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JOURNAL ARTICLE
Yaqi Zhao, A Douglas Laird, Kathryn G Roberts, Rolla L Yafawi, Hagop M Kantarjian, Daniel J DeAngelo, Matthias Stelljes, Michaela Liedtke, Wendy Stock, Nicola Gökbuget, Susan M O'Brien, Elias J Jabbour, Ryan D Cassaday, Melanie R Loyd, Scott R Olsen, Geoffrey A Neale, Xueli Liu, Erik Vandendries, Anjali S Advani, Charles G Mullighan
The phase 3 INO-VATE trial demonstrated higher rates of remission, measurable residual disease negativity, and improved overall survival for patients with relapsed/refractory (R/R) acute lymphoblastic leukemia (ALL) who received inotuzumab ozogamicin (InO) vs standard of care chemotherapy (SC). Here we examined associations between genomic alterations and the efficacy of InO. Of 326 randomized patients, 91 (InO, n=43; SC, n=48) had samples evaluable for genomic analysis. The spectrum of gene fusions and other genomic alterations observed was comparable with prior studies of adult ALL...
March 26, 2024: Blood Advances
#2
JOURNAL ARTICLE
Xin Huang, Yizhen Li, Jingliao Zhang, Lei Yan, Huanbin Zhao, Liang Ding, Sheetal Bhatara, Xu Yang, Satoshi Yoshimura, Wenjian Yang, Seth E Karol, Hiroto Inaba, Charles Mullighan, Mark Litzow, Xiaofan Zhu, Yingchi Zhang, Wendy Stock, Nitin Jain, Elias Jabbour, Steven M Kornblau, Marina Konopleva, Ching-Hon Pui, Elisabeth Paietta, William Evans, Jiyang Yu, Jun J Yang
Leukemia can arise at various stages of the hematopoietic differentiation hierarchy, but the impact of developmental arrest on drug sensitivity is unclear. Applying network-based analyses to single-cell transcriptomes of human B cells, we define genome-wide signaling circuitry for each B cell differentiation stage. Using this reference, we comprehensively map the developmental states of B cell acute lymphoblastic leukemia (B-ALL), revealing its strong correlation with sensitivity to asparaginase, a commonly used chemotherapeutic agent...
April 8, 2024: Cancer Cell
#3
Vasiliki Leventaki, Timothy Shaw, Stanley Pounds, Xueyuan Cao, Jing Ma, Gustavo Palacios, John Mason, Sherrie Perkins, Gang Wu, Yiping Fan, Jian Wang, Xin Zhou, Alyssa Obermayer, Marsha Kinney, Jacqueline Kraveka, Thomas Gross, John Sandlund, Jinghui Zhang, Charles Mullighan, Megan Lim
Anaplastic large cell lymphoma (ALCL) is a mature T-cell lymphoma that accounts for for 10-15% of childhood lymphomas. Despite the observation that more than 90% of pediatric cases harbor the anaplastic lymphoma kinase (ALK) rearrangement resulting in aberrant ALK kinase expression, there is significant clinical, morphologic, and biological heterogeneity. To gain insights into the genomic aberrations and molecular heterogeneity within ALK-positive ALCL(ALK+ ALCL), we analyzed 46 pediatric ALK+ ALCLs by whole-exome sequencing, RNA-sequencing, and DNA methylation profiling...
March 28, 2024: Research Square
#4
JOURNAL ARTICLE
Yaqi Zhao, Nicholas J Short, Hagop M Kantarjian, Ti-Cheng Chang, Pankaj S Ghate, Chunxu Qu, Walid Macaron, Nitin Jain, Beenu Thakral, Aaron Phillips, Joseph D Khoury, Guillermo Garcia-Manero, Wenchao Zhang, Yiping Fan, Hui Yang, Rebecca Garris, Lewis Fady Nasr, Richard Kriwacki, Kathryn G Roberts, Marina Y Konopleva, Elias J Jabbour, Charles G Mullighan
Inotuzumab ozogamicin (InO) is an antibody-drug conjugate that delivers calicheamicin to CD22-expressing cells. In a retrospective cohort of InO-treated patients with B-cell acute lymphoblastic leukemia, we sought to understand the genomic determinants of response and resistance to InO. Pre- and post-InO patient samples were analyzed by whole genome, exome, and/or transcriptome sequencing. Acquired CD22 mutations were observed in 11% (3/27) of post-InO relapsed tumor samples, but not in refractory samples (0/16)...
March 29, 2024: Blood
#5
JOURNAL ARTICLE
Klara Klein, Sebastian Kollmann, Angela Hiesinger, Julia List, Jonatan Kendler, Thorsten Klampfl, Mehak Randhawa, Jana Trifinopoulos, Barbara Maurer, Reinhard Grausenburger, Christof A Bertram, Richard H Moriggl, Thomas Rülicke, Charles G Mullighan, Agnieszka Witalisz-Siepracka, Wencke Walter, Gregor Hoermann, Veronika Sexl, Dagmar Gotthardt
Patients with T- and NK-cell neoplasms frequently have somatic STAT5B gain-of-function mutations. The most frequent STAT5B mutation is STAT5BN642H, which is known to drive murine T-cell leukemia although its role in NK-cell malignancies is unclear. Introduction of the STAT5BN642H mutation into human NK-cell lines enhances their potential to induce leukemia in mice. We have generated a mouse model that enables tissue-specific expression of STAT5BN642H and have selectively expressed the mutated STAT5B in hematopoietic cells (N642Hvav/+) or exclusively in NK cells (N642HNK/NK)...
March 18, 2024: Blood
#6
Andy G X Zeng, Ilaria Iacobucci, Sayyam Shah, Amanda Mitchell, Gordon Wong, Suraj Bansal, Qingsong Gao, Hyerin Kim, James A Kennedy, Mark D Minden, Torsten Haferlach, Charles G Mullighan, John E Dick
Initial classification of acute leukemia involves the assignment of blasts to cell states within the hematopoietic hierarchy based on morphological and immunophenotypic features. Yet, these traditional classification approaches lack precision, especially at the level of immature blasts. Single-cell RNA-sequencing (scRNA-seq) enables precise determination of cell state using thousands of markers, thus providing an opportunity to re-examine present-day classification schemes of acute leukemia. Here, we developed a detailed reference map of human bone marrow hematopoiesis from 263,519 single-cell transcriptomes spanning 55 cellular states...
December 27, 2023: bioRxiv
#7
JOURNAL ARTICLE
Gisele Nishiguchi, Lauren G Mascibroda, Sarah M Young, Elizabeth A Caine, Sherif Abdelhamed, Jeffrey J Kooijman, Darcie J Miller, Sourav Das, Kevin McGowan, Anand Mayasundari, Zhe Shi, Juan M Barajas, Ryan Hiltenbrand, Anup Aggarwal, Yunchao Chang, Vibhor Mishra, Shilpa Narina, Melvin Thomas, Allister J Loughran, Ravi Kalathur, Kaiwen Yu, Suiping Zhou, Xusheng Wang, Anthony A High, Junmin Peng, Shondra M Pruett-Miller, Danette L Daniels, Marjeta Urh, Anang A Shelat, Charles G Mullighan, Kristin M Riching, Guido J R Zaman, Marcus Fischer, Jeffery M Klco, Zoran Rankovic
Molecular-glue degraders are small molecules that induce a specific interaction between an E3 ligase and a target protein, resulting in the target proteolysis. The discovery of molecular glue degraders currently relies mostly on screening approaches. Here, we describe screening of a library of cereblon (CRBN) ligands against a panel of patient-derived cancer cell lines, leading to the discovery of SJ7095, a potent degrader of CK1α, IKZF1 and IKZF3 proteins. Through a structure-informed exploration of structure activity relationship (SAR) around this small molecule we develop SJ3149, a selective and potent degrader of CK1α protein in vitro and in vivo...
January 16, 2024: Nature Communications
#8
JOURNAL ARTICLE
Oscar Molina, Carmen Ortega-Sabater, Namitha Thampi, Narcís Fernández-Fuentes, Mercedes Guerrero-Murillo, Alba Martínez-Moreno, Meritxell Vinyoles, Talía Velasco-Hernández, Clara Bueno, Juan L Trincado, Isabel Granada, Diana Campos, Carles Giménez, Judith M Boer, Monique L den Boer, Gabriel F Calvo, Mireia Camós, Jose-Luis Fuster, Pablo Velasco, Paola Ballerini, Franco Locatelli, Charles G Mullighan, Diana C J Spierings, Floris Foijer, Víctor M Pérez-García, Pablo Menéndez
Chromosomal instability (CIN) lies at the core of cancer development leading to aneuploidy, chromosomal copy-number heterogeneity (chr-CNH) and ultimately, unfavorable clinical outcomes. Despite its ubiquity in cancer, the presence of CIN in childhood B-cell acute lymphoblastic leukemia (cB-ALL), the most frequent pediatric cancer showing high frequencies of aneuploidy, remains unknown. Here, we elucidate the presence of CIN in aneuploid cB-ALL subtypes using single-cell whole-genome sequencing of primary cB-ALL samples and by generating and functionally characterizing patient-derived xenograft models (cB-ALL-PDX)...
December 15, 2023: EMBO Molecular Medicine
#9
JOURNAL ARTICLE
Kelly R Barnett, Robert J Mobley, Jonathan D Diedrich, Brennan P Bergeron, Kashi Raj Bhattarai, Alexander C Monovich, Shilpa Narina, Wenjian Yang, Kristine R Crews, Christopher S Manring, Elias Jabbour, Elisabeth Paietta, Mark R Litzow, Steven M Kornblau, Wendy Stock, Hiroto Inaba, Sima Jeha, Ching-Hon Pui, Charles G Mullighan, Mary V Relling, Shondra M Pruett-Miller, Russell J H Ryan, Jun J Yang, William E Evans, Daniel Savic
B cell lineage acute lymphoblastic leukemia (B-ALL) is composed of diverse molecular subtypes, and while transcriptional and DNA methylation profiling has been extensively examined, the chromatin landscape is not well characterized for many subtypes. We therefore mapped chromatin accessibility using ATAC-seq in primary B-ALL cells from 156 patients spanning ten molecular subtypes and present this dataset as a resource. Differential chromatin accessibility and transcription factor (TF) footprint profiling were employed and identified B-ALL cell of origin, TF-target gene interactions enriched in B-ALL, and key TFs associated with accessible chromatin sites preferentially active in B-ALL...
December 13, 2023: Cell Genom
#10
Yaqi Zhao, Nicholas J Short, Hagop M Kantarjian, Ti-Cheng Chang, Pankaj S Ghate, Chunxu Qu, Walid Macaron, Nitin Jain, Beenu Thakral, Aaron H Phillips, Joseph Khoury, Guillermo Garcia-Manero, Wenchao Zhang, Yiping Fan, Hui Yang, Rebecca S Garris, Lewis F Nasr, Richard W Kriwacki, Kathryn G Roberts, Marina Konopleva, Elias J Jabbour, Charles G Mullighan
UNLABELLED: Inotuzumab ozogamicin (InO) is an antibody-drug conjugate that delivers calicheamicin to CD22-expressing cells. In a retrospective cohort of InO treated patients with B-cell acute lymphoblastic leukemia, we sought to understand the genomic determinants of response to InO. Acquired CD22 mutations were observed in 11% (3/27) of post-InO relapsed tumor samples. There were multiple CD22 mutations per sample and the mechanisms of CD22 escape included protein truncation, protein destabilization, and epitope alteration...
December 9, 2023: medRxiv
#11
Ilaria Iacobucci, Andy G X Zeng, Qingsong Gao, Laura Garcia-Prat, Pradyumna Baviskar, Sayyam Shah, Alex Murison, Veronique Voisin, Michelle Chan-Seng-Yue, Cheng Cheng, Chunxu Qu, Colin Bailey, Matthew Lear, Matthew T Witkowski, Xin Zhou, Airen Zaldivar Peraza, Karishma Gangwani, Anjali S Advani, Selina M Luger, Mark R Litzow, Jacob M Rowe, Elisabeth M Paietta, Wendy Stock, John E Dick, Charles G Mullighan
Sequencing of bulk tumor populations has improved genetic classification and risk assessment of B-ALL, but does not directly examine intratumor heterogeneity or infer leukemia cellular origins. We profiled 89 B-ALL samples by single-cell RNA-seq (scRNA-seq) and compared them to a reference map of normal human B-cell development established using both functional and molecular assays. Intra-sample heterogeneity was driven by cell cycle, metabolism, differentiation, and inflammation transcriptional programs. By inference of B lineage developmental state composition, nearly all samples possessed a high abundance of pro-B cells, with variation between samples mainly driven by sub-populations...
December 9, 2023: bioRxiv
#12
JOURNAL ARTICLE
Bruno A Cardoso, Mafalda Duque, Ana Gírio, Rita Fragoso, Mariana L Oliveira, James R Allen, Leila R Martins, Nádia C Correia, André Bortolini Silveira, Alexandra Veloso, Shunsuke Kimura, Lisa Demoen, Filip Matthijssens, Sima Jeha, Cheng Cheng, Ching-Hon Pui, Ana R Grosso, João L Neto, Sérgio F De Almeida, Pieter Van Vlieberghe, Charles G Mullighan, J Andres Yunes, David M Langenau, Françoise Pflumio, João T Barata
CASZ1 is a conserved transcription factor involved in neural development, blood vessel assembly and heart morphogenesis. CASZ1 has been implicated in cancer, either suppressing or promoting tumor development depending on the tissue. However, the impact of CASZ1 on hematological tumors remains unknown. Here, we show that the T-cell oncogenic transcription factor TAL1 is a direct positive regulator of CASZ1, that T-cell acute lymphoblastic leukemia (T-ALL) samples at diagnosis overexpress CASZ1b isoform, and that CASZ1b expression in patient samples correlates with PI3KAKT- mTOR signaling pathway activation...
December 7, 2023: Haematologica
#13
Shunsuke Kimura, Petri Polonen, Lindsey Montefiori, Chun Shik Park, Ilaria Iacobucci, Allen Ej Yeoh, Andishe Attarbaschi, Andrew S Moore, Anthony Brown, Atsushi Manabe, Barbara Buldini, Burgess B Freeman, Chelsey Chen, Cheng Cheng, Chiew Kean Hui, Chi-Kong Li, Ching-Hon Pui, Chunxu Qu, Daisuke Tomizawa, David T Teachey, Elena Varotto, Elisabeth M Paietta, Elizabeth D Arnold, Franco Locatelli, Gabriele Escherich, Hannah Elisa Muhle, Hanne Vibeke Marquart, Hester A de Groot-Kruseman, Jacob M Rowe, Jan Stary, Jan Trka, John Kim Choi, Jules P P Meijerink, Jun J Yang, Junko Takita, Katarzyna Pawinska-Wasikowska, Kathryn G Roberts, Katie Han, Kenneth J Caldwell, Kjeld Schmiegelow, Kristine R Crews, Mariko Eguchi, Martin Schrappe, Martin Zimmerman, Masatoshi Takagi, Mellissa Maybury, Michael Svaton, Michaela Reiterova, Michal Kicinski, Mollie S Prater, Motohiro Kato, Noemi Reyes, Orietta Spinelli, Paul Thomas, Pauline Mazilier, Qingsong Gao, Riccardo Masetti, Rishi S Kotecha, Rob Pieters, Sarah Elitzur, Selina M Luger, Sharnise Mitchell, Shondra M Pruett-Miller, Shuhong Shen, Sima Jeha, Stefan Köhrer, Steven M Kornblau, Szymon Skoczeń, Takako Miyamura, Tiffaney L Vincent, Toshihiko Imamura, Valentino Conter, Yanjing Tang, Yen-Chun Liu, Yunchao Chang, Zhaohui Gu, Zhongshan Cheng, Zhou Yinmei, Hiroto Inaba, Charles G Mullighan
PURPOSE: Gamma delta T-cell receptor-positive acute lymphoblastic leukemia (γδ T-ALL) is a high-risk but poorly characterized disease. METHODS: We studied clinical features of 200 pediatric γδ T-ALL, and compared the prognosis of 93 cases to 1,067 protocol-matched non-γδ T-ALL. Genomic features were defined by transcriptome and genome sequencing. Experimental modeling was used to examine the mechanistic impacts of genomic alterations...
November 8, 2023: medRxiv
#14
Kai Tan, Jason Xu, Changya Chen, Tiffaney Vincent, Petri Pölönen, Jianzhong Hu, Satoshi Yoshimura, Wenbao Yu, Jonathan Sussman, Chia-Hui Chen, Elizabeth Li, Caroline Diorio, Rawan Shraim, Haley Newman, Lahari Uppuluri, Alexander Li, Gregory Chen, Shovik Bandyopadhyay, David Wu, Yang-Yang Ding, Jessica Xu, Tristan Lim, Miles Hsu, Anusha Thadi, Kyung Jin Ahn, Chi-Yun Wu, Jacqueline Peng, Yusha Sun, Alice Wang, Rushabh Mehta, David Frank, Lauren Meyer, Mignon Loh, Elizabeth Raetz, Zhiguo Chen, Brent Wood, Meenakshi Devidas, Kimberly Dunsmore, Stuart Winter, Ti-Cheng Chang, Gang Wu, Stanley Pounds, Nancy Zhang, William Carroll, Stephen Hunger, Kathrin Bernt, Jun Yang, Charles Mullighan, David Teachey
Refractoriness to initial chemotherapy and relapse after remission are the main obstacles to cure in T-cell Acute Lymphoblastic Leukemia (T-ALL). Biomarker guided risk stratification and targeted therapy have the potential to improve outcomes in high-risk T-ALL; however, cellular and genetic factors contributing to treatment resistance remain unknown. Previous bulk genomic studies in T-ALL have implicated tumor heterogeneity as an unexplored mechanism for treatment failure. To link tumor subpopulations with clinical outcome, we created an atlas of healthy pediatric hematopoiesis and applied single-cell multiomic (CITE-seq/snATAC-seq) analysis to a cohort of 40 cases of T-ALL treated on the Children's Oncology Group AALL0434 clinical trial...
October 30, 2023: Research Square
#15
JOURNAL ARTICLE
Karen R Rabin, Meenakshi Devidas, Zhiguo Chen, Lingyun Ji, John Kairalla, Johann K Hitzler, Jun J Yang, Andrew J Carroll, Nyla A Heerema, Michael J Borowitz, Brent L Wood, Kathryn G Roberts, Charles G Mullighan, Richard C Harvey, I-Ming Chen, Cheryl L Willman, Shalini C Reshmi, Julie M Gastier-Foster, Deepa Bhojwani, Susan R Rheingold, Kelly W Maloney, Leonard A Mattano, Eric C Larsen, Reuven J Schore, Michael J Burke, Wanda L Salzer, Naomi J Winick, William L Carroll, Elizabeth A Raetz, Mignon L Loh, Stephen P Hunger, Anne L Angiolillo
PURPOSE: Patients with Down syndrome (DS) and B-ALL experience increased rates of relapse, toxicity, and death. We report results for patients with DS B-ALL enrolled on Children's Oncology Group trials between 2003 and 2019. METHODS: We analyzed data for DS (n = 743) and non-DS (n = 20,067) patients age 1-30 years on four B-ALL standard-risk (SR) and high-risk trials. RESULTS: Patients with DS exhibited more frequent minimal residual disease (MRD) ≥0...
January 10, 2024: Journal of Clinical Oncology
#16
REVIEW
Rob Pieters, Charles G Mullighan, Stephen P Hunger
Systemic combination chemotherapy and intrathecal chemotherapy markedly increased the survival rate of children with ALL. In the past two decades, the use of minimal (measurable) residual disease (MRD) measurements early in therapy improved risk group stratification with subsequent treatment intensifications for patients at high risk of relapse, and enabled a reduction of treatment for low-risk patients. The recent development of more sensitive MRD technologies may further affect risk stratification. Molecular genetic profiling has led to the discovery of many new subtypes and their driver genetic alterations...
December 20, 2023: Journal of Clinical Oncology
#17
JOURNAL ARTICLE
Swarnendu Tripathi, Hazheen K Shirnekhi, Scott D Gorman, Bappaditya Chandra, David W Baggett, Cheon-Gil Park, Ramiz Somjee, Benjamin Lang, Seyed Mohammad Hadi Hosseini, Brittany J Pioso, Yongsheng Li, Ilaria Iacobucci, Qingsong Gao, Michael N Edmonson, Stephen V Rice, Xin Zhou, John Bollinger, Diana M Mitrea, Michael R White, Daniel J McGrail, Daniel F Jarosz, S Stephen Yi, M Madan Babu, Charles G Mullighan, Jinghui Zhang, Nidhi Sahni, Richard W Kriwacki
Fusion oncoproteins (FOs) arise from chromosomal translocations in ~17% of cancers and are often oncogenic drivers. Although some FOs can promote oncogenesis by undergoing liquid-liquid phase separation (LLPS) to form aberrant biomolecular condensates, the generality of this phenomenon is unknown. We explored this question by testing 166 FOs in HeLa cells and found that 58% formed condensates. The condensate-forming FOs displayed physicochemical features distinct from those of condensate-negative FOs and segregated into distinct feature-based groups that aligned with their sub-cellular localization and biological function...
September 28, 2023: Nature Communications
#18
JOURNAL ARTICLE
Shawn H R Lee, Emily Ashcraft, Wenjian Yang, Kathryn G Roberts, Yoshihiro Gocho, Lauren Rowland, Hiroto Inaba, Seth E Karol, Sima Jeha, Kristine R Crews, Charles G Mullighan, Mary V Relling, William E Evans, Cheng Cheng, Jun J Yang, Ching-Hon Pui
PURPOSE: High hyperdiploidy, the largest and favorable subtype of childhood ALL, exhibits significant biological and prognostic heterogeneity. However, factors contributing to the varied treatment response and the optimal definition of hyperdiploidy remain uncertain. METHODS: We analyzed outcomes of patients treated on two consecutive frontline ALL protocols, using six different definitions of hyperdiploidy: chromosome number 51-67 (Chr51-67); DNA index (DI; DI1...
December 10, 2023: Journal of Clinical Oncology
#19
JOURNAL ARTICLE
Jonathan Paolino, Boris Dimitrov, Beth Apsel Winger, Angelica Sandoval-Perez, Amith Vikram Rangarajan, Nicole Ocasio-Martinez, Harrison K Tsai, Yuting Li, Amanda L Robichaud, Delan Khalid, Charlie Hatton, Riaz Gillani, Petri Polonen, Anthony Dilig, Giacomo Gotti, Julia Kavanagh, Asmani A Adhav, Sean Gow, Jonathan Tsai, Yen Der Li, Benjamin L Ebert, Eliezer M Van Allen, Jacob Bledsoe, Annette S Kim, Sarah K Tasian, Stacy L Cooper, Todd M Cooper, Nobuko Hijiya, Maria Luisa Sulis, Neerav N Shukla, Jeffrey A Magee, Charles G Mullighan, Michael J Burke, Marlise R Luskin, Brenton G Mar, Matthew P Jacobson, Marian H Harris, Kimberly Stegmaier, Andrew E Place, Yana Pikman
PURPOSE: Patients with relapsed or refractory T-cell acute lymphoblastic leukemia (T-ALL) or lymphoblastic lymphoma (T-LBL) have limited therapeutic options. Clinical use of genomic profiling provides an opportunity to identify targetable alterations to inform therapy. EXPERIMENTAL DESIGN: We describe a cohort of 14 pediatric patients with relapsed or refractory T-ALL enrolled on the Leukemia Precision-based Therapy (LEAP) Consortium trial (NCT02670525) and a patient with T-LBL, discovering alterations in platelet-derived growth factor receptor-α (PDGFRA) in 3 of these patients...
September 19, 2023: Clinical Cancer Research
#20
JOURNAL ARTICLE
Lauren Rowland, Brandon Smart, Anthony Brown, Gino M Dettorre, Yoshihiro Gocho, Jeremy Hunt, Wenjian Yang, Satoshi Yoshimura, Noemi Reyes, Guoqing Du, August John, Dylan Maxwell, Wendy Stock, Steven Kornblau, Mary V Relling, Hiroto Inaba, Ching-Hon Pui, Jean-Pierre Bourquin, Seth E Karol, Charles G Mullighan, William E Evans, Jun J Yang, Kristine R Crews
Resistance of acute lymphoblastic leukemia (ALL) cells to chemotherapy, whether present at diagnosis or acquired during treatment, is a major cause of treatment failure. Primary ALL cells are accessible for drug sensitivity testing at the time of new diagnosis or at relapse, but there are major limitations with current methods for determining drug sensitivity ex vivo. Here, we describe a functional precision medicine method using a fluorescence imaging platform to test drug sensitivity profiles of primary ALL cells...
August 5, 2023: Bio-protocol
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