms of wing development in lepidopteran insects, and these differentially expressed genes may be targets for Lepidoptera pest control.

Genomic and clinical characteristics of MET exon14 alterations in a large cohort of Chinese cancer patients revealed distinct features and a novel resistance mechanism for crizotinib

Background: Alterations in MET exon 14 (METex14) and its flanking intronic regions have been identified in a variety of cancers. Patients with METex14 alterations often benefit from MET inhibitors such as crizotinib. Given the unique mutation profiles of Chinese lung cancer patients, it is necessary to investigate the prevalence of METex14 alterations in a large cohort of cancer patients. Patients and methods: Cases carrying METex14 alterations were screened from 26,391 Chinese cancer patients by next-generation sequencing (NGS), and the clinicopathologic and molecular characteristics were reviewed. Results: Compared to Western population (~3%), the frequency of METex14 alterations is much lower in Chinese cancer patients (0.7%, n=184) and lung cancer patients (1.1%, n=175). Seventy-eight distinct METex14 alterations, including several novel alteration types were detected. Concurrent MET copy gain and non-exon14 MET mutations were also found. EGFR copy gain (11%) and mutations (8%), KRAS (5%) and PIK3CA (5%), appeared in a mutually exclusive pattern. Female patients contain much less TP53 mutations than male patients (65% vs. 24%, FDR = 0.01). Co-amplification of CDK4 and MDM2, CDK6 and EGFR were identified, which indicated cell cycle dysregulation and EGFR alteration are important co-occurring features in patients with METex 14 alteration. Of 9 tissue specimens having PD-L1 immunohistochemistry (IHC) results, 5 of them (55.5%) were found PD-L1 positive, which is comparable to other types of tumor. In 14 crizotinib-treated patients, the median progression free survival (mPFS) was 7 months. Upon resistance to crizotinib, two patients acquired secondary mutations in MET and one patient acquired BRAF p.K601E that can be a novel resistance mechanism. Conclusion: Chinese cancer patients have a relatively lower frequency of METex14 alterations compared to Western patients. Patients with METex14 alterations showed distinct molecular characteristics and the representative case study showed responses to MET tyrosine kinase inhibitor (TKI).

Multi-Responsive Silk Fibroin-Based Nanoparticles for Drug Delivery

Silk fibroin has the merits of biocompatibility, biodegradability, ease of processing, and feasibility of modification, which present it as a promising drug delivery material. This review focuses on the structures of silk fibroin, the controlled transformation of secondary structures, and the formation mechanism of silk fibroin-based nanoparticles (SFNPs). We also discuss the intrinsic multi-responsive, surface functionalization, and transgenic modification of SFNPs for drug delivery.

Identification and effect of Zf-AD-containing C2H2 zinc finger genes on BmNPV replication in the silkworm (Bombyx mori)

Zf-AD-containing C2H2 zinc -finger genes (ZAD) are uniquely present and have lineage-specific expansion in arthropods. Arthropods are also the hosts of Baculoviruses. We studied the possible relationship between the lineage-specific expansion of ZAD genes and arthropod-Baculovirus co-evolution. We used the silkworm (Bombyx mori) as a model. We identified 73 ZAD genes (BmZAD) in the silkworm. Sequence-based similarity analysis showed that nine clusters involving 28 BmZADs may have undergone species-specific expansion in the silkworm. Expression pattern analysis showed that the BmZADs were divided into five groups. Group I comprised 10 genes with high expression in multiple tissues, suggesting that BmZADs may play roles in the development of various tissues. We identified six BmZADs that could be induced by the Nucleopolyhedrovirus (BmNPV). Among them, BmZAD69 expression is capable of responding to BmNPV infection, and the ZAD domain is indispensable for the function of BmZAD69 in BmNPV replication. We also detected a 3 bp deletion at 1.7 kb upstream of BmZAD69, which may make it more sensitive to BmNPV infection, and thus elevate the BmNPV resistance in Qiufeng_N, a strain with strong virus resistance. These data suggest that BmZADs may be involved in BmNPV infection and that ZAD genes may play a role in arthropod-Baculovirus co-evolution.

Unusual tertiary pairs in eukaryotic tRNAAla

tRNA molecules have well-defined sequence conservations that reflect the conserved tertiary pairs maintaining their architecture and functions during the translation processes. An analysis of aligned tRNA sequences present in the GtRNAdb database (the Lowe Laboratory, University of California, Santa Cruz) led to surprising conservations on some cytosolic tRNAs specific for alanine compared to other tRNA species, including tRNAs specific for glycine. First, besides the well-known G3oU70 base pair in the amino acid stem, there is the frequent occurrence of a second wobble pair at G30oU40, a pair generally observed as a Watson-Crick pair throughout phylogeny. Second, the tertiary pair R15/Y48 occurs as a purine-purine R15/A48 pair. Finally, the conserved T54/A58 pair maintaining the fold of the T-loop is observed as a purine-purine A54/A58 pair. The R15/A48 and A54/A58 pairs always occur together. The G30oU40 pair occurs alone or together with these other two pairs. The pairing variations are observed to a variable extent depending on phylogeny. Among eukaryotes, insects display all variations simultaneously, whereas mammals present either the G30oU40 pair or both R15/A48 and A54/A58. tRNAs with the anticodon 34A(I)GC36 are the most prone to display all those pair variations in mammals and insects. tRNAs with anticodon Y34GC36 have preferentially G30oU40 only. These unusual pairs are not observed in bacterial, nor archaeal, tRNAs, probably because of the avoidance of A34-containing anticodons in four-codon boxes. Among eukaryotes, these unusual pairing features were not observed in fungi and nematodes. These unusual structural features may affect, besides aminoacylation, transcription rates (e.g., 54/58) or ribosomal translocation (30/40).

Whole-genome resequencing reveals loci under selection during silkworm improvement

Breeding or genetic improvement refers to the process of artificial selection following domestication; as such, it has had a major influence on modern agriculture and animal production. Improvement generally focuses on traits that greatly affect the economic performance. Therefore, understanding the genetic basis underlying improvement will contribute to the identification of genes controlling economic traits and will facilitate future crop and animal breeding. However, genome-wide study of the molecular basis underlying improvement remains rare. The silkworm is a unique, entirely domesticated economically important invertebrate; genetic improvement has had a huge effect on the silkworm regarding silk-related traits. Herein, we performed whole-genomic sequencing on local and genetically improved silkworm lines to identify the genomic regions under strong selection in silkworm breeding/improvement. By genomic-wide selective sweeping analysis, we identified 24 genomic regions with strong selection signals, eight of which contained 13 candidate genes underlying silkworm breeding. Interestingly, six of these genes were annotated with functions related to neural signal response. Among the six genes, BGIBMGA004050 encodes silkworm CREB-regulated_transcription_coactivator_1 (BmCRTC1), which was reported to be involved in energy-sensing pathways. These results suggested that improvement may have affected the nervous system of the silkworm. This research will provide new insights into the genetic basis underlying the genetic improvement of silkworms and possibly of other species.

Cocoonase is indispensable for Lepidoptera insects breaking the sealed cocoon

Many insects spin cocoons to protect the pupae from unfavorable environments and predators. After emerging from the pupa, the moths must escape from the sealed cocoons. Previous works identified cocoonase as the active enzyme loosening the cocoon to form an escape-hatch. Here, using bioinformatics tools, we show that cocoonase is specific to Lepidoptera and that it probably existed before the occurrence of lepidopteran insects spinning cocoons. Despite differences in cocooning behavior, we further show that cocoonase evolved by purification selection in Lepidoptera and that the selection is more intense in lepidopteran insects spinning sealed cocoons. Experimentally, we applied gene editing techniques to the silkworm Bombyx mori, which spins a dense and sealed cocoon, as a model of lepidopteran insects spinning sealed cocoons. We knocked out cocoonase using the CRISPR/Cas9 system. The adults of homozygous knock-out mutants were completely formed and viable but stayed trapped and died naturally in the cocoon. This is the first experimental and phenotypic evidence that cocoonase is the determining factor for breaking the cocoon. This work led to a novel silkworm strain yielding permanently intact cocoons and provides a new strategy for controlling the pests that form cocoons.

Spinning and cocooning are the instincts of many insects, providing a shelter to the residing pupae to resist adverse factors. After the metamorphosis of pupa into adult, the adult must break open the cocoon to emerge, which is called decocooning. We have bioinformatically identified that cocoonase is specific to Lepidoptera, and demonstrated that it is the determining factor for breaking the sealed cocoon experimentally for the first time. This work led to a novel silkworm strain yielding permanently intact cocoons and provides a new strategy for controlling the pests that form cocoons and for breeding.

Molecular and clinicopathological characteristics of ROS1-rearranged non-small-cell lung cancers identified by next-generation sequencing

ROS1 gene rearrangements have been reported in diverse cancer types including non-small-cell lung cancer (NSCLC), and with a notably higher prevalence in lung adenocarcinoma. The tyrosine kinase inhibitors, crizotinib, lorlatinib, and entrectinib, have demonstrated favorable efficacy in treating ROS1-rearranged NSCLCs. Herein, we retrospectively reviewed 17 158 NSCLC patients whose tumor specimen and/or circulating cell-free DNA underwent comprehensive genomic profiling. A total of 258 unique patients were identified with ROS1 rearrangements, representing an overall prevalence of approximately 1.5% of ROS1 fusions in newly diagnosed and relapsed NSCLC patients. CD74 (38%) was the most common fusion partner of ROS1, followed by EZR (13%), SDC4 (13%), SLC34A2 (10%), and other recurrent fusion partners with lower frequencies, including TPM3, MYH9, and CCDC6. Variant breakpoints occurred in ROS1 introns 33 (37%), 31 (25%), 32 (17%), and 34 (11%) with no obvious hotspots. CD74 (63%) and EZR (50%) were more frequently fused to ROS1 intron 33 than other introns, while ROS1 intron 31 was most frequently fused with SDC4 (79%) and SLC34A2 (81%). Crizotinib progression-free survival (PFS) was not significantly different between fusion variants involving breakpoints in different ROS1 introns, nor was there a significant difference in PFS between CD74-ROS1 and non-CD74-ROS1 groups of patients. Furthermore, TP53 was most frequently mutated in patients who progressed on crizotinib, and TP53 mutations were significantly associated with shorter crizotinib PFS. ROS1 mutations, including G2032R, were observed in approximately 33% of post-crizotinib samples. Collectively, we report the prevalence of ROS1 fusions in a large-scale NSCLC population and the efficacy of crizotinib in treating patients with ROS1-rearranged NSCLC.

Abstract 1324: Genomic and clinical characteristics of MET exon14 alterations in 26,391 Chinese cancer patients

Background: Alterations in MET exon 14 (METex14) and its flanking intronic regions have been identified in a variety of cancers, and suggested to cause enhanced MET activity and oncogenesis. Clinical evidences suggested that patients with METex14 alterations often benefit from MET inhibitors such as crizotinib. Given the unique mutation profiles of Chinese lung cancer patients, it is necessary to investigate the prevalence of METex14 alterations in a large cohort of cancer patients.

Patients and methods: Cases carrying METex14 alterations were screened from 26,391 Chinese cancer patients, and the clinicopathologic and molecular characteristics of the cohort were reviewed. PD-L1 immunohistochemistry and the treatment response to MET inhibitors were also analyzed for cases with such information available.

Results: Compared to Western cancer population (3~7%), the frequency of METex14 alterations is much lower in Chinese cancer patients (0.7%, n=184) and in Chinese lung cancer patients (1.1%, n=175). Seventy-eight distinct METex14 alterations were detected, with majority of alterations are base substitutions at splice donor site (42%) and insertion/deletions (indels) in intron 13 (28%). Concurrent MET copy gain and non-exon14 MET mutations were found in 4% and 11% of cases, respectively. Other driver alterations, such as EGFR copy gain (11%) and mutations (8%), KRAS (5%) and PIK3CA (5%), appeared in a mutually exclusive pattern. In 71 patients sequenced by 425-gene panel, gene copy gains were prevalent in MDM2 (24%), CDK4 (14%), MCL1 (13%), TERT (13%), MYC (11%), CD274 (7%) and CDK6 (6%). Female patients contain much less TP53 mutations than male patients (65% vs. 24%, FDR = 0.01). Of 9 tissue specimens having PD-L1 immunohistochemistry (IHC) results, 5 of them (55.5%) were found PD-L1 positive, indicating the option for immunotherapy. In 14 patients who received crizotinib-treatment, the median progression free survival (mPFS) was 7 months with the longest PFS of 17 months. Upon resistance to crizotinib, two patients acquired secondary mutations in MET and one patient acquired BRAF p.K601E that can be a novel resistance mechanism to crizotinib treatment.

Conclusion: Chinese cancer patients have a relatively lower frequency of METex14 alterations compared to Western patients, and these patients can be potentially treated by immunotherapy and crizotinib.

Citation Format: Sisi Liu, Danni Song, Xiaoling Tong, Xue Wu, Xiaonan Wang, Yang Washington Shao. Genomic and clinical characteristics of MET exon14 alterations in 26,391 Chinese cancer patients [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1324.

Abstract 730: Validation of a NGS-based MSI testing workflow in liquid biopsy

Background

Microsatellite instability (MSI) is a molecular phenotype characterized by the lengthening or shortening of tandem DNA repeats within the human genome. MSI phenomenon has been reported in various solid tumors as the consequence of DNA mismatch repair deficiency. It is generally associated with good prognosis and effective immunotherapy treatment. The current MSI tests are based on various methodologies, including immunohistochemistry, polymerase chain reactions, or next-generation sequencing (NGS). Each testing methodology has its own technical advantages, but they either fail at liquid biopsy specimen or implement complicated and expensive experimental interventions.

Methods

A designated analysis pipeline was developed individually for tissue biopsy and liquid biopsy to evaluate the stability of MSI sites within a NGS panel testing targeting over 400 genes at a common depth of coverage (&lt;1000X for tissue biopsy and &lt;5000X for liquid biopsy). The liquid biopsy algorithm implements a signal enhancing module based on a pool of normal samples to boost assay performance. We validated the tissue biopsy testing with an exploratory cohort of 90 gastrointestinal tract cancer patients. Retrospective review of over 10,000 pan-cancer patient-matched tissue-cfDNA sample pairs permitted a comprehensive evaluation of the liquid biopsy MSI testing performance.

Results

For tissue biopsy specimen validation, the assay system displayed 0.97 area-under-the-curve (AUC) in receiver operative characteristics (ROC) curve analysis against the comparator assay, out-performing publicly available MSI analysis software. Unfortunately, the tissue MSI analysis pipeline and publicly available software fails with less than 10% sensitivity and 0.55 AUC when applied to liquid biopsy specimen with the patient-matched tissue MSI status used as the gold standard. In contrast, the dedicated cfDNA analysis pipeline significantly boosted the assay performance to 0.73 without additional experimental interventions, such as wild-type allele depletion or molecular barcode.

Conclusions

MSI testing in liquid biopsy specimen remains challenging due to the low fraction of tumor originated cfDNA and consequently weak signal intensity. The implementation of the signal enhancing MSI analysis algorithm demonstrated high proficiency at improving the signal-to-noise ratio. This bioinformatics approach offered a cost-effective and non-invasive alternative for MSI testing without significantly modifying the NGS library preparation protocols.

Citation Format: Xiangyuan Ma, Hua Bao, Xiaoling Tong, Zhili Chang, Xunbiao Liu, Xiuyan Zhang, Ryan S. Robetyore, Xue Wu, Yang W. Shao. Validation of a NGS-based MSI testing workflow in liquid biopsy [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 730.

Abstract 741: Molecular and clinicopathological characteristics of Chinese non-small cell lung cancers with ROS1 gene fusions identified by next-generation sequencing

Background ROS1 gene rearrangements are reported at a prevalence of 1-2% in unselected cancer populations including non-small cell lung cancer (NSCLC), and notably higher in lung adenocarcinoma. More than twenty ROS1 fusion partners have been identified, which continues to increase due to the adoption of next-generation sequencing (NGS) for genetic testing. The tyrosine kinase inhibitors (TKIs) including crizotinib, lorlatinib, and entrectinib, have demonstrated favorable efficacy in the treatment of ROS1-rearranged NSCLCs.

Methods A total of 17,158 Chinese non-small cell lung cancer (NSCLC) patients whose tumor specimen and/or circulating cell-free DNA (cfDNA) underwent genomic profiling by hybridization capture-based targeted NGS of exons and introns of cancer related genes were retrospectively reviewed. Clinical characteristics, treatment history, and progression-free survival (PFS) for crizotinib of a subset of 37 patients were further evaluated.

Results A total of 288 ROS1-positive NSCLC patients were identified in the cohort at a frequency of 1.7% (288/17158). ROS1 fusions retaining the intact ROS1 kinase domain were confirmed in a subset of 258 patients (1.5%) with the most common fusion partner being CD74 (104/258, 40%), followed by EZR (34/258, 13%), SDC4 (28/258, 11%), SLC34A2 (27/258, 11%), and other recurrent ones at low frequency including TPM3, GOPC, MYH9, and CCDC6. Most frequent breakpoints on ROS1 are spreading in introns 33 (37%), 31 (25%), 32 (17%) and 34 (11%) with no obvious hotspots. 5.4% of cases (14/258) were fused to intergenic regions (IGR), mainly on the same chromosome of ROS1, with unknown fusion products. Notably, CD74 (63%) and EZR (50%) are more frequently fused with ROS1 intron 33, while ROS1 intron 31 was the most common breakpoint region of fusion events involving SDC4 (79%) and SLC34A2 (81%). Median PFS (mPFS) was not significantly different between fusions involving breakpoints in ROS1 introns 31-34 for crizotinib treatment, whereas non-CD74 patients (n=23) trended to demonstrate longer mPFS than that of CD74-ROS1 cases (n=14) (12.0 versus 9.9 months). Previously reported acquired resistance to crizotinib in ROS1-rearranged patients, including ROS1 G2032R and S1986F mutations, were observed in 11 out of 37 patients upon disease progression. In addition, two out of three patients who had uncharacterized fusion partners (IGR-ROS1) achieved durable clinical benefit on crizotinib.

Conclusion We hereby report the prevalence of ROS1 fusions of 1.7% in a large Chinses NSCLC population detected by NGS testing and the most frequent fusion partners including CD74, EZR, SDC4, and SLC34A2. Crizotinib has demonstrated robust response in treating ROS1-rearranged NSCLC, particularly in non-CD74 ROS1-positive patients.

Keywords ROS1, gene fusion, non-small cell lung cancer, crizotinib, breakpoint, next-generation sequencing

Citation Format: Dongling Gao, Yuchen Han, Zhihua Zhao, Qiuxiang Ou, Xiaoling Tong, Ruiying Zhao, Nan Dong, Xue Wu, Wencai Li, Guozhong Jiang. Molecular and clinicopathological characteristics of Chinese non-small cell lung cancers with ROS1 gene fusions identified by next-generation sequencing [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 741.

Resveratrol elongates the lifespan and improves antioxidant activity in the silkworm Bombyx mori

A number of research has shown that the plant polyphenol resveratrol, one of the most prominent small molecules, has beneficial protective effects in multiple organisms, including worms, flies, and killifish. To understand the effects of resveratrol on lifespan, we evaluated its effects in the silkworm Bombyx mori. In this study, we found that lifespan was significantly prolonged in both female and male silkworms treated with resveratrol. Silkworm larval weight was significantly increased from day 3 of the 5th larval instar (L5D3) to day 7 of the 5th larval instar (L5D7). However, the weight of the pupa, cocoon, and total cocoon was not significantly different in female silkworms with resveratrol treatment than that in controls. Meanwhile, resveratrol significantly improved the thermotolerance of the silkworms, which enhanced their survival rate. Moreover, antioxidant activity was increased by resveratrol in both female and male silkworms. Furthermore, an antioxidant-related signalling pathway, SIRT7-FoxO-GST, was activated in silkworms with resveratrol treatment. Collectively, these results help us to understand the molecular pathways underlying resveratrol induced pro-longevity effects and indicate that silkworm is a promising animal model for evaluating the effects of lifespan-extending drugs.

Variability of EGFR exon 20 insertions in 24 468 Chinese lung cancer patients and their divergent responses to EGFR inhibitors

EGFR exon 20 insertions (EGFR e20ins) account for up to 10% of EGFR mutations in lung cancer; however, tumors with EGFR e20ins had poor response rates to EGFR tyrosine kinase inhibitors (TKIs) including gefitinib, erlotinib, afatinib, and osimertinib, and the heterogeneity of EGFR e20ins further complicates the clinical studies. Here, we retrospectively screened next‐generation sequencing (NGS) data from 24 468 lung cancer patients, and a total of 85 unique EGFR e20ins variants were identified in 547 cases (2.24%), with p.A767_V769dup (25.1%) and p.S768_D770dup (17.6%) being the most prevalent ones. Comprehensive genomic profiling revealed that TP53 mutations frequently coexisted with p.H773dup (77.8%, P = 0.0558) and p.A767_V769dup (62.8%, P = 0.0325), while RB1 mutations usually co‐occurred with p.H773_V774insAH (33.3%, P = 0.0551), implying that different EGFR e20ins variants might require distinct genomic context for tumorigenesis and/or maintenance. Despite that treatment regimens were highly diverse for EGFR e20ins‐positive patients, we observed an overall response rate of 14% and a disease control rate (DCR) of 38.4% in 65 patients who received at least one EGFR TKI. The progression‐free survival (PFS) differs significantly in six representative EGFR e20ins variants (P = 0.017), and EGFR p.A763_Y764insFQEA was associated with better PFS than other EGFR e20ins when treating with various EGFR TKIs. Some EGFR e20ins variants showed at least partial response to first‐generation EGFR TKIs, including p.A767_V769dup, p.S768_D770dup, p.N771_H773dup, p.A763_Y764insFQEA, and p.D770_N771insG. Poziotinib achieved higher DCR for p.S768_D770dup than for p.A767_V769dup, whereas osimertinib showed limited effects for these two insertions when used as the first‐line treatment. Overall, our results demonstrated that EGFR e20ins were highly diversified in terms of insertion patterns and co‐occurring mutations and these EGFR e20ins variants showed different clinical responses to various EGFR TKIs, suggesting the clinical importance of selecting proper EGFR TKI treatment based on the specific EGFR e20ins type.

Genomic landscape and clinicopathological characteristics of lung cancer in young Chinese patients

e13520

Background: Approximately 2-3% of lung cancer (LC) was found in very young patients (≤ 45 years old) and they were reported to have different clinical characteristics and genetic profiles when compared to older patients. However, it is still lack of large-scale genomic studies that could provide deep insights into the tumorigenesis, precision treatment and prognosis for this particular population. Methods: Clinically annotated data of targeted next generation sequencing (NGS) on 7858 tumor tissue specimens from LC patients were analyzed. For all specimens, a total of 422 or 425 cancer-related genes were interrogated with a mean coverage depth greater than 500x. Results: Of 7858 LC cases, 814 of them were younger than 45 (age at diagnosis), which were compared to 7044 old LC cases ( > 45 years old). Clinical information showed that young LC are more prevalent in female, to be more advanced disease and to have more adenocarcinoma in histology. Somatic genomic data analysis revealed that compared to old LC, young LC has significantly higher ALK/ROS1/RET fusions, ERBB2 mutations and 5q amplification(FDR < 0.1), but lower mutational frequencies in KRAS, CDKN2A, ERBB4, FAT1, NF1, lower copy number gain (CNG) of PIK3CA, MDM2, FGFR1, and less 5q deletion(FDR < 0.1). Interestingly, in young LC, genetic differences between female and male are not significant, with TP53 and EGFR being most frequently mutated in both sexes. Similarly, the differences between young and old female LC are also limit, with young female LC having more ALK fusions (13.43% vs. 5.1%, FDR < 0.01), less EGFR mutations and MDM2 CNG than old female. On the contrary, male patients demonstrated much wide disparity between young and old LC: young LC was enriched with ALK/ROS1/RET/ERBB2 fusions and mutations in EGFR, ERBB2 and SMAD2, while old LC have more mutations in KRAS, TP53, CDKN2A, and CNG of PIK3CA (all FDR < 0.1). We also found that EGFR exon19 deletion (19del) was significantly enriched in young LC, especially in male, while p.L858R showed preference in old LC. Conclusions: The data suggest that the prevalence of different genetic alterations is both age and sex related. The high level of ALK/ROS1/RET fusions and less CNV in young LC could potentially lead to more effective treatment and better prognosis. We also noted that genomic alterations in young LC were not significantly different across sexes, but the disparity by sex was enormously enlarged in old LC, which might be correlated to their life-long exposures, such as smoking, life styles and sex-affected factors.

Metformin prolongs lifespan through remodeling the energy distribution strategy in silkworm, Bombyx mori

Metformin is a hypoglycemic agent used clinically in the treatment of type 2 diabetics. In addition, metformin is being investigated as a potential geroprotector. Here, we investigated the effects of metformin silkworm lifespan and the underlying molecular pathways involved. We found that metformin prolonged the lifespan of the male silkworm without reducing body weight, which suggests metformin can increase lifespan through remodeling of the animal's energy distribution strategy. Consistent with that idea, metformin reduced silk production and thus the energy devoted to that process. Metformin also increased fasting tolerance and levels of the antioxidant glutathione, and also activated an adenosine monophosphate-activated protein kinase-p53-forkhead box class O signaling pathway in silkworm. These results suggest that activity in this pathway may contribute to metformin-induced lifespan extension in silkworm by increasing stress resistance and antioxidative capacity while reducing energy output for silk product. The results also show that the silkworm is a potential useful animal model for evaluating the effects of small molecules with potential clinical utility.

Evaluation of the silkworm lemon mutant as an invertebrate animal model for human sepiapterin reductase deficiency

Human sepiapterin reductase (SR) deficiency is an inherited disease caused by SPR gene mutations and is a monoamine neurotransmitter disorder. Here, we investigated whether the silkworm lemon mutant could serve as a model of SR deficiency. A point mutation in the BmSPR gene led to a five amino acid deletion at the carboxyl terminus in the lemon mutant. In addition, classical phenotypes seen in SR deficient patients were observed in the lemon mutant, including a normal phenylalanine level, a decreased dopamine and serotonin content, and an increased neopterin level. A recovery test showed that the replenishment of l-dopa significantly increased the dopamine level in the lemon mutant. The silkworm lemon mutant also showed negative behavioural abilities. These results suggest that the silkworm lemon mutant has an appropriate genetic basis and meets the biochemical requirements to be a model of SR deficiency. Thus, the silkworm lemon mutant can serve as a candidate animal model of SR deficiency, which may be helpful in facilitating accurate diagnosis and effective treatment options of SR deficiency.

HP-CagA+ Regulates the Expression of CDK4/CyclinD1 via reg3 to Change Cell Cycle and Promote Cell Proliferation

Previous studies have shown that regeneration gene 3 (reg3) is significantly expressed in gastric mucosa tissues with Helicobacter pylori (HP) cytotoxin-associated gene A (CagA)-positive (HP-CagA+). CagA-positive HP increases the risk of gastric cancer. The purpose of this study was to investigate the correlation between reg3 and HP-CagA+ and explore the effects of reg3 on the proliferation of gastric cancer cells and the development of tissues and organs. We analyzed the expression of reg3 in human tissues and organs. The results showed that reg3 expression in gastric tissues was significantly higher than that in other tissues and organs. In addition, reg3 influenced the prognosis of gastric, lung, and ovarian cancers. Immunohistochemical analysis indicated that the expression of reg3 and CagA in cancerous tissues was higher than that in adjacent tissues. HP-CagA⁺ infection of gastric cancer cells promotes reg3 expression, suggesting that reg3 may be a target gene of CagA in gastric cancer, which together affects the formation and development of gastric cancer. reg3 and CagA promote cell proliferation, and then affect the development of mouse tissues and organs by regulating G1/S phase transition of the cell cycle via the formation of the cell cycle-dependent complex CDK4/CyclinD1. This is the first study that shows the influence of CagA on the cell cycle and induction of cell proliferation by promoting reg3 expression.