FlowCytoNews
Flow cytometry, gated weekly.
ISSUE #3 · MONDAY EDITION · THE LITERATURE · OCT 5, 2026
Welcome to the Monday edition of FlowCytoNews. Monday is The Literature: the cytometry papers and preprints that went online in the last two weeks, who did the work, and the number that matters from each abstract. Wednesday brings On the Calendar and Friday brings Industry Moves. This fortnight: one model for flow, CyTOF and CITE-seq data, ten years of EuroFlow AML files put to work, and a tissue map for NK clonality. Tell us what we missed — hit reply.
■ The Literature
No new OMIP appeared in Cytometry Part A this fortnight. Cytometry Part B's new clinical panel series, announced Sep 16, has not published its first panel yet.
One model now integrates flow, CyTOF and CITE-seq data
Florian Ingelfinger and Nir Yosef (Weizmann Institute of Science; Yosef also at UC Berkeley), with Ido Amit and 12 co-authors, present CytoVI, a deep generative model for antibody-based single-cell data. It "generates informative cell embeddings, imputes missing measurements, performs differential protein expression testing and automates annotation of cells in a single probabilistic model," across flow cytometry, mass cytometry and CITE-seq. The team used it to build "an integrated B cell maturation atlas spanning 350 proteins," and in patients with B-cell non-Hodgkin lymphoma profiled by both flow and CITE-seq, "CytoVI uncovered disease-associated T cell states." It is open source in scvi-tools. No industry affiliations are listed.
▪ Nature Methods · Sep 30 · 10.1038/s41592-026-03224-5
Why it matters: Imputing markers a panel never measured is what lets you merge datasets stained with different panels on different platforms, the request every core eventually gets. Treat imputed values as predictions to confirm at the bench, not as measurements.
Ten years of standardized EuroFlow AML files predict the genetic subtype in 77% of cases
Sarah Bonte and Yvan Saeys (VIB-UGent, Ghent) with Vincent van der Velden (Erasmus MC, Rotterdam), and Alberto Orfao and Jacques van Dongen (University of Salamanca) among 14 authors, pooled "5366 flow cytometry files from 885 AML patients, stained with the EuroFlow acute leukemia orientation tube (ALOT) and AML/MDS panel, acquired in a standardized way at eight centers over a period of 10 years." A machine-learning model trained to predict WHO genetic classes from the immunophenotype "allowed accurate prediction in 77% of cases, reproducible in an independent validation cohort." Some classes, such as AML with RUNX1::RUNX1T1 or PML::RARA, "showed homogeneous immunophenotypes." No company affiliations are listed.
▪ Cytometry Part B · Sep 29 · 10.1002/cyto.b.70077
Why it matters: The bigger result is in the conclusion: "EuroFlow standardized protocols allow analysis of multi-centric data measured over an extended period of time." Files acquired under locked settings become a research dataset years later; ad hoc files do not. See Bench Notes.
NK receptor patterns differ by tissue, and that changes how you call an NK clone
Valerie Woodings and Afshin Shameli (University of Washington, Seattle), with a co-author at MD Anderson, built a flow panel for NK-cell immunophenotyping and clonality and "applied it to 120 specimens, including normal peripheral blood (PB), bone marrow (BM), lymph node (LN), and body fluids, as well as a series of NK-cell neoplasms and NK-cell clones of uncertain significance (NK-CUS)." NK cells in lymph node and fluid samples were enriched for a different CD56 subset than those in blood and marrow, "resulting in higher CD94/NKG2A and lower KIR expression compared to PB." "Twelve cases fulfilled the proposed criteria for NK-CUS," including putative CMV-related clones. No industry co-authors.
▪ Cytometry Part B · Oct 1 · 10.1002/cyto.b.70078
Why it matters: This is the data companion to last week's multi-institution NK best-practices paper (10.1002/cyto.b.70076). If your normal KIR reference patterns come from blood, do not apply them to a lymph node or an effusion.
Venetoclax plus inotuzumab cleared flow MRD in 16 of 18 patients with relapsed ALL
Marlise Luskin and Daniel DeAngelo (Dana-Farber Cancer Institute) report a phase 1 trial (NCT05016947) of venetoclax plus standard-dose inotuzumab ozogamicin in 23 adults with relapsed or refractory CD22+ B-ALL or lymphoblastic lymphoma. "Of 22 evaluable patients, 21 (95.5%) achieved complete remission, including 19 after one cycle." MRD "cleared in 16/18 (88.9%) by flow cytometry (<10⁻⁴) and 14/19 (73.7%) by next-generation sequencing (<10⁻⁶)." Four patients (17.4%) developed sinusoidal obstruction syndrome. No industry affiliations are listed.
▪ Blood · Sep 25 · 10.1182/blood.2026035238
Why it matters: Flow and NGS were scored at thresholds two logs apart, so the two percentages are not a head-to-head comparison. A flow-negative result at 10⁻⁴ is not an NGS-negative result at 10⁻⁶; your report should state the threshold every time.
A dim CD25 conjugate called about one in four ATLL cases CD25-negative
Feng Zhang and Chenqing Zhang (Fujian Medical University Union Hospital, Fuzhou), with co-author Yanrong Liu of Beijing GoBroad Hospital ("Department of Flow Cytometry, Beijing GoBroad Hospital, GoBroad Healthcare Group", a private hospital group), reviewed morphology, flow and clinical records for 58 people diagnosed with adult T-cell leukemia/lymphoma between 2010 and 2024. "CD25 was negative in 26.3% of cases when assessed with a weakly conjugated fluorochrome," and "FCM detected BM infiltration more sensitively than conventional BM smears." Their peripheral-blood tumor-load index "outperformed the Japan Clinical Oncology Group prognostic index" (AUC 0.871 vs 0.738, DeLong's p = 0.024); the authors call the findings "exploratory" and say they need independent validation.
▪ Cytometry Part B · Sep 21 · 10.1002/cyto.b.70074
Why it matters: CD25 is a defining ATLL marker. If it sits on a dim fluorochrome in your T-cell tube, a negative result may be a panel-design artifact; move it to a bright one before you call a case CD25-negative.
A filter-free cytometer reads cells off a chip of photon counters, with no focusing
Kunihiko Iizuka (University of Tokyo; also Lab Arco Limited, Osaka) and corresponding author Soo Hyeon Kim (Institute of Industrial Science, University of Tokyo) built "two-dimensionally expanded flow cytometry (2DFC)" on an array of time-gated single-photon avalanche diodes. Gating the detectors after a pulsed laser separates fluorescence from excitation light "in the time domain, enabling direct detection of fluorescence from cells flowing over the SPAD array without the need for optical filters." It resolves cellular fluorescence "at a cell concentration of 1 × 10⁶ cells/mL and a volumetric flow rate of up to 1 mL/min without fluidic focusing mechanisms," and detects both single cells and multicellular clusters.
▪ Biosensors and Bioelectronics · Oct 1 · 10.1016/j.bios.2026.119290
Why it matters: Sheathless, filter-free detection is one route to large-volume measurement of cell clusters that conventional flow cells exclude or clog on. This is a detector demonstration, not an instrument you can buy.
Also out
How to use MRD around transplant in AML. Hatem Ellaithy and Yi-Bin Chen (Mass General Brigham) and Christopher Hourigan (Fralin Biomedical Research Institute, Virginia Tech) walk through "four representative cases," covering selection for transplant, conditioning intensity, post-transplant surveillance and maintenance or pre-emptive therapy. — Blood · Sep 22 · 10.1182/blood.2025032501
When a Luminex crossmatch can stand in for the flow crossmatch. All six authors are at Dr. Lal PathLabs (a commercial reference lab, New Delhi). In 3,711 donor-recipient pairs, class I at MFI 1000 predicted T-cell flow crossmatch positivity "with 77% sensitivity, 98% specificity, and 96.8% accuracy"; cut-offs of <500 and >1000 "accurately predict FCXM outcomes," but flow crossmatch "remains crucial for weak positive LXM (MFI 500-1000) cases." — Transplant Immunology · Sep 21 · 10.1016/j.trim.2026.102461
A dye that separates EVs from lipoproteins on nano-flow. Sean Carey Winoto and Guillermo Bazan (National University of Singapore) use conjugated oligoelectrolytes, which have shorter fluorescence lifetimes in lipid monolayers than in bilayers, to "discriminate red blood cell-derived extracellular vesicles from very-low-density lipoproteins." — Angewandte Chemie · Sep 30 · 10.1002/anie.9487218
Urinary EVs swing 100-fold between people. Samantha Upson and Uta Erdbrügger (University of Virginia, with the UVA Flow Cytometry Core) collected every void over 24 hours from 13 healthy adults and used single-EV flow, NTA and cryo-EM; concentrations tracked urine creatinine and TSG101, "allowing normalization of uEVs to urine creatinine and TSG101." — AJP Renal Physiology · Sep 23 · 10.1152/ajprenal.00129.2026
Gating guidelines for immunological assays. Janet Staats, Anagha Divekar (BioLegend, San Diego), J. Philip McCoy and Holden Maecker (Stanford) fill a gap they state plainly: "there are no comprehensive guidelines across the various types of immunological assays performed in research settings using flow cytometry." A chapter in the Immunophenotyping volume of Methods in Molecular Biology (vol. 3087). — Methods Mol Biol · Oct 1 · 10.1007/978-1-0716-5607-5_14
Magnesium inside organelles, read by flow. Michael Brady and Daniela Buccella (NYU and Emory) report MagZet2 ratiometric indicators and "the first organelle-resolved Mg2+ detection by flow cytometry." — ACS Sensors · Sep 21 · 10.1021/acssensors.6c01904
ZAP-70 in CLL, reviewed. Riya Thapa and Shivkanya Fuloria (AIMST University, Malaysia) cover flow assessment and standardization, and note ZAP-70 "is no longer considered a standard-of-care prognostic marker where contemporary molecular prognostic testing is available." — Clinica Chimica Acta · Sep 28 · 10.1016/j.cca.2026.122858
"Closing the gap between non-measurable residual disease and true absence of minimal residual disease." A commentary from Avraham Frisch (Rambam Health Care Campus, Haifa). No abstract online, so title only. — Haematologica · Sep 24 · 10.3324/haematol.2026.301948
Preprints
Three surface markers to replace CCR7/CD45RA for memory CD8 T cells. Pavla Bohacova and Maxim Artyomov (Washington University School of Medicine, St. Louis) show that "conventional CCR7-CD45RA gating generates heterogeneous populations containing extensive mixtures of transcriptionally and epigenetically distinct CD8 T cell states," and propose a CD55/CD319/CX3CR1 framework that "enables direct isolation of viable cells, including GZMK-expressing cells." — bioRxiv · Sep 21 · 10.64898/2026.09.15.751807
Aligning protein data across platforms without flipping marker order. RAMP, from Q. Xu and Ye Zheng (MD Anderson Cancer Center), harmonizes cytometry, CITE-seq and spatial proteomics; "Across seven integration tasks, RAMP achieved the strongest overall balance of batch correction and cell-type preservation." — bioRxiv · Oct 1 · 10.64898/2026.09.25.754510
■ Bench Notes
Acquire today's diagnostic files so they can be pooled in ten years
The EuroFlow AML paper above (10.1002/cyto.b.70077) worked because 5,366 files from eight centers were "acquired in a standardized way." To make your own archive reusable:
Lock instrument settings to target values, not to the last run. Set PMT voltages or gains so reference beads hit fixed target MFIs, and re-check them daily. The EuroFlow SOP (Kalina et al., Leukemia 2012, 10.1038/leu.2012.122) is the worked template.
Version your panels. Record clone, fluorochrome, vendor and lot for every tube, with the date each change took effect. Any reanalysis will need to split the archive at those dates.
Keep raw files. Save the original FCS files as acquired (FCS 3.1 or 3.2; Spidlen et al., Cytometry A 2021, 10.1002/cyto.a.24225) with their compensation or unmixing matrices, not just gated exports or PDFs.
Capture MIFlowCyt metadata at acquisition. Instrument, configuration, sample prep and controls (Lee et al., Cytometry A 2008, 10.1002/cyto.a.20623) are hard to reconstruct later.
Keep a de-identified key to diagnosis and genetics. The AML model was only possible because WHO genetic class was linked to each file.
Check before you plan a public deposit. FlowRepository is online, but its homepage says new experiment creation is temporarily suspended because it is running out of space.
What did we miss? Hit reply — corrections run at the top of the next edition. If a colleague signs out clinical flow, runs a core or builds analysis pipelines, forward this to them.