[Update on collaborative autopsy-based research in German pathology, neuropathology, and forensic medicine]

BACKGROUND

Autopsies are a valuable tool for understanding disease, including COVID-19.

MATERIALS AND METHODS

The German Registry of COVID-19 Autopsies (DeRegCOVID), established in April 2020, serves as the electronic backbone of the National Autopsy Network (NATON), launched in early 2022 following DEFEAT PANDEMIcs.

RESULTS

The NATON consortium's interconnected, collaborative autopsy research is enabled by an unprecedented collaboration of 138 individuals at more than 35 German university and non-university autopsy centers through which pathology, neuropathology, and forensic medicine autopsy data including data on biomaterials are collected in DeRegCOVID and tissue-based research and methods development are conducted. More than 145 publications have now emerged from participating autopsy centers, highlighting various basic science and clinical aspects of COVID-19, such as thromboembolic events, organ tropism, SARS-CoV‑2 detection methods, and infectivity of SARS-CoV-2 at autopsy.

CONCLUSIONS

Participating centers have demonstrated the high value of autopsy and autopsy-derived data and biomaterials to modern medicine. The planned long-term continuation and further development of the registry and network, as well as the open and participatory design, will allow the involvement of all interested partners.

P6149Coronary computed tomographic angiography (CTA) for risk stratification in the diagnostic triage of patients undergoing liver transplantation (LT): A long-term outcome study

Background

Cardiovascular (CV) risk stratification in patients with end-stage liver disease (ESLD) prior to liver transplantation (LT) is crucial: CV-disease poses a major threat for posttransplant survival.

Therefore, our purpose was to assess safety of coronary computed tomographic angiography (CTA) in patients prior to orthotopic LT over a long-term follow up period, and its value for CV risk stratification.

Methods

In this single center, retrospective observational study 458 patients underwent coronary calcium score (CCS) and coronary CTA for pre-LT risk stratification between 2005 and 2016. CTA was evaluated for 1) stenosis severity (CADRADS: 4-severe>70%/3-intermediate50–70%/2-mild<50%/1-minimal<25%/0=no CAD) 2) plaque burden (SIS, G-score), 3) high–risk plaque features (Napkin Ring Sign, low attenuation plaque, positive remodelling) and 4) Coronary Calcium Score. Primary endpoint was mortality (all-cause and cardiovascular), secondary endpoint major cardiovascular events (MACE).

Results

Finally 270 patients (79.3% males, age 61±8.5 years) who underwent orthotopic LT were included (mean follow-up 7.5 years±3.1, range 2–13). 87 (32.2%) had CCS zero and 60 (22.2%) CCS >300 Agatston Units (CCS 335.6 AU± 868.9). 248 patients underwent CTA after CCS. The majority had CAD (n=173, 72.3%) by CTA while only 75 (27.7%) had no CAD. 102 patients (38.8%) had minimal-or-mild stenosis<50% (CADRADS 1–2), 34 (12.9%) intermediate and 17 (6.5%) severe stenosis.Out of CCS 0 patients, 13 had non-calcified plaque.

All-cause mortality rate was 46 (17.0%), with the majority of patients (43 (93.5%) experiencing non-cardiac death and 3 (6.5%) cardiovascular death due to 1 myocardial infarction and 2 cardiopulmonary failure. CADRADS predicted mortality (Kaplan Meir, p<0.001). On multivariate Cox Regression modell, SIS and G-score predicted all-cause mortality (HR 1.1:p=0.034; 95% CI: 0.649–0.983 and HR 1.1, p=0.029; 95% CI: 1.0–1.6), while Calcium Score did not. There were 6 MACE (3 STEMI, 3 NSTEMI). MACE rate was 0% in CADRADS 0 or 1, 1 in CADRADS-2 and increasing to 5 in CADRADS 3 and 4 groups.

Coronary CTA for LT risk stratification

Conclusion

Cardiac CT is a reliable non-invasive modality for pre-LT assessment of CV-risk over a long-term period, with 0% MACE in patients with no CAD or minimal CAD. CTA allows for an improved CV-risk stratification by stenosis severity (CADRADS) and plaque burden as compared to calcium scoring.

Treatment of perianal sepsis and long-term outcome of recurrence and continence

AIM

The study investigated the fate of patients with perianal sepsis of cryptoglandular origin.

METHOD

All patients treated for perianal sepsis between January 1994 and December 2000 were retrospectively analysed regarding recurrence and faecal incontinence. Data collection was conducted by chart review and by telephone questionnaire using the Vaizey incontinence score.

RESULTS

One hundred seventy-three (58%) of 300 patients were available for follow-up at a median period of 121 (77-171) months. Fistula-in-ano was diagnosed in 156 (90%) patients. After a single surgical procedure, 55 (32%) patients had no recurrence of perianal sepsis. In 118 (68%), recurrence required multiple procedures (median 3, range 2-19). If only a single incision and drainage was performed (n = 10, 6%), no faecal incontinence occurred. Drainage with fistulotomy (n = 45, 26%) induced mild incontinence in 9% and severe incontinence in 4%. After multiple procedures that were required in 118 (68%) patients, mild and severe faecal incontinence was found in 16% and 4% of them, respectively.

CONCLUSION

Treatment of anal sepsis is associated with a high recurrence rate and a substantial risk of faecal incontinence.

Structural analysis of free and enzyme-bound amaranth alpha-amylase inhibitor: classification within the knottin fold superfamily and analysis of its functional flexibility

The three-dimensional structure of the amaranth alpha-amylase inhibitor (AAI) adopts a knottin fold of abcabc topology. Upon binding to alpha-amylase, it adopts a more compact conformation characterized by an increased number of intramolecular hydrogen bonds, a decreased volume and in addition a trans to cis isomerization of Pro20. A systematic analysis of the 3-D structural databanks revealed that similar proteins and domains share with AAI the characteristic presence of proline residues, many of which are in a cis backbone conformation. As these proteins fulfil a variety of functional roles and are expressed in very different organisms, we conclude that the structure of the knottin fold, including the propensity of the cis bond, are the result of convergent evolution.

Structural basis for possible calcium-induced activation mechanisms of calpains

The calpains form a growing family of structurally related intracellular multidomainal cysteine proteinases, which exhibit a catalytic domain distantly related to papain. In contrast to papain, however, their activity in most cases depends on calcium. The calpains are believed to play important roles in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction, but have also been implicated in muscular dystrophy, ischemia, traumatic brain injury, neurodegenerative diseases, rheumatoid arthritis and cataract formation. The best characterized calpains are the ubiquitously expressed mu- and m-calpains, consisting of a common 30 kDa small S-subunit (domains V and VI) and slightly differing 80 kDa large L-subunits (domains I to IV). We have recently determined the 2.3 A structure of recombinant full-length human m-calpain in the absence of calcium, which reveals that the catalytic domain and the two calmodulin-like domains, previously believed to represent the unique calcium switch, are not positioned adjacent to each other, but are separated by the beta-sandwich domain III, which distantly resembles C2 domains. Although the catalytic domain of apocalpain is strongly disrupted compared to papain (which explains its inactivity in the absence of calcium), the crystal structure reveals several sites where calcium could bind, thereby causing a subdomain fusion to form a papain-like catalytic center. All current evidence points to the cooperative interaction of several calcium binding sites. Sites identified include the three EF-hand binding sites in each calmodulin-like domain, the negatively charged segments arranged around the active-site cleft (provided by both catalytic subdomains), as well as an exposed acidic loop of domain III, whose charge compensation could allow the adjacent barrel-like subdomain IIb to move toward the helical subdomain IIa. The Gly-rich S-chain N-terminus and the calcium-loaded acidic loop could target the conventional calpains to cellular/nuclear membranes, thereby explaining their strongly reduced calcium requirement in vivo and in vitro in the presence of acidic phospholipids.

The crystal structure of calcium-free human m-calpain suggests an electrostatic switch mechanism for activation by calcium

Calpains (calcium-dependent cytoplasmic cysteine proteinases) are implicated in processes such as cytoskeleton remodeling and signal transduction. The 2.3-A crystal structure of full-length heterodimeric [80-kDa (dI-dIV) + 30-kDa (dV+dVI)] human m-calpain crystallized in the absence of calcium reveals an oval disc-like shape, with the papain-like catalytic domain dII and the two calmodulin-like domains dIV+dVI occupying opposite poles, and the tumor necrosis factor alpha-like beta-sandwich domain dIII and the N-terminal segments dI+dV located between. Compared with papain, the two subdomains dIIa+dIIb of the catalytic unit are rotated against one another by 50 degrees, disrupting the active site and the substrate binding site, explaining the inactivity of calpains in the absence of calcium. Calcium binding to an extremely negatively charged loop of domain dIII (an electrostatic switch) could release the adjacent barrel-like subdomain dIIb to move toward the helical subdomain dIIa, allowing formation of a functional catalytic center. This switch loop could also mediate membrane binding, thereby explaining calpains' strongly reduced calcium requirements in vivo. The activity status at the catalytic center might be further modulated by calcium binding to the calmodulin domains via the N-terminal linkers.

Crystallization and preliminary X-ray analysis of recombinant full-length human m-calpain

m-Calpain constitutes the prototype of the superfamily of neutral calcium-activated cysteine proteinases. It is a heterodimer consisting of an 80 and a 30 kDa subunit. Recombinant full-length human m-calpain has been crystallized using macro-seeding techniques and vapour-diffusion methods. Two different monoclinic crystal forms (space group P2(1)) were obtained from a solution containing polyethylene glycol (M(W) = 10 000) as a precipitating agent. Complete data sets have been collected to 2.3 and 3.0 A resolution using cryo-cooling conditions and synchrotron radiation. The unit-cell parameters are a = 64.86, b = 133.97, c = 78.00 A, beta = 102.43 degrees and a = 51.80, b = 171.36, c = 64.66 A, beta = 94.78 degrees, respectively. The V(m) values indicate that there is one heterodimer in each asymmetric unit.

Cycling of human dendritic cell effector phenotypes in response to TNF-alpha: modification of the current 'maturation' paradigm and implications for in vivo immunoregulation

Dendritic cells (DCs) are potent antigen presenting cells reported to undergo irreversible functional 'maturation' in response to inflammatory signals such as TNF-alpha. The current paradigm holds that this DC maturation event is required for full functional capacity and represents terminal differentiation of this cell type, culminating in apoptotic cell death. This provides a possible mechanism for avoiding dysregulated immunostimulatory activity, but imposes constraints on the capacity of DCs to influence subsequent immune responses and to participate in immunological memory. We report that the cell surface and functional effects induced by TNF-alpha are reversible and reinducible. These effects are accompanied by a concordant modulation of cytokine mRNA expression that includes the induction of proinflammatory factors (IL-15, IL-12, LT-alpha, LT-beta, TNF-alpha, RANTES) which is coincident with the down-regulation of counter-regulatory cytokines (IL-10, TGF-beta1, TGF-beta2, IL-1 RA, MCP-1). The resultant net effect is a dendritic cell activation state characterized by a transient proinflammatory posture. These results demonstrate that 1) human DCs do not undergo terminal 'maturation' in response to TNF-alpha, 2) DC phenotypes are more pleiotropic than previously thought, and 3) DCs are potential immunoregulatory effector cells with implications for control of immune responses in both in vivo and in vitro systems.

Specific inhibition of insect alpha-amylases: yellow meal worm alpha-amylase in complex with the amaranth alpha-amylase inhibitor at 2.0 A resolution

BACKGROUND

alpha-Amylases constitute a family of enzymes that catalyze the hydrolysis of alpha-D-(1,4)-glucan linkages in starch and related polysaccharides. The Amaranth alpha-amylase inhibitor (AAI) specifically inhibits alpha-amylases from insects, but not from mammalian sources. AAI is the smallest proteinaceous alpha-amylase inhibitor described so far and has no known homologs in the sequence databases. Its mode of inhibition of alpha-amylases was unknown until now.

RESULTS

The crystal structure of yellow meal worm alpha-amylase (TMA) in complex with AAI was determined at 2.0 A resolution. The overall fold of AAI, its three-stranded twisted beta sheet and the topology of its disulfide bonds identify it as a knottin-like protein. The inhibitor binds into the active-site groove of TMA, blocking the central four sugar-binding subsites. Residues from two AAI segments target the active-site residues of TMA. A comparison of the TMA-AAI complex with a modeled complex between porcine pancreatic alpha-amylase (PPA) and AAI identified six hydrogen bonds that can be formed only in the TMA-AAI complex.

CONCLUSIONS

The binding of AAI to TMA presents a new inhibition mode for alpha-amylases. Due to its unique specificity towards insect alpha-amylases, AAI might represent a valuable tool for protecting crop plants from predatory insects. The close structural homology between AAI and 'knottins' opens new perspectives for the engineering of various novel activities onto the small scaffold of this group of proteins.

The 2.2 A crystal structure of human chymase in complex with succinyl-Ala-Ala-Pro-Phe-chloromethylketone: structural explanation for its dipeptidyl carboxypeptidase specificity

Human chymase (HC) is a chymotrypsin-like serine proteinase expressed by mast cells. The 2.2 A crystal structure of HC complexed to the peptidyl inhibitor, succinyl-Ala-Ala-Pro-Phe-chloromethylketone (CMK), was solved and refined to a crystallographic R-factor of 18.4 %. The HC structure exhibits the typical folding pattern of a chymotrypsin-like serine proteinase, and shows particularly similarity to rat chymase 2 (rat mast cell proteinase II) and human cathepsin G. The peptidyl-CMK inhibitor is covalently bound to the active-site residues Ser195 and His57; the peptidyl moiety juxtaposes the S1 entrance frame segment 214-217 by forming a short antiparallel beta-sheet. HC is a highly efficient angiotensin-converting enzyme. Modeling of the chymase-angiotensin I interaction guided by the geometry of the bound chloromethylketone inhibitor indicates that the extended substrate binding site contains features that may generate the dipeptidyl carboxypeptidase-like activity needed for efficient cleavage and activation of the hormone. The C-terminal carboxylate group of angiotensin I docked into the active-site cleft, with the last two residues extending beyond the active site, is perfectly localized to make a favorable hydrogen bond and salt bridge with the amide nitrogen of the Lys40-Phe41 peptide bond and with the epsilon-ammonium group of the Lys40 side-chain. This amide positioning is unique to the chymase-related proteinases, and only chymases from primates possess a Lys residue at position 40. Thus, the structure conveniently explains the preferred conversion of angiotensin I to angiotensin II by human chymase.

Phase I trial of anti-CD3-stimulated CD4+ T cells, infusional interleukin-2, and cyclophosphamide in patients with advanced cancer

PURPOSE

We performed a phase I trial to determine whether in vivo expansion of activated CD4+ T cells was possible in cancer patients. 111Indium labeling was used to observe trafficking patterns of the infused stimulated CD4+ T cells. The influence of cyclophosphamide (CTX) dosing on immunologic outcome was also examined.

PATIENTS AND METHODS

Patients with advanced solid tumors or non-Hodgkin's lymphoma received CTX at 300 or 1,000 mg/m2 intravenously (i.v.). Leukapheresis was performed to harvest peripheral-blood mononuclear cells (PBMCs) either just before the CTX dose, or when the patient was either entering or recovering from the leukocyte nadir induced by CTX. An enriched population of CD4+ T cells was obtained by negative selection. The CD4+ T cells were activated ex vivo with anti-CD3, cultured with interleukin-2 (IL-2) for 4 days, and adoptively transferred. After adoptive transfer, patients received IL-2 (9.0 x 10(6) IU/m2/d) by continuous infusion for 7 days.

RESULTS

The absolute number of CD4+, CD4+/DR+, and CD4+/CD45RO+ T cells increased in a statistically significant fashion in all cohorts after the first course of therapy. The degree of CD4 expansion was much greater than CD8 expansion, which resulted in a CD4:CD8 ratio that increased in 26 of 31 patients. The greatest in vivo CD4 expansion occurred when cells were harvested as patients entered the CTX-induced nadir. One complete response (CR), two partial responses (PRs), and eight minor responses were observed. Trafficking of 111Indium-labeled CD4 cells to subcutaneous melanoma deposits was also documented.

CONCLUSION

CD4+ T cells can be expanded in vivo in cancer patients, which results in increased CD4:CD8 ratios. The timing of pheresis in relation to CTX administration influences the degree of CD4 expansion. Tumor responses with this regimen were observed in a variety of tumors, including melanoma and non-Hodgkin's lymphoma; a high percentage of patients had at least some tumor regression from the regimen that produced the greatest CD4+ T-cell expansion.

A novel strategy for inhibition of alpha-amylases: yellow meal worm alpha-amylase in complex with the Ragi bifunctional inhibitor at 2.5 A resolution

BACKGROUND

alpha-Amylases catalyze the hydrolysis of alpha-D-(1,4)-glucan linkages in starch and related compounds. There is a wide range of industrial and medical applications for these enzymes and their inhibitors. The Ragi bifunctional alpha-amylase/trypsin inhibitor (RBI) is the prototype of the cereal inhibitor superfamily and is the only member of this family that inhibits both trypsin and alpha-amylases. The mode of inhibition of alpha-amylases by these cereal inhibitors has so far been unknown.

RESULTS

The crystal structure of yellow meal worm alpha-amylase (TMA) in complex with RBI was determined at 2.5 A resolution. RBI almost completely fills the substrate-binding site of TMA. Specifically, the free N terminus and the first residue (Ser1) of RBI interact with all three acidic residues of the active site of TMA (Asp185, Glu222 and Asp287). The complex is further stabilized by extensive interactions between the enzyme and inhibitor. Although there is no significant structural reorientation in TMA upon inhibitor binding, the N-terminal segment of RBI, which is highly flexible in the free inhibitor, adopts a 3(10)-helical conformation in the complex. RBI's trypsin-binding loop is located opposite the alpha-amylase-binding site, allowing simultaneous binding of alpha-amylase and trypsin.

CONCLUSIONS

The binding of RBI to TMA constitutes a new inhibition mechanism for alpha-amylases and should be general for all alpha-amylase inhibitors of the cereal inhibitor superfamily. Because RBI inhibits two important digestive enzymes of animals, it constitutes an efficient plant defense protein and may be used to protect crop plants from predatory insects.

Crystal structure of yellow meal worm alpha-amylase at 1.64 A resolution

The three-dimensional structure of the alpha-amylase from Tenebrio molitor larvae (TMA) has been determined by molecular replacement techniques using diffraction data of a crystal of space group P212121 (a=51.24 A; b=93.46 A; c=96.95 A). The structure has been refined to a crystallographic R-factor of 17.7% for 58,219 independent reflections in the 7.0 to 1.64 A resolution range, with root-mean-square deviations of 0.008 A for bond lengths and 1.482 degrees for bond angles. The final model comprises all 471 residues of TMA, 261 water molecules, one calcium cation and one chloride anion. The electron density confirms that the N-terminal glutamine residue has undergone a post-transitional modification resulting in a stable 5-oxo-proline residue. The X-ray structure of TMA provides the first three-dimensional model of an insect alpha-amylase. The monomeric enzyme exhibits an elongated shape approximately 75 Ax46 Ax40 A and consists of three distinct domains, in line with models for alpha-amylases from microbial, plant and mammalian origin. However, the structure of TMA reflects in the substrate and inhibitor binding region a remarkable difference from mammalian alpha-amylases: the lack of a highly flexible, glycine-rich loop, which has been proposed to be involved in a "trap-release" mechanism of substrate hydrolysis by mammalian alpha-amylases. The structural differences between alpha-amylases of various origins might explain the specificity of inhibitors directed exclusively against insect alpha-amylases.

The alpha-amylase from the yellow meal worm: complete primary structure, crystallization and preliminary X-ray analysis

The alpha-amylase from Tenebrio molitor larvae (TMA) was purified from a crude larval extract. After removal of the N-terminal pyroglutamate residue and identification of the following 17 residues by Edman sequencing, the cDNA of mature TMA was cloned from larval mRNA. The encoded enzyme consists of 471 amino acid residues and has 57-79% sequence identity to other insect alpha-amylases and also shows high homology to the mammalian enzymes. TMA was crystallized in form of well-ordered orthorhombic crystals of space group P2(1)2(1)2(1) diffracting beyond 1.6 A resolution with unit cell dimensions of a = 51.24 A, b = 93.46 A, c = 96.95 A. TMA may serve as model system for the future analysis of interactions between insect alpha-amylase and proteinaceous plant inhibitors on the molecular level.

Determination of the three-dimensional structure of the bifunctional alpha-amylase/trypsin inhibitor from ragi seeds by NMR spectroscopy

The three-dimensional structure of the bifunctional alpha-amylase/trypsin inhibitor (RBI) from seeds of ragi (Eleusine coracana Gaertneri) has been determined in solution using multidimensional 1H and 15N NMR spectroscopy. The inhibitor consists of 122 amino acids, with 5 disulfide bridges, and belongs to the plant alpha-amylase/trypsin inhibitor family for which no three-dimensional structures have yet been available. The structure of the inhibitor was determined on the basis of 1131 interresidue interproton distance constraints derived from nuclear Overhauser enhancement measurements and 52 phi angles, supplemented by 9 psi and 51 chi 1 angles. RBI consists of a globular four-helix motif with a simple "up-and-down" topology. The helices are between residues 18-29, 37-51, 58-65, and 87-94. A fragment from Val 67 to Ser 69 and Gln 73 to Glu 75 forms an antiparallel beta-sheet. The fold of RBI represents a new motif among the serine proteinase inhibitors. The trypsin binding loop of RBI adopts the "canonical", substrate-like conformation which is highly conserved among serine proteinase inhibitors. The binding loop is stabilized by the two adjacent alpha-helices 1 and 2. This motif is also novel and not found in known structures of serine proteinase inhibitors. The three-dimensional structure of RBI together with biochemical data suggests the location of the alpha-amylase binding site on the face of the molecule opposite to the site of the trypsin binding loop. The RBI fold should be general for all members of the RBI family because conserved residues among the members of the family from the core of the structure.

Specificity of the Mnt protein. Independent effects of mutations at different positions in the operator

The relative binding affinities of Mnt protein are determined for each possible base-pair at position 15 of the operator sequence, and for all combinations of G.C base-pairs at positions 15 and 17. The partitioning of each operator sequence is determined quantitatively with restriction enzymes. At position 15, the wild-type G.C base-pair provides the highest binding affinity but, unlike position 17, the primary distinction is between purine and pyrimidine bases on the top strand. The information content at position 15 is only about 0.16 bit. In comparison with previous measurements at position 17, it is determined that the interactions of the Mnt protein with positions 15 and 17 are independent, i.e. the specific binding energies for the two positions are additive. The relative binding affinities at position 17 are also determined in the background of a G to T mutation at position 5, the position equivalent to 17 on the other half of the symmetric operator. The relative affinities at position 17 are independent of whether position 5 is wild-type or mutant.