Rearrangement Sequence Research Articles

Development of B-lymphoblastic leukemia in patients treated for multiple myeloma – A case series of 14 patients

Abstract Development of B-lymphoblastic leukemia/lymphoma (BALL) is uncommon in patients with plasma cell neoplasm (PCN). Currently, little is known about risk factors for and characteristics of BALL arising in patients who have undergone treatment for PCN. We reviewed the clinicopathologic features of 14 patients with PCN who developed subsequent BALL and assessed the clonal relationship between these two neoplasms in 5 of the 14 patients. Clinical and laboratory data were extracted from the electronic medical record in accordance with an institutional review board-approved protocol. For the IgH clonality studies DNA was extracted from formalin fixed paraffin embedded tissue and analyzed utilizing the LymphoTrack® IGH FR2/3 Assay -- S5/PGM™ reagents from Invivoscribe Technologies. Next-generation sequencing of libraries was performed on a ThermoFisher Scientific Ion Torrent S5™ sequencer. The LymphoTrack® Software - S5/PGM™ Version 2.4.5 was used to analyze the IGH rearrangement sequences and relative proportion of the sequences was determined as a percentage of total sequencing reads. All PCN patients in our cohort received an autologous stem cell transplant (auto-SCT) with subsequent lenalidomide maintenance therapy. The mean time from the start of lenalidomide treatment after auto-SCT to BALL development was 62 months. None of the BALL cases were Philadelphia chromosome-positive. There was increased incidence of TP53 mutations and deletions (36%). IgH clones were identified in all but one sample. Comparison of the IgH clones from the original PCN and subsequent BALL revealed distinct clones in all 5 patients tested. In 2 of the 5 patients, the original PCN clone was also identified along with the distinct BALL clone. Our study reveals that BALL cases arising in patients with treated PCN are not clonally related to the original disease, and may represent therapy-related malignancy associated to prior treatment including lenalidomide maintenance therapy. More studies are needed to establish the incidence and understand the pathogenesis of this possible therapy-related complication.

Concise syntheses and anti-inflammatory effects of isocorniculatolide B and corniculatolide B and C

The first total syntheses of isocorniculatolide B, corniculatolide B, and corniculatolide C, consisting of isomeric corniculatolide skeletons, have been accomplished in a divergent manner. The key features of the synthesis involve the construction of diaryl ether linkages by nucleophilic aromatic substitution, installation of a C14-substituted alkyl side chain via a sequence of Baeyer-Villiger reaction and Claisen rearrangement, and efficient construction of corniculatolide and isocorniculatolide frameworks, including 17-membered (exterior) macrolactone skeletons from a versatile diaryl ether intermediate by Mitsunobu macrolactonization. Moreover, we prepared the structural congeners of isomeric corniculatolides via diverted total synthesis approach including desmethyl analogues and related dimeric macrolides. The anti-inflammatory activities of the synthesized natural products, analogues and synthetic intermediates were also investigated. In particular, corniculatolide B significantly inhibited the protein expression of COX-2 and the mRNA expressions of TNF-α, IL-1β and IL-6 by inhibiting of NF-κB signaling in intestinal epithelial cells induced by lipopolysaccharide treatment. It also significantly inhibited the promoter activity and the phosphorylation of subunits p50 and p65 of NF-κB to the same extent as Bay 11-7082, a potent IκB kinase inhibitor. These results suggest that corniculatolide B might have therapeutic potential in inflammatory bowel disease via NF-κB signaling pathway.

Sequential Rearrangement of Information in Formation of Patterns

Sequential Rearrangement of Information in Formation of Patterns

Total Syntheses of the C19 Diterpenoid Alkaloids (-)-Talatisamine, (-)-Liljestrandisine, and (-)-Liljestrandinine by a Fragment Coupling Approach.

The C19 diterpenoid alkaloids (C19 DTAs) are a large family of natural products, many of which modulate the activity of ion channels in vivo and are therefore of interest for the study of neurological and cardiovascular diseases. The complex architectures of these molecules continue to challenge the state-of-the art in chemical synthesis, particularly with respect to efficient assembly of their polcyclic ring systems. Here, we report the total syntheses of (−)-talatisamine, (−)-liljestrandisine, and (−)-liljestrandinine, three aconitine-type C19 DTAs, using a fragment coupling strategy. Key to this approach is a 1,2-addition/semipinacol rearrangement sequence which efficiently joins two complex fragments and sets an all-carbon quaternary center.

Total synthesis of (±)-erythrodiene and (±)-spirojatamol

A unique synthetic strategy toward (±)-erythrodiene and (±)-spirojatamol was achieved from cyclobutone and isobutyraldehyde through an 11-step synthetic route. During the work, a tandem Castro-Stephens coupling/1, 3-acyloxy shift/cyclization/semipinacol rearrangement sequence, which was developed recently by the same group, was used as the key step to build the crucial spirocyclic intermediate 5b.

High Throughput Immunoprofiling of Low Count B Lymphocytosis Reveals a Distinct T Cell Receptor Repertoire from Chronic Lymphocytic Leukemia

Mounting evidence supports the notion that T cells are crucial for the survival and expansion of the malignant clone in chronic lymphocytic leukemia (CLL). Recently, NGS immunoprofiling of the T cell receptor (TR) gene repertoire in CLL revealed “disease-specific” TR clonotypes shared by different patients that persisted and further expanded over time, suggesting that antigen drive likely underlies T-cell expansions in CLL. CLL-like Monoclonal B-cell Lymphocytosis (MBL) is characterized by the presence of CLL-like clonal B cells in lower numbers compared to CLL with no other evidence of disease. MBL is distinguished into high and low count (HC-MBL and LC-MBL, respectively). HC-MBL may evolve to CLL requiring treatment and is considered a pre-leukemic condition, while LC-MBL has an unclear, if any, link to CLL, posing a particular conundrum, especially considering that despite sharing CLL-associated genomic aberrations it displays a distinct immunoglobulin gene repertoire. The precise mechanisms underlying MBL onset and/or progression into overt CLL remain unknown. Arguably, these could entail the acquisition of particular genetic lesions and/or extrinsic signals delivered to the clonal B cells, including those emanating from T cells. Considering the above, here we aimed at characterizing T cells in the early steps of CLL ontogeny by detailed immunoprofiling of the TR gene repertoire in LC-MBL, a thus far unexplored area.The study group comprised 43 individuals with CLL-like (CD5+) LC-MBL and 7 individuals with non CLL-like LC-MBL (atypical CLL-like and CD5- LC-MBL). The presence of a LC-MBL population was confirmed by a standardized flow cytometry protocol. TR beta chain (TRB) gene rearrangements were RT-PCR amplified with the use of the BIOMED 2 protocol. Sequencing libraries were prepared with the TruSeq DNA LT Kit and run on the MiSeq Sequencer using the MiSeq Reagent Kit v3 (500 cycles). Raw NGS reads were subjected to data filtering based on read length and quality. Filtered-in sequences were submitted to IMGT/HighV-QUEST and an in-house bioinformatics pipeline for clonotype computation and repertoire characterization.Overall, 9,385,319 productive filtered-in TRBV-TRBD-TRBJ rearrangement sequences were evaluated corresponding to an average of 32,205 different (unique) clonotypes/sample (clonotype: same TRBV gene and CDR3 amino acid sequence). Skewing of the TRBV repertoire was identified in both LC-MBL categories. In specific, the 4/5 most frequently utilized TRBV genes were identical between the 2 categories (TRBV29-1, TRBV12-3, TRBV19, TRBV6-5) and cumulatively accounted for a virtually identical part of the respective repertoire (28.7% versus 28.6%). Comparison to our published data from CLL revealed similarities regarding TRBV gene usage, particularly for CLL-like LC-MBL. Oligoclonality was evident in both MBL categories with the 10 most frequent clonotypes accounting for 21.3% of the total repertoire in CLL-like LC-MBL and 20.3% in non CLL-like LC-MBL, again not differing significantly from CLL (26.3%). All the above 3 entities were clearly more oligoclonal in comparison to 2 healthy control samples from aged-matched used as a reference. Cluster analysis among the 10 most frequent clonotypes of all LC-MBL and CLL samples revealed infrequent matches between: (i) different CLL-like LC-MBL samples (24/430, 0.055%); (ii) CLL-like and non CLL-like LC-MBL (8/500, 0.016%); and, (iii) CLL-like LC-MBL and CLL (2/680, 0.002%).Altogether, these findings indicate that, similar to CLL, antigen drive likely underlies T-cell expansions also in LC-MBL. However, despite similar TRBV gene usage and degree of oligoclonality, scant shared clonotypes were identified, thus indicating that the antigenic stimuli and/or immune processes shaping the TR profiles in LC-MBL and CLL are distinct. DisclosuresAgathangelidis:Gilead Sciences: Research Funding. Stamatopoulos:Gilead: Consultancy, Honoraria, Research Funding; Novartis SA: Research Funding; Abbvie: Honoraria, Research Funding; Janssen Pharmaceuticals: Honoraria, Research Funding. Ghia:Gilead: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Janssen Pharmaceuticals: Honoraria, Research Funding; AbbVie: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Roche: Honoraria.

Synergistic Pd(0)/Rh(II) Dual Catalytic [6 + 3] Dipolar Cycloaddition for the Synthesis of Monocyclic Nine-Membered N,O-Heterocycles and Their Alder-ene Rearrangement to Fused Bicyclic Compounds.

The catalytic construction of a monocyclic medium-sized N,O-heterocyclic ring represents a formidable challenge in organic synthesis. Herein we report the synergistic palladium(0)/rhodium(II) dual catalytic cycloaddition of vinylpropylene carbonates with N-sulfonyl-1,2,3-triazoles to afford monocyclic nine-membered N,O-heterocycles. The catalytically generated 1,6-dipole-equivalent zwitterionic π-allyl palladium(II) complex and the 1,3-dipole-equivalent α-imino rhodium(II) carbenoid intermediate react with each other in a formal [6 + 3] dipolar cycloaddition to furnish nine-membered oxazonines, which can be transformed into cis-fused [4.3.0] bicyclic compounds via a transannular Alder-ene rearrangement. The tandem one-pot cycloaddition/Alder-ene rearrangement sequence is also possible.

Single-Cell Sequencing Confirms Transcripts and VHDJH Rearrangements of Immunoglobulin Genes in Human Podocytes.

Most glomerular diseases are associated with inflammation caused by deposited pathogenic immunoglobulins (Igs), which are believed to be produced by B cells. However, our previous study indicated that the human podocyte cell line can produce IgG. In this study, we aimed to confirm the transcripts and characterize the repertoires of Igs in primary podocytes at single cell level. First, single-cell RNA sequencing of cell suspensions from “normal” kidney cortexes by a 10xGenomics Chromium system detected Ig transcripts in 7/360 podocytes and Ig gene segments in 106/360 podocytes. Then, we combined nested PCR with Sanger sequencing to detect the transcripts and characterize the repertoires of Igs in 48 single podocytes and found that five classes of Ig heavy chains were amplified in podocytes. Four-hundred and twenty-nine VHDJH rearrangement sequences were analyzed; podocyte-derived Igs exhibited classic VHDJH rearrangements with nucleotide additions and somatic hypermutations, biased VH1 usage and restricted diversity. Moreover, compared with the podocytes from healthy control that usually expressed one class of Ig and one VHDJH pattern, podocytes from patients expressed more classes of Ig, VHDJH patterns and somatic hypermutations. These findings suggested that podocytes can express Igs in normal condition and increase diversity in pathological situations.

Identification of the first Alu-mediated gross deletion involving the BCKDHA gene in a compound heterozygous patient with maple syrup urine disease

AimsTo investigate a family with clinical symptoms of maple syrup urine disease and reveal a genetic cause underlying this disease. MethodsTargeted capture sequencing was used to screen for mutations in the patient. Real-Time PCR was carried out to perform exon 1, 5, 9 CNV analysis of samples from the patient’s father, mother and sister. Whole genome sequencing was performed to map the approximate location of the break points of the gross deletion. Long-range PCR and Sanger sequencing were performed to identify the length of the deletion and to locate the break points. ResultsThe patient is a compound heterozygous mutation including a small deletion mutation (c.1227_1229del chr19: 41930402) and a gross novel deletion including exon1-9 in BCKDHA. The junction site of the gross deletion was localized within a microhomologous sequence in two Alu elements. ConclusionsThis study is the first time report on rearrangement sequences in BCKDHA mediated by Alu element, which resulted in MSUD. Our results may also offer new insights into the formation and pathogenicity of MSUD, and may be useful to genetic counseling and genetic testing.

Palladium-Catalyzed Cascade Carbonylative Synthesis of 1,2,4-Triazol-3-ones from Hydrazonoyl Chlorides and NaN3.

A palladium-catalyzed three-component carbonylative reaction for the synthesis of 3H-1,2,4-triazol-3-ones from hydrazonoyl chlorides and NaN3 has been achieved. The reaction presumably proceeds through a cascade carbonylation, acyl azide formation, Curtius rearrangement, and intramolecular nucleophilic addition sequence. A wide variety of structurally diverse 3H-1,2,4-triazol-3-ones were constructed in moderate to excellent yields. Benzene-1,3,5-triyl triformate (TFBen) was applied as a solid and convenient CO surrogate.

Inside Back Cover: Seven‐Step Synthesis of All‐Nitrogenated Sugar Derivatives Using Sequential Overman Rearrangements (Angew. Chem. Int. Ed. 10/2021)

All-nitrogenated sugars (ANSs), in which all hydroxy groups in a carbohydrate are replaced with amino groups, are anticipated to be privileged structures with useful biological activities. In their Communication on page 5193, Takaaki Sato, Noritaka Chida, and co-workers report the synthesis, transformation, and biological tests of ANS derivatives. The key to success was a seven-step synthesis of ANSs by a sequential Overman rearrangement enabling formal simultaneous substitution of four or five hydroxy groups in monosaccharides with amino groups.

8‐Prenylflavanones through Microwave Promoted Tandem Claisen Rearrangement/6‐endo‐trig Cyclization and Cross Metathesis

Prenylated flavanones were obtained from ortho‐allyloxy chalcones through a one‐pot sequence of Claisen rearrangement and 6‐endo‐trig cyclization, followed by olefin cross metathesis of the intermediate allyl flavanones with 2‐methyl‐2‐butene. The synthetic utility of this route is illustrated for the synthesis of several naturally occurring prenyl flavanones.

Efficient and Chemoselective Procedure for Conversion of Rhodanine Derivatives into 1,3‐Thiazolidine‐2,4‐diones via 1,3‐Dipolar Cycloaddition Reaction and Rearrangement Sequences

AbstractHerein, we report a chemoselective 1,3‐dipolar cycloaddition reaction between 5‐alkylidene‐ or 5‐arylidene rhodanine derivatives and nitrile oxide generated in situ from dibromoformaldoxime to construct 1,3‐thiazolidine‐2,4‐dione scaffold under mild conditions. This strategy exhibits a distinguished manner to afford thiazolidine derivatives in a simple, rapid and practical route. The results proved that the reaction proceeds through an unpredictable rearrangement and no spirocyclic product is generated. The structures of the target molecules were confirmed by IR, 1H NMR, 13C NMR, mass spectra and unambiguously X‐ray crystal structure analysis.

Altered 3D chromatin structure permits inversional recombination at the IgH locus.

Immunoglobulin heavy chain (IgH) genes are assembled by two sequential DNA rearrangement events that are initiated by recombination activating gene products (RAG) 1 and 2. Diversity (DH) gene segments rearrange first, followed by variable (VH) gene rearrangements. Here, we provide evidence that each rearrangement step is guided by different rules of engagement between rearranging gene segments. DH gene segments, which recombine by deletion of intervening DNA, must be located within a RAG1/2 scanning domain for efficient recombination. In the absence of intergenic control region 1, a regulatory sequence that delineates the RAG scanning domain on wild-type IgH alleles, VH and DH gene segments can recombine with each other by both deletion and inversion of intervening DNA. We propose that VH gene segments find their targets by distinct mechanisms from those that apply to DH gene segments. These distinctions may underlie differential allelic choice associated with each step of IgH gene assembly.

Acid-Catalyzed Rearrangements of 3-Aryloxirane-2-Carboxamides: Novel DFT Mechanistic Insights.

Efficient synthesis of 3‐arylquinolin‐2(1H)‐ones and N‐(2‐carboxyaryl)‐oxalamides from protic acid‐catalyzed rearrangements of 3‐aryloxirane‐2‐carboxamides was achieved recently but not well understood. In contrast to the classical Meinwald rearrangement, extensive DFT calculations reveal that the proximal aryl and amide groups have strong synergetic effects to control the amide‐aided and aryl‐directed oxirane‐opening and further rearrangement sequences. The ortho‐nitro substituent of the proximal aryl is directly involved in a nucleophilic oxirane ring‐opening, the amide C=O is an important proton shuttle for facile H‐shifts, while the N‐aryl may act as a potential ring‐closing site via Friedel‐Crafts alkylation. The mechanistic insights are useful for rational design of novel synthesis by changing the aryl and amide functional groups proximal to the oxirane ring.

Sequential delithiation behavior and structural rearrangement of a nanoscale composite-structured Li1.2Ni0.2Mn0.6O2 during charge\u2013discharge cycles

Lithium- and manganese-rich layered oxides (LMRs) are promising positive electrode materials for next-generation rechargeable lithium-ion batteries. Herein, the structural evolution of Li1.2Ni0.2Mn0.6O2 during the initial charge–discharge cycle was examined using synchrotron-radiation X-ray diffraction, X-ray absorption spectroscopy, and nuclear magnetic resonance spectroscopy to elucidate the unique delithiation behavior. The pristine material contained a composite layered structure composed of Ni-free and Ni-doped Li2MnO3 and LiMO2 (M = Ni, Mn) nanoscale domains, and Li ions were sequentially and inhomogeneously extracted from the composite structure. Delithiation from the LiMO2 domain was observed in the potential slope region associated with the Ni2+/Ni4+ redox couple. Li ions were then extracted from the Li2MnO3 domain during the potential plateau and remained mostly in the Ni-doped Li2MnO3 domain at 4.8 V. In addition, structural transformation into a spinel-like phase was partly observed, which is associated with oxygen loss and cation migration within the Li2MnO3 domain. During Li intercalation, cation remigration and mixing resulted in a domainless layered structure with a chemical composition similar to that of LiNi0.25Mn0.75O2. After the structural activation, the Li ions were reversibly extracted from the newly formed domainless structure.

AgNO3·SiO2: Convenient AgNPs source for the sustainable hydrofunctionalization of allenyl-indoles using heterogeneous catalysis

Supported silver nitrate in silica gel has been demonstrated as an excellent heterogeneous catalytic system for the selective hydroarylation of indole-tethered allenes, with a selectivity reversal in comparison with homogeneous gold catalysis. In this way, the controlled preparation of 1,2-disubstituted-9H-carbazoles, 1,2-disubstituted-4,9-dihydro-1H-carbazoles, and 2,4-disubstituted-spiro[cyclopentane-1,3′-indol]-3-enes has been accomplished. Control experiments supported by Density Functional Theory calculations strongly suggest that indole-tethered allenes react through a 5-endo-dig-carbometallation/rearrangement sequence, which contrasts to the previously reported 6-endo-dig-carbometallation pathway promoted by [Au(I)]-catalysts in related systems.

Rearrangement of 3-Hydroxyazetidines into 2-Oxazolines.

A novel rearrangement sequence of 3-hydroxyazetidines via a Ritter initiated cascade provides highly substituted 2-oxazolines in high yields. The reaction conditions and substrate scope of the transformation have been studied demonstrating the generality of the process. The derived products can also be functionalized in order to undergo further intramolecular cyclization leading to a new class of macrocycle. The final cyclization step was shown to be a transformation amenable to continuous flow processing allowing for a dramatic reduction in the reaction time and simple scale-up.

Altered 3D chromatin structure permits inversional recombination at the IgH locus

Abstract Immunoglobulin heavy chain (IgH) genes are assembled by two sequential DNA rearrangement events that are initiated by recombinase activating gene products (RAG) 1 and 2. Diversity gene segments (DH) rearrange first, followed by variable (VH) gene rearrangements. Here we provide evidence that each rearrangement step is guided by different rules of engagement between rearranging gene segments. DH gene segments, that recombine by deletion of intervening DNA, must be located within a RAG1/2 scanning domain for efficient recombination. In the absence of intergenic control region 1, a regulatory sequence that delineates the RAG scanning domain on WT IgH alleles, VH and DH gene segments can recombine with each other by both deletion and inversion of intervening DNA. We propose that VH gene segments find their targets by diffusion-controlled mechanisms. These distinct mechanisms may underlie differential allelic choice associated with each step of IgH gene assembly.

Cytoskeletal control of the developing and mature B cell antigen receptor repertoire

Abstract The existence of diverse B cell antigen receptor (BCR) specificities is essential for development of protective antibody responses against a wide variety of pathogens. In developing B cells, the BCR repertoire is crafted through sequential rearrangements of heavy and light chain genes, and involves both combinatorial and junctional diversification catalyzed by recombinases and nucleases. Mature B cells undergo further diversification in peripheral lymphoid organs through isotype switching and somatic hypermutations in response to foreign antigens; although these events are not known to alter BCR antigen specificity. Cytoskeletal proteins modulate BCR signal strength and thereby antibody responses, but it is not known if they play a role in the generation of BCR diversity. Using next generation sequencing, and iRepertoire, Inc and ImMunoGeneTics (IMGT) software platforms we examined BCR repertoires in developing and mature B cells that lack the expression of Ezrin, a prominent cytoskeletal regulator of BCR organization, signaling and activation. We show that Ezrin deficiency impacts the generation of BCR repertoire diversity during B cell development, as well as the mature BCR repertoire. Our analysis provides a window into the major processes involved in diversifying the B cell repertoire in control and Ezrin-deficient B cells, including V gene usage, number, frequency and length of unique CDR3s, nucleotide additions and trimming, and shared and unique clonotypes. Our data suggest that the Ezrin cytoskeleton in B cells impacts humoral immunity not only through modulation of B cell activation upon foreign antigen encounter, but also through qualitative and quantitative modulation of the available BCR repertoire.