Research
Our research focuses the dissection of mechanisms that underlie response and resistance to immunotherapies and on the longitudinal tracking of tumor cell evolution using single-cell lineage-tracing approaches based on interrogation of natural barcodes like somatic nuclear or mitochondrial DNA mutations.
Highlighted
![Integrative genotyping of cancer and immune phenotypes by long-read sequencing](https://github.com/mehdiborji/nanoranger/blob/main/nanoranger_schema.png?raw=true)
Integrative genotyping of cancer and immune phenotypes by long-read sequencing
Nature Communications
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02 Jan 2024
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doi:10.1038/s41467-023-44137-7
Targeted genotyping of scRNA-seq cDNA libraries using long-read sequencing with Oxford Nanopore
![Mechanisms of response and resistance to combined decitabine and ipilimumab for advanced myeloid disease](https://ars.els-cdn.com/content/image/1-s2.0-S0006497123002355-BLOOD_BLD-2022-018246-fx1_lrg.jpg)
Mechanisms of response and resistance to combined decitabine and ipilimumab for advanced myeloid disease
Blood
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13 Apr 2023
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doi:10.1182/blood.2022018246
Single cell RNA sequencing analysis dissecting responses to ipilimumab treatment of relapsed AML/MDS with and without stem cell transplantation.
![Longitudinal Single-Cell Dynamics of Chromatin Accessibility and Mitochondrial Mutations in Chronic Lymphocytic Leukemia Mirror Disease History](https://aacr.silverchair-cdn.com/aacr/content_public/journal/cancerdiscovery/11/12/10.1158_2159-8290.cd-11-12-iti/1/m_2945photo4.jpeg)
Longitudinal Single-Cell Dynamics of Chromatin Accessibility and Mitochondrial Mutations in Chronic Lymphocytic Leukemia Mirror Disease History
Cancer Discovery
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01 Dec 2021
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doi:10.1158/2159-8290.CD-21-0276
First demonstration that longitudinal changes of mitochondrial DNA mutations reflect therapeutic bottlenecks.
All
2024
Oncogene induced TIM-3 ligand expression dictates susceptibility to anti-TIM-3 therapy in mice
Journal of Clinical Investigation
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25 Jun 2024
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doi:10.1172/JCI177460
![Single-cell genomics-based immune and disease monitoring in blood malignancies](https://s3.amazonaws.com/production.scholastica/public/attachments/a18131cc-e507-48ab-b237-b2c703a1cbf5/large/image5.png)
Single-cell genomics-based immune and disease monitoring in blood malignancies
Clinical Hematology International
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14 Jun 2024
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doi:10.46989/001c.117961
Single-cell genomics-based immune and disease monitoring in blood malignancies
![Integrative genotyping of cancer and immune phenotypes by long-read sequencing](https://github.com/mehdiborji/nanoranger/blob/main/nanoranger_schema.png?raw=true)
Integrative genotyping of cancer and immune phenotypes by long-read sequencing
Nature Communications
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02 Jan 2024
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doi:10.1038/s41467-023-44137-7
Targeted genotyping of scRNA-seq cDNA libraries using long-read sequencing with Oxford Nanopore
2023
![Preexisting tumor-resident T cells with cytotoxic potential associate with response to neoadjuvant anti–PD-1 in head and neck cancer](https://www.science.org/cms/asset/6ebfa65f-a3b0-4247-951e-8afbee7d1a10/sciimmunol.2023.8.issue-87.largecover.jpg)
Preexisting tumor-resident T cells with cytotoxic potential associate with response to neoadjuvant anti–PD-1 in head and neck cancer
Science Immunology
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29 Sep 2023
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doi:10.1126/sciimmunol.adf4968
First demonstration that preexisting tumor-resident T cells associate with response to neoadjuvant anti-PD-1 in head and neck cancer
![Mechanisms of response and resistance to combined decitabine and ipilimumab for advanced myeloid disease](https://ars.els-cdn.com/content/image/1-s2.0-S0006497123002355-BLOOD_BLD-2022-018246-fx1_lrg.jpg)
Mechanisms of response and resistance to combined decitabine and ipilimumab for advanced myeloid disease
Blood
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13 Apr 2023
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doi:10.1182/blood.2022018246
Single cell RNA sequencing analysis dissecting responses to ipilimumab treatment of relapsed AML/MDS with and without stem cell transplantation.
![Ipilimumab plus decitabine for patients with MDS or AML in posttransplant or transplant-naïve settings](/images/publications/2023-Blood-Garcia.png)
Ipilimumab plus decitabine for patients with MDS or AML in posttransplant or transplant-naïve settings
Blood
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13 Apr 2023
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doi:10.1182/blood.2022017686
Clinical study of CTLA-4 blockade and decitabine in relapsed AML/MDS with or without stem cell transplantation.
2022
![<i>In Vivo</i>Modeling of CLL Transformation to Richter Syndrome Reveals Convergent Evolutionary Paths and Therapeutic Vulnerabilities](https://aacr.silverchair-cdn.com/aacr/content_public/journal/bloodcancerdiscov/issue/4/2/1/m_bloodcandisc_4_2_cover.png)
In VivoModeling of CLL Transformation to Richter Syndrome Reveals Convergent Evolutionary Paths and Therapeutic Vulnerabilities
Blood Cancer Discovery
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06 Dec 2022
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doi:10.1158/2643-3230.BCD-22-0082
![Mitochondrial DNA Mutations as Natural Barcodes for Lineage Tracing of Murine Tumor Models](https://aacr.silverchair-cdn.com/aacr/content_public/journal/cancerres/issue/83/5/4/m_canres_83_5_cover.png)
Mitochondrial DNA Mutations as Natural Barcodes for Lineage Tracing of Murine Tumor Models
Cancer Research
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05 Dec 2022
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doi:10.1158/0008-5472.CAN-22-0275
First demonstration of mtDNA mutation-based lineage-tracing in murine cancer models.
![Immune Phenotypes and Target Antigens of Clonally Expanded Bone Marrow T Cells in Treatment-Naïve Multiple Myeloma](https://aacr.silverchair-cdn.com/aacr/content_public/journal/cancerimmunolres/issue/10/11/2/m_canimm_10_11_cover.png)
Immune Phenotypes and Target Antigens of Clonally Expanded Bone Marrow T Cells in Treatment-Naïve Multiple Myeloma
Cancer Immunology Research
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19 Sep 2022
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doi:10.1158/2326-6066.CIR-22-0434
![AML relapse after a TIGIT race](/images/publications/2022-Blood-Penter.png)
AML relapse after a TIGIT race
Blood
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15 Sep 2022
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doi:10.1182/blood.2022017614
Comment on Gournay et al. describing post-transplant immune reconstitution dynamics.
Rapid single-cell identification of Epstein–Barr virus-specific T-cell receptors for cellular therapy
Cytotherapy
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01 Aug 2022
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doi:10.1016/j.jcyt.2022.03.005
![Improved T-cell Immunity Following Neoadjuvant Chemotherapy in Ovarian Cancer](https://aacr.silverchair-cdn.com/aacr/content_public/journal/clincancerres/issue/28/15/2/m_clincanres_28_15_cover.png)
Improved T-cell Immunity Following Neoadjuvant Chemotherapy in Ovarian Cancer
Clinical Cancer Research
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20 Apr 2022
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doi:10.1158/1078-0432.CCR-21-2834
![Natural Barcodes for Longitudinal Single Cell Tracking of Leukemic and Immune Cell Dynamics](https://www.frontiersin.org/files/Articles/788891/fimmu-12-788891-HTML/image_m/fimmu-12-788891-g001.jpg)
Natural Barcodes for Longitudinal Single Cell Tracking of Leukemic and Immune Cell Dynamics
Frontiers in Immunology
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03 Jan 2022
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doi:10.3389/fimmu.2021.788891
2021
![Longitudinal Single-Cell Dynamics of Chromatin Accessibility and Mitochondrial Mutations in Chronic Lymphocytic Leukemia Mirror Disease History](https://aacr.silverchair-cdn.com/aacr/content_public/journal/cancerdiscovery/11/12/10.1158_2159-8290.cd-11-12-iti/1/m_2945photo4.jpeg)
Longitudinal Single-Cell Dynamics of Chromatin Accessibility and Mitochondrial Mutations in Chronic Lymphocytic Leukemia Mirror Disease History
Cancer Discovery
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01 Dec 2021
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doi:10.1158/2159-8290.CD-21-0276
First demonstration that longitudinal changes of mitochondrial DNA mutations reflect therapeutic bottlenecks.
![Coevolving JAK2V617F+relapsed AML and donor T cells with PD-1 blockade after stem cell transplantation: an index case](/images/publications/2021-Blood-Advances-Penter.png)
Coevolving JAK2V617F+relapsed AML and donor T cells with PD-1 blockade after stem cell transplantation: an index case
Blood Advances
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18 Nov 2021
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doi:10.1182/bloodadvances.2021004335
Integrated analysis of exceptional response to PD-1 inhibition in relapsed sAML after allogeneic stem cell transplantation with scRNA-seq, CITE-seq, scATAC-seq and CyTOF.
![Molecular and cellular features of CTLA-4 blockade for relapsed myeloid malignancies after transplantation](/images/publications/2021-Blood-Penter.png)
Molecular and cellular features of CTLA-4 blockade for relapsed myeloid malignancies after transplantation
Blood
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16 Mar 2021
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doi:10.1182/blood.2021010867
Dissection of exceptional responses to CTLA-4 blockade in relapsed leukemia cutis after allogeneic stem cell transplantation.
2020
![Personal tumor antigens in blood malignancies: genomics-directed identification and targeting](https://dm5migu4zj3pb.cloudfront.net/manuscripts/129000/129209/medium/JCI129209.f1.jpg)
Personal tumor antigens in blood malignancies: genomics-directed identification and targeting
Journal of Clinical Investigation
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27 Jan 2020
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doi:10.1172/JCI129209
Review of targets for cellular immunotherapies in blood malignancies.
2019
![Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)](https://onlinelibrary.wiley.com/cms/asset/8f22b04f-5691-4d44-aff2-2bf43eb3a8ca/eji.v49.10.cover.jpg)
Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)
European Journal of Immunology
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01 Oct 2019
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doi:10.1002/eji.201970107
Best practices for flow cytometry.
Localization-associated immune phenotypes of clonally expanded tumor-infiltrating T cells and distribution of their target antigens in rectal cancer
OncoImmunology
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24 Mar 2019
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doi:10.1080/2162402X.2019.1586409
Phenotypes and T cell receptor sequences of tumor-infiltrating lymphocytes compared to physiologic tissue-resident T cells.
2018
![FACS single cell index sorting is highly reliable and determines immune phenotypes of clonally expanded T cells](https://onlinelibrary.wiley.com/cms/asset/ff97c041-128f-4ec7-bdbf-d64149611b0b/eji4220-gra-0001-m.png)
FACS single cell index sorting is highly reliable and determines immune phenotypes of clonally expanded T cells
European Journal of Immunology
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03 Apr 2018
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doi:10.1002/eji.201847507
Demonstration of the high accuracy of FACS index sorting using single T and B cell receptor sequencing.
2017
![Clonal Expansion and Interrelatedness of Distinct B-Lineage Compartments in Multiple Myeloma Bone Marrow](https://aacr.silverchair-cdn.com/aacr/content_public/journal/cancerimmunolres/issue/5/9/3/m_canimm_5_9_cover.png)
Clonal Expansion and Interrelatedness of Distinct B-Lineage Compartments in Multiple Myeloma Bone Marrow
Cancer Immunology Research
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31 Aug 2017
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doi:10.1158/2326-6066.cir-17-0012
Identification of myeloma clones in phenotypically healthy B cell compartment using B cell receptor sequencing.
2015
![Ruxolitinib in corticosteroid-refractory graft-versus-host disease after allogeneic stem cell transplantation: a multicenter survey](https://static-content.springer.com/cover/journal/41375/29/10.jpg)
Ruxolitinib in corticosteroid-refractory graft-versus-host disease after allogeneic stem cell transplantation: a multicenter survey
Leukemia
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31 Jul 2015
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doi:10.1038/leu.2015.212
![A rapid screening system evaluates novel inhibitors of DNA methylation and suggests F-box proteins as potential therapeutic targets for high-risk neuroblastoma](https://static-content.springer.com/cover/journal/11523/10/4.jpg)
A rapid screening system evaluates novel inhibitors of DNA methylation and suggests F-box proteins as potential therapeutic targets for high-risk neuroblastoma
Targeted Oncology
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06 Jan 2015
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doi:10.1007/s11523-014-0354-5