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1.
Blood Adv ; 2022 Jan 11.
Artigo em Inglês | MEDLINE | ID: mdl-35015819

RESUMO

PD-1 blockade enhances the function of anti-tumor T-cells and antibody-dependent cell-mediated cytotoxicity (ADCC) of NK cells. In a single-center, open-label, phase 2 trial, we tested the combination of pembrolizumab, an anti-PD-1 monoclonal antibody and rituximab, an anti-CD20 monoclonal antibody that induces ADCC, in 30 follicular lymphoma (FL) patients with rituximab-sensitive disease who relapsed after ≥1 prior therapy. Pembrolizumab was administered at 200mg IV every 3 weeks for up to 16 cycles and rituximab was given at 375mg/m2 IV weekly for 4 weeks in cycle 1 only. The most common grade 3/4 adverse events (AE) were liver enzyme abnormalities (3%), diarrhea (3%), nausea (3%), aseptic meningitis (3%) and pancreatitis (3%). Low-grade immune-related AEs were reported for 80% of patients, including diarrhea (43%), liver enzyme abnormalities (33%), thyroid dysfunction (27%), and rash (23%). Grade 3 or 4 immune related AEs occurred in 13% of patients. Treatment-related AEs led to discontinuation in 6 (20%) patients. Overall response rate (primary endpoint) was 67% and complete response rate was 50%. Median progression-free survival (PFS) was 12.6 months (95% CI, 8.2-27.6 months), the 3-year overall survival rate was 97%, and 23% of patients were in remission at a median follow up of 35 months. Presence of a high CD8+ T-effector score at baseline in the tumor was associated with induction of a complete response and improved PFS. In this single arm, phase 2 study, the combination of pembrolizumab and rituximab demonstrates favorable efficacy and safety profile in relapsed FL. This trial is registered at www.clinicaltrials.gov: NCT02446457.

2.
Cold Spring Harb Protoc ; 2022(1): pdb.prot100701, 2022 Jan 04.
Artigo em Inglês | MEDLINE | ID: mdl-34983856

RESUMO

If labeled oligonucleotides are to be used only as probes in hybridization experiments, complete removal of unincorporated label is generally not necessary. However, to reduce background to a minimum, the bulk of the unincorporated label should be separated from the labeled oligonucleotide. Most of the residual unincorporated precursors can be removed from the preparation by differential precipitation with ethanol, as described in this protocol, if the oligonucleotide is >18 nt in length.

3.
Cold Spring Harb Protoc ; 2022(1): pdb.prot100735, 2022 Jan 04.
Artigo em Inglês | MEDLINE | ID: mdl-34983857

RESUMO

In this protocol, hybridization is first performed in conventional aqueous solvents at a temperature well below the melting temperature, and the hybrids are then washed at higher stringency in buffers containing quaternary alkylammonium salts. TMACl is used with probes that are 14-50 nt in length, whereas TEACl is used with oligonucleotides that are 50-200 nt in length.

4.
Cold Spring Harb Protoc ; 2022(1): pdb.top100578, 2022 Jan 04.
Artigo em Inglês | MEDLINE | ID: mdl-34983861

RESUMO

Labeled nucleic acids and oligonucleotides are typically generated by enzymatic methods such as end-labeling, random priming, nick translation, in vitro transcription, and variations of the polymerase chain reaction (PCR). Some of these methods place the label in specific locations within the nucleic acid (e.g., at the 5' or 3' terminus); others generate molecules that are labeled internally at multiple sites. Some methods yield labeled single-stranded products, whereas others generate double-stranded nucleic acids. Finally, some generate probes of defined length, whereas others yield a heterogeneous population of labeled molecules. Options available for generating and detecting labeled nucleic acids, as well as advice on designing oligonucleotides for use as probes, is included here.

5.
Cold Spring Harb Protoc ; 2021(12): pdb.prot101691, 2021 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-34853119

RESUMO

Isolation of RNA from yeast is complicated by the need to first break the thick, rigid cell wall. The protocol provided here uses a cycle of heating and freezing of cells in the presence of phenol and the detergent sodium dodecyl sulfate (SDS). The extraction is performed in the presence of low salt so that, following separation of the aqueous and phenol phases by centrifugation, DNA can be collected from the interface while RNA remains in the aqueous phase. This protocol should yield ∼50-250 µg of RNA from 10 mL of culture. The RNA isolated using this approach is suitable for most follow-up applications such as northern blot hybridization, reverse transcriptase-polymerase chain reaction (RT-PCR), and cDNA construction.

6.
Artigo em Inglês | MEDLINE | ID: mdl-34907077

RESUMO

In molecular cloning, digoxigenin is used as a ligand that can be incorporated into DNA and RNA probes and detected after hybridization with an anti-digoxigenin-antibody enzyme conjugate. Methods to label nucleic acids with digoxigenin and to detect digoxigenin-labeled probes are introduced here.

7.
Artigo em Inglês | MEDLINE | ID: mdl-34907078

RESUMO

The polymerase chain reaction (PCR) can be used to produce both nonradiolabeled DNA probes and radiolabeled DNA probes with high specific activity. In this protocol, PCR is used to generate double-stranded probes. Related methods, including the generation of asymmetric probes by PCR, are also discussed.

8.
Cold Spring Harb Protoc ; 2021(11): pdb.prot100438, 2021 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-34725171

RESUMO

Alkaline agarose gels are run at high pH, which causes each thymine and guanine residue to lose a proton and thus prevents the formation of hydrogen bonds with their adenine and cytosine partners. The denatured DNA is maintained in a single-stranded state and migrates through an alkaline agarose gel as a function of its size. Other denaturants such as formamide and urea do not work well because they cause the agarose to become rubbery.

9.
Cold Spring Harb Protoc ; 2021(11): pdb.prot101212, 2021 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-34725172

RESUMO

This protocol describes a convenient method for the preparation, use, and storage of competent Escherichia coli The reported transformation efficiency of this method is ∼5 × 107 transformants/µg of plasmid DNA.

10.
Cold Spring Harb Protoc ; 2021(11): pdb.top101170, 2021 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-34725175

RESUMO

Plasmids occupy a place of honor in molecular cloning: They were used in the first recombinant DNA experiments and, 40 or more years later, they remain as the carriage horses of molecular cloning. After almost half a century of sequential improvement in design, today's plasmid vectors are available in huge variety, are often optimized for specific purposes, and bear only passing resemblance to their forebears. Here, various features of plasmid vectors and methods for transforming E. coli cells are introduced.

11.
Cancer Res ; 81(23): 6029-6043, 2021 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-34625423

RESUMO

The family of PIM serine/threonine kinases includes three highly conserved oncogenes, PIM1, PIM2, and PIM3, which regulate multiple prosurvival pathways and cooperate with other oncogenes such as MYC. Recent genomic CRISPR-Cas9 screens further highlighted oncogenic functions of PIMs in diffuse large B-cell lymphoma (DLBCL) cells, justifying the development of small-molecule PIM inhibitors and therapeutic targeting of PIM kinases in lymphomas. However, detailed consequences of PIM inhibition in DLBCL remain undefined. Using chemical and genetic PIM blockade, we comprehensively characterized PIM kinase-associated prosurvival functions in DLBCL and the mechanisms of PIM inhibition-induced toxicity. Treatment of DLBCL cells with SEL24/MEN1703, a pan-PIM inhibitor in clinical development, decreased BAD phosphorylation and cap-dependent protein translation, reduced MCL1 expression, and induced apoptosis. PIM kinases were tightly coexpressed with MYC in diagnostic DLBCL biopsies, and PIM inhibition in cell lines and patient-derived primary lymphoma cells decreased MYC levels as well as expression of multiple MYC-dependent genes, including PLK1. Chemical and genetic PIM inhibition upregulated surface CD20 levels in an MYC-dependent fashion. Consistently, MEN1703 and other clinically available pan-PIM inhibitors synergized with the anti-CD20 monoclonal antibody rituximab in vitro, increasing complement-dependent cytotoxicity and antibody-mediated phagocytosis. Combined treatment with PIM inhibitor and rituximab suppressed tumor growth in lymphoma xenografts more efficiently than either drug alone. Taken together, these results show that targeting PIM in DLBCL exhibits pleiotropic effects that combine direct cytotoxicity with potentiated susceptibility to anti-CD20 antibodies, justifying further clinical development of such combinatorial strategies. SIGNIFICANCE: These findings demonstrate that inhibition of PIM induces DLBCL cell death via MYC-dependent and -independent mechanisms and enhances the therapeutic response to anti-CD20 antibodies by increasing CD20 expression.

12.
Cold Spring Harb Protoc ; 2021(10): pdb.prot100693, 2021 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-34599075

RESUMO

In this method, a short primer is hybridized to an oligonucleotide template whose sequence is the complement of the desired radiolabeled probe. The primer is then extended using the Klenow fragment to incorporate [α-32P]dNTPs in a template-directed manner. After the reaction, the template and product are separated by denaturation followed by electrophoresis through a polyacrylamide gel under denaturing conditions. With this method, it is possible to generate oligonucleotide probes that contain several radioactive atoms per molecule of oligonucleotide and to achieve specific activities as high as 2 × 1010 cpm/µg of probe. Because the end product of the reaction is dsDNA, whose strands must be separated and the labeled product isolated, this method is generally not used to prepare nonradiolabeled oligonucleotides.

13.
Cold Spring Harb Protoc ; 2021(10): pdb.prot100719, 2021 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-34599076

RESUMO

When labeled oligonucleotides are to be used in enzymatic reactions such as primer extension, virtually all of the unincorporated label must be removed from the oligonucleotide. For this purpose, chromatographic methods or gel electrophoresis are superior to differential precipitation of the oligonucleotide with ethanol or cetylpyridinium bromide (CPB). This protocol describes a method to separate labeled oligonucleotides from unincorporated label that takes advantage of differences in mobility between oligonucleotides and mononucleotides during size-exclusion chromatography. Although size-exclusion chromatography can, in principle, be used to purify either radiolabeled or nonradiolabeled oligonucleotides, this protocol is geared toward purifying radiolabeled oligonucleotides, whose elution from the column is monitored using a minimonitor and whose separation from unincorporated nucleotides is monitored by liquid scintillation counting.

14.
Cold Spring Harb Protoc ; 2021(10): pdb.top100776, 2021 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-34599078

RESUMO

Biotin is a water-soluble vitamin that can be attached to a variety of proteins and nucleic acids, often without altering their properties. Its use in molecular biology is introduced here.

15.
Blood ; 2021 Oct 03.
Artigo em Inglês | MEDLINE | ID: mdl-34601571

RESUMO

Majority of RUNX1 mutations in AML are missense or deletion-truncation and behave as loss-of-function mutations. Following standard therapy, AML patients expressing mtRUNX1 exhibit inferior clinical outcome than those without mutant RUNX1. Studies presented here demonstrate that as compared to AML cells lacking mtRUNX1, their isogenic counterparts harboring mtRUNX1 display impaired ribosomal biogenesis and differentiation, as well as exhibit reduced levels of wild-type RUNX1, PU.1 and c-Myc. Compared to AML cells with only wild-type RUNX1, AML cells expressing mtRUNX1 were also more sensitive to the protein translation inhibitor homoharringtonine (omacetaxine) and BCL2 inhibitor venetoclax. HHT treatment repressed enhancers and their BRD4 occupancy, as well as was associated with reduced levels of c-Myc, c-Myb, MCL1 and Bcl-xL. Consistent with this, co-treatment with omacetaxine and venetoclax or BET inhibitor induced synergistic in vitro lethality in AML expressing mtRUNX1. Compared to each agent alone, co-treatment with omacetaxine and venetoclax or BET inhibitor also displayed improved in vivo anti-AML efficacy, associated with improved survival of immune depleted mice engrafted with AML cells harboring mtRUNX1. These findings highlight superior efficacy of omacetaxine-based combination therapies for AML harboring mtRUNX1.

16.
Nat Commun ; 12(1): 6071, 2021 10 18.
Artigo em Inglês | MEDLINE | ID: mdl-34663807

RESUMO

In contrast to the curative effect of allogenic stem cell transplantation in acute myeloid leukemia via T cell activity, only modest responses are achieved with checkpoint-blockade therapy, which might be explained by T cell phenotypes and T cell receptor (TCR) repertoires. Here, we show by paired single-cell RNA analysis and TCR repertoire profiling of bone marrow cells in relapsed/refractory acute myeloid leukemia patients pre/post azacytidine+nivolumab treatment that the disease-related T cell subsets are highly heterogeneous, and their abundance changes following PD-1 blockade-based treatment. TCR repertoires expand and primarily emerge from CD8+ cells in patients responding to treatment or having a stable disease, while TCR repertoires contract in therapy-resistant patients. Trajectory analysis reveals a continuum of CD8+ T cell phenotypes, characterized by differential expression of granzyme B and a bone marrow-residing memory CD8+ T cell subset, in which a population with stem-like properties expressing granzyme K is enriched in responders. Chromosome 7/7q loss, on the other hand, is a cancer-intrinsic genomic marker of PD-1 blockade resistance in AML. In summary, our study reveals that adaptive T cell plasticity and genomic alterations determine responses to PD-1 blockade in acute myeloid leukemia.


Assuntos
Inibidores de Checkpoint Imunológico/uso terapêutico , Leucemia Mieloide Aguda/tratamento farmacológico , Receptor de Morte Celular Programada 1/antagonistas & inibidores , Receptores de Antígenos de Linfócitos T/metabolismo , Linfócitos T/efeitos dos fármacos , Idoso , Idoso de 80 Anos ou mais , Azacitidina/uso terapêutico , Medula Óssea/efeitos dos fármacos , Medula Óssea/imunologia , Linfócitos T CD8-Positivos/efeitos dos fármacos , Linfócitos T CD8-Positivos/imunologia , Linfócitos T CD8-Positivos/metabolismo , Deleção Cromossômica , Cromossomos Humanos Par 7/genética , Resistencia a Medicamentos Antineoplásicos/genética , Granzimas/metabolismo , Humanos , Leucemia Mieloide Aguda/genética , Leucemia Mieloide Aguda/imunologia , Pessoa de Meia-Idade , Nivolumabe/uso terapêutico , Receptores de Antígenos de Linfócitos T/genética , Análise de Célula Única , Subpopulações de Linfócitos T/efeitos dos fármacos , Subpopulações de Linfócitos T/imunologia , Subpopulações de Linfócitos T/metabolismo , Linfócitos T/imunologia , Linfócitos T/metabolismo , Transcriptoma/efeitos dos fármacos
18.
Cold Spring Harb Protoc ; 2021(9): pdb.prot101311, 2021 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-34470863

RESUMO

This protocol describes the use of TOPO-activated TA vectors for cloning. Manufacturers of cloning kits provide excellent manuals that explain in detail what to do and why to do it. This makes TOPO cloning easy, but not foolproof. When setting up TOPO cloning for the first time, set up a trial experiment as described here.

19.
Cold Spring Harb Protoc ; 2021(9): pdb.top101345, 2021 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-34470865

RESUMO

This introduction outlines various methods to clone amplified DNAs and to facilitate the construction of complex multicomponent genetic units. Because of the ease with which the termini of amplified DNAs can be tailored by polymerase chain reaction (PCR), many of the methods outlined here use PCR not only to synthesize DNAs but also to link them together into purpose-designed constructs. The most recent refinements however have been the development of modular genetic units that can be harnessed to target DNAs not by PCR but by site-specific recombination enzymes.

20.
Cold Spring Harb Protoc ; 2021(8): pdb.prot100677, 2021 Aug 02.
Artigo em Inglês | MEDLINE | ID: mdl-34341177

RESUMO

The removal of 5' phosphates from nucleic acids with phosphatases and their readdition in radiolabeled form by bacteriophage T4 polynucleotide kinase is a widely used technique for generating 32P-labeled probes. When the reaction is performed efficiently, 40%-50% of the protruding 5' termini in the reaction becomes radiolabeled. However, the specific activity of the resulting probes is not as high as that obtained by other radiolabeling methods because only one radioactive atom is introduced per DNA molecule. Nevertheless, the availability of [γ-32P]ATP with specific activities in the 3000-7000 Ci/mmol range allows the synthesis of probes suitable for many purposes. This protocol includes procedures for labeling the 5' ends of dsDNA and oligonucleotides.

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