Sequencing-based analysis of clonal evolution of 25 mantle cell lymphoma patients at diagnosis and after failure of standard immunochemotherapy.

Our knowledge of genetic aberrations, that is, variants and copy number variations (CNVs), associated with mantle cell lymphoma (MCL) relapse remains limited. A cohort of 25 patients with MCL at diagnosis and the first relapse after the failure of standard immunochemotherapy was analyzed using whole-exome sequencing. The most frequent variants at diagnosis and at relapse comprised six genes: TP53, ATM, KMT2D, CCND1, SP140, and LRP1B. The most frequent CNVs at diagnosis and at relapse included TP53 and CDKN2A/B deletions, and PIK3CA amplifications. The mean count of mutations per patient significantly increased at relapse (n = 34) compared to diagnosis (n = 27). The most frequent newly detected variants at relapse, LRP1B gene mutations, correlated with a higher mutational burden. Variant allele frequencies of TP53 variants increased from 0.35 to 0.76 at relapse. The frequency and length of predicted CNVs significantly increased at relapse with CDKN2A/B deletions being the most frequent. Our data suggest, that the resistant MCL clones detected at relapse were already present at diagnosis and were selected by therapy. We observed enrichment of genetic aberrations of DNA damage response pathway (TP53 and CDKN2A/B), and a significant increase in MCL heterogeneity. We identified LRP1B inactivation as a new potential driver of MCL relapse.

Chondrosarcoma with Target-Like Chondrocytes: Update on Molecular Profiling and Specific Morphological Features.

This is the first histological and molecular analysis of two chondrosarcomas with target-like chondrocytes that were compared with a group of conventional chondrosarcomas and enchondromas. The unique histological feature of target-like chondrocytes is the presence of unusual hypertrophic eosinophilic APAS-positive perichondrocytic rings (baskets). In the sections stained with Safranin O/Fast green, the outer part of the ring was blue and the material in the lacunar space stained orange, similarly to intercellular regions. Immunohistochemical examination showed strong positivity for vimentin, factor XIIIa, cyclin D1, osteonectin, B-cell lymphoma 2 apoptosis regulator (Bcl-2), p53 and p16. The S-100 protein was positive in 25 % of neoplastic cells. Antibodies against GFAP, D2-40 (podoplanin), CD99, CKAE1.3 and CD10 exhibited weak focal positivity. Pericellular rings/baskets contained type VI collagen in their peripheral part, in contrast to the type II collagen in intercellular interterritorial spaces. Ultrastructural examination revealed that pericellular rings contained an intralacunar component composed of microfibrils with abundant admixture of aggregates of dense amorphous non-fibrillar material. The outer extralacunar zone was made up of a layer of condensed thin collagen fibrils with admixture of non-fibrillar dense material. NGS sequencing identified a fusion transcript involving fibronectin 1 (FN1) and fibroblast growth factor receptor 2 (FGFR2) at the RNA level. At the DNA level, no significant variant was revealed except for the presumably germline variant in the SPTA1 gene.

Chondrosarcoma with Target-Like Chondrocytes: Update on Molecular Profiling and Specific Morphological Features.

The original article was published in Folia Biologica (Praha) Volume 68, No. 3 (2022), 112-124.

Comprehensive Analysis of PTEN in Primary Cutaneous Melanoma.

Phosphatase and tensin homologue (PTEN) is a tumour suppressor gene implicated in tumorigenesis of melanoma, with distinct cytoplasmic and nuclear functions. Cytoplasmic PTEN negatively regulates the PI3K/AKT/mTOR signalling pathway, while nuclear PTEN works as a tumour suppressor. Clinical data suggest that the loss of PTEN function in melanoma is associated with aggressive tumour behaviour. We performed a comprehensive analysis of PTEN in 112 primary cutaneous melanomas including immunohistochemical (IHC), fluorescent in situ hybridization (FISH), next-generation sequencing (NGS), and epigenetic analysis. The goal of our study was to: (a) correlate PTEN expression with selected clinico-pathological variables, and assess its prognostic significance; (b) correlate molecular aberrations with PTEN expression to consider the utility of immunohistochemical analysis of PTEN protein expression for screening PTEN genetic alterations; (c) review the literature and evaluate the PTEN expression level in melanoma with respect to possible therapeutic targeting. Our results showed that PTEN molecular alterations were present in 4/20 (20 %) cases with a loss of expression, 3/11 (27 %) cases with clonal-like expression, and 1/81 (1 %) cases with positive PTEN expression. No PTEN promoter methylation was found in any of the cases. Even though the value of our observation is limited by the low number of cases fully evaluated by IHC (112 cases), FISH (19 cases) and NGS (30 cases), our data suggest that IHC is not an appropriate method for the screening of PTEN genetic alterations. Our survival analysis suggests that patients with positive cytoplasmic PTEN expression show better disease-free survival (P < 0.05).

Chromosomal assignment of porcine EAD, EAO, LPR and P3 genes by linkage analysis.

A two-point linkage analysis was performed between blood group (14), allotype (8), polymorphic protein (11), DNA type I (2), and microsatellite (2) loci in Wild Boar x Pietrain and Meishan x Pietrain three-generation families. The following new pairwise linkages were detected: LPR-EAN (Zmax = 60.68, theta = 0.055), EAD-GH1 (Zmax = 17.43, theta = 0.246), EAO-P3 (Zmax = 15.81, theta = 0.239), and P3-S0003 (Zmax = 5.43, theta = 0.312). This study and published mapping data enabled the localization of LPR (LPR allotype) to chromosome 9, EAD (erythrocyte antigen D) to chromosome 12, and EAO (erythrocyte antigen O) and P3 (P3 allotype) to the q arm of chromosome 6 with gene order S0003-P3-EAO, EAO being the most distal.

Relations between genetic distance of parental pig breeds and heterozygosity of their F1 crosses measured by genetic markers.

The aim of this paper is to examine the extent to which increment of heterozygosity in F1 crosses can be predicted from genetic distance of parental breeds. For this purpose, 38 polymorphic marker loci (blood groups, allotypes, polymorphic proteins and enzymes) were tested in 1115 purebred animals (Duroc, Hampshire and Czech Meat Pig as sire breeds; Landrace, Large White and Black Pied Prestice as dam breeds) and in 1428 crossbred animals of the resulting nine crossbred groups. The number of animals in each genetic group ranged from 75 to 230. On the basis of the allele frequencies of the scored loci, three measures of genetic diversity (heterozygosity, standardized heterozygosity, effective number of alleles) were calculated in all 15 genetic groups. Furthermore, two measures of genetic distance (Nei's standard genetic distance and Gregorius' absolute genetic distance) were calculated between the parental populations. High correlations (Pearson product-moment correlation 0.62 to 0.73; Spearman rank correlation 0.58 to 0.85) were found between the increment of heterozygosity in the crosses (in relation to the mean of the heterozygosities of parental populations) and the genetic distance between the parental populations.

Identification of new apolipoprotein B epitopes and haplotypes and their distribution in swine populations.

Results from comparative immunogenetic studies on inheritance and identification of four new apolipoprotein B (apoB) allotypes and three additional apoB haplotypes and their distribution in miniature and domestic swine are presented. Immunological surveys on the four new and 16 previously described Lpb allotypes and genetic analysis of their segregation in progenies, of miniature and domestic swine and their crosses, indicate that three new allotypes designated Lpb9, Lpb10 and Lpb101 are individual (mutant) apoB epitopes, each representing a discriminating marker for one of the new apoB haplotypes specified by three new apoB alleles designated Lpb9, Lpb10 and Lpb101. The fourth allotype, Lpb20, is one of the common epitopes forming the alternative epitope pair with Lpb10, and is a constituent of each of the eight previously described and two new apoB haplotypes. The new apoB alleles have so far been found only in miniature swine, with Lpb10 being the most frequent in the Göttingen, Vietnamese Pot-belly and Japanese Miniature, Lpb9 was detected only in Minnesota Miniature and Lpb101 only in Vietnamese Potbelly. The common allotype, Lpb20, shares immunological similarities with human apoB indicating its ancestral origin, whereas none of the alloreagents detecting the three individual apoB variants, Lpb9, Lpb10 or Lpb101, showed cross-reactivity with human apoB, suggesting their exclusive swine origin and evolvement during speciation through mutations.

The porcine M blood group system: evidence to suggest assignment of its M1 factor to a new system (P).

A new allele Maejm and a more precise genetic analysis of the Ml factor previously assigned to the M system are described after screening three generation families (Wild Boar x Pietrain, Meishan x Pietrain) for the M blood group system using a complete set of 13 M reagents. From informative families with proven parental M genotypes it was shown that the Ml antigen is controlled by an allele from another system. We propose to designate this new system P and to change the factor designation from Ml to Pa.

A new lipoprotein allotype Lpr3 and allele Lpr1,3 in the pig.

Specific alloprecipitins were found in blood plasma of pigs, immunized by sera of Lpr1 positive donors. These precipitins detected a new allotype of the lipoprotein Lpr system which was designated Lpr3. Genetic studies confirmed its codominant inheritance and subgroup character. This linear subgroup of allotype Lpr1 is controlled by the allele Lpr1,3. Investigations in populations of 14 pig breeds showed significant interbreed differences in the frequencies of alleles Lpr1, Lpr2 and Lpr1,3.

An additional locus (PI4) in the protease inhibitor (PI) gene cluster of pigs.

A further alpha-protease inhibitor system, PI4, was detected in porcine sera using either 2D agarose gel, pH 5.0-PAGE, pH 9.0, or 1D PAGE followed by immunoblotting with rabbit anti-porcine PI2 or PI3 antisera. PI4 inhibited chymotrypsin, but not trypsin. Seven allelic variants of PI4 were described. By haplotyping of alpha-protease inhibitor systems in 52 complete families it was shown that PI4 locus belongs to the PI gene cluster. The probable order of the PI loci was: PI1, PO1A, PI2, PI4, PI3.

New blood group factors Es, Et and a new allele Ebdgjmt (E16) in the pig E blood group system.

By immunizing a miniature sow a monovalent reagent (later designated anti-Es) was prepared, detecting an alternative antigen to the Ej. Blood group factors Ej and Es thus form the fifth genetically closed E subsystem. Analyses of selected raw sera containing anti-Ej led to the determination of a further Ej subgroup (designated Et) which is antithetical, mutually excluding with the blood factor Er. New blood factor Et is inherited by alleles Edeghjmnt (= E9) and (= E16). The investigation in pig breeds kept in CSFR indicated that allele Edeghjmnt occurs in Black and White Prestice breed (qE9 = 0.076 +/- 0.010) while allele Edeghjmnr (= E14) only in miniature pigs (qE9 = 0.147 +/- 0.011) and in wild pigs. In an élite herd of Swedish Landrace kept in CSFR a new complex allele Ebdgjmt (= E16) was found. Its frequency in the population studied was 0.058 +/- 0.022.

Two new common alleles of erythrocyte adenosine deaminase (ADA) in pigs.

New adenosine deaminase variants ADA C and ADA D were found by means of agarose gel electrophoresis in pig erythrocytes. Family data supported the hypothesis that these are controlled by codominant alleles ADAC and ADAD. The ADAC allele was present in Large White (q = 0.076), Landrace (q = 0.037) and their crosses with other breeds. The ADAD allele was present in Duroc (q = 0.067) and its crosses. Allele frequencies for six pig breeds are given.

Polymorphism of pig serum alpha-protease inhibitor-3 (PI3) and assignment of the locus to the Pi1, Po1A, Po1B, Pi2, Igh linkage group.

Polymorphism of an alpha-protease inhibitor, PI3, in pig serum samples was detected using 2D agarose gel (pH 5.4)--polyacrylamide gel (pH 9.0) electrophoresis. Evidence was obtained that the five variants observed (A, B1, B2, C and D) are under genetic control by codominant alleles (Pi3A, Pi3B1, Pi3B2, Pi3C and Pi3D) at one autosomal locus. Variants A, B1, B2 and C inhibited chymotrypsin; there was no appreciable inhibition of trypsin and papain. Variant D did not inhibit chymotrypsin, and therefore its classification as a PI3 variant was put in question. PI3 typing was not possible in about 50% of the studied pigs since in those cases the PI3 variants were either too weak or absent. On the basis of backcross matings and haplotyping in complete families for protease inhibitor loci Pi1, Po1A, Pi2 and Pi3 it was proved that the Pi3 locus belongs to the protease inhibitor gene cluster, and the position of the locus in the linkage group was proposed as being Pi1-Po1A-(Po1B)-Pi3-Pi2-(Igh1, Igh2, Igh3, Igh4).

Plasma alpha-protease inhibitors in Norwegian Landrace and Czech Landrace pigs.

The studies on alpha-protease inhibitors systems, controlled by four tightly linked loci, were performed within 159 families of Norwegian Landrace (NL) and 40 families of Czech Landrace (CL) pigs. Significant differences in allele and haplotype frequencies between the two breeds were shown. The SE-F and SSsS haplotypes (Pi1, Po1A, Po1B, Pi2 loci) appeared to be the most frequent haplotypes in NL and CL breeds respectively. This system of blood plasma proteins can be very useful for studying the relationship between breeds.

Absence of detectable linkage between the G and H blood group loci in the pig.

Morton's lod score method used for the analysis of data from 168 backcross matings (1094 offspring) did not indicate linkage between the G and H blood group loci of the pig. Linkage closer than 0.413 could be excluded at the 1% significance level.

Localization of the Po2 locus in the S, Phi, Hal, H, Po2, Pgd linkage group in pigs.

The localization of the Po2 locus controlling a polymorphic serum postalbumin was studied in 41 families of the Czech Landrace breed. The haplotypes involving six closely linked loci (S, Phi, Hal, H, Po2, Pgd) were determined for each family member. The crossovers observed between the H, Po2 and Pgd loci indicated that Po2 is located between H and Pgd. The Po2 locus appears to be closer to H [theta = 0.54% (0.06%-1.92%)] than to Pgd [theta = 4.02% (1.67%-7.96%)]. A strong Ha-Po2S association (r = 0.96, P less than 0.001) and H-PO2 linkage disequilibrium (D = 0.2218, P less than 0.01, D/DMax = 0.98) were found.

Serum allotypes in ovarian follicular fluids of pigs.

Sera and ovarian follicular fluids of 158 sows were tested with 27 allotype reagents. Immunodiffusion in agar gel (microtest) and haemagglutination inhibition were used as detection methods. Out of eight 'individual' (Lpb 1,-2,-3,-4,-5,-6,-7,-9) and four 'common' (Lpb 12,-13,-14,-16) specificities of serum beta-lipoproteins (LDL), 11 were present in sera, but none in follicular fluids. On the other hand, Lpr 1 and Lpr (x) allotypes of the VHDL + VLDL beta-lipoprotein system were detected both in sera and in follicular fluids. Of four antigens of the Gp system (Gp A,-a, -B,-b), only the 'dominant' characters, Gp A and Gp B, occurred in the follicular fluid. The typing of polymorphic IgG immunoglobulins (IgG-a or IgG-b system) showed that B1 or A2, B2 or A1 and B3 or A(x) allotypes could be detected both in serum and follicular fluid. Among allotypes that were not yet genetically classified, only the P3 specificity was not found in the population tested. The G1 allotype (preliminarily described as an alpha-globulin) was present in sera only, and the remaining allotypes, G9, P1, P16 and P23 (alpha- or beta-globulins) were present both in sera and follicular fluids. The mechanism of the transmission of serum proteins into ovarian follicles and their possible importance is discussed.

Development of a semi-inbred line of Landrace pigs. I. Breeding performance and immunogenetic characteristics.

During 15 years of inbreeding of pigs (Canadian Landrace) a semi-inbred line has been developed. The inbreeding coefficient (FX) is 0.84, which theoretically corresponds to between 8-9 generations of brother/sister matings. At the highest inbreeding level (0.84) the mean number of newborn piglets in the litter was 7.2 (5 litters, n = 36) including 5 stillborn (13.8%). The mean birth weight of the litter was 8.56 kg (5 litters, n = 31) the mean piglet birth weight was 1.23 kg and at the age of 21 days the mean weight of a litter was 33.24 kg with a mean piglet weight of 5.44 kg. During inbreeding, immunogenetic alloantigenic systems were investigated. Of 15 known erythrocyte systems, alleles of loci J, K, and of the most polymorphic system E, segregated. As to other immunogenetic systems (histocompatibility, leucocyte and allotypes) 2 SLA haplotypes (major histocompatibility complex) and 2 alleles of the SLC leucocyte system segregated. Allotransplants of the skin in SLA compatible siblings survived for a mean of 50.7 days (n = 77) compared with 10.8 days (n = 29) in non-inbred siblings. Tests of blastic transformation activated by T and B lymphocyte mitogens revealed a normal cell-mediated immune response. After immunization with some cell membrane alloantigens a normal humoral response was also recorded. All tested animals were halothane-resistant and tolerated a 10-min exposure to 5% without developing malignant hyperthermia. Depression due to inbreeding was manifested by a reduced reproductive ability (smaller number of piglets, frequent incidence of gonadal hypoplasia, diminution or loss of libido).

Gene order and recombination rates in the linkage group S-Phi-Hal-H-(Po2)-Pgd in pigs.

Families of Czech Landrace (94 litters and 636 offspring) were tested for halothane sensitivity, A-O (S), H, PHI and PGD phenotypes. Informative matings for the estimation of recombination rates between marker loci were selected. The following recombination frequencies were established: S - Phi = 4.8% (2.5%-10.7%); S - H = 6.8% (4.3%-11.7%); Phi - H = 2.6% (0.9%-5.3%); H - Pgd = 4.4% (1.6%-8.0%). Cross-overs were observed also between S - Hal, Hal - H and Hal - Pgd, but were not found between Phi - Hal. On the basis of these results it has been possible to revise the position of the S locus in this linkage group. The most probable gene order would be: S - Phi - Hal (or Hal - Phi) - H - (Po2) - Pgd. A striking difference was found between the number of halothane-sensitive pigs (87) and HalnHaln genotypes determined by haplotyping (123). Segregation rates in 19 backcross matings and experimental matings of the animals proved that this difference is mostly due to incomplete penetrance or low expression of halothane sensitivity.