Carl D NovinaHarvard Medical School | HMS · Department of Microbiology and Immunobiology
Carl D Novina
MD,PhD
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112
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Introduction
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September 2006 - present
July 2004 - present
October 2004 - present
Publications
Publications (112)
Long noncoding RNAs (lncRNA) can drive tumorigenesis and are susceptible to therapeutic intervention. Here, we used a large-scale CRISPR interference viability screen to interrogate cell growth dependency to lncRNA genes in multiple myeloma (MM), and identified a prominent role for the miR-17-92 cluster host gene (MIR17HG). We show that a MIR17HG-d...
The Front Cover shows light‐induced activation of CAR T cells. Antibodies are coupled to small molecules protected by ultraviolet‐light‐sensitive cages, which can bind to proteins common to tumors and normal tissues. Only when tumors are exposed to ultraviolet light, cages dissociate from the small molecules, enabling small‐molecule‐specific CAR T...
Major challenges to chimeric antigen receptor (CAR) T cell therapies include uncontrolled immune activity, off‐tumor toxicities and tumor heterogeneity. To overcome these challenges, we engineered CARs directed against small molecules. By conjugating the same small molecule to distinct tumor‐targeting antibodies, we show that small molecule specifi...
3′ untranslated region (3′UTR) variants are strongly associated with human traits and diseases, yet few have been causally identified. We developed the massively parallel reporter assay for 3′UTRs (MPRAu) to sensitively assay 12,173 3′UTR variants. We applied MPRAu to six human cell lines, focusing on genetic variants associated with genome-wide as...
How hematopoietic stem cells (HSCs) coordinate their divisional axis and whether this orientation is important for stem cell–driven hematopoiesis is poorly understood. Single-cell RNA sequencing data from patients with Shwachman-Diamond syndrome (SDS), an inherited bone marrow failure syndrome, show that ARHGEF2, a RhoA-specific guanine nucleotide...
3'untranslated region (3'UTR) variants are strongly associated with human traits and diseases, yet few have been causally identified. We developed the Massively Parallel Reporter Assay for 3'UTRs (MPRAu) to sensitively assay 12,173 3'UTR variants. We applied MPRAu to six human cell lines, focusing on genetic variants associated with genome-wide ass...
Long noncoding RNA (lncRNAs) are key epigenetic factors that drive the origin and progression of human cancers via mechanisms that are largely unknown. We have previuosly reported the clinical significance of a lncRNA signature in multiple myeloma (MM) as independent risk predictor for clinical outcome; and recently identified a lncRNA RROL (RNA Re...
The inaccessibility of living bone marrow (BM) hampers the study of its pathophysiology under myelotoxic stress induced by drugs, radiation or genetic mutations. Here, we show that a vascularized human BM-on-a-chip (BM chip) supports the differentiation and maturation of multiple blood cell lineages over 4 weeks while improving CD34⁺ cell maintenan...
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Long non-coding RNAs (lncRNAs) are critical regulators of numerous physiological processes and diseases, especially cancers. However, development of lncRNA-based therapies is limited because the mechanisms of many lncRNAs are obscure, and interactions with functional partners, including proteins, remain uncharacterized. The lncRNA SLNCR1 binds to a...
How hematopoietic stem cells (HSCs) coordinate their divisional axis relative to supportive niche cells and whether or not their divisional orientation is important for stem cell-driven hematopoiesis is poorly understood. Single cell RNA sequencing data from patients with the inherited bone marrow failure Shwachman-Diamond syndrome (SDS) show that...
Long noncoding RNAs (lncRNA) are major regulators of chromatin dynamics and gene expression. We have recently performed deep RNA sequencing of CD138+ cells from 360 uniformly-treated, newly-diagnosed multiple myeloma (MM) patients (IFM/DFCI 2009) and described the lncRNA landscape and their role as independent risk predictors for clinical outcome i...
Shwachman-Diamond Syndrome (SDS) is a rare and clinically-heterogeneous bone marrow (BM) failure syndrome caused by mutations in the Shwachman-Bodian-Diamond Syndrome (SBDS) gene. Although SDS was described over 50 years ago, the molecular pathogenesis is poorly understood due, in part, to the rarity and heterogeneity of the affected hematopoietic...
Melanoma is the deadliest form of skin cancer, affecting men more frequently and severely than women. Although recent studies suggest that differences in activity of the androgen receptor (AR) underlie the observed sex bias, little is known about AR activity in melanoma. Here we show that AR and EGR1 bind to the long non-coding RNA SLNCR and increa...
Monosomy 7 or deletion of 7q (del(7q)) are common clonal cytogenetic abnormalities associated with high grade myelodysplastic syndrome (MDS) arising in inherited and acquired bone marrow failure. Current non-transplant approaches to treat marrow failure may be complicated by stimulation of clonal outgrowth. To study the biological consequences of d...
Mammalian gene expression is a complex process regulated in part by CpG methylation. The ability to target methylation for de novo gene regulation could have therapeutic and research applications. We have previously developed a dCas9-MC/MN protein for targeting CpG methylation. dCas9-MC/MN is composed of an artificially split M.SssI methyltransfera...
Understanding human bone marrow (BM) pathophysiology in the context of myelotoxic stress induced by drugs, radiation, or genetic mutations is of critical importance in clinical medicine. However, study of these dynamic cellular responses is hampered by the inaccessibility of living BM in vivo. Here, we describe a vascularized human Bone Marrow-on-a...
INTRODUCTION
T cells play a central role in our immune system’s responses to infections. Recent promising clinical studies have shown that the immune system can be ‘engineered’ to recognize and kill tumor cells by binding to specific proteins found on the tumor cell surface. The use of ‘chimeric antigen receptor’ (CAR) T cells, now approved for the...
Diamond Blackfan Anemia (DBA) is a congenital red blood cell aplasia usually caused by haploinsufficiency of selected ribosomal protein genes. Approximately 10% of DBA patients are anemic at birth, and 80% of DBA patients present by 6 months. These and other data suggest that the DBA erythroid defect is exacerbated by the switch from fetal to adult...
Monosomy 7 or deletion of 7q (del(7q)) are common cytogenetic abnormalities in pediatric MDS. Monosomy 7/del(7q) frequently arises in the context of inherited bone marrow failure (BMF) syndromes such as Shwachman Diamond Syndrome (SDS), an autosomal recessive disorder caused by biallelic mutations in the SBDS gene. Monosomy 7/del(7q) is associated...
Mammalian genomes exhibit complex patterns of gene expression regulated, in part, by DNA methylation. The advent of engineered DNA methyltransferases (MTases) to target DNA methylation to specific sites in the genome will accelerate many areas of biological research. However, targeted MTases require clear design rules to direct site-specific DNA me...
p>Through an shRNA screen we identified the protein arginine methyltransferase Prmt1 as a vulnerable intervention point in murine p53/Rb-null osteosarcomas, the human counterpart of which lacks effective therapeutic options. Depletion of Prmt1 in p53-deficient cells impaired tumor initiation and maintenance in vitro and in vivo . Mechanistic studie...
During infection, antigen-specific T cells undergo tightly regulated developmental transitions controlled by transcriptional and post-transcriptional regulation of gene expression. We found that the microRNA miR-31 was strongly induced by activation of the T cell antigen receptor (TCR) in a pathway involving calcium and activation of the transcript...
Long non-coding RNAs (lncRNAs) regulate critical cellular processes and their dysregulation contributes to multiple diseases. Although only a few lncRNAs have defined mechanisms, many of these characterized lncRNAs interact with transcription factors to regulate gene expression, suggesting a common mechanism of action. Identifying RNA-bound transcr...
Shwachman-Diamond Syndrome (SDS) is an inherited bone marrow failure caused by mutations in SBDS, which encodes a conserved ribosome assembly factor. Despite simple genetic underpinnings, SDS is surprisingly complex. Patients suffer varying degrees of neutropenia, thrombocytopenia and anemia, and are predisposed to myelodysplasia and acute myeloid...
Myelodysplastic syndrome (MDS) caused by monosomy 7 or del(7q) is a frequent clonal abnormality that arises in the context of inherited bone marrow failure syndromes, such as Shwachman Diamond Syndrome (SDS). Monosomy 7/del(7q) also develops in a subset of patients with acquired aplastic anemia or de novo MDS in the general population. Monosomy 7/d...
Small molecules and antisense oligonucleotides that inhibit the translation initiation factors eIF4A1 and eIF4E have been explored as broad-based therapeutic agents for cancer treatment, based on the frequent upregulation of these two subunits of the eIF4F cap-binding complex in many cancer cells. Here we provide support for these therapeutic appro...
Tumor-stroma interactions are critical for epithelial-derived tumors, and among the stromal cell types, cancer-associated fibroblasts (CAFs) exhibit multiple functions that fuel growth, dissemination, and drug resistance. However, these interactions remain insufficiently characterized in non-epithelial tumors such as malignant melanoma. We generate...
Long non-coding RNAs (lncRNAs) have been implicated in numerous physiological processes and diseases, most notably cancers. However, little is known about the mechanism of many functional lncRNAs. We identified an abundantly expressed lncRNA associated with decreased melanoma patient survival. Increased expression of this lncRNA, SLNCR1, mediates m...
Impaired erythropoiesis in the deletion 5q (del(5q)) subtype of myelodysplastic syndrome (MDS) has been linked to heterozygous deletion of RPS14, which encodes the ribosomal protein small subunit 14. We generated mice with conditional inactivation of Rps14 and demonstrated an erythroid differentiation defect that is dependent on the tumor suppresso...
Diamond Blackman Anemia (DBA) is a severe erythroid hypoplasia that usually presents during the first year of life. Most cases are due to heterozygous mutations in ribosomal protein genes including RPS19, RPL5 and RPL11. Ribosomal stress-induced p53 activation is thought to play a major role in DBA, leading to apoptosis and/or cell cycle arrest in...
With its unique ability to produce high-voltage electric discharges in excess of 600 volts, the South American strong voltage electric eel (Electrophorus electricus) has played an important role in the history of science. Remarkably little is understood about the molecular nature of its electric organs.
We present an in-depth analysis of the genome...
Little is known about the genetic basis of convergent traits that originate repeatedly over broad taxonomic scales. The myogenic electric organ has evolved six times in fishes to produce electric fields used in communication, navigation, predation, or defense. We have examined the genomic basis of the convergent anatomical and physiological origins...
Little is known about the genetic basis of convergent traits that originate repeatedly over broad taxonomic scales. The myogenic
electric organ has evolved six times in fishes to produce electric fields used in communication, navigation, predation, or
defense. We have examined the genomic basis of the convergent anatomical and physiological origins...
The oncogenic transcription factor TAL1/SCL is aberrantly expressed in 60% of cases of human T cell acute lymphoblastic leukemia (T-ALL) and initiates T-ALL in mouse models. By performing global microRNA (miRNA) expression profiling after depletion of TAL1, together with genome-wide analysis of TAL1 occupancy by chromatin immunoprecipitation couple...
A high-throughput RNA interference (RNAi) screen targeting 542 genes of the human kinome was used to discover regulators of RNAi. Here we report that the proto-oncogene Akt-3/PKBγ (Akt3) phosphorylates Argonaute 2 (Ago2) at S387, which downregulates cleavage and upregulates translational repression of endogenous microRNA (miRNA)-targeted messenger...
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The oncogenic transcription factor TAL1/SCL is aberrantly expressed in over 40% of cases of human T-cell acute lymphoblastic leukemia (T-ALL) and causes T-ALL in murine transgenic models, emphasizing its importance in the molecular pathogenesis of this disease. However, the mechanism by which TAL1 leads to transformation of thymocytes is uncle...
MicroRNAs (miRNAs) are small noncoding RNAs that post-transcriptionally regulate protein output from the majority of human mRNAs. In contrast to the consensus view that all miRNAs are associated with Argonaute (Ago) proteins, we determine that miRNAs are expressed in a 13-fold excess relative to Agos in HeLa cells and that miRNAs are bound to mRNAs...
MicroRNAs (miRNAs) regulate physiological and pathological processes by inducing posttranscriptional repression of target messenger RNAs (mRNAs) via incompletely understood mechanisms. To discover factors required for human miRNA activity, we performed an RNAi screen using a reporter cell line of miRNA-mediated repression of translation initiation....
MicroRNAs (miRNAs) are endogenous, ~22-nucleotide-long, noncoding RNAs that play critical roles in physiology and disease via mechanisms that remain obscure. Although numerous studies implicate miRNAs in repression of translation, more recent reports suggest that the major role of miRNAs is in reduction of target mRNA stability. Because mRNA transl...
Primers used in these studies.
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Intronic and intergenic miRNAs that decrease at least two fold after U1 (SNRNP70+PRP8) knockdown in melanoma cell lines 451LU and 501mel as detected by the microarray; #, miRNA* strand; N/A, not detected by the microarray.
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Cooperativity between splicing and microprocessing is miRNA- and intronic context-independent. (A) Replacing miR-211 with a SCR sequence in the melastatin mini-gene decreases miR-211 expression and exon 6-exon 7 splicing, but not steady-state mini-gene levels. WT or SCR melastatin mini-gene were transfected into HeLa cells, and the levels of miRNAs...
Endogenous miR-211-containing intron 6 of melastatin is preferentially spliced in a Microprocessor-dependent manner. (A) Relative copy numbers of indicated exon-exon junctions, based on standard curves produced using cloned melastatin cDNA, were determined by qRT-PCR and normalized to Actin in primary melanocytes (PM) and melanoma cell lines (UACC6...
The spliceosome and the Microprocessor are mechanistically and physically coupled. (A) Knockdown efficiencies of indicated splicing factors (PRP8, U2AF65, and SNRNP70) in HeLa cells were assessed by qRT-PCR and normalized to Actin. (B) Knockdown of U1 (SNRPNP70+PRP8) and U2 (U2AF65+PRP8) splicing factors decreases exon 6-exon 7 splicing but not min...
Validation of miRNA expression profiling data. Intronic miRNAs that decreased more than two-fold after U1 (SNRNP70+PRP8) knockdown as assessed by the microarray were validated by qRT-PCR and normalized to U48 in the indicated melanoma cell lines.
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Normalized miRNA expression levels (Ct value threshold ≤30) after U1 (SNRNP70+PRP8) knockdown in melanoma cell lines 451LU and 501mel as detected by the microarray.
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Author Summary
MicroRNA (miRNA) genes are transcribed as long primary RNAs containing local hairpins that are excised by the Microprocessor complex minimally composed of Drosha and DGCR8. Most mammalian miRNAs reside in introns of protein-encoding and non-coding genes, but it is unclear how microprocessing of an intronic miRNA and splicing at the h...
Comment on: Chan E, et al. Cell Cycle 2011; 10:1845-52.
The NOTCH1 signaling pathway is a critical determinant of cell fate decisions and drives oncogenesis through mechanisms that are incompletely understood. Using an established mouse model of T cell acute lymphoblastic leukemia (T-ALL), here we report that induction of intracellular Notch1 (ICN1) leads to repression of miR-451 and miR-709. ICN1 decre...
Hierarchical clustering of miRNAs expressed in CLL, control B cell, and activated B cells. Heatmap of miRNA expression across 38 patient-derived CLL samples, 9 donor B cell samples, and 6 CpG activated donor B cell samples. miRNA expression is hierarchically clustered on the Y-axis and patient-derived CLL samples or control B cell donors are hierar...
Comparative marker selective view alignment miRNA expression distinguishes miRNA expression between unactivated donor B cells from CLL cells. Comparative marker selective view alignment distinguishes upregulated miRNA expression in 9 control, unactivated B cell sample (Y-axis, red) and in 38 CLL cell patient samples (X-axis, blue). Score (Y-axis) r...
miRNA expression profiling in CD5+B cells in comparison to CD5- B cells. B cells were isolated from four donors and six CLL patient samples by CD19+selection. Control B cells were stained with anti-human CD5 and CD19 antibodies, FACS sorted for CD5-CD19+(CD5-) and CD5+CD19+(CD5+) B cells and miRNA expression was analyzed by RT-PCR. Relative express...
Signature miRNA expression is not significantly altered in CLL cells before and after CD19 positive selection. Total RNA extracted from PBMC or purified CD19+CLL cells from three CLL patient samples with high white blood cell counts (>50×103/mL blood) (CLL) were analyzed by miRNA-specific RT-PCR. The relative expression of miR-26a, miR-29a, miR-29b...
Inhibition of miR-155 expression by MEK and JNK inhibitors. A. Relative expression of miR-155 in CLL cells treated with MEK (PD98059; PD) and JNK (SP600125; SP) inhibitors. B. Relative expression of miR-155 in CpG-activated B cell treated with PD98059 and SP600125 inhibitors. Cells were cultured with DMSO as a control (DMSO).
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Purity of CLL sample after CD19 positive selection. FACS analysis was performed on PBMCs (PBMC) and purified CLL cells (CLL) using anti-human CD19 and anti-human CD5 antibodies. The purity of the CLL cells was shown as the percentage number on the CD5+CD19+population.
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miRNA expression distinguishes unstimulated B cells from activated B cells. A. anti-IgM was used to activate B cells for 24 or 48 hrs and miRNA-specific RT-PCRs was performed on control B cells before and after activation. B. The same analysis as in (A) by CD40L for 24 hr or 48 hrs. Co-culturing with the 3T3 feeder cells as the control. C. The same...
miRNAs tested in FlexmiR v2 expression profiling.
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Cell surface marker expression is compared among unactivated donor B cells, anti-IgM-activated donor B cells, and CLL cells. FACS analysis was performed using FITC-labeled different surface marker antibodies. 16 different CLL samples (L#), 5 donor control B cell samples (CB) and 3 activated B cell samples by anti-IgM F(ab')2 are shown.
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miRNAs correlated with ZAP70 and IgVH status. Wilcoxon rank sum tests were used for whether there were any differences on miRNA expression pattern between patients with different clinical features such as (S4A) ZAP70 status, and (S4B) IgVH status. p-value and q-value for each miRNA are shown. N: patient number.
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CLL-specific miRNA signatures identified by different groups.
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Summary of clinical parameters of CLL patients samples used in these studies.
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Chronic lymphocytic leukemia (CLL) is thought to be a disease of resting lymphocytes. However, recent data suggest that CLL cells may more closely resemble activated B cells. Using microRNA (miRNA) expression profiling of highly-enriched CLL cells from 38 patients and 9 untransformed B cells from normal donors before acute CpG activation and 5 matc...
When it escapes early detection, malignant melanoma becomes a highly lethal and treatment-refractory cancer. Melastatin is greatly downregulated in metastatic melanomas and is widely believed to function as a melanoma tumor suppressor. Here we report that tumor suppressive activity is not mediated by melastatin but instead by a microRNA (miR-211) h...
Argonaute (AGO) proteins bind to small RNAs and mediate small RNA-induced silencing in eukaryotes. Using a minimal in vitro system, we show that bacterially expressed human AGO1 and AGO2 but not AGO3 and AGO4 possess strand-dissociating activity of microRNA (miRNA) duplexes. Both AGO1 and AGO2 function as RNA chaperones, capable of performing multi...
MicroRNAs (miRNAs) are abundant ∼22 nucleotide-long endogenous RNAs that have profound impact on eukaryotic biology by mechanisms that are incompletely understood. miRNAs guide protein complexes (miRNPs) to partially complementary target mRNAs and downregulate their expression by at least two mechanisms: repression of mRNA translation and accelerat...
Epstein-Barr Virus (EBV) establishes a long-term latent infection and is associated with a number of human malignancies that are thought to arise from deregulation of different stages of the viral life cycle. Recently, a large number of microRNAs (miRNAs) have been described for EBV, and it has been suggested that their expression may vary between...
