Papers by Praveen Baskaran
Journal of Cell Biology
Progressive accrual of senescent cells in aging and chronic diseases is associated with detriment... more Progressive accrual of senescent cells in aging and chronic diseases is associated with detrimental effects in tissue homeostasis. We found that senescent fibroblasts and epithelia were not only refractory to macrophage-mediated engulfment and removal, but they also paralyzed the ability of macrophages to remove bystander apoptotic corpses. Senescent cell-mediated efferocytosis suppression (SCES) was independent of the senescence-associated secretory phenotype (SASP) but instead required direct contact between macrophages and senescent cells. SCES involved augmented senescent cell expression of CD47 coinciding with increased CD47-modifying enzymes QPCT/L. SCES was reversible by interfering with the SIRPα-CD47-SHP-1 axis or QPCT/L activity. While CD47 expression increased in human and mouse senescent cells in vitro and in vivo, another ITIM-containing protein, CD24, contributed to SCES specifically in human epithelial senescent cells where it compensated for genetic deficiency in CD4...
American Journal of Respiratory Cell and Molecular Biology
Cytotoxic CD8+ T lymphocytes (CTLs) are key players of adaptive anti-tumor immunity based on thei... more Cytotoxic CD8+ T lymphocytes (CTLs) are key players of adaptive anti-tumor immunity based on their ability to specifically recognize and destroy tumor cells. Many cancer immunotherapies rely on unleashing CTL function. However, tumors can evade killing through strategies which are not yet fully elucidated. To provide deeper insight into tumor evasion mechanisms in an antigen-dependent manner, we established a human co-culture system composed of tumor and primary immune cells. Using this system, we systematically investigated intrinsic regulators of tumor resistance by conducting a complementary CRISPR screen approach. By harnessing CRISPR activation (CRISPRa) and CRISPR knockout (KO) technology in parallel, we investigated gene gain-of-function as well as loss-of-function across genes with annotated function. CRISPRa and CRISPR KO screens uncovered 186 and 704 hits respectively, with 60 gene hits overlapping between both. These data confirmed the role of interferon-γ (IFN-γ), tumor ...
Supplemental figures, tables, and data. PDF file with supplemental figures, tables, and data. (PD... more Supplemental figures, tables, and data. PDF file with supplemental figures, tables, and data. (PDF 800 kb)
Table with expression fold changes and p-values. Excel file with all expression FPKM values for a... more Table with expression fold changes and p-values. Excel file with all expression FPKM values for all genes, fold changes and FDR corrected p-values for all genes that were found to be significantly differentially expressed in at least one comparison. The file also includes the assignments of genes to expression biclusters. (XLS 19558 kb)
The CRISPR Journal, 2021
Mutations in the human b-globin gene are the cause of b-hemoglobinopathies, one of the most commo... more Mutations in the human b-globin gene are the cause of b-hemoglobinopathies, one of the most common inherited single-gene blood disorders in the world. Novel therapeutic approaches are based on lentiviral vectors (LVs) or CRISPR-Cas9-mediated gene disruption to express adult hemoglobin (HbA), or to reactivate the completely functional fetal hemoglobin, respectively. Nonetheless, LVs present a risk of insertional mutagenesis, while gene-disrupting transcription factors (BCL11A, KLF1) involved in the fetal-to-adult hemoglobin switch might generate dysregulation of other cellular processes. Therefore, universal gene addition/correction approaches combining CRISPR-Cas9 and homology directed repair (HDR) by delivering a DNA repair template through adeno-associated virus could mitigate the limitations of both lentiviral gene transfer and gene disruption strategies, ensuring targeted integration and controlled transgene expression. In this study, we attained high rates of gene addition (up to 12%) and gene correction (up to 38%) in hematopoietic stem and progenitor cells from healthy donors without any cell sorting/enrichment or the application of HDR enhancers. Furthermore, these approaches were tested in heterozygous (b 0 /b +) and homozygous (b 0 /b 0 , b + /b +) b-thalassemia patients, achieving a significant increase in HbA and demonstrating the universal therapeutic potential of this study for the treatment of b-hemoglobinopathies.
Additional file 3: Table S3. High impact Namchi breed specific SNP. Table S4. High impact Kapsiki... more Additional file 3: Table S3. High impact Namchi breed specific SNP. Table S4. High impact Kapsiki breed specific SNP. Table S5. High impact Red Fulani breed specific SNP. Table S6. High impact White Fulani breed specific SNP. Table S7. High impact Gudali breed specific SNP. Table S8. High impact Brahman breed specific SNP. Table S9. High impact Holstein breed specific SNP. Table S10. High impact N'Dama breed specific SNP.
Additional file 2: Figure S2. Distribution of SNPs, InDels and breed-specific SNPs per chromosome... more Additional file 2: Figure S2. Distribution of SNPs, InDels and breed-specific SNPs per chromosome and breed. Bar plot illustrates the number of SNPs found in at least two breeds (green), breed-specific SNPs (blue) and InDels (orange) across all the breeds for each chromosome.
Additional file 1: Table S1. Pairwise alignment of contigs assembled from unmapped reads to the n... more Additional file 1: Table S1. Pairwise alignment of contigs assembled from unmapped reads to the non-redundant nucleotide database.
Data S1 The complete amino acid sequences of the HBB targeting ZFNs. Table S1 TALE FLASH IDs and ... more Data S1 The complete amino acid sequences of the HBB targeting ZFNs. Table S1 TALE FLASH IDs and RVDs targeting the promoter of HBB gene. Table S2 Details of ssODNs (sequence, symmetry, and length of homology arms). Table S3 Barcode and sample details of next-generation sequencing. Table S4 Details of off-target position, primer details, and indel frequency. (PDF 601 kb)
Figure S1. Strategy for targeting the promoter and IVS1–110 mutation of the HBB gene. A) The prom... more Figure S1. Strategy for targeting the promoter and IVS1–110 mutation of the HBB gene. A) The promoter region of HBB gene targeted with three different gene-editing tools, HBBIVS1–110 targeted with CRISPR/Cas9. B) The design of three different gene-editing tools at sequence level. Figure S2 Comparison of three different gene-editing tools at HBB promoter. The complete raw data of Fig. 1a. Figure S3 Gene correction of HBBIVS1–110 in CD34+ HSCs using pX330.sg HBBIVS1–110 and ssODNs. A) CD34+ HSCs nucleofected with pX330.sg HBBIVS1–110 plasmid and ssODNs and measured for indel rate by T7 assay and HDR by TIDE analysis. Only 5TS resulted 3% HDR rate in TIDE analysis (as in Fig. 2a). B) Gene-editing capacity of pDNA-encoded Cas9 and mRNA-encoded Cas9 were compared, and superiority of Cas9 mRNA was observed (P
Insects and nematodes represent the most species-rich animal taxa and they occur together in a va... more Insects and nematodes represent the most species-rich animal taxa and they occur together in a variety of associations. Necromenic nematodes of the genus Pristionchus are found on scarab beetles with more than 30 species known from worldwide samplings. However, little is known about the dynamics and succession of nematodes and bacteria during the decomposition of beetle carcasses. Here, we study nematode and bacterial succession of the decomposing rhinoceros beetle Oryctes borbonicus on La Réunion Island. We show that Pristionchus pacificus exits the arrested dauer stage seven days after the beetles´ deaths. Surprisingly, new dauers are seen after 11 days, suggesting that some worms return to the dauer stage after one reproductive cycle. We used high-throughput sequencing of the 16S rRNA genes of decaying beetles, beetle guts and nematodes to study bacterial communities in comparison to soil. We find that soil environments have the most diverse bacterial communities. The bacterial community of living and decaying beetles are more stable but one single bacterial family dominates the microbiome of decaying beetles. In contrast, the microbiome of nematodes is relatively similar even across different families. This study represents the first characterization of the dynamics of nematode-bacterial interactions during the decomposition of insects
Gene duplication is a major mechanism that plays a vital role in different evolutionary innovatio... more Gene duplication is a major mechanism that plays a vital role in different evolutionary innovations, ranging from generating novel traits to phenotypic plasticity. Evolutionary impact of gene duplication and the fate of duplicated genes has been studied in detail. However, little is known about the impact of gene duplication on gene expression with respect to different evolutionary time scales. Here, we study genome-wide patterns of gene duplications in nematodes and assess their effect on expression levels. This study encompasses various macroevolutionary comparisons at different time scales and microevolutionary comparisons within the species Pristionchus pacificus. At the macroevolutionary level, by comparing species separated more than 280 million years ago, we found various lineage-specific expansions in multiple gene families along the Pristionchus lineage. Moreover, we found that duplicated genes are highly enriched among developmentally regulated genes. Interestingly, the re...
Haematologica, 2020
In situ follicular neoplasia (ISFN) is the earliest morphologically identifiable precursor of fol... more In situ follicular neoplasia (ISFN) is the earliest morphologically identifiable precursor of follicular lymphoma (FL). Although it is genetically less complex than FL and has low risk for progression, ISFN already harbors secondary genetic alterations, in addition to the defining t(14;18)(q32;q21) translocation. FL, in turn, frequently progresses to diffuse large B-cell lymphoma (DLBCL) or high-grade B-cell lymphoma (HGBL). By BCL2 staining of available reactive lymphoid tissue obtained at any time point in patients with aggressive B-cell lymphoma (BCL), we identified ten paired cases of ISFN and DLBCL/HGBL, including six de novo tumors and four tumors transformed from FL as an intermediate step, and investigated their clonal evolution using microdissection and next-generation sequencing. A clonal relationship between ISFN and aggressive BCL was established by immunoglobulin and/or BCL2 rearrangements and/or the demonstration of shared somatic mutations for all ten cases. Targeted ...
Scientific Reports, 2020
β-hemoglobinopathies are caused by abnormal or absent production of hemoglobin in the blood due t... more β-hemoglobinopathies are caused by abnormal or absent production of hemoglobin in the blood due to mutations in the β-globin gene (HBB). Imbalanced expression of adult hemoglobin (HbA) induces strong anemia in patients suffering from the disease. However, individuals with natural-occurring mutations in the HBB cluster or related genes, compensate this disparity through γ-globin expression and subsequent fetal hemoglobin (HbF) production. Several preclinical and clinical studies have been performed in order to induce HbF by knocking-down genes involved in HbF repression (KLF1 and BCL11A) or disrupting the binding sites of several transcription factors in the γ-globin gene (HBG1/2). In this study, we thoroughly compared the different CRISPR/Cas9 gene-disruption strategies by gene editing analysis and assessed their safety profile by RNA-seq and GUIDE-seq. All approaches reached therapeutic levels of HbF after gene editing and showed similar gene expression to the control sample, while...
BackgroundWest African indigenous taurine cattle display unique adaptive traits shaped by husband... more BackgroundWest African indigenous taurine cattle display unique adaptive traits shaped by husbandry management, regional climate and exposure to endemic pathogens. They are less productive with respect to milk and meat production which has been associated with a number of factors, amongst others small size, traditional beliefs and husbandry practices. This resulted in the severe dwindling of their populations size rendering them vulnerable to extinction. The Namchi (Doayo) taurine cattle breed has documented resistance traits against trypanosome infection and exposure to tick infestation. Nonetheless, the historically later introduced Zebu cattle are the main cattle breeds in Africa today, even though they suffer more from locally prevailing pathogens. By using a reference-based whole genome sequencing approach, we sequenced for the first time the genomes of five cattle breeds from Cameroon: the Namchi (Doayo), an endangered trypanotolerant taurine breed, the Kapsiki, an indigenous ...
Molecular and Cellular Pediatrics, 2018
Background: β-Thalassemia is an inherited hematological disorder caused by mutations in the human... more Background: β-Thalassemia is an inherited hematological disorder caused by mutations in the human hemoglobin beta (HBB) gene that reduce or abrogate β-globin expression. Although lentiviral-mediated expression of β-globin and autologous transplantation is a promising therapeutic approach, the risk of insertional mutagenesis or low transgene expression is apparent. However, targeted gene correction of HBB mutations with programmable nucleases such as CRISPR/Cas9, TALENs, and ZFNs with non-viral repair templates ensures a higher safety profile and endogenous expression control. Methods: We have compared three different gene-editing tools (CRISPR/Cas9, TALENs, and ZFNs) for their targeting efficiency of the HBB gene locus. As a proof of concept, we studied the personalized gene-correction therapy for a common β-thalassemia splicing variant HBB IVS1-110 using Cas9 mRNA and several optimally designed singlestranded oligonucleotide (ssODN) donors in K562 and CD34 + hematopoietic stem cells (HSCs). Results: Our results exhibited that indel frequency of CRISPR/Cas9 was superior to TALENs and ZFNs (P < 0.0001). Our designed sgRNA targeting the site of HBB IVS1-110 mutation showed indels in both K562 cells (up to 77%) and CD34 + hematopoietic stem cells-HSCs (up to 87%). The absolute quantification by next-generation sequencing showed that up to 8% site-specific insertion of the NheI tag was achieved using Cas9 mRNA and a chemically modified ssODN in CD34 + HSCs. Conclusion: Our approach provides guidance on non-viral gene correction in CD34 + HSCs using Cas9 mRNA and chemically modified ssODN. However, further optimization is needed to increase the homology directed repair (HDR) to attain a real clinical benefit for β-thalassemia.
Neuro-Oncology, 2018
NEURO-ONCOLOGY • NOVEMBER 2018 tosis (NF) type II. MRI obtained 4 weeks after initial resection r... more NEURO-ONCOLOGY • NOVEMBER 2018 tosis (NF) type II. MRI obtained 4 weeks after initial resection revealed local progression. Gross total resection(GTR) of residual tumor was performed. In view of rapid progression, chemotherapy was initiated 12 weeks from diagnosis, as per Dana Farber Protocol 02-294 for ATRT (Atypical Teratoid Rhabdoid Tumor). Therapy related complications included-febrile neutropenia, Candida rugosa fungemia, loss of vision in right eye and right ear sensorineural hearing loss. The patient continues to be in remission 1 year after completion of his therapy. There are no established guidelines for the management of pediatric rhabdoid meningiomas. Multiagent chemotherapy as per DFCI ATRT 02-294 along with GTR should be considered as a potential treatment option for papillary rhabdoid meningioma. Radiation therapy should be excluded in younger patients due to risk of neuro-cognitive sequelae. Patients with meningioma associated with NF II need to have lifelong follow up.
Development (Cambridge, England), Jul 2, 2018
Sulfation of biomolecules, like phosphorylation, is one of the most fundamental and ubiquitous bi... more Sulfation of biomolecules, like phosphorylation, is one of the most fundamental and ubiquitous biochemical modifications with important functions during detoxification. This process is reversible, involving two enzyme classes: a sulfotransferase, which adds a sulfo group to a substrate; and a sulfatase that removes the sulfo group. However, unlike phosphorylation, the role of sulfation in organismal development is poorly understood. In this study, we find that two independent sulfation events regulate the development of mouth morphology in the nematode This nematode has the ability to form two alternative mouth morphologies depending on environmental cues, an example of phenotypic plasticity. We found that, in addition to a previously described sulfatase, a sulfotransferase is involved in regulating the mouth-form dimorphism in However, it is unlikely that both of these sulfation-associated enzymes act upon the same substrates, as they are expressed in different cell types. Furtherm...
PLOS ONE, 2017
Cystic Fibrosis (CF) is the most common monogenic disease among people of Western European descen... more Cystic Fibrosis (CF) is the most common monogenic disease among people of Western European descent and caused by mutations in the CFTR gene. However, the disease severity is immensely variable even among patients with similar CFTR mutations due to the possible effect of 'modifier genes'. To identify genetic modifiers, we applied RNA-seq based transcriptomic analyses in CF patients with a mild and severe lung phenotype. Global gene expression and enrichment analyses revealed that genes of the type I interferon response and ribosomal stalk proteins are potential modifiers of CF related lung dysfunction. The results provide a new set of CF modifier genes with possible implications as new therapeutic targets for the treatment of CF.
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Papers by Praveen Baskaran