Publications by authors named "Wandi Zhang"

51 Publications

Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer.

Nat Biotechnol 2021 Oct 18. Epub 2021 Oct 18.

Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA, USA.

Tumor-associated epitopes presented on MHC-I that can activate the immune system against cancer cells are typically identified from annotated protein-coding regions of the genome, but whether peptides originating from novel or unannotated open reading frames (nuORFs) can contribute to antitumor immune responses remains unclear. Here we show that peptides originating from nuORFs detected by ribosome profiling of malignant and healthy samples can be displayed on MHC-I of cancer cells, acting as additional sources of cancer antigens. We constructed a high-confidence database of translated nuORFs across tissues (nuORFdb) and used it to detect 3,555 translated nuORFs from MHC-I immunopeptidome mass spectrometry analysis, including peptides that result from somatic mutations in nuORFs of cancer samples as well as tumor-specific nuORFs translated in melanoma, chronic lymphocytic leukemia and glioblastoma. NuORFs are an unexplored pool of MHC-I-presented, tumor-specific peptides with potential as immunotherapy targets.
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http://dx.doi.org/10.1038/s41587-021-01021-3DOI Listing
October 2021

Phenotype, specificity and avidity of antitumour CD8 T cells in melanoma.

Nature 2021 08 21;596(7870):119-125. Epub 2021 Jul 21.

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.

Interactions between T cell receptors (TCRs) and their cognate tumour antigens are central to antitumour immune responses; however, the relationship between phenotypic characteristics and TCR properties is not well elucidated. Here we show, by linking the antigenic specificity of TCRs and the cellular phenotype of melanoma-infiltrating lymphocytes at single-cell resolution, that tumour specificity shapes the expression state of intratumoural CD8 T cells. Non-tumour-reactive T cells were enriched for viral specificities and exhibited a non-exhausted memory phenotype, whereas melanoma-reactive lymphocytes predominantly displayed an exhausted state that encompassed diverse levels of differentiation but rarely acquired memory properties. These exhausted phenotypes were observed both among clonotypes specific for public overexpressed melanoma antigens (shared across different tumours) or personal neoantigens (specific for each tumour). The recognition of such tumour antigens was provided by TCRs with avidities inversely related to the abundance of cognate targets in melanoma cells and proportional to the binding affinity of peptide-human leukocyte antigen (HLA) complexes. The persistence of TCR clonotypes in peripheral blood was negatively affected by the level of intratumoural exhaustion, and increased in patients with a poor response to immune checkpoint blockade, consistent with chronic stimulation mediated by residual tumour antigens. By revealing how the quality and quantity of tumour antigens drive the features of T cell responses within the tumour microenvironment, we gain insights into the properties of the anti-melanoma TCR repertoire.
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http://dx.doi.org/10.1038/s41586-021-03704-yDOI Listing
August 2021

Longitudinal Single-Cell Dynamics of Chromatin Accessibility and Mitochondrial Mutations in Chronic Lymphocytic Leukemia Mirror Disease History.

Cancer Discov 2021 Jun 10. Epub 2021 Jun 10.

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.

While cancers evolve during disease progression and in response to therapy, temporal dynamics remain difficult to study in humans due to the lack of consistent barcodes marking individual clones . We employ mitochondrial single-cell assay for transposase-accessible chromatin with sequencing to profile 163,279 cells from 9 patients with chronic lymphocytic leukemia (CLL) collected across disease course and utilize mitochondrial DNA (mtDNA) mutations as natural genetic markers of cancer clones. We observe stable propagation of mtDNA mutations over years in the absence of strong selective pressure, indicating clonal persistence, but dramatic changes following tight bottlenecks, including disease transformation and relapse posttherapy, paralleled by acquisition of copy-number variants and changes in chromatin accessibility and gene expression. Furthermore, we link CLL subclones to distinct chromatin states, providing insight into nongenetic sources of relapse. mtDNA mutations thus mirror disease history and provide naturally occurring genetic barcodes to enable patient-specific study of cancer subclonal dynamics. SIGNIFICANCE: Single-cell multi-omic profiling of CLL reveals the utility of somatic mtDNA mutations as barcodes, which mark subclones that can evolve over time along with changes in accessible chromatin and gene expression profiles to capture dynamics of disease evolution.
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http://dx.doi.org/10.1158/2159-8290.CD-21-0276DOI Listing
June 2021

Molecular and cellular features of CTLA-4 blockade for relapsed myeloid malignancies after transplantation.

Blood 2021 06;137(23):3212-3217

Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD; and.

Relapsed myeloid disease after allogeneic stem cell transplantation (HSCT) remains largely incurable. We previously demonstrated the potent activity of immune checkpoint blockade in this clinical setting with ipilimumab or nivolumab. To define the molecular and cellular pathways by which CTLA-4 blockade with ipilimumab can reinvigorate an effective graft-versus-leukemia (GVL) response, we integrated transcriptomic analysis of leukemic biopsies with immunophenotypic profiling of matched peripheral blood samples collected from patients treated with ipilimumab following HSCT on the Experimental Therapeutics Clinical Trials Network 9204 trial. Response to ipilimumab was associated with transcriptomic evidence of increased local CD8+ T-cell infiltration and activation. Systemically, ipilimumab decreased naïve and increased memory T-cell populations and increased expression of markers of T-cell activation and costimulation such as PD-1, HLA-DR, and ICOS, irrespective of response. However, responding patients were characterized by higher turnover of T-cell receptor sequences in peripheral blood and showed increased expression of proinflammatory chemokines in plasma that was further amplified by ipilimumab. Altogether, these data highlight the compositional T-cell shifts and inflammatory pathways induced by ipilimumab both locally and systemically that associate with successful GVL outcomes. This trial was registered at www.clinicaltrials.gov as #NCT01822509.
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http://dx.doi.org/10.1182/blood.2021010867DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8351891PMC
June 2021

Personal neoantigen vaccines induce persistent memory T cell responses and epitope spreading in patients with melanoma.

Nat Med 2021 03 21;27(3):515-525. Epub 2021 Jan 21.

Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.

Personal neoantigen vaccines have been envisioned as an effective approach to induce, amplify and diversify antitumor T cell responses. To define the long-term effects of such a vaccine, we evaluated the clinical outcome and circulating immune responses of eight patients with surgically resected stage IIIB/C or IVM1a/b melanoma, at a median of almost 4 years after treatment with NeoVax, a long-peptide vaccine targeting up to 20 personal neoantigens per patient ( NCT01970358 ). All patients were alive and six were without evidence of active disease. We observed long-term persistence of neoantigen-specific T cell responses following vaccination, with ex vivo detection of neoantigen-specific T cells exhibiting a memory phenotype. We also found diversification of neoantigen-specific T cell clones over time, with emergence of multiple T cell receptor clonotypes exhibiting distinct functional avidities. Furthermore, we detected evidence of tumor infiltration by neoantigen-specific T cell clones after vaccination and epitope spreading, suggesting on-target vaccine-induced tumor cell killing. Personal neoantigen peptide vaccines thus induce T cell responses that persist over years and broaden the spectrum of tumor-specific cytotoxicity in patients with melanoma.
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http://dx.doi.org/10.1038/s41591-020-01206-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8273876PMC
March 2021

A large peptidome dataset improves HLA class I epitope prediction across most of the human population.

Nat Biotechnol 2020 02 16;38(2):199-209. Epub 2019 Dec 16.

Broad Institute of MIT and Harvard, Cambridge, MA, USA.

Prediction of HLA epitopes is important for the development of cancer immunotherapies and vaccines. However, current prediction algorithms have limited predictive power, in part because they were not trained on high-quality epitope datasets covering a broad range of HLA alleles. To enable prediction of endogenous HLA class I-associated peptides across a large fraction of the human population, we used mass spectrometry to profile >185,000 peptides eluted from 95 HLA-A, -B, -C and -G mono-allelic cell lines. We identified canonical peptide motifs per HLA allele, unique and shared binding submotifs across alleles and distinct motifs associated with different peptide lengths. By integrating these data with transcript abundance and peptide processing, we developed HLAthena, providing allele-and-length-specific and pan-allele-pan-length prediction models for endogenous peptide presentation. These models predicted endogenous HLA class I-associated ligands with 1.5-fold improvement in positive predictive value compared with existing tools and correctly identified >75% of HLA-bound peptides that were observed experimentally in 11 patient-derived tumor cell lines.
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http://dx.doi.org/10.1038/s41587-019-0322-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7008090PMC
February 2020

Mitochondrial Reprogramming Underlies Resistance to BCL-2 Inhibition in Lymphoid Malignancies.

Cancer Cell 2019 10 19;36(4):369-384.e13. Epub 2019 Sep 19.

Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Dana Building, Room DA-520, Boston MA 02215-02115, USA; Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA.

Mitochondrial apoptosis can be effectively targeted in lymphoid malignancies with the FDA-approved B cell lymphoma 2 (BCL-2) inhibitor venetoclax, but resistance to this agent is emerging. We show that venetoclax resistance in chronic lymphocytic leukemia is associated with complex clonal shifts. To identify determinants of resistance, we conducted parallel genome-scale screens of the BCL-2-driven OCI-Ly1 lymphoma cell line after venetoclax exposure along with integrated expression profiling and functional characterization of drug-resistant and engineered cell lines. We identified regulators of lymphoid transcription and cellular energy metabolism as drivers of venetoclax resistance in addition to the known involvement by BCL-2 family members, which were confirmed in patient samples. Our data support the implementation of combinatorial therapy with metabolic modulators to address venetoclax resistance.
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http://dx.doi.org/10.1016/j.ccell.2019.08.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6801112PMC
October 2019

Growth dynamics in naturally progressing chronic lymphocytic leukaemia.

Nature 2019 06 29;570(7762):474-479. Epub 2019 May 29.

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.

How the genomic features of a patient's cancer relate to individual disease kinetics remains poorly understood. Here we used the indolent growth dynamics of chronic lymphocytic leukaemia (CLL) to analyse the growth rates and corresponding genomic patterns of leukaemia cells from 107 patients with CLL, spanning decades-long disease courses. We found that CLL commonly demonstrates not only exponential expansion but also logistic growth, which is sigmoidal and reaches a certain steady-state level. Each growth pattern was associated with marked differences in genetic composition, the pace of disease progression and the extent of clonal evolution. In a subset of patients, whose serial samples underwent next-generation sequencing, we found that dynamic changes in the disease course of CLL were shaped by the genetic events that were already present in the early slow-growing stages. Finally, by analysing the growth rates of subclones compared with their parental clones, we quantified the growth advantage conferred by putative CLL drivers in vivo.
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http://dx.doi.org/10.1038/s41586-019-1252-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6630176PMC
June 2019

Conversion of Aldehydes to Branched or Linear Ketones via Regiodivergent Rhodium-Catalyzed Vinyl Bromide Reductive Coupling-Redox Isomerization Mediated by Formate.

J Am Chem Soc 2019 05 18;141(17):6864-6868. Epub 2019 Apr 18.

Department of Chemistry , University of Texas at Austin , Austin , Texas 78712 , United States.

A regiodivergent catalytic method for direct conversion of aldehydes to branched or linear alkyl ketones is described. Rhodium complexes modified by P BuMe catalyze formate-mediated aldehyde-vinyl bromide reductive coupling-redox isomerization to form branched ketones. Use of the less strongly coordinating ligand, PPh, promotes vinyl- to allylrhodium isomerization en route to linear ketones. This method bypasses the 3-step sequence often used to convert aldehydes to ketones involving the addition of pre-metalated reagents to Weinreb or morpholine amides.
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http://dx.doi.org/10.1021/jacs.9b03113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602061PMC
May 2019

Rhodium-Catalyzed Aldehyde Arylation via Formate-Mediated Transfer Hydrogenation: Beyond Metallic Reductants in Grignard/Nozaki-Hiyami-Kishi-Type Addition.

J Am Chem Soc 2019 02 29;141(5):1828-1832. Epub 2019 Jan 29.

Department of Chemistry , University of Texas at Austin , Austin , Texas 78712 , United States.

The first intermolecular carbonyl arylations via transfer hydrogenative reductive coupling are described. Using rhodium catalysts modified by BuPMe, sodium formate-mediated reductive coupling of aryl iodides with aldehydes occurs in a chemoselective fashion in the presence of protic functional groups and lower halides. This work expands the emerging paradigm of transfer hydrogenative coupling as an alternative to pre-formed carbanions or metallic reductants in C═X addition.
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http://dx.doi.org/10.1021/jacs.8b13652DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6376962PMC
February 2019

Bone marrow transplantation for adolescents and young adults with sickle cell disease: Results of a prospective multicenter pilot study.

Am J Hematol 2019 04 11;94(4):446-454. Epub 2019 Feb 11.

Division of Hematology/Oncology, Department of Pediatrics, UCSF Benioff Children's Hospital of Oakland, Oakland, California.

We conducted a multicenter pilot investigation of the safety and feasibility of bone marrow transplantation (BMT) in adults with severe sickle cell disease (SCD) (NCT 01565616) using a reduced toxicity preparative regimen of busulfan (13.2 mg/kg), fludarabine (175 mg/m ) and thymoglobulin (6 mg/kg) and cyclosporine or tacrolimus and methotrexate for graft-vs-host disease (GVHD) prophylaxis. Twenty-two patients (median age 22 years; range 17-36) were enrolled at eight centers. Seventeen patients received marrow from an HLA-identical sibling donor and five patients received marrow from an 8/8 HLA-allele matched unrelated donor. Before BMT, patients had stroke, acute chest syndrome, recurrent pain events, were receiving regular red blood cell transfusions, or had an elevated tricuspid regurgitant jet (TRJ) velocity, which fulfilled eligibility criteria. Four patients developed grades II-III acute GVHD (18%) and six developed chronic GVHD (27%) that was moderate in two and severe in one patient. One patient died of intracranial hemorrhage and one of GVHD. Nineteen patients had stable donor chimerism, 1-year post-transplant. One patient who developed secondary graft failure survives disease-free after a second BMT. The one-year overall survival and event-free survival (EFS) are 91% (95% CI 68%-98%) and 86% (95% CI, 63%-95%), respectively, and 3-year EFS is 82%. Statistically significant improvements in the pain interference and physical function domains of health-related quality of life were observed. The study satisfied the primary endpoint of 1-year EFS ≥70%. This regimen is being studied in a prospective clinical trial comparing HLA-matched donor BMT with standard of care in adults with severe SCD (NCT02766465).
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http://dx.doi.org/10.1002/ajh.25401DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6542639PMC
April 2019

Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial.

Nature 2019 01 19;565(7738):234-239. Epub 2018 Dec 19.

Oncovir Inc, Washington, DC, USA.

Neoantigens, which are derived from tumour-specific protein-coding mutations, are exempt from central tolerance, can generate robust immune responses and can function as bona fide antigens that facilitate tumour rejection. Here we demonstrate that a strategy that uses multi-epitope, personalized neoantigen vaccination, which has previously been tested in patients with high-risk melanoma, is feasible for tumours such as glioblastoma, which typically have a relatively low mutation load and an immunologically 'cold' tumour microenvironment. We used personalized neoantigen-targeting vaccines to immunize patients newly diagnosed with glioblastoma following surgical resection and conventional radiotherapy in a phase I/Ib study. Patients who did not receive dexamethasone-a highly potent corticosteroid that is frequently prescribed to treat cerebral oedema in patients with glioblastoma-generated circulating polyfunctional neoantigen-specific CD4 and CD8 T cell responses that were enriched in a memory phenotype and showed an increase in the number of tumour-infiltrating T cells. Using single-cell T cell receptor analysis, we provide evidence that neoantigen-specific T cells from the peripheral blood can migrate into an intracranial glioblastoma tumour. Neoantigen-targeting vaccines thus have the potential to favourably alter the immune milieu of glioblastoma.
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http://dx.doi.org/10.1038/s41586-018-0792-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6546179PMC
January 2019

A cloning and expression system to probe T-cell receptor specificity and assess functional avidity to neoantigens.

Blood 2018 11 27;132(18):1911-1921. Epub 2018 Aug 27.

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA.

Recent studies have highlighted the promise of targeting tumor neoantigens to generate potent antitumor immune responses and provide strong motivation for improving our understanding of antigen-T-cell receptor (TCR) interactions. Advances in single-cell sequencing technologies have opened the door for detailed investigation of the TCR repertoire, providing paired information from TCRα and TCRβ, which together determine specificity. However, a need remains for efficient methods to assess the specificity of discovered TCRs. We developed a streamlined approach for matching TCR sequences with cognate antigen through on-demand cloning and expression of TCRs and screening against candidate antigens. Here, we first demonstrate the system's capacity to identify viral-antigen-specific TCRs and compare the functional avidity of TCRs specific for a given antigen target. We then apply this system to identify neoantigen-specific TCR sequences from patients with melanoma treated with personalized neoantigen vaccines and characterize functional avidity of neoantigen-specific TCRs. Furthermore, we use a neoantigen-prediction pipeline to show that an insertion-deletion mutation in a putative chronic lymphocytic leukemia (CLL) driver gives rise to an immunogenic neoantigen mut- and use this approach to identify the mut--specific TCR sequence. This approach provides a means to identify and express TCRs, and then rapidly assess antigen specificity and functional avidity of a reconstructed TCR, which can be applied for monitoring antigen-specific T-cell responses, and potentially for guiding the design of effective T-cell-based immunotherapies.
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http://dx.doi.org/10.1182/blood-2018-04-843763DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6213317PMC
November 2018

Selection between Diastereomeric Kinetic vs Thermodynamic Carbonyl Binding Modes Enables Enantioselective Iridium-Catalyzed anti-(α-Aryl)allylation of Aqueous Fluoral Hydrate and Difluoroacetaldehyde Ethyl Hemiacetal.

J Am Chem Soc 2018 08 18;140(30):9392-9395. Epub 2018 Jul 18.

Department of Chemistry , University of Texas at Austin , Austin , Texas 78712 , United States.

Enantioselectivity increases with increasing carbonyl electrophilicity in 2-propanol-mediated reductive couplings of aldehydes with branched aryl-substituted allylic acetates to form products of carbonyl anti-(α-aryl)allylation. This unusual phenomenon is caused by aldehyde coordination to diastereomeric kinetic vs thermodynamic carbonyl binding sites that deliver enantiomeric products. Exploiting this effect, anti-diastereo- and enantioselective (α-aryl)allylations of fluoral hydrate and difluoroacetaldehyde ethyl hemiacetal were developed.
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http://dx.doi.org/10.1021/jacs.8b05725DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6206506PMC
August 2018

The evolutionary landscape of chronic lymphocytic leukemia treated with ibrutinib targeted therapy.

Nat Commun 2017 12 19;8(1):2185. Epub 2017 Dec 19.

Broad Institute, Cambridge, MA, 02142, USA.

Treatment of chronic lymphocytic leukemia (CLL) has shifted from chemo-immunotherapy to targeted agents. To define the evolutionary dynamics induced by targeted therapy in CLL, we perform serial exome and transcriptome sequencing for 61 ibrutinib-treated CLLs. Here, we report clonal shifts (change >0.1 in clonal cancer cell fraction, Q < 0.1) in 31% of patients during the first year of therapy, associated with adverse outcome. We also observe transcriptional downregulation of pathways mediating energy metabolism, cell cycle, and B cell receptor signaling. Known and previously undescribed mutations in BTK and PLCG2, or uncommonly, other candidate alterations are present in seventeen subjects at the time of progression. Thus, the frequently observed clonal shifts during the early treatment period and its potential association with adverse outcome may reflect greater evolutionary capacity, heralding the emergence of drug-resistant clones.
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http://dx.doi.org/10.1038/s41467-017-02329-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5736707PMC
December 2017

Carbonyl anti-(α-Amino)allylation via Ruthenium Catalyzed Hydrogen Autotransfer: Use of an Acetylenic Pyrrole as an Allylmetal Pronucleophile.

Org Lett 2017 09 29;19(18):4876-4879. Epub 2017 Aug 29.

University of Texas at Austin, Department of Chemistry , Austin, Texas 78712, United States.

A single ruthenium complex catalyzes two discrete transformations resulting in the net conversion of an acetylenic pyrrole and alcohols to products of carbonyl anti-(α-amino)allylation. An initial catalytic process enables isomerization of an alkyne to a kinetically more reactive allene. A second catalytic process promotes alcohol-to-allene hydrogen transfer to form an aldehyde-allylruthenium pair that engages in regio- and diastereoselective carbonyl addition. A related reductive coupling of aldehydes mediated by 2-propanol also is described. The present catalytic processes represent rare examples of the use of alkynes as nucleophilic allylmetal precursors.
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http://dx.doi.org/10.1021/acs.orglett.7b02336DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5637530PMC
September 2017

Catalytic Enantioselective Carbonyl Allylation and Propargylation via Alcohol-Mediated Hydrogen Transfer: Merging the Chemistry of Grignard and Sabatier.

Acc Chem Res 2017 09 9;50(9):2371-2380. Epub 2017 Aug 9.

Department of Chemistry, University of Texas at Austin , Welch Hall (A5300), 105 East 24th Street, Austin, Texas 78712, United States.

Merging the characteristics of transfer hydrogenation and carbonyl addition, we have developed a new class of catalytic enantioselective C-C bond formations. In these processes, hydrogen transfer between alcohols and π-unsaturated reactants generates carbonyl-organometal pairs that combine to deliver products of addition. On the basis of this mechanistic paradigm, lower alcohols are converted directly to higher alcohols in the absence of premetalated reagents or discrete alcohol-to-carbonyl redox reactions. In certain cases, due to a pronounced kinetic preference for primary versus secondary alcohol dehydrogenation, diols and higher polyols are found to engage in catalytic stereo- and site-selective C-C bond formation-a capability that further enhances efficiency by enabling skeletal construction events without extraneous manipulations devoted to the installation and removal of protecting groups. While this Account focuses on redox-neutral couplings of alcohols, corresponding aldehyde reductive couplings mediated by 2-propanol were developed in parallel for most of the catalytic transformations reported herein. Mechanistically, two distinct classes of alcohol C-H functionalizations have emerged, which are distinguished by the mode of pronucleophile activation, specifically, processes wherein alcohol oxidation is balanced by (a) π-bond hydrometalation or (b) C-X bond reductive cleavage. Each pathway offers access to allylmetal or allenylmetal intermediates and, therefrom, enantiomerically enriched homoallylic or homopropargylic alcohol products, respectively. In the broadest terms, carbonyl addition mediated by premetalated reagents has played a central role in synthetic organic chemistry for well over a century, but the requisite organometallic reagents pose issues of safety, require multistep syntheses, and generate stoichiometric quantities of metallic byproducts. The concepts and catalytic processes described in this Account, conceived and developed wholly within the author's laboratory, signal a departure from the use of stoichiometric organometallic reagents in carbonyl addition. Rather, they reimagine carbonyl addition as a hydrogen autotransfer process or cross-coupling in which alcohol reactants, by virtue of their native reducing ability, drive the generation of transient organometallic nucleophiles and, in doing so, serve dually as carbonyl proelectrophiles. The catalytic allylative and propargylative transformations developed to date display capabilities far beyond their classical counterparts, and their application to the total synthesis of type-I polyketide natural products have evoked a step-change in efficiency. More importantly, the present data suggest that diverse transformations traditionally reliant on premetalated reagents may now be conducted catalytically without stoichiometric metals. This Account provides the reader and potential practitioner with a catalog of enantioselective alcohol-mediated carbonyl additions-a user's guide, 10-year retrospective, and foundation for future work in this emerging area of catalytic C-C bond formation.
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http://dx.doi.org/10.1021/acs.accounts.7b00308DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5641472PMC
September 2017

An immunogenic personal neoantigen vaccine for patients with melanoma.

Nature 2017 07 5;547(7662):217-221. Epub 2017 Jul 5.

Center for Immuno-Oncology (CIO), Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.

Effective anti-tumour immunity in humans has been associated with the presence of T cells directed at cancer neoantigens, a class of HLA-bound peptides that arise from tumour-specific mutations. They are highly immunogenic because they are not present in normal tissues and hence bypass central thymic tolerance. Although neoantigens were long-envisioned as optimal targets for an anti-tumour immune response, their systematic discovery and evaluation only became feasible with the recent availability of massively parallel sequencing for detection of all coding mutations within tumours, and of machine learning approaches to reliably predict those mutated peptides with high-affinity binding of autologous human leukocyte antigen (HLA) molecules. We hypothesized that vaccination with neoantigens can both expand pre-existing neoantigen-specific T-cell populations and induce a broader repertoire of new T-cell specificities in cancer patients, tipping the intra-tumoural balance in favour of enhanced tumour control. Here we demonstrate the feasibility, safety, and immunogenicity of a vaccine that targets up to 20 predicted personal tumour neoantigens. Vaccine-induced polyfunctional CD4 and CD8 T cells targeted 58 (60%) and 15 (16%) of the 97 unique neoantigens used across patients, respectively. These T cells discriminated mutated from wild-type antigens, and in some cases directly recognized autologous tumour. Of six vaccinated patients, four had no recurrence at 25 months after vaccination, while two with recurrent disease were subsequently treated with anti-PD-1 (anti-programmed cell death-1) therapy and experienced complete tumour regression, with expansion of the repertoire of neoantigen-specific T cells. These data provide a strong rationale for further development of this approach, alone and in combination with checkpoint blockade or other immunotherapies.
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http://dx.doi.org/10.1038/nature22991DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5577644PMC
July 2017

Evaluation of carbon emission reductions promoted by private driving restrictions based on automatic fare collection data in Beijing, China.

J Air Waste Manag Assoc 2017 11 28;67(11):1249-1257. Epub 2017 Apr 28.

c Beijing Transportation Information Center , Beijing , People's Republic of China.

Public transportation automatic fare collection (AFC) systems are able to continuously record large amounts of passenger travel information, providing massive, low-cost data for research on regulations pertaining to public transport. These data can be used not only to analyze characteristics of passengers' trips but also to evaluate transport policies that promote a travel mode shift and emission reduction. In this study, models combining card, survey, and geographic information systems (GIS) data are established with a research focus on the private driving restriction policies being implemented in an ever-increasing number of cities. The study aims to evaluate the impact of these policies on the travel mode shift, as well as relevant carbon emission reductions. The private driving restriction policy implemented in Beijing is taken as an example. The impact of the restriction policy on the travel mode shift from cars to subways is analyzed through a model based on metro AFC data. The routing paths of these passengers are also analyzed based on the GIS method and on survey data, while associated carbon emission reductions are estimated. The analysis method used in this study can provide reference for the application of big data in evaluating transport policies.

Implications: Motor vehicles have become the most prevalent source of emissions and subsequently air pollution within Chinese cities. The evaluation of the effects of driving restriction policies on the travel mode shift and vehicle emissions will be useful for other cities in the future. Transport big data, playing an important support role in estimating the travel mode shift and emission reduction considered, can help related departments to estimate the effects of traffic jam alleviation and environment improvement before the implementation of these restriction policies and provide a reference for relevant decisions.
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http://dx.doi.org/10.1080/10962247.2017.1320597DOI Listing
November 2017

Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction.

Immunity 2017 02;46(2):315-326

Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA; Harvard Medical School, Boston, MA, 02115, USA. Electronic address:

Identification of human leukocyte antigen (HLA)-bound peptides by liquid chromatography-tandem mass spectrometry (LC-MS/MS) is poised to provide a deep understanding of rules underlying antigen presentation. However, a key obstacle is the ambiguity that arises from the co-expression of multiple HLA alleles. Here, we have implemented a scalable mono-allelic strategy for profiling the HLA peptidome. By using cell lines expressing a single HLA allele, optimizing immunopurifications, and developing an application-specific spectral search algorithm, we identified thousands of peptides bound to 16 different HLA class I alleles. These data enabled the discovery of subdominant binding motifs and an integrative analysis quantifying the contribution of factors critical to epitope presentation, such as protein cleavage and gene expression. We trained neural-network prediction algorithms with our large dataset (>24,000 peptides) and outperformed algorithms trained on datasets of peptides with measured affinities. We thus demonstrate a strategy for systematically learning the rules of endogenous antigen presentation.
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http://dx.doi.org/10.1016/j.immuni.2017.02.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5405381PMC
February 2017

Transcriptomic Characterization of SF3B1 Mutation Reveals Its Pleiotropic Effects in Chronic Lymphocytic Leukemia.

Cancer Cell 2016 Nov 3;30(5):750-763. Epub 2016 Nov 3.

Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.

Mutations in SF3B1, which encodes a spliceosome component, are associated with poor outcome in chronic lymphocytic leukemia (CLL), but how these contribute to CLL progression remains poorly understood. We undertook a transcriptomic characterization of primary human CLL cells to identify transcripts and pathways affected by SF3B1 mutation. Splicing alterations, identified in the analysis of bulk cells, were confirmed in single SF3B1-mutated CLL cells and also found in cell lines ectopically expressing mutant SF3B1. SF3B1 mutation was found to dysregulate multiple cellular functions including DNA damage response, telomere maintenance, and Notch signaling (mediated through KLF8 upregulation, increased TERC and TERT expression, or altered splicing of DVL2 transcript, respectively). SF3B1 mutation leads to diverse changes in CLL-related pathways.
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http://dx.doi.org/10.1016/j.ccell.2016.10.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5127278PMC
November 2016

Iridium-Catalyzed C-C Coupling of a Simple Propargyl Ether with Primary Alcohols: Enantioselective Homoaldol Addition via Redox-Triggered (Z)-Siloxyallylation.

J Am Chem Soc 2015 Dec 15;137(51):16024-7. Epub 2015 Dec 15.

Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States.

A chiral iridium complex formed in situ from [Ir(cod)Cl]2 and (R)-H8-BINAP is found to catalyze the direct enantioselective C-C coupling of a simple propargyl ether, TIPSOCH2C≡CH, with primary alcohols to form γ-hydroxy (Z)-enol silanes with uniformly high enantioselectivity and complete alkene (Z)-stereoselectivity. As corroborated by deuterium labeling studies, these studies represent the first examples of 1,2-hydride shift-enabled π-allyl formation in the context of iridium catalysis.
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http://dx.doi.org/10.1021/jacs.5b12131DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4697880PMC
December 2015

Ruthenium Catalyzed Diastereo- and Enantioselective Coupling of Propargyl Ethers with Alcohols: Siloxy-Crotylation via Hydride Shift Enabled Conversion of Alkynes to π-Allyls.

J Am Chem Soc 2015 Oct 29;137(40):13066-71. Epub 2015 Sep 29.

Department of Chemistry, University of Texas at Austin , 1 University Station, Welch Hall A5300, Austin, Texas 78712, United States.

The first enantioselective carbonyl crotylations through direct use of alkynes as chiral allylmetal equivalents are described. Chiral ruthenium(II) complexes modified by Josiphos (SL-J009-1) catalyze the C-C coupling of TIPS-protected propargyl ether 1a with primary alcohols 2a-2o to form products of carbonyl siloxy-crotylation 3a-3o, which upon silyl deprotection-reduction deliver 1,4-diols 5a-5o with excellent control of regio-, anti-diastereo-, and enantioselectivity. Structurally related propargyl ethers 1b and 1c bearing ethyl- and phenyl-substituents engage in diastereo- and enantioselective coupling, as illustrated in the formation of adducts 5p and 5q, respectively. Selective mono-tosylation of diols 5a, 5c, 5e, 5f, 5k, and 5m is accompanied by spontaneous cyclization to deliver the trans-2,3-disubstituted furans 6a, 6c, 6e, 6f, 6k, and 6m, respectively. Primary alcohols 2a, 2l, and 2p were converted to the siloxy-crotylation products 3a, 3l, and 3p, which upon silyl deprotection-lactol oxidation were transformed to the trans-4,5-disubstituted γ-butyrolactones 7a, 7l, and 7p. The formation of 7p represents a total synthesis of (+)-trans-whisky lactone. Unlike closely related ruthenium catalyzed alkyne-alcohol C-C couplings, deuterium labeling studies provide clear evidence of a novel 1,2-hydride shift mechanism that converts metal-bound alkynes to π-allyls in the absence of intervening allenes.
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http://dx.doi.org/10.1021/jacs.5b08019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4688008PMC
October 2015

Enantioselective ruthenium-catalyzed carbonyl allylation via alkyne-alcohol C-C bond-forming transfer hydrogenation: allene hydrometalation vs oxidative coupling.

J Am Chem Soc 2015 Mar 3;137(9):3161-4. Epub 2015 Mar 3.

Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States.

Chiral ruthenium(II) complexes modified by Josiphos ligands catalyze the reaction of alkynes with primary alcohols to form homoallylic alcohols with excellent control of regio-, diastereo-, and enantioselectivity. These processes represent the first examples of enantioselective carbonyl allylation using alkynes as allylmetal equivalents.
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http://dx.doi.org/10.1021/jacs.5b00747DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4385519PMC
March 2015

Assessing cholesterol storage in live cells and C. elegans by stimulated Raman scattering imaging of phenyl-Diyne cholesterol.

Sci Rep 2015 Jan 22;5:7930. Epub 2015 Jan 22.

1] Interdisciplinary Life Science Program, Purdue University, West Lafayette, IN, USA [2] Department of Chemistry, Purdue University, West Lafayette, IN, USA [3] Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.

We report a cholesterol imaging method using rationally synthesized phenyl-diyne cholesterol (PhDY-Chol) and stimulated Raman scattering (SRS) microscope. The phenyl-diyne group is biologically inert and provides a Raman scattering cross section that is 88 times larger than the endogenous C = O stretching mode. SRS microscopy offers an imaging speed that is faster than spontaneous Raman microscopy by three orders of magnitude, and a detection sensitivity of 31 μM PhDY-Chol (~1,800 molecules in the excitation volume). Inside living CHO cells, PhDY-Chol mimics the behavior of cholesterol, including membrane incorporation and esterification. In a cellular model of Niemann-Pick type C disease, PhDY-Chol reflects the lysosomal accumulation of cholesterol, and shows relocation to lipid droplets after HPβCD treatment. In live C. elegans, PhDY-Chol mimics cholesterol uptake by intestinal cells and reflects cholesterol storage. Together, our work demonstrates an enabling platform for study of cholesterol storage and trafficking in living cells and vital organisms.
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http://dx.doi.org/10.1038/srep07930DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4302291PMC
January 2015

Locally disordered methylation forms the basis of intratumor methylome variation in chronic lymphocytic leukemia.

Cancer Cell 2014 Dec;26(6):813-825

Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Division of Hematology/Oncology, Children's Hospital, Boston, MA 02115, USA. Electronic address:

Intratumoral heterogeneity plays a critical role in tumor evolution. To define the contribution of DNA methylation to heterogeneity within tumors, we performed genome-scale bisulfite sequencing of 104 primary chronic lymphocytic leukemias (CLLs). Compared with 26 normal B cell samples, CLLs consistently displayed higher intrasample variability of DNA methylation patterns across the genome, which appears to arise from stochastically disordered methylation in malignant cells. Transcriptome analysis of bulk and single CLL cells revealed that methylation disorder was linked to low-level expression. Disordered methylation was further associated with adverse clinical outcome. We therefore propose that disordered methylation plays a similar role to that of genetic instability, enhancing the ability of cancer cells to search for superior evolutionary trajectories.
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http://dx.doi.org/10.1016/j.ccell.2014.10.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4302418PMC
December 2014

Synthesis of nitriles via palladium-catalyzed water shuffling from amides to acetonitrile.

Org Biomol Chem 2014 Dec;12(45):9109-12

Department of Chemistry and Center for Cancer Research, Purdue University, 720 Clinic Drive, West Lafayette, IN 47907, USA.

Palladium-catalyzed synthesis of nitriles from amides has been described. Two similar, but complementary reaction conditions have been identified to convert various amides including α,β,γ,δ-unsaturated amides, cinnamides, aromatic amides and alkyl amides to the corresponding nitriles in good to excellent yield.
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http://dx.doi.org/10.1039/c4ob01825gDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4213294PMC
December 2014

Systematic identification of personal tumor-specific neoantigens in chronic lymphocytic leukemia.

Blood 2014 Jul 2;124(3):453-62. Epub 2014 Jun 2.

Cancer Vaccine Center and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA;

Genome sequencing has revealed a large number of shared and personal somatic mutations across human cancers. In principle, any genetic alteration affecting a protein-coding region has the potential to generate mutated peptides that are presented by surface HLA class I proteins that might be recognized by cytotoxic T cells. To test this possibility, we implemented a streamlined approach for the prediction and validation of such neoantigens derived from individual tumors and presented by patient-specific HLA alleles. We applied our computational pipeline to 91 chronic lymphocytic leukemias (CLLs) that underwent whole-exome sequencing (WES). We predicted ∼22 mutated HLA-binding peptides per leukemia (derived from ∼16 missense mutations) and experimentally confirmed HLA binding for ∼55% of such peptides. Two CLL patients that achieved long-term remission following allogeneic hematopoietic stem cell transplantation were monitored for CD8(+) T-cell responses against predicted or confirmed HLA-binding peptides. Long-lived cytotoxic T-cell responses were detected against peptides generated from personal tumor mutations in ALMS1, C6ORF89, and FNDC3B presented on tumor cells. Finally, we applied our computational pipeline to WES data (N = 2488 samples) across 13 different cancer types and estimated dozens to thousands of predicted neoantigens per individual tumor, suggesting that neoantigens are frequent in most tumors.
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http://dx.doi.org/10.1182/blood-2014-04-567933DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4102716PMC
July 2014

Somatic mutation as a mechanism of Wnt/β-catenin pathway activation in CLL.

Blood 2014 Aug 28;124(7):1089-98. Epub 2014 Apr 28.

Cancer Vaccine Center, and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.

One major goal of cancer genome sequencing is to identify key genes and pathways that drive tumor pathogenesis. Although many studies have identified candidate driver genes based on recurrence of mutations in individual genes, subsets of genes with nonrecurrent mutations may also be defined as putative drivers if they affect a single biological pathway. In this fashion, we previously identified Wnt signaling as significantly mutated through large-scale massively parallel DNA sequencing of chronic lymphocytic leukemia (CLL). Here, we use a novel method of biomolecule delivery, vertical silicon nanowires, to efficiently introduce small interfering RNAs into CLL cells, and interrogate the effects of 8 of 15 mutated Wnt pathway members identified across 91 CLLs. In HEK293T cells, mutations in 2 genes did not generate functional changes, 3 led to dysregulated pathway activation, and 3 led to further activation or loss of repression of pathway activation. Silencing 4 of 8 mutated genes in CLL samples harboring the mutated alleles resulted in reduced viability compared with leukemia samples with wild-type alleles. We demonstrate that somatic mutations in CLL can generate dependence on this pathway for survival. These findings support the notion that nonrecurrent mutations at different nodes of the Wnt pathway can contribute to leukemogenesis.
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http://dx.doi.org/10.1182/blood-2014-01-552067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4133483PMC
August 2014
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