Laser microdissection, proteomics, and multiplex immunohistochemistry: a bumpy ride into the study of paraffin-embedded fetal and pediatric lung tissues

Background: Knowledge about lung development or lung disease is mainly derived from data extrapolated from mouse models. This has obvious drawbacks in developmental diseases, particularly due to species differences. Our objective is to describe the development of complementary analysis methods that will allow a better understanding of the molecular mechanisms involved in the pathogenesis of rare congenital diseases. Methods: Paraffin-embedded human pediatric and fetal lung samples were laser microdissected to enrich different lung regions, namely, bronchioli or alveoli. These samples were analyzed by data-independent acquisition-based quantitative proteomics, and the lung structures were subsequently compared. To confirm the proteomic data, we employed an optimized Sequential ImmunoPeroxidase Labeling and Erasing (SIMPLE) staining for specific proteins of interest. Results: By quantitative proteomics, we identified typical pulmonary proteins from being differentially expressed in different regions. While the receptor for advanced glycation end products (RAGE) and the surfactant protein C (SFTPC) were downregulated, tubulin beta 4B (TUBB4B) was upregulated in bronchioli, compared to alveoli. In fetal tissues, CD31 was downregulated in fetal bronchioli compared to canaliculi. Moreover, we confirmed their presence using SIMPLE staining. Some expected proteins did not show up in the proteomic data, such as SOX-9, which was only detected by means of immunohistochemistry in the SIMPLE analysis. Conclusion: Our data underline the robustness and applicability of this type of experimental approach, especially for rare paraffin-embedded tissue samples. It also strengthens the importance of these methods for future studies, particularly when considering developmental lung diseases, such as congenital lung anomalies.</p

Early life exposure to nicotine modifies lung gene response after elastase-induced emphysema

Background: Chronic obstructive pulmonary disease (COPD) is among the top 5 causes of mortality in the world and can develop as a consequence of genetic and/or environmental factors. Current efforts are focused on identifying early life insults and how these contribute to COPD development. In line with this, our study focuses on the influence of early life nicotine exposure and its potential impact on (a) lung pulmonary functions, and (b) elastase-induced emphysema in adulthood.Methods: To address this hypothesis, we developed a model of 2 hits, delivered at different time points: mouse pups were first exposed to nicotine/placebo in utero and during lactation, and then subsequently received elastase/placebo at the age of 11 weeks. The effect of nicotine pretreatment and elastase instillation was assessed by (a) measurement of pulmonary function at post-elastase day (ped) 21, and (b) transcriptomic profiling at ped3 and 21, and complementary protein determination. Statistical significance was determined by 3- and 2-way ANOVA for pulmonary functions, and RNAseq results were analyzed using the R project.Results: We did not observe any impact of nicotine pre- and early post-natal exposure compared to control samples on lung pulmonary functions in adulthood, as measured by FLEXIVENT technology. After elastase instillation, substantial lung damage was detected by x-ray tomography and was accompanied by loss in body weight at ped3 as well as an increase in cell numbers, inflammatory markers in BAL and lung volume at ped21. Lung functions showed a decrease in elastance and an increase in deep inflation volume and pressure volume (pv) loop area in animals with emphysema at ped21. Nicotine had no effect on elastance and deep inflation volume, but did affect the pv loop area in animals with emphysema at ped21. Extensive transcriptomic changes were induced by elastase at ped3 both in the nicotine-pretreated and the control samples, with several pathways common to both groups, such as for cell cycle, DNA adhesion and DNA damage. Nicotine pretreatment affected the number of lymphocytes present in BAL after elastase instillation and some of the complement pathway related proteins, arguing for a slight modification of the immune response, as well as changes related to general body metabolism. The majority of elastase-induced transcriptomic changes detected at ped3 had disappeared at ped21. In addition, transcriptomic profiling singled out a common gene pool that was independently activated by nicotine and elastase.Conclusions: Our study reports a broad spectrum of transient transcriptomic changes in mouse emphysema and identifies nicotine as influencing the emphysema-associated immune system response.</p

Elliptic anisotropy measurement of the f0_0(980) hadron in proton-lead collisions and evidence for its quark-antiquark composition

International audienceDespite the f$_0$(980) hadron having been discovered half a century ago, the question about its quark content has not been settled: it might be an ordinary quark-antiquark ($\mathrm{q\bar{q}}$) meson, a tetraquark ($\mathrm{q\bar{q}q\bar{q}}$) exotic state, a kaon-antikaon ($\mathrm{K\bar{K}}$) molecule, or a quark-antiquark-gluon ($\mathrm{q\bar{q}g}$) hybrid. This paper reports strong evidence that the f$_0$(980) state is an ordinary $\mathrm{q\bar{q}}$ meson, inferred from the scaling of elliptic anisotropies ($v_2$) with the number of constituent quarks ($n_\mathrm{q}$), as empirically established using conventional hadrons in relativistic heavy ion collisions. The f$_0$(980) state is reconstructed via its dominant decay channel f$_0$(980) $\to$$\pi^+\pi^-$, in proton-lead collisions recorded by the CMS experiment at the LHC, and its $v_2$ is measured as a function of transverse momentum ($p_\mathrm{T}$). It is found that the $n_q$ = 2 ($\mathrm{q\bar{q}}$ state) hypothesis is favored over $n_q$ = 4 ($\mathrm{q\bar{q}q\bar{q}}$ or $\mathrm{K\bar{K}}$ states) by 7.7, 6.3, or 3.1 standard deviations in the $p_\mathrm{T}$$\lt$ 10, 8, or 6 GeV/$c$ ranges, respectively, and over $n_\mathrm{q}$ = 3 ($\mathrm{q\bar{q}g}$ hybrid state) by 3.5 standard deviations in the $p_\mathrm{T}$$\lt$ 8 GeV/$c$ range. This result represents the first determination of the quark content of the f$_0$(980) state, made possible by using a novel approach, and paves the way for similar studies of other exotic hadron candidates

Extracting the speed of sound in the strongly interacting matter created in ultrarelativistic lead-lead collisions at the LHC

International audienceUltrarelativistic nuclear collisions create a strongly interacting state of hot and dense quark-gluon matter that exhibits a remarkable collective flow behavior with minimal viscous dissipation. To gain deeper insights into its intrinsic nature and fundamental degrees of freedom, we extracted the speed of sound in this medium created using lead-lead (PbPb) collisions at a center-of-mass energy per nucleon pair of 5.02 TeV. The data were recorded by the CMS experiment at the CERN LHC and correspond to an integrated luminosity of 0.607 nb$^{-1}$. The measurement is performed by studying the multiplicity dependence of the average transverse momentum of charged particles emitted in head-on PbPb collisions. Our findings reveal that the speed of sound in this matter is nearly half the speed of light, with a squared value of 0.241 $\pm$ 0.002 (stat) $\pm$ 0.016 (syst) in natural units. The effective medium temperature, estimated using the mean transverse momentum, is 219 $\pm$ 8 (syst) MeV. The measured squared speed of sound at this temperature aligns precisely with predictions from lattice quantum chromodynamic (QCD) calculations. This result provides a stringent constraint on the equation of state of the created medium and direct evidence for a deconfined QCD phase being attained in relativistic nuclear collisions

Search for CPCP violation in D0^0→\to KS0^0_\mathrm{S}KS0^0_\mathrm{S} decays in proton-proton collisions at s\sqrt{s} = 13 TeV

International audienceA search is reported for charge-parity D$^0$$\to$ K$^0_\mathrm{S}$K$^0_\mathrm{S}$$CP$ violation in D$^0$$\to$ K$^0_\mathrm{S}$K$^0_\mathrm{S}$ decays, using data collected in proton-proton collisions at $\sqrt{s}$ = 13 TeV recorded by the CMS experiment in 2018. The analysis uses a dedicated data set that corresponds to an integrated luminosity of 41.6 fb$^{-1}$, which consists of about 10 billion events containing a pair of ẖadrons, nearly all of which decay to charm hadrons. The flavor of the neutral D meson is determined by the pion charge in the reconstructed decays D$^{*+}$$\to$ D$^0\pi^+$ and D$^{*-}$$\to$ D$^0\pi^-$. The D$^0$$\to$ K$^0_\mathrm{S}$K$^0_\mathrm{S}$$CP$ asymmetry in D$^0$$\to$ K$^0_\mathrm{S}$K$^0_\mathrm{S}$ is measured to be $A_{CP}$( K$^0_\mathrm{S}$K$^0_\mathrm{S}$) = (6.2 $\pm$ 3.0 $\pm$ 0.2 $\pm$ 0.8)%, where the three uncertainties represent the statistical uncertainty, the systematic uncertainty, and the uncertainty in the measurement of the D$^0$ $\to$ K$^0_\mathrm{S}$K$^0_\mathrm{S}$ $CP$ asymmetry in the D$^0$ $\to$ K$^0_\mathrm{S}\pi^+\pi^-$ decay. This is the first D$^0$ $\to$ K$^0_\mathrm{S}$K$^0_\mathrm{S}$ $CP$ asymmetry measurement by CMS in the charm sector as well as the first to utilize a fully hadronic final state

Measurement of multijet azimuthal correlations and determination of the strong coupling in proton-proton collisions at s\sqrt{s} = 13 TeV

International audienceA measurement is presented of a ratio observable that provides a measure of the azimuthal correlations among jets with large transverse momentum $p_\mathrm{T}$. This observable is measured in multijet events over the range of $p_\mathrm{T}$ = 360-3170 GeV based on data collected by the CMS experiment in proton-proton collisions at a centre-of-mass energy of 13 TeV, corresponding to an integrated luminosity of 134 fb$^{-1}$. The results are compared with predictions from Monte Carlo parton-shower event generator simulations, as well as with fixed-order perturbative quantum chromodynamics (pQCD) predictions at next-to-leading-order (NLO) accuracy obtained with different parton distribution functions (PDFs) and corrected for nonperturbative and electroweak effects. Data and theory agree within uncertainties. From the comparison of the measured observable with the pQCD prediction obtained with the NNPDF3.1 NLO PDFs, the strong coupling at the Z boson mass scale is $\alpha_\mathrm{S}(m_\mathrm{Z})$ = 0.1177 $\pm$ 0.0013 (exp) $_{-0.0073}^{+0.0116}$ (theo) = 0.1177$_{-0.0074}^{+0.0117}$, where the total uncertainty is dominated by the scale dependence of the fixed-order predictions. A test of the running of $\alpha_\mathrm{S}(m_\mathrm{Z})$ in the TeV region shows no deviation from the expected NLO pQCD behaviour

Performance of CMS muon reconstruction from proton-proton to heavy ion collisions

International audienceThe performance of muon tracking, identification, triggering, momentum resolution, and momentum scale has been studied with the CMS detector at the LHC using data collected at $\sqrt{s_\mathrm{NN}}$ = 5.02 TeV in proton-proton (pp) and lead-lead (PbPb) collisions in 2017 and 2018, respectively, and at $\sqrt{s_\mathrm{NN}}$ = 8.16 TeV in proton-lead (pPb) collisions in 2016. Muon efficiencies, momentum resolutions, and momentum scales are compared by focusing on how the muon reconstruction performance varies from relatively small occupancy pp collisions to the larger occupancies of pPb collisions and, finally, to the highest track multiplicity PbPb collisions. We find the efficiencies of muon tracking, identification, and triggering to be above 90% throughout most of the track multiplicity range. The momentum resolution and scale are unaffected by the detector occupancy. The excellent muon reconstruction of the CMS detector enables precision studies across all available collision systems

Test of lepton flavor universality in B± ⁣→ ⁣K±μ+μ− {\mathrm{B}^{\pm}} \!\to\! \mathrm{K^{\pm}}\mu^{+}\mu^{-} and B± ⁣→ ⁣K±e+e− {\mathrm{B}^{\pm}} \!\to\! \mathrm{K^{\pm}}\mathrm{e}^+\mathrm{e}^- decays in proton-proton collisions at s= \sqrt{s} = 13 TeV

A test of lepton flavor universality in ${\mathrm{B}^{\pm}} \!\to\! \mathrm{K^{\pm}}\mu^{+}\mu^{-}$ and ${\mathrm{B}^{\pm}} \!\to\! \mathrm{K^{\pm}}\mathrm{e}^+\mathrm{e}^-$ decays, as well as a measurement of differential and integrated branching fractions of a nonresonant ${\mathrm{B}^{\pm}} \!\to\! \mathrm{K^{\pm}}\mu^{+}\mu^{-}$ decay are presented. The analysis is made possible by a dedicated data set of proton-proton collisions at $\sqrt{s} =$ 13 TeV recorded in 2018, by the CMS experiment at the LHC, using a special high-rate data stream designed for collecting about 10 billion unbiased b hadron decays. The ratio of the branching fractions $\mathcal{B}({\mathrm{B}^{\pm}} \!\to\! \mathrm{K^{\pm}}\mu^{+}\mu^{-})$ to $\mathcal{B}({\mathrm{B}^{\pm}} \!\to\! \mathrm{K^{\pm}}\mathrm{e}^+\mathrm{e}^-)$ is determined from the measured double ratio $R(\mathrm{K})$ of these decays to the respective branching fractions of the ${\mathrm{B}^{\pm}} \!\to\! {\mathrm{J}/\psi} \mathrm{K^{\pm}}$ with ${\mathrm{J}/\psi} \!\to\!\mu^{+}\mu^{-}$ and $\mathrm{e}^+\mathrm{e}^-$ decays, which allow for significant cancellation of systematic uncertainties. The ratio $R(\mathrm{K})$ is measured in the range 1.1 $< q^2 <$ 6.0 GeV$^2$, where $q$ is the invariant mass of the lepton pair, and is found to be $R(\mathrm{K})=$ 0.78 $^{+0.47}_{-0.23}$, in agreement with the standard model expectation $R(\mathrm{K}) \approx$ 1. This measurement is limited by the statistical precision of the electron channel. The integrated branching fraction in the same $q^2$ range, $\mathcal{B}({\mathrm{B}^{\pm}} \!\to\! \mathrm{K^{\pm}}\mu^{+}\mu^{-}) =$ (12.42 $\pm$ 0.68) $\times$ 10$^{-8}$, is consistent with the present world-average value and has a comparable precision.A test of lepton flavor universality in B$^{\pm}$$\to$ K$^{\pm}\mu^+\mu^-$ and B$^{\pm}$$\to$ K$^{\pm}$e$^+$e$^-$ decays, as well as a measurement of differential and integrated branching fractions of a nonresonant B$^{\pm}$$\to$ K$^{\pm}\mu^+\mu^-$ decay are presented. The analysis is made possible by a dedicated data set of proton-proton collisions at $\sqrt{s}$ = 13 TeV recorded in 2018, by the CMS experiment at the LHC, using a special high-rate data stream designed for collecting about 10 billion unbiased b hadron decays. The ratio of the branching fractions $\mathcal{B}$(B$^{\pm}$$\to$ K$^{\pm}\mu^+\mu^-$) to $\mathcal{B}$(B$^{\pm}$$\to$ K$^{\pm}$e$^+$e$^-$) is determined from the measured double ratio $R$(K) of these decays to the respective branching fractions of the B$^\pm$$\to$ J/$\psi$K$^\pm$ with J/$\psi$$\to$$\mu^+\mu^-$ and e$^+$e$^-$ decays, which allow for significant cancellation of systematic uncertainties. The ratio $R$(K) is measured in the range 1.1 $\lt q^2 \lt$ 6.0 GeV$^2$, where $q$ is the invariant mass of the lepton pair, and is found to be $R$(K) = 0.78$^{+0.47}_{-0.23}$, in agreement with the standard model expectation $R$(K) $\approx$ 1. This measurement is limited by the statistical precision of the electron channel. The integrated branching fraction in the same $q^2$ range, $\mathcal{B}$(B$^{\pm}$$\to$ K$^{\pm}\mu^+\mu^-$) = (12.42 $\pm$ 0.68) $\times$ 10$^{-8}$, is consistent with the present world-average value and has a comparable precision

Elliptic anisotropy measurement of the f0_0(980) hadron in proton-lead collisions and evidence for its quark-antiquark composition

International audienceDespite the f$_0$(980) hadron having been discovered half a century ago, the question about its quark content has not been settled: it might be an ordinary quark-antiquark ($\mathrm{q\bar{q}}$) meson, a tetraquark ($\mathrm{q\bar{q}q\bar{q}}$) exotic state, a kaon-antikaon ($\mathrm{K\bar{K}}$) molecule, or a quark-antiquark-gluon ($\mathrm{q\bar{q}g}$) hybrid. This paper reports strong evidence that the f$_0$(980) state is an ordinary $\mathrm{q\bar{q}}$ meson, inferred from the scaling of elliptic anisotropies ($v_2$) with the number of constituent quarks ($n_\mathrm{q}$), as empirically established using conventional hadrons in relativistic heavy ion collisions. The f$_0$(980) state is reconstructed via its dominant decay channel f$_0$(980) $\to$$\pi^+\pi^-$, in proton-lead collisions recorded by the CMS experiment at the LHC, and its $v_2$ is measured as a function of transverse momentum ($p_\mathrm{T}$). It is found that the $n_q$ = 2 ($\mathrm{q\bar{q}}$ state) hypothesis is favored over $n_q$ = 4 ($\mathrm{q\bar{q}q\bar{q}}$ or $\mathrm{K\bar{K}}$ states) by 7.7, 6.3, or 3.1 standard deviations in the $p_\mathrm{T}$$\lt$ 10, 8, or 6 GeV/$c$ ranges, respectively, and over $n_\mathrm{q}$ = 3 ($\mathrm{q\bar{q}g}$ hybrid state) by 3.5 standard deviations in the $p_\mathrm{T}$$\lt$ 8 GeV/$c$ range. This result represents the first determination of the quark content of the f$_0$(980) state, made possible by using a novel approach, and paves the way for similar studies of other exotic hadron candidates

Search for new Higgs bosons via same-sign top quark pair production in association with a jet in proton-proton collisions at s= \sqrt{s}= 13 TeV

A search is presented for new Higgs bosons in proton-proton (pp) collision events in which a same-sign top quark pair is produced in association with a jet, via the $\mathrm{p}\mathrm{p}\to \mathrm{t}\mathrm{H}/\mathrm{A} \to\mathrm{t}\mathrm{t}\overline{\mathrm{c}}$ and $\mathrm{p}\mathrm{p}\to \mathrm{t}\mathrm{H}/\mathrm{A} \to\mathrm{t}\mathrm{t}\overline{\mathrm{u}}$ processes. Here, H and A represent the extra scalar and pseudoscalar boson, respectively, of the second Higgs doublet in the generalized two-Higgs-doublet model (g2HDM). The search is based on pp collision data collected at a center-of-mass energy of 13 TeV with the CMS detector at the LHC, corresponding to an integrated luminosity of 138 fb$^{-1}$. Final states with a same-sign lepton pair in association with jets and missing transverse momentum are considered. New Higgs bosons in the 200-1000 GeV mass range and new Yukawa couplings between 0.1 and 1.0 are targeted in the search, for scenarios in which either H or A appear alone, or in which they coexist and interfere. No significant excess above the standard model prediction is observed. Exclusion limits are derived in the context of the g2HDM.A search is presented for new Higgs bosons in proton-proton (pp) collision events in which a same-sign top quark pair is produced in association with a jet, via the pp $\to$ tH/A $\to$ t$\mathrm{\bar{t}}$c and pp $\to$ tH/A $\to$ t$\mathrm{\bar{t}}$u processes. Here, H and A represent the extra scalar and pseudoscalar boson, respectively, of the second Higgs doublet in the generalized two-Higgs-doublet model (g2HDM). The search is based on pp collision data collected at a center-of-mass energy of 13 TeV with the CMS detector at the LHC, corresponding to an integrated luminosity of 138 fb$^{-1}$. Final states with a same-sign lepton pair in association with jets and missing transverse momentum are considered. New Higgs bosons in the 200-1000 GeV mass range and new Yukawa couplings between 0.1 and 1.0 are targeted in the search, for scenarios in which either H or A appear alone, or in which they coexist and interfere. No significant excess above the standard model prediction is observed. Exclusion limits are derived in the context of the g2HDM